@article{Kar2022,
title = {In vitro and in silico study of mixtures cytotoxicity of metal oxide nanoparticles to Escherichia coli: a mechanistic approach},
author = {Supratik Kar, Kavitha Pathakoti, Danuta Leszczynska, Paul B. Tchounwou & Jerzy Leszczynski},
doi = {10.1080/17435390.2022.2123750},
year  = {2022},
date = {2022-09-23},
journal = {Nanotoxicology},
abstract = {Metal oxide nanoparticles (MONPs) are commonly found in the aquatic and terrestrial systems as chemical mixtures. Assessment of cytotoxicity associated with single and combination of MONPs can truly identify the concerned environmental risk. Thus, using Escherichia coli as a test model, in vitro cytotoxicity of 6 single MONPs, 15 binary and 20 tertiary mixtures with equitoxic ratios was evaluated following standard bioassay protocols. Assessment of oxidative stress suggested that the production of reactive oxygen species (ROS) was negligible, and the release of metal zinc ions played an important role in the toxicity of MONP mixtures. From our experimental data points, seven quantitative structure-activity relationships (QSARs) models were developed to model the cytotoxicity of these MONPs, based on our created periodic table-based descriptors and experimentally analyzed Zeta-potential. Two strategic approaches i.e. pharmacological and mathematical hypotheses were considered to identify the mixture descriptors pool for modeling purposes. The stringent validation criteria suggested that the model (Model M4) developed with mixture descriptors generated by square-root mole contribution outperformed the other six models considering validation criteria. While considering the pharmacological approach, the ‘independent action’ generated descriptor pool offered the best model (Model M2), which firmly confirmed that each MONP in the mixture acts through ‘independent action’ to induce cytotoxicity to E. colii nstead of fostering an additive, antagonistic or synergistic effect among MONPs. The total metal electronegativity in a specific metal oxide relative to the number of oxygen atoms and metal valence was associated with a positive contribution to cytotoxicity. At the same time, the core count, which gives a measure of molecular bulk and Zeta potential, had a negative contribution to cytotoxicity.},
note = {NSF/CREST HRD-1547754},
keywords = {E. coli, in silico, In vitro, mixtures, Nanoparticles, Toxicity},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko2022,
title = {NTO Degradation by Nitroreductase: A DFT Study},
author = {Liudmyla K. Sviatenko, Leonid Gorb, and Jerzy Leszczynski},
doi = {10.1021/acs.jpcb.2c04153},
year  = {2022},
date = {2022-08-04},
journal = {J. Phys. Chem. B},
volume = {126},
number = {32},
pages = {5991\textendash6006},
abstract = {NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of the possible mechanism for all steps of reduction of NTO by oxygen-insensitive nitroreductase, as one of the pathways for NTO environmental degradation, was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Obtained results reveal an overall sequence for NTO transformation into ATO (5-amino-1,2,4-triazol-3-one) with the flavin mononucleotide (FMN) cofactor of nitroreductase. Reduction of the nitro group to the nitroso group and the nitroso group to the hydroxylamino group follow a similar mechanism that consists of the sequential electron and proton transfer from the flavin cofactor. The hydride transfer mechanism may contribute to reduction of the nitroso group by the anionic form of the reduced flavin cofactor. Reduction of 5-(hydroxylamino)-1,2,4-triazol-3-one by the neutral form of the reduced flavin is impossible, whereas reduction of the hydroxylamino group to the amino group occurs with the anionic form of the reduced cofactor by a mechanism involving an initial proton transfer from the hydroxonium ion followed by two electrons and one proton transfers from the flavin cofactor. Small activation energies and high exothermicity support the significant contribution of oxygen-insensitive nitroreductase and other enzymes, containing FMN as a cofactor, to NTO degradation in the environment.},
note = {ARO W911NF-20-1-0116; XSEDE DMR110088
},
keywords = {NTO},
pubstate = {published},
tppubtype = {article}
}
@article{De2022,
title = {Repurposing FDA approved drugs as possible anti-SARS-CoV-2 medications using ligand-based computational approaches: sum of ranking difference-based model selection},
author = {Priyanka De, Vinay Kumar, Supratik Kar, Kunal Roy, Jerzy Leszczynski},
doi = {10.1007/s11224-022-01975-3},
year  = {2022},
date = {2022-06-07},
journal = {Struct. Chem. },
volume = {33},
pages = {1741\textendash1753},
abstract = {The worldwide burden of coronavirus disease 2019 (COVID-19) is still unremittingly prevailing, with more than 440 million infections and over 5.9 million deaths documented so far since the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic. The non-availability of treatment further aggravates the scenario, thereby demanding the exploration of pre-existing FDA-approved drugs for their effectiveness against COVID-19. The current research aims to identify potential anti-SARS-CoV-2 drugs using a computational approach and repurpose them if possible. In the present study, we have collected a set of 44 FDA-approved drugs of different classes from a previously published literature with their potential antiviral activity against COVID-19. We have employed both regression- and classification-based quantitative structure\textendashactivity relationship (QSAR) modeling to identify critical chemical features essential for anticoronaviral activity. Multiple models with the consensus algorithm were employed for the regression-based approach to improve the predictions. Additionally, we have employed a machine learning-based read-across approach using Read-Across-v3.1 available from https://sites.google.com/jadavpuruniversity.in/dtc-lab-software/home and linear discriminant analysis for the efficient prediction of potential drug candidate for COVID-19. Finally, the quantitative prediction ability of different modeling approaches was compared using the sum of ranking differences (SRD). Furthermore, we have predicted a true external set of 98 pharmaceuticals using the developed models for their probable anti-COVID activity and their prediction reliability was checked employing the “Prediction Reliability Indicator” tool available from https://dtclab.webs.com/software-tools. Though the present study does not target any protein of viral interaction, the modeling approaches developed can be helpful for identifying or screening potential anti-coronaviral drug candidates.},
note = {NSF/CREST HRD-1547754},
keywords = {COVID-19, In silico approaches, Quantitative structure\textendashactivity relationship, Read-across, SARS-CoV-2},
pubstate = {published},
tppubtype = {article}
}
@article{Gorb2022,
title = {Decomposition of 2,4,6-trinitrotoluene (TNT) and 5-nitro-2,4- dihydro-3H-1,2,4-triazol-3-one (NTO) by Fe13O13 nanoparticle: density functional theory study},
author = {Leonid Gorb, Mykola Ilchenko, Jerzy Leszczynski},
doi = {10.1007/s11356-022-20547-w},
year  = {2022},
date = {2022-05-11},
journal = {Environ. Sci. Pollut. Res.},
volume = {29},
pages = {68522\textendash68531},
abstract = {To obtain more insight into the mechanisms of the decomposition of energetic compounds, we performed a computational study of the interaction of Fe13O13 nanoparticles with two energetic molecules such as 2,4,6-trinitrotoluene (TNT) and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The density functional theory using M06-2X, B3LYP, and BLYP density functionals was applied. We found that the reactivity of these molecules strongly depends on the place of adsorption (so-called top and bottom planes of Fe13O13). Namely, only the interaction with the bottom plane results in the thermodynamic characteristics of the decomposition that provide a medium reaction rate for the studied processes. Several pathways for such decomposition were found. One of them is the inter-complex oxygen transfer of nitro-group oxygen to Fe13O13. This pathway results in the formation of adsorbed nitroso compounds. The second pathway describes a more complex decomposition that includes the transfer of the nitro-group oxygen accompanied by the hydrogen transfer. In all cases, the interaction of energetic molecules with Fe13O13 nanoparticles takes place along with a barrier-less electron transfer from Fe13O13 to TNT or NTO species.},
note = {ARO grant W911NF-20-1-0116
},
keywords = {Decomposition, Density functional theory, Iron oxide, Nano-cluster, Nanoparticles, NTO, TNT},
pubstate = {published},
tppubtype = {article}
}
@article{Kumar2022,
title = {Identification of potential antivirals against 3CLpro enzyme for the treatment of SARS-CoV-2: A multi-step virtual screening study},
author = {V. Kumar, S. Kar, P. De, K. Roy & J. Leszczynski},
doi = {10.1080/1062936X.2022.2055140},
year  = {2022},
date = {2022-04-05},
journal = {SAR QSAR Environ. Res.},
volume = {33},
number = {5},
pages = {357-386},
abstract = {The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak is posing a serious public health threat worldwide in the form of COVD-19. Herein, we have performed two-dimensional quantitative structure\textendashactivity relationship (2D-QSAR) and three-dimensional pharmacophore modelling analysis employing inhibitors of 3-chymotrypsin-like protease (3CLpro), the leading protease that is crucial for the replication of SARS-CoV-2. The investigation aims to identify the important structural features responsible for the enzyme inhibition and the search for novel 3CLpro enzyme inhibitors as effective therapeutics for treating SARS-CoV-2. Furthermore, we carried out molecular docking studies using the most and least active compounds in the dataset, aiming to validate the contributions of various features as appeared in the QSAR models. Later, the stringently validated 2D-QSAR model was used to estimate the 3CLpro inhibitory activity of compounds from five chemical databases. Compounds with the significant predicted activity were then subjected to pharmacophore-based virtual screening to screen the top-rated compounds, which were then further subjected to molecular docking analysis, absorption, distribution, metabolism, excretion \textendash toxicity (ADMET) profiling, and molecular dynamics (MD) simulation. The multi-step virtual screening analyses suggested that compounds CASAntiV-865453-58-3, CASAntiV-865453-40-3, and CASAntiV-2043031-84-9 could be used as effective therapeutic agents for the treatment of SARS-CoV-2.},
note = {NSF/CREST HRD-1547754},
keywords = {2D-QSAR, 3CLpro, 3D-QSAR, ADMET docking, SARS CoV-2},
pubstate = {published},
tppubtype = {article}
}
@article{Gorb2022b,
title = {A density functional theory study of the simplest adsorption forms of perfluorooctanoic and perfluorooctanesulphonic acids by graphene oxide and fluorinated graphene oxide.},
author = {Leonid Gorb, Mykola Ilchenko & Jerzy Leszczynski},
doi = {10.1080/00268976.2022.2053218},
year  = {2022},
date = {2022-03-19},
journal = {Molecular Physics},
abstract = {A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate the simplest adsorption structure models of perfluorooctanoic and perfluorooctanesulphonic acids adsorbed from a water solution by the surfaces of graphene oxide and fluorinated graphene oxide. It has been revealed that both hydrophilic and hydrophobic sites can adsorb the anions of the investigated acids. The results of our calculations suggest preference in the adsorption ability of graphene oxide compared to its fluorinated counterpart.},
note = {ERDC W912HZ-20-20069
NSF-PREM grant no. DMR-1826886 },
keywords = {adsorption, fluorinated graphene oxide, graphene oxide, Perfluorooctanoic acid, perfluorooctansulphonic acid},
pubstate = {published},
tppubtype = {article}
}
@article{Wang2021,
title = {Theoretical DFT Study on the Mechanisms of CO/CO2 Conversion in Chemical Looping Catalyzed by Calcium Ferrite},
author = {Jing Wang, Jiande Gu, Asif Rony, Maohong Fan, and Jerzy Leszczynski},
doi = {https://doi.org/10.1021/acs.jpca.1c04431},
year  = {2021},
date = {2021-09-10},
journal = {J. Phys. Chem. A },
volume = {125},
number = {37},
pages = {8159\textendash8167},
abstract = {The CO/CO2 conversion mechanism on the calcium ferrite (CFO) surface in chemical looping was explored by a computational study using the density functional theory approach. The CFO catalytic reaction pathway of 2CO + O2 → 2CO2 conversion has been elucidated. Our results show that the Fe center in CFO plays the key role as a catalyst in the CO/CO2 conversion. Two energetically stable spin states of CFO, quintet and septet, serve as the effective catalysts. The presence of the triplet O2 molecule caused the conversion of these two spin-state structures into each other along the catalytic reaction pathway. A double release of CO2 was predicted following this reaction mechanism. The rate-determining step is the formation of the 2CO2\textendashCFO complex (P4) in the quintet state (19.0 kcal/mol). The predicted energy barriers for all the steps suggest that the proposed pathway is plausible.},
keywords = {Chemical Looping, DFT, Mechanisms of CO/CO2 Conversion},
pubstate = {published},
tppubtype = {article}
}
@article{Cingireddy2021,
title = {Preliminary Screening of COVID-19 Infection Employing Machine Learning Techniques From Simple Blood Profile},
author = {Anirudh Reddy Cingireddy, Robin Ghosh, Supratik Kar, Venkata Melapu, Sravanthi Joginipeli, Jerzy Leszczynski},
doi = {http://doi.org/10.4018/IJQSPR.2021070103},
year  = {2021},
date = {2021-09-01},
journal = {Int J Quantum Struc Prop Rel },
volume = {6},
number = {3},
pages = {35-47},
abstract = {Frequent testing of the entire population would help to identify individuals with active COVID-19 and allow us to identify concealed carriers. Molecular tests, antigen tests, and antibody tests are being widely used to confirm COVID-19 in the population. Molecular tests such as the real-time reverse transcription-polymerase chain reaction (rRT-PCR) test will take a minimum of 3 hours to a maximum of 4 days for the results. The authors suggest using machine learning and data mining tools to filter large populations at a preliminary level to overcome this issue. The ML tools could reduce the testing population size by 20 to 30%. In this study, they have used a subset of features from full blood profile which are drawn from patients at Israelita Albert Einstein hospital located in Brazil. They used classification models, namely KNN, logistic regression, XGBooting, naive Bayes, decision tree, random forest, support vector machine, and multilayer perceptron with k-fold cross-validation, to validate the models. Na\"{i}ve bayes, KNN, and random forest stand out as the most predictive ones with 88% accuracy each.},
keywords = {Blood Test, COVID-19, Decision Tree, KNN, Logistic Regression, Machine learning, Molecular Tests, Multilayer Perceptron, Naive Bayes, Random Forest, Support Vector Machine, XGBooting},
pubstate = {published},
tppubtype = {article}
}
@inbook{Kar2021,
title = {Chapter: QSAR and machine learning modeling of toxicity of nanomaterials: a risk assessment approach},
author = {Supratik Kar and Jerzy Leszczynski},
editor = {J. Njuguna, K. Pielichowski, H. Zhu},
doi = {https://doi.org/10.1016/B978-0-12-820505-1.00016-X},
year  = {2021},
date = {2021-07-30},
pages = {417-441},
publisher = {WOODHEAD PUBLISHING, ELSEVIER},
edition = {2nd},
chapter = {16},
series = {Health and Environmental Safety of Nanomaterials: Polymer Nanocomposites and Other Materials Containing Nanoparticles},
abstract = {The advancement of nanoscience and enormous use of nanomaterials (NMs) in the form of coated nanoparticles, engineered metal oxide nanomaterials (MONMs), single- and multiwalled carbon nanotubes, fullerenes (C60/C70), and silica NMs open up multifaceted possibilities of inflicting toxicity on the environment. With the implications of NMs in medicine, cars, batteries, solar panels, textiles, toys, electronics, etc., one can’t control the safe release of NMs into the ecosystem, which directly affects the organisms present in the aquatic and terrestrial environment and indirectly affects humans' lives. The testing of each individual form of NMs on diverse species as well as different response/endpoints by traditional experimental assays is an impossible task. Thus in most cases, environment regulatory bodies, industries, and environmental scientists largely depend on in silico methods like quantitative structure\textendashactivity relationships (QSARs) and machine learning approaches. In a relatively short time, these models can be prepared with the expertise of cheminformaticians and can be employed for the prediction of future NMs as well as the already existing ones in the ecosystem. Since the beginning of 2010, a huge number of in silico models have been developed in combination with in vivo and in vitro analysis, and the present number of such models exceeds 150. The successful models cover eukaryotic to prokaryotic organisms and cell lines including cytotoxicity, genotoxicity, enzymatic inhibition, egg hatching, cellular viability, and cellular uptake. Most of the models can identify the mechanistic interpretation behind the toxicity of NMs toward specific organisms/cell lines. This is helpful for the safe design of NMs for the future along with risk assessment.},
keywords = {Machine learning, Metal oxide, Nanomaterial, QSAR, Toxicity},
pubstate = {published},
tppubtype = {inbook}
}
@inbook{Samanta2021,
title = {Chapter: Delving charge-transfer excitations in hybrid organic-inorganic hetero junction of dye-sensitized solar cell: Assessment of excitonic optical properties using the GW and Bethe-Salpeter Green’s function formalisms},
author = {P. Samanta, J. Leszczynski},
editor = { J. Roy, S. Kar, J. Leszczynski (eds.)},
doi = {https://doi.org/10.1007/978-3-030-69445-6_5},
isbn = {978-3-030-69445-6},
year  = {2021},
date = {2021-05-13},
volume = {32},
pages = {99-126},
publisher = {Springer, Cham},
series = {Development of Solar Cells. Challenges and Advances in Computational Chemistry and Physics},
abstract = {First-principles modeling of charge-neutral excitations with the recognition of charge-transfer and Rydberg states and probing the mechanism of charge-carrier generation from the photoexcited electron\textendashhole pair for the hybrid organic\textendashinorganic photovoltaic materials remain as a cornerstone problem within the framework of time-dependent density functional theory (TDDFT) . The many-body Green’s function Bethe\textendashSalpeter formalism based on a Dyson-like equation for the two-particle correlation function, which accounts for the exchange and attractive screened Coulomb interactions between photoexcited electrons and holes, has emerged as a decent approach to study the photoemission properties including the Frenkel and charge-transfer excitations in an assortment of finite and extended systems of optoelectronic materials. The key ideas of practical implementation of Bethe\textendashSalpeter equation (BSE) involving the computations of single-particle states, quasi-particle energy levels, and the screened Coulomb interaction with the aid of Gaussian atomic basis sets and resolution-of-identity techniques are discussed. The work revisits the computational aspects for the evaluation of electronic, spectroscopic, and photochromic properties of the dye-sensitized solar cell (DSSC) constituents by considering the excitonic effects that renormalize the energy levels and coalesce the single-particle transitions. The most recent advancements in theoretical methods that employ the maximally localized Wannier’s function (MLWF) and curtail the overall scaling of BSE calculations are also addressed, and the viable applications are subsequently illustrated with selected examples. Finally, the review reveals some computational challenges that need to be resolved to expand the applicability of BSE in designing solar cell materials, and to unravel the intricate mechanism of ultrafast excited-state processes.},
keywords = {BSE, DSSC, Exciton, GW},
pubstate = {published},
tppubtype = {inbook}
}
@inbook{Roy2021c,
title = {Chapter: Computational screening of organic dye-sensitizers for dye-sensitized solar cells: DFT/TDDFT approach},
author = {J. Roy, S. Kar, J. Leszczynski},
editor = {J. Roy, S. Kar, J. Leszczynski (eds.)},
doi = {https://doi.org/10.1007/978-3-030-69445-6_8},
isbn = {978-3-030-69445-6},
year  = {2021},
date = {2021-05-13},
volume = {32},
pages = {187-206},
publisher = {Springer, Cham},
series = {Development of Solar Cells. Challenges and Advances in Computational Chemistry and Physics},
abstract = {Dye-sensitized solar cells (DSSCs) represent a promising third-generation photovoltaic technology due to their ease in fabrication, low cost, ability to operate in diffused light, flexibility, and being lightweight. Organic dye-sensitizers are vital components of the DSSCs. Comprehensive theoretical study of the dye’s spectroscopic properties, including excitation energies ground- and excited-state oxidation potential, allows to design and screen organic dye-sensitizers for an efficient DSSC. Density functional theory (DFT) and time-dependent DFT (TDDFT) approaches have been efficiently used to estimate different optoelectronic properties of sensitizers. This chapter outlined the use of the DFT and TDDFT framework to design organic dye-sensitizers for DSSCs to predict different photophysical properties. Prediction of essential factors such as short-circuit current density (JSC), open-circuit voltage (VOC), along with charge transfer phenomena, will help experimental groups to fabricate DSSCs with higher photoconversion efficiency (PCE). Besides, this chapter includes a basic understanding of the mechanism of DSSCs, based on the energetics of the various constituents of the heterogeneous device.},
keywords = {DFT, DSSC, Organic Sensitizer, TD-DFT},
pubstate = {published},
tppubtype = {inbook}
}
@inbook{Majumdar2021,
title = {Chapter: Slater-Type Orbitals},
author = {Devashis Majumdar, Pabitra Narayan Samanta, Szczepan Roszak, and Jerzy Leszczynski},
editor = {Eva Perlt},
doi = {https://doi.org/10.1007/978-3-030-67262-1_2},
issn = {2192-6603},
year  = {2021},
date = {2021-05-07},
volume = {107},
pages = {17-40},
publisher = {Springer, Cham.},
chapter = {2},
series = {Lecture Notes in Chemistry},
abstract = {The key concept of Slater-type orbitals (STOs) underpinning quantum chemical calculations of polyatomic systems has been elucidated via a discourse on mathematical challenges of solving immanent multicenter integrals in density functional theory (DFT). Two types of orbitals viz. Gaussian-type orbitals (GTOs) and STOs are being discussed about their importance in atomic orbital-based calculations and compared their advantages and disadvantages in solving chemistry-related problems of molecules. The third type of orbitals obtained through plane-wave basis sets are excluded in this discussion, as they are mostly used to solve condensed-phase problems. The rudiments of STOs have been discussed without radical analysis of programmatic implementations of mathematical algorithms. The discussions are mainly focused on the DFT calculations, and the concepts of various Slater atomic basis sets are being introduced. In the final part of the article, a few specific examples are considered related to the application of DFT-STOs to different chemical problems. We place emphasis on benchmark studies of simple molecular structures, excitation energy calculations, excitation energy spectrum of UO22+ as well as resonance Raman spectrum analysis.},
type = {Book: Basis Sets in Computational Chemistry},
keywords = {Benchmark studies, Excitation energy calculations, Resonance Raman spectrum analysis, Slater-type orbitals},
pubstate = {published},
tppubtype = {inbook}
}
@article{Rozhenko2021,
title = {Z,E-Isomerism in a Series of Substituted Iminophosphonates: Quantum Chemical Research},
author = {Alexander B. Rozhenko, Andrey A. Kyrylchuk, Yuliia O. Lapinska, Yuliya V. Rassukana, Vladimir V. Trachevsky, Volodymyr V. Pirozhenko, Jerzy Leszczynski and Petro P. Onysko},
doi = {https://doi.org/10.3390/org2020008},
year  = {2021},
date = {2021-04-23},
journal = {Organics},
volume = {2},
number = {2},
pages = {84-97},
abstract = {Esters of iminophosphonic acids (iminophosphonates, or IPs), including a fragment, >P(=O)-C=N, can be easily functionalized, for instance to aminophosphonic acids with a wide range of biological activity. Depending on the character of the substitution, the Z- or E-configuration is favorable for IPs, which in turn can influence the stereochemistry of the products of chemical transformations of IPs. While the Z,E-isomerism in IPs has been thoroughly studied by NMR spectroscopy, the factors stabilizing a definite isomer are still not clear. In the current work, density functional theory (DFT, using M06-2X functional) and ab initio spin-component\textendashscaled second-order M\oller\textendashPlesset perturbation theory (SCS-MP2) calculations were carried out for a broad series of IPs. The calculations reproduce well a subtle balance between the preferred Z-configuration inherent for C-trifluoromethyl substituted IPs and the E-form, which is more stable for C-alkyl- or aryl-substituted IPs. The predicted trend of changing activation energy values agrees well with the recently determined experimental ΔG≠298 magnitudes. Depending on the substitution in the aromatic moiety, the Z/E-isomerization of N-aryl-substituted IPs proceeds via two types of close-in energy transition states. Not a single main factor but a combination of various contributions should be considered in order to explain the Z/E-isomerization equilibrium for different IPs.},
keywords = {DFT calculations; SCS-MP2 calculations; Z, E-isomerism; Iminophosphonates; Thermodynamic stability},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2021,
title = {Using quasi-SMILES for the predictive modeling of the safety of 574 metal oxide nanoparticles measured in different experimental conditions},
author = {Alla P. Toropova, Andrey A. Toropov, Jerzy Leszczynski, Natalia Sizochenko},
doi = {https://doi.org/10.1016/j.etap.2021.103665},
year  = {2021},
date = {2021-04-22},
journal = {ENVIRON TOXICOL PHAR},
volume = {86},
pages = {103665},
abstract = {The production of nanomaterials continues its rapid growth; however, newly manufactured nanomaterials' environmental and health safety are among the most significant concerns. A safety assessment is usually a lengthy and costly process, so computational studies are often used to complement experimental testing. One of the most time-efficient techniques is structure-activity relationships (SAR) modeling. In this project, we analyzed the Sustainable Nanotechnology (S2NANO) dataset that contains 574 experimental cell viability and toxicity datapoints for Al2O3, CuO, Fe2O3, Fe3O4, SiO2, TiO2, and ZnO measured in different conditions. We aimed to develop classification- and regression-based structure-activity relationship models using quasi-SMILES molecular representation. Introduced quasi-SMILES took into consideration all available information, including structural features of nanoparticles (molecular structure, core size, etc.) and related experimental parameters (cell line, dose, exposure time, assay, hydrodynamic size, surface charge, etc.). Resultant regression models demonstrated sufficient predictive power, while classification models demonstrated higher accuracy.},
keywords = {CORAL software, Metal oxide nanoparticles, Molecular representation, Monte carlo optimization, Nano-QSAR, Nano-SAR, Quasi-SMILES},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2021,
title = {Zeta potentials (ζ) of metal oxide nanoparticles: A meta-analysis of experimental data and a predictive neural networks modeling},
author = {Natalia Sizochenko, Alicja Mikolajczyk, Michael Syzochenko, Tomasz Puzyn, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.impact.2021.100317},
year  = {2021},
date = {2021-04-16},
journal = {Nanoimpact},
volume = {22},
pages = {100317},
abstract = {Zeta potential is usually measured to estimate the surface charge and the stability of nanomaterials, as changes in these characteristics directly influence the biological activity of a given nanoparticle. Nowadays, theoretical methods are commonly used for a pre-screening safety assessments of nanomaterials. At the same time, the consistency of data on zeta potential measurements in the context of environmental impact is an important challenge. The inconsistency of data measurements leads to inaccuracies in predictive modeling. In this article, we report a new curated dataset of zeta potentials measured for 208 silica- and metal oxide nanoparticles in different media. We discuss the data curation framework for zeta potentials designed to assess the quality and usefulness of the literature data for further computational modeling. We also provide an analysis of specific trends for the datapoints harvested from different literature sources. In addition to that, we present for the first time a structure-property relationship model for nanoparticles (nano-SPR) that predicts values of zeta potential values measured in different environmental conditions (i.e., biological media and pH).},
keywords = {Computational modeling, Metal oxide nanoparticles, Toxicological profile, Weight of evidence, Zeta potential},
pubstate = {published},
tppubtype = {article}
}
@article{Ivashchenko2021,
title = {Phase diagram, electronic, mechanical and thermodynamic properties of TiB2\textendashZrB2 solid solutions: A first-principles study},
author = {V.I. Ivashchenko, P.E.A. Turchi, V.I. Shevchenko, N.R. Mediukh, Leonid Gorb, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.matchemphys.2021.124340},
year  = {2021},
date = {2021-04-15},
journal = {Mater. Chem. Phys.},
volume = {263},
pages = {124340},
abstract = {The stability, electronic and phonon structures, mechanical and thermodynamic properties as well optical spectra of the Ti1−xZrxB2 solid solutions were investigated in the framework of a first-principles approach. The miscibility gap was predicted with the consolute temperature TC = 1973 K and composition xC = 0.4. The negative deviation of the calculated bulk, shear, Young moduli, Debye temperature, Vickers hardness and fracture toughness from the mixing rule is observed. The ideal shear stress of 41.1 GPa for Ti0.5Zr0.5B2 was found to be lower compared to that for TiB2 (43.5 GPa) and ZrB2 (43.1 GPa). The calculated elastic moduli and Poisson ratio exhibit the spatial anisotropy inherent to hexagonal structures. It was shown that the thermodynamic characteristics of the Zr-rich solid solutions could be well reproduced in a temperature range up to 1000\textendash1400 K using the harmonic approximation. The calculated dielectric constants  and , and optical reflectivity spectra  for Ti1−xZrxB2 were analyzed in comparison with available optical spectra of parent diborides from other authors.},
keywords = {BSE, DSSC, Elastic properties, Electronic properties, Exciton, First-principles, GW, Optical properties, Ti-Zr-B2},
pubstate = {published},
tppubtype = {article}
}
@article{Borysenko2021,
title = {Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction},
author = {Iryna O. Borysenko, Liudmyla K. Sviatenko, Sergiy I. Okovytyy, Jerzy Leszczynski},
doi = {https://doi.org/10.1007/s11224-020-01663-0},
year  = {2021},
date = {2021-04-15},
journal = {Struct. Chem.},
volume = {32},
pages = {581 - 589},
abstract = {Algorithm for generation and assessment of probability of possible reaction pathways for multiple-channel bimolecular interactions is presented. The proposed algorithm comprises a combination of few steps. They include conformational search for reaction intermediate using the molecular mechanics (MMX) approach, based on the obtained conformation construction of structures of transition states and pre-reaction complexes, and calculation activation energies to further determine the probable reaction pathways. The proposed algorithm could be adopted for investigation of chemical and biochemical reactions of different types. Here, we have considered the reaction of bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine (1) with glycidyl ether (2) in a neutral environment that proceeds through SN2-like mechanism forming bipolar ion (3) which is a good starting point for identification of the reaction channels. Conformational properties of intermediate (3) have been investigated using stochastic conformational search. From the 95 localized conformations within 10 kcal/mol of global minimum that have been obtained, 63 unique transition state conformations were generated and optimized by using the PM7 and M062X/6-31G(d) methods for accurate estimation of overall rate constant of reaction. The most energetically favorable pathways have been investigated at the M062X/6-31G(d) level of theory taking into account the influence of solvent.},
keywords = {DFT, Epoxide ring opening reaction},
pubstate = {published},
tppubtype = {article}
}
@article{Roy2021,
title = {Interaction of epoxy-based hydrogels and water: A molecular dynamics simulation study},
author = {Juganta K. Roy, Henry P. Pinto, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.jmgm.2021.107915},
year  = {2021},
date = {2021-04-13},
journal = {J MOL GRAPH MODEL},
volume = {106},
pages = {107915},
abstract = {Biomaterials play a crucial role in tissue engineering as a functional replacement, regenerative medicines, supportive scaffold for guided tissue growth, and drug delivery devices. The term biomaterial refers to metals, ceramics, and polymers account for the vast majority. In the case of polymers, hydrogels have emerged as active materials for an immense variety of applications. Epoxy-based hydrogels possess a unique network structure that enables very high levels of hydrophilicity and biocompatibility. Hydrogel such as Medipacs Epoxy Polymers (MEPs) models were constructed to understand water’s behavior at the water/hydrogel interface and hydrogel network. We computed the Gibbs dividing surface (GDS) to define the MEP/water interface, and all the physicochemical properties were computed based on GDS. We calculated the radial distribution function (RDF), the 2D surface roughness of the immersed MEPs. RDF analysis confirmed that the first hydration shell is at a distance of 1.86 r{A}, and most of the water molecules are near the hydroxyl group of the MEPs network. Hydrogen bonds (H-bonds) analysis was performed, and the observation suggested that the disruption of the H-bonds between MEP chains leads to an increase in the polymer matrix’s void spaces. These void spaces are filled with diffused water molecules, leading to swelling of the MEP hydrogel. The swelling parameter was estimated from the fitted curve of the yz-lattice of the simulation cell. The MEP/water interface simulation results provide insightful information regarding the design strategy of epoxy-based hydrogel and other hydrogels vital for biomedical applications.},
keywords = {Atomistic MD simulation, Biomaterials, Epoxy-based hydrogel, Gibbs dividing surface, Surface roughness, Swelling behavior},
pubstate = {published},
tppubtype = {article}
}
@inbook{Kar2021b,
title = {Chapter: Drug Databases for Development of Therapeutics Against Coronaviruses},
author = {S. Kar, J. Leszczynski},
editor = {K. Roy, Ed},
doi = {https://doi.org/10.1007/7653_2020_66},
isbn = {978-1-0716-1366-5},
year  = {2021},
date = {2021-04-06},
pages = {761-780},
publisher = {Springer, New York, NY},
series = {In Silico Modeling of Drugs Against Coronaviruses. Methods in Pharmacology and Toxicology. },
abstract = {Within a span of 11 months starting from December 2019, around 47.6 million people have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including the number of deaths touching 1,215,601 on November 3, 2020. The number increases at an alarming rate with a possible second wave of Coronavirus Disease 2019 (COVID-19) throughout the world. A clear threat of another lockdown is looming over the social life and economy. Thus, scientists worldwide are running against the time to find small drug molecules as therapeutics and possible vaccines to relieve the world. Over the past months, computational chemistry and computer-aided drug design (CADD) have shown encouraging promises in generating multiple lead/hit compounds by employing powerful virtual screening techniques (VS) and drug repurposing of various approved and experimental drugs. The present chapter has enlisted and discussed the top 25 small molecule databases, including both synthetic as well as natural compounds. Most of the databases are freely available for research purposes, which can be strategically screened employing multiple computational techniques to discover therapeutics for COVID-19.},
keywords = {Antiviral, COVID-19, Database Repurposing, SARS-CoV-2, Virtual screening},
pubstate = {published},
tppubtype = {inbook}
}
@article{Skretna2021,
title = {The kernel weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models.},
author = {Agnieszka Gajewicz Skretna, Supratik Kar, Magdalena Piotrowska, Jerzy Leszczynski},
doi = {https://doi.org/10.1186/s13321-021-00484-5},
year  = {2021},
date = {2021-02-12},
journal = {J. Cheminform.},
volume = {13},
number = {9},
pages = {1-20},
abstract = {The ability of accurate predictions of biological response (biological activity/property/toxicity) of a given chemical makes the quantitative structure‐activity/property/toxicity relationship (QSAR/QSPR/QSTR) models unique among the in silico tools. In addition, experimental data of selected species can also be used as an independent variable along with other structural as well as physicochemical variables to predict the response for different species formulating quantitative activity\textendashactivity relationship (QAAR)/quantitative structure\textendashactivity\textendashactivity relationship (QSAAR) approach. Irrespective of the models' type, the developed model's quality, and reliability need to be checked through multiple classical stringent validation metrics. Among the validation metrics, error-based metrics are more significant as the basic idea of a good predictive model is to improve the predictions' quality by lowering the predicted residuals for new query compounds. Following the concept, we have checked the predictive quality of the QSAR and QSAAR models employing kernel-weighted local polynomial regression (KwLPR) approach over the traditional linear and non-linear regression-based approaches tools such as multiple linear regression (MLR) and k nearest neighbors (kNN). Five datasets which were previously modeled using linear and non-linear regression method were considered to implement the KwPLR approach, followed by comparison of their validation metrics outcomes. For all five cases, the KwLPR based models reported better results over the traditional approaches. The present study's focus is not to develop a better or improved QSAR/QSAAR model over the previous ones, but to demonstrate the advantage, prediction power, and reliability of the KwLPR algorithm and establishing it as a novel, powerful cheminformatic tool. To facilitate the use of the KwLPR algorithm for QSAR/QSPR/QSTR/QSAAR modeling, the authors provide an in-house developed KwLPR.RMD script under the open-source R programming language.},
keywords = {kernel weighted local polynomial regression, QSAR},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2021c,
title = {Evaluating the cytotoxicity of a large pool of metal oxide nanoparticles to Escherichia coli: Mechanistic understanding through In Vitro and In Silico studies},
author = {Supratik Kar, Kavitha Pathakoti, Paul B. Tchounwou, Danuta Leszczynska, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.chemosphere.2020.128428},
year  = {2021},
date = {2021-02-11},
journal = {Chemosphere},
volume = {264},
pages = {128428},
abstract = {The toxic effect of eight metal oxide nanoparticles (MONPs) on Escherichia coli was experimentally evaluated following standard bioassay protocols. The obtained cytotoxicity ranking of these studied MONPs is Er2O3, Gd2O3, CeO2, Co2O3, Mn2O3, Co3O4, Fe3O4/WO3 (in descending order). The computed EC50 values from experimental data suggested that Er2O3 and Gd2O3 were the most acutely toxic MONPs to E. coli. To identify the mechanism of toxicity of these 8 MONPs along with 17 other MONPs from our previous study, we employed seven classifications and machine learning (ML) algorithms including linear discriminant analysis (LDA), na\"{i}ve bayes (NB), multinomial logistic regression (MLogitR), sequential minimal optimization (SMO), AdaBoost, J48, and random forest (RF). We also employed 1st and 2nd generation periodic table descriptors developed by us (without any sophisticated computing facilities) along with experimentally analyzed Zeta-potential, to model the cytotoxicity of these MONPs. Based on qualitative validation metrics, the LDA model appeared to be the best among the 7 tested models. The core environment of metal defined by the ratio of the number of core electrons to the number of valence electrons and the electronegativity count of oxygen showed a positive impact on toxicity. The identified properties were important for understanding the mechanisms of nanotoxicity and for predicting the potential environmental risk associated with MONPs exposure. The developed models can be utilized for environmental risk assessment of any untested MONP to E. coli, thereby providing a scientific basis for the design and preparation of safe nanomaterials.},
keywords = {Classification, in silico, In vitro, Machine learning, Metal oxide, Nanoparticles, Toxicity},
pubstate = {published},
tppubtype = {article}
}
@article{Kapusta2021,
title = {Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling.},
author = {Karina Kapusta, Supratik Kar, Jasmine T. Collins, Latasha M. Franklin, Wojciech Kolodziejczyk, Jerzy Leszczynski & Glake A. Hill},
doi = {https://doi.org/10.1080/07391102.2020.1806930},
year  = {2021},
date = {2021-02-10},
journal = {J. Biomol. Struct. Dyn. },
volume = {39},
number = {17},
pages = {6810-6827},
abstract = {Due to an outbreak of COVID-19, the number of research papers devoted to in-silico drug discovery of potential antiviral drugs is increasing every day exponentially. Still, there is no specific drug to prevent or treat this novel coronavirus (SARS-CoV-2) disease. Thus, the screening for a potential remedy presents a global challenge for scientists. Up to date over a hundred crystallographic structures of SARS-CoV-2 Mpro have been deposited to Protein Data Bank. With many known proteins, the demand for a reliable target has become higher than ever, so as the choice of an efficient computational methods. Therefore, in this study comparative methods have been used for receptor-based virtual screening, targeting 9 selected structures of viral Mpro. Reliability analyses followed by re-docking of the specific co-crystallized ligand provided the best reproductivity for structures with PDB ID 6LU7, 6Y2G and 6Y2F. The influence of crystallographic water on an outcome of a virtual screening against selected targets was also investigated. Once the most reliable targets were selected, the library of easy purchasable natural compounds were retrieved from the MolPort database (10,305 compounds) and docked against the selected Mpro proteins. To ensure the efficiency of the selected compounds, binding energies for top-15 hit ligands were calculated using Molecular Mechanics as well as their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were predicted. Based on predicted binding energies and toxicities, top-5 compounds were selected and subjected to Molecular Dynamics simulation and found to be stable in complex to act as possible inhibitors for SARS-CoV-2.},
keywords = {Docking, Molecular dynamics, Natural compounds, Protein reliability, SARS-CoV-2, Virtual screening},
pubstate = {published},
tppubtype = {article}
}
@article{Ojha2021,
title = {Therapeutics for COVID-19: from computation to practices\textemdashwhere we are, where we are heading to.},
author = {Probir Kumar Ojha, Supratik Kar, Jillella Gopala Krishna, Kunal Roy, Jerzy Leszczynski},
url = {https://link.springer.com/article/10.1007/s11030-020-10134-x#Ack1},
doi = {10.1007/s11030-020-10134-x},
year  = {2021},
date = {2021-02-01},
journal = {Mol. Divers.},
volume = {25},
pages = {625\textendash659 },
abstract = {After the 1918 Spanish Flu pandemic caused by the H1N1 virus, the recent coronavirus disease 2019 (COVID-19) brought us to the time of serious global health catastrophe. Although no proven therapies are identified yet which can offer a definitive treatment of the COVID-19, a series of antiviral, antibacterial, antiparasitic, immunosuppressant drugs have shown clinical benefits based on repurposing theory. However, these studies are made on small number of patients, and, in majority of the cases, have been carried out as nonrandomized trials. As society is running against the time to combat the COVID-19, we present here a comprehensive review dealing with up-to-date information of therapeutics or drug regimens being utilized by physicians to treat COVID-19 patients along with in-depth discussion of mechanism of action of these drugs and their targets. Ongoing vaccine trials, monoclonal antibodies therapy and convalescent plasma treatment are also discussed. Keeping in mind that computational approaches can offer a significant insight to repurposing based drug discovery, an exhaustive discussion of computational modeling studies is performed which can assist target-specific drug discovery.},
note = {NSF/CREST HRD-1547754
NSF/RISE HRD-1547836},
keywords = {Computational, Coronavirus, COVID-19, Drug, SARS-CoV-2, Vaccine},
pubstate = {published},
tppubtype = {article}
}
@article{Vijayan2020,
title = {Evaluating Donor Effects in Isoindigo-Based Small Molecular Fluorophores},
author = {Sajith M. Vijayan, Nicholas Sparks, Juganta K. Roy, Cameron Smith, Christopher Tate, Nathan I. Hammer, Jerzy Leszczynski, and Davita L. Watkins},
url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpca.0c07796},
doi = {https://doi.org/10.1021/acs.jpca.0c07796},
year  = {2020},
date = {2020-12-11},
journal = {J. Phys. Chem. A },
volume = {124},
number = {51},
pages = {10777-10786},
abstract = {Small molecular organic fluorophores have garnered significant interest because of their indispensable use in fluorescence imaging (FI) and optoelectronic devices. Herein, we designed triphenylamine (TPA)-capped donor\textendashacceptor\textendashdonor (D\textendashA\textendashD)-based fluorophores having a variation at the heterocyclic donor (D) units, 3,4-ethylenedioxythiophene (EDOT), furan (FURAN), thiophene (THIO), and 1-methyl-1H-pyrrole (MePyr), with isoindigo as the core electron acceptor (A) unit. Synthesis of these fluorophores (II-X-TPA) resulted in four symmetrical dye molecules: II-EDOT-TPA, II-FURAN-TPA, II-THIO-TPA, and II-MePyr-TPA, where TPA functioned as a terminal unit and a secondary electron donor group. Photophysical, electrochemical, and computational analyses were conducted to investigate the effect of heterocyclic donor units on the II-X-TPA derivatives. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations provided insightful features of structural and electronic properties of each fluorophore and correlated well with experimental observations. Electron density distribution maps, overlapping frontier molecular orbital diagrams, and highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) electron transfer indicated intramolecular charge transfer (ICT). Theoretical studies confirmed the experimental HOMO energy trend and demonstrated its crucial importance in understanding each heterocycle’s donor ability. Stokes shifts of up to ∼178 nm were observed, whereas absorptions and emissions were shifted deeper into the NIR region, resulting from ICT. Results suggest that this isoindigo fluorophore series has potential as a molecular scaffold for the development of efficient FI agents. The studied fluorophores can be further tuned with different donor fragments to enhance the ICT and facilitate in shifting the optical properties further into the NIR region.},
keywords = {Computational analyses, electrochemical, Photophysical, Small molecular organic fluorophores, TD-DFT},
pubstate = {published},
tppubtype = {article}
}
@article{P.Toropova2020,
title = {How the CORAL software can be used to select compounds for efficient treatment of neurodegenerative diseases?},
author = {Alla P.Toropova, Andrey A.Toropov, Danuta Leszczynska, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.taap.2020.115276},
year  = {2020},
date = {2020-12-01},
journal = {Toxicol. Appl. Pharm.},
volume = {408},
pages = {115276},
abstract = {Recommendations on the efficient application of CORAL software (http://www.insilico.eu/coral) to establish quantitative structure-property/activity relationships (QSPRs/QSARs) are provided. The predictive potential of the approach has been demonstrated for QSAR models developed for inhibitor concentrations (negative decimal logarithm of IC50) of derivatives of N-methyl-d-aspartate (NMDA) receptor, leucine-rich repeat kinase 2 (LRRK2), and tropomyosin receptor kinase A (TrkA). The above three protein targets are related to various neurodegenerative diseases such as Alzheimer's and Parkinson's. Each model was checked using several splits of the data for the training and the validation sets. The index of ideality of correlation (IIC) represents a tool to improve the predictive potential for an arbitrary model. However, the use of the IIC should be carried out according to rules, described in this work.},
keywords = {Alzheimer's DiseaseParkinson's DiseaseNeuroprotectionNeurodegenerative DiseasesBioinformaticsIn Silico Design},
pubstate = {published},
tppubtype = {article}
}
@article{Tang2020,
title = {Unveiling the critical role of p-d hybridization interaction in M13-nGan clusters on CO2 adsorption},
author = {Qingli Tang, Feng Shi, Kan Li, Wenchao Ji, Jerzy Leszczynski, Armistead G. Russell, Eric G. Eddings, Zhemin Shen, Maohong Fan},
doi = {https://doi.org/10.1016/j.fuel.2020.118446},
year  = {2020},
date = {2020-11-15},
journal = {Fuel},
volume = {280},
pages = {118446},
abstract = {Inspired by conclusions of previous studies that Ga has the promoting effect on CO2 conversion, we performed density functional theory (DFT) investigations of CO2 adsorption on forty icosahedral (Ih) symmetry 13-atom clusters. They include M13, Ga-centered M12Ga, M-centered M12Ga, Ga-centered M11Ga2 and M-centered M11Ga2 clusters (M = Fe, Co, Ni, Cu, Ru, Rh, Pd and Ag). Initially, the stabilities of these clusters were studied. The results show that Ga doped Cu, Pd, and Ag clusters are more stable than their pure metal analogues, and except Pd and Ag clusters, M-centered species are more stable than Ga-centered clusters. In addition, the activation of CO2 on these clusters was studied. The results show that most of M-centered M12Ga clusters transfer more electron density to CO2 than other corresponding Ga-doped analogues. The amount of Bader charge transfers has noteworthy linear relationship with the structural parameters of CO2. DOS analyses show that empty σ orbital of CO2 is acceptor of electrons from cluster. It is worth to mention that Ag13−nGan clusters have little interaction with CO2. To explain the effects of Ga on the adsorption of CO2, the electronic properties of clusters were studied. The projected density of states (PDOSs), charge density differences, Bader charge transfers and electron localization functions (ELFs) analyses show that Ga transfers electron density to M atom, and the effective interaction is attributed to the p orbitals of Ga with the d orbitals of M near Fermi level(0), mainly responsible for the activation of CO2.},
keywords = {13-Atom clusters, CO2 adsorption, Effects of Ga, Electronic properties},
pubstate = {published},
tppubtype = {article}
}
@article{Toropov2020,
title = {Advancement of predictive modeling of zeta potentials (ζ) in metal oxide nanoparticles with correlation intensity index (CII)},
author = {Andrey A. Toropov, Natalia Sizochenko, Alla P. Toropova, Danuta Leszczynska, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.molliq.2020.113929},
year  = {2020},
date = {2020-11-01},
journal = {J. Mol. Liq.},
volume = {317},
pages = {113929},
abstract = {It was expected that index of the ideality of correlation (IIC) and correlation intensity index (CII) could be used as possible tools to improve the predictive power of the quantitative model for zeta potential of nanoparticles. In this paper, we test how the statistical quality of quantitative structure-activity models for zeta potentials (ζ, a common measurement that reflects surface charge and stability of nanomaterial) could be improved with the use of these two indexes. Our hypothesis was tested using the benchmark data set that consists of 87 measurements of zeta potentials in water. We used quasi-SMILES molecular representation to take into consideration the size of nanoparticles in water and calculated optimal descriptors and predictive models based on the Monte Carlo method. We observed that the models developed with utilization of CII are statistically more reliable than models obtained with the IIC. However, the described approach gives an improvement of the statistical quality of these models for the external validation sets to the detriment for the training sets. Nevertheless, this circumstance is rather an advantage than a disadvantage.},
keywords = {Correlation intensity index, Index of ideality of correlation, Metal oxide nanoparticles, Nano-QSPR, Quasi-SMILES, Zeta potential},
pubstate = {published},
tppubtype = {article}
}
@article{Borysenko2020,
title = {Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction},
author = {Iryna O. Borysenko, Liudmyla K. Sviatenko, Sergiy I. Okovytyy, Jerzy Leszczynski},
doi = {https://doi.org/10.1007/s11224-020-01663-0},
year  = {2020},
date = {2020-10-19},
journal = {Struct. Chem.},
volume = {32},
pages = {581\textendash589},
abstract = {Algorithm for generation and assessment of probability of possible reaction pathways for multiple-channel bimolecular interactions is presented. The proposed algorithm comprises a combination of few steps. They include conformational search for reaction intermediate using the molecular mechanics (MMX) approach, based on the obtained conformation construction of structures of transition states and pre-reaction complexes, and calculation activation energies to further determine the probable reaction pathways. The proposed algorithm could be adopted for investigation of chemical and biochemical reactions of different types. Here, we have considered the reaction of bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine (1) with glycidyl ether (2) in a neutral environment that proceeds through SN2-like mechanism forming bipolar ion (3) which is a good starting point for identification of the reaction channels. Conformational properties of intermediate (3) have been investigated using stochastic conformational search. From the 95 localized conformations within 10 kcal/mol of global minimum that have been obtained, 63 unique transition state conformations were generated and optimized by using the PM7 and M062X/6-31G(d) methods for accurate estimation of overall rate constant of reaction. The most energetically favorable pathways have been investigated at the M062X/6-31G(d) level of theory taking into account the influence of solvent.},
keywords = {Conformational analysis, Epoxide cycle opening, Glycidyl ethers, Multiple-channel bimolecular reaction},
pubstate = {published},
tppubtype = {article}
}
@article{Wu2020,
title = {Negative thermal quenching of photoluminescence in a copper\textendashorganic framework emitter},
author = {Ting Wu, Shenlong Jiang, Pabitra Narayan Samanta, Yangbin Xie, Jipeng Li, Xiaoling Wang, Majumdar Devashis, Xiangwei Gu, Yusong Wang, Wei Huang, Qun Zhang, Jerzy Leszczynski, and Dayu Wu},
doi = {https://doi.org/10.1039/d0cc04788k},
year  = {2020},
date = {2020-10-14},
journal = {Chem. Commun.},
volume = {56},
number = {80},
pages = {12057-12060},
abstract = {Negative thermal quenching (NTQ), an abnormal phenomenon that the intensity of photoluminescence (PL) increases with increasing temperature, has essentially been restricted to either bulk semiconductors or very low temperatures. Here, we report a delayed fluorescence copper-organic framework exhibiting negative thermal quenching (NTQ) of photoluminescence, which is driven by the fluctuation between the localized and delocalized form of its imidazole ligand. The process is completely reversible on cooling/heating cycles. This study opens a new avenue to explore the electronically switchable NTQ effect in coordination networks and further to develop the NTQ-based light-emitting diodes.},
keywords = {Copper-organic framework, Delayed fluorescence, Negative thermal quenching (NTQ), SOC-TDDFT},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2020b,
title = {Is intraspecies QSTR model answer to toxicity data gap filling: Ecotoxicity modeling of chemicals to avian species},
author = {Supratik Kar, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.scitotenv.2020.139858},
year  = {2020},
date = {2020-10-10},
journal = {Sci. Total Environ.},
volume = {738},
pages = {139858},
abstract = {Interspecies model represents an established approach for the response data gap filling for regulatory agencies and researchers. We propose a novel approach of intraspecies modeling within the animals of the same species, instead of animals from different species. The proposed intraspecies model is capable of more precise extrapolation of data than the interspecies model, as animals under the same species share a similar mechanism of action (MOA) and target sites for the response. Along with the advantage of better prediction over the interspecies model, the intraspecies model has all the significant features like recognition of MOA, species-specific toxicity, reduction of animal experimentation, and money and time. To establish and test the intraspecies modeling approach, we have modeled ecotoxicity of organic chemicals to three avian species: Anas platyrhynchos, Colinus virginianus, and Phasianus colchicus. The intraspecies models offer to identify the mechanistic interpretation of the ecotoxicity of the studied chemicals along with the toxicity data gap filling. The success of the intraspecies modeling relies on connecting the missing dots of toxicity for the regulatory purposes, especially when there is a scarcity of ecotoxicity experimental data and in silico models for avian species.},
keywords = {Avian; Ecotoxicity; Intraspecies; QSTR; Regulatory},
pubstate = {published},
tppubtype = {article}
}
@article{Gorb2020,
title = {Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study},
author = {Leonid Gorb, Anatolii Pekh, Alexey Nyporko, Mykola Ilchenko, Anastasiia Golius, Tetiana Zubatiuk, Roman Zubatyuk, Igor Dubey, Dmytro M. Hovorun, and Jerzy Leszczynski},
doi = {https://doi.org/10.1021/acs.jpcb.0c06154},
year  = {2020},
date = {2020-09-25},
journal = {J. Phys. Chem. B},
volume = {124},
number = {42},
pages = {9343-9353},
abstract = {We report a comprehensive quantum-chemical study on d(A)5·d(T)5 and d(G)5·d(C)5 DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG]. The research was performed to model the evolution of the spatial structure of d(A)5·d(T)5 and d(G)5 d(C)5 DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included. Also, for comparison, limited calculations have been carried out on the Dickerson dodecamer. The study has been performed at the density functional theory level using B97D3 and ωB97XD exchange\textendashcorrelation functionals augmented by the Def2SVP basis set. We found that the (dA)5·(dT)5 anion when placed in vacuum forms a DNA duplex, which possesses an intermediate form between a helix and a ladder. The presence of compensating Na+ counterions or explicit microhydration of minor and major grooves stabilizes a DNA mini-helix of B-shape. Factors such as water bulk play a minor role. Somewhat different behavior has been found in the case of the (dG)5·(dC)5 duplex. In this case, we observe the formation of B-type mini-helixes even for the (dG)5·(dC)5 anion placed in vacuum. This is due to an additional stabilization originated from the appearance of an extra hydrogen bond, compared to an AT base pair. To assess whether the obtained results are transferable to different sizes of mini-helixes, similar calculations have been performed for the duplex formed by the Dickerson dodecamer which contains a total of 12 dG·dC and dA·dT base pairs. It has been found that in vacuum, analogous to the d(A)5·d(T)5 duplex, this system possesses a shape which is also quite close to a ladder. However, the presence of factors such as hydration restores the B-type geometry. Also, our results completely in line with the results of electrospray-ionization experiments suggest that uncompensated by counterions the DNA backbone preserves the duplex geometry in vacuum. We present arguments that this state is kinetically unstable.},
keywords = {DFT, Dickerson Dodecamer, DNA Mini-Helixes},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2020,
title = {From Animal to Human: Interspecies Analysis Provides a Novel Way of Ascertaining and Fighting COVID-19},
author = {Supratik Kar and Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.xinn.2020.100021},
year  = {2020},
date = {2020-08-28},
journal = {The Innovation},
volume = {1},
number = {2},
pages = {100021},
abstract = {There is a strong risk of mutations in the genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in animals. Consequently, a possibility of zoonotic transfer of a much stronger form of the present virus from animal to human is also very feasible in the near future. Thus, recent incidents of SARS-CoV-2 infection in animals need to be studied very carefully to protect against any future transmissions. Interspecies analysis from animal to human or vice versa is the tool of choice at the present time for understanding zoonotic transfer and improving/accelerated drug discovery for COVID-19.},
keywords = {COVID-19, Interspecies Analysis},
pubstate = {published},
tppubtype = {article}
}
@article{Kapusta2020,
title = {Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling},
author = {Karina Kapusta, Supratik Kar, Jasmine T. Collins, Latasha M. Franklin, Wojciech Kolodziejczyk, Jerzy Leszczynski & Glake A. Hill},
doi = {https://doi.org/10.1080/07391102.2020.1806930},
year  = {2020},
date = {2020-08-14},
journal = {J. Biomol. Struct. Dyn.},
volume = {39},
number = {17},
pages = {6810-6827},
abstract = {Due to an outbreak of COVID-19, the number of research papers devoted to in-silico drug discovery of potential antiviral drugs is increasing every day exponentially. Still, there is no specific drug to prevent or treat this novel coronavirus (SARS-CoV-2) disease. Thus, the screening for a potential remedy presents a global challenge for scientists. Up to date over a hundred crystallographic structures of SARS-CoV-2 Mpro have been deposited to Protein Data Bank. With many known proteins, the demand for a reliable target has become higher than ever, so as the choice of an efficient computational methods. Therefore, in this study comparative methods have been used for receptor-based virtual screening, targeting 9 selected structures of viral Mpro. Reliability analyses followed by re-docking of the specific co-crystallized ligand provided the best reproductivity for structures with PDB ID 6LU7, 6Y2G and 6Y2F. The influence of crystallographic water on an outcome of a virtual screening against selected targets was also investigated. Once the most reliable targets were selected, the library of easy purchasable natural compounds were retrieved from the MolPort database (10,305 compounds) and docked against the selected Mpro proteins. To ensure the efficiency of the selected compounds, binding energies for top-15 hit ligands were calculated using Molecular Mechanics as well as their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were predicted. Based on predicted binding energies and toxicities, top-5 compounds were selected and subjected to Molecular Dynamics simulation and found to be stable in complex to act as possible inhibitors for SARS-CoV-2.},
keywords = {Docking, Molecular dynamics, Natural compounds, Protein reliability, SARS-CoV-2, Virtual screening},
pubstate = {published},
tppubtype = {article}
}
@article{Roy2020,
title = {Revealing the Photophysical Mechanism of N,N′-Diphenyl-aniline Based Sensitizers with the D\textendashD−π\textendashA Framework: Theoretical Insights},
author = {Juganta K. Roy, Supratik Kar, and Jerzy Leszczynski},
doi = {https://doi.org/10.1021/acssuschemeng.0c04061},
year  = {2020},
date = {2020-08-10},
journal = {ACS Sustainable Chem. Eng.},
volume = {8},
number = {35},
pages = {13328\textendash13341},
abstract = {The D\textendashD−π\textendashA framework based dyes are competent for lowering the aggregation and reducing the charge recombination inherently due to their 3D structures. Seven D\textendashD−π\textendashA-based N,N′-diphenyl-aniline (NNdPA) dyes are designed and investigated using cluster and periodic density functional theory (DFT) approaches to evaluate their prospect of application in the future dye-sensitized solar cells (DSSCs). The critical parameters related to short-circuit photocurrent density (JSC) and open-circuit voltage (VOC) of the considered dyes such as the driving force of electron injection (ΔGInject), the spontaneity of dye regeneration (ΔGReg), the exciton binding synergy (Eb), the charge transfer length (dCT), the reorganization energy (λTotal), the shift of the conduction band of TiO2 (ΔECB), the projected density of states (PDOS), and the chemical reactivity parameters were computed. Computed results implied that the fused π-conjugation bridge, along with the benzothiadiazole (BTD) unit, improves the absorption spectrum and charge separation. Also, incorporation of the benzene ring lowers λTotal with balancing its counterparts’ reorganization energy. Considering the dye characteristics after electron injection, NNdPA04 with large Stokes shift would possess the most stable excited state due to longer excited state lifetime, τe, with the lowest driving force between excited state oxidation potential and conduction band minimum of TiO2. We found that the presence of the benzene ring in the fused π-conjugation unit increases the light harvesting by shifting the UV\textendashvis spectrum to a longer wavelength. The values of ΔECB and ΔGReg suggest that the NNdPA04 and NNdPA10 would be able to suppress the charge recombination and thus enhance VOC of NNdPA-based dyes. The outcomes inferred that the designed NNdPA04 dye could be the lead candidate for the photoefficient NNdPA-based DSSCs. Our work also provides a rational insight into designing the D\textendashD−π\textendashA dyes with a fused π-conjugation.},
keywords = {Charge recombination, DFT, DSSCs, Fused π-conjugation, Organic dyes},
pubstate = {published},
tppubtype = {article}
}
@article{Leszczynski2020,
title = {Open access in silico tools to predict the ADMET profiling of drug candidates, Expert Opinion on Drug Discovery},
author = {Supratik Kar & Jerzy Leszczynski},
doi = {https://doi.org/10.1080/17460441.2020.1798926},
year  = {2020},
date = {2020-07-31},
journal = {Expert Opin. Drug Discov.},
volume = {15},
number = {12},
pages = {1473-1487},
abstract = {Introduction: We are in an era of bioinformatics and cheminformatics where we can predict data in the fields of medicine, the environment, engineering and public health. Approaches with open access in silico tools have revolutionized disease management due to early prediction of the absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles of the chemically designed and eco-friendly next-generation drugs.

Areas covered: This review meticulously encompasses the fundamental functions of open access in silico prediction tools (webservers and standalone software) and advocates their use in drug discovery research for the safety and reliability of any candidate-drug. This review also aims to help support new researchers in the field of drug design.

Expert opinion: The choice of in silico tools is critically important for drug discovery and the accuracy of ADMET prediction. The accuracy largely depends on the types of dataset, the algorithm used, the quality of the model, the available endpoints for prediction, and user requirement. The key is to use multiple in silico tools for predictions and comparing the results, followed by the identification of the most probable prediction.},
keywords = {ADMET profiling, Drug candidates, in silico, Open access},
pubstate = {published},
tppubtype = {article}
}
@article{Gorb2020b,
title = {A density functional theory study of simplest nanocomposites formed by graphene oxide and polyvinyl alcohol: geometry, interaction energy and vibrational spectrum},
author = {Leonid Gorb, Mykola Ilchenko, Jerzy Leszczynski},
doi = {https://doi.org/10.1007/s00894-020-04447-9},
year  = {2020},
date = {2020-06-25},
journal = {J.Mol. Model.},
volume = {26},
number = {7},
pages = {183},
abstract = {A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of electrostatic and dispersion components. Also, we computationally generated IR spectra of intercalates and compared them with those experimentally obtained. Two sources of interaction energy to stabilize the intercalates between graphene oxide and PVA are suggested. They are the electrostatic and dispersion (van-der-Waals) components. We also revealed that ωB97XD density functional in conjunction with 6-31G(d,p) basis set is qualitatively able to describe IR spectra of considered species.},
keywords = {Density functional theory; Graphene oxide; IR spectra; Intercalates, interaction energy; Polyvinyl alcohol.},
pubstate = {published},
tppubtype = {article}
}
@article{Zhou2020,
title = {Relative order of acidity among hydroxyl groups of oxyluciferin and emission light colors in aqueous solution},
author = {Jian-Ge Zhou, Shan Yang, Zhen-Yan Deng, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.jphotochem.2020.112504},
year  = {2020},
date = {2020-06-15},
journal = {J. Photoch. Photobio. A},
volume = {397},
pages = {112504},
abstract = {The magnitude of the acidity of the oxyluciferin in water in the ground and excited state is investigated, and it is found for the first time using computational approach that the enol group of the phenol-enol species is the most acidic in the ground state, but the deprotonation of the phenol of the phenol-keto form is the most favored in the excited state. The relative order of the acidity among the hydroxyl groups in the oxyluciferin is attributed to the sequence of the Osingle bondH bond lengths in the enol and phenol group of the phenol-enol form, and the phenol group of the phenol-keto species. The mechanism of determining the dominant emissive species in the excited state is proposed, and the dependence of emission light colors on the photoexcitation energy is elucidated by the high relative concentration of six chemical forms in the ground state and the absorption efficiency.},
keywords = {Absorption and emission spectra, Excited state proton transfer, Firefly luciferin, pKa},
pubstate = {published},
tppubtype = {article}
}
@article{Ghosh2020,
title = {Chemometric Modeling of the Ecotoxicity of Industrial Chemicals to an Avian Species Anas Platyrhynchos},
author = {Shinjita Ghosh, Supratik Kar, Jerzy Leszczynski},
doi = {http://dx.doi.org/10.4018/IJQSPR.2020040101},
year  = {2020},
date = {2020-04-01},
journal = {Int J Quantum Struc Prop Rel },
volume = {5},
number = {2},
pages = {1-16},
abstract = {Birds or avians have been imperative species in the ecology, having been evaluated in an effort to understand the toxic effects of endocrine disruption. The ecotoxicity of 56 industrial chemicals classified as endocrine disruptors were modeled employing classification and regression-based quantitative structure-activity relationship (QSAR) models to an important avian species, Anas platyrhynchos. The classification- and regression-based QSAR models were developed using linear discriminant analysis (LDA) and partial least squares (PLS) tools, respectively. All models were validated meticulously by employing internal and external validation metrics followed by randomization test, applicability domain (AD) study, and intelligent consensus prediction of all individual models. Features like topological distance of 1, 3, and 5 between atoms O-P, C-P, and N-S, correspondingly, along with the CR3X fragment, can be responsible for an increase in toxicity. On the contrary, the presence of S-Cl with topological distance 6 is accountable for lowering the toxicity of towards A. platyrhynchos. The developed chemometric models can offer significant evidence and guidance in the framework of virtual screening as well as a toxicity prediction of new and/or untested chemical libraries towards this specific avian species.
},
keywords = {Avian Species, Chemometric Modeling, Ecotoxicity},
pubstate = {published},
tppubtype = {article}
}
@article{Krishna2020,
title = {Chemometric modeling of power conversion efficiency of organic dyes in dye sensitized solar cells for the future renewable energy},
author = {Jillella Gopala Krishna, Probir Kumar Ojha, Supratik Kar, Kunal Roy, Jerzy Leszczynski},
doi = {https://doi.org/10.1016/j.nanoen.2020.104537},
year  = {2020},
date = {2020-04-01},
journal = {Nano Energy},
volume = {70},
pages = {104537},
abstract = {The present study reports chemometric modeling of power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs) using the biggest available data set till date which comprises around 1200 dyes covering 7 chemical classes. To extract the best structural features required for higher PCE, we have developed multiple partial least squares (PLS) quantitative structure-property relationship (QSPR) models for the Triphenylamine, Phenothiazine, Indoline, Porphyrin, Coumarin, Carbazole and Diphenylamine chemical classes using descriptors derived from the best subset selection method followed by selection of best five models in each dataset based on the Mean Absolute Error (MAE) values. The models were validated both internally and externally followed by the consensus predictions employing “Intelligent Consensus Predictor” tool to examine whether the quality of predictions can be improved with the “intelligent” selection of multiple PLS models. The quality of predictions for the respective external sets showed that the consensus models (CM) are better than the individual models (IM) in most of the cases. From the insights of the developed models, we concluded that attributes like a packed structure toward higher conductivity of electrons, auxiliary donor fragment of aromatic tertiary amines, number of thiophenes inducing the bathochromic shift and augmenting the absorption, presence of additional electron donors, enhancement of electron-donating abilities, number of non-aromatic conjugated C(sp2) which helps as conjugation extension units to broaden the absorption and highly conjugated π-systems exert positive contributions to the PCE. On the contrary, features negatively contributing to PCE are the followings: fragments which lower the tendency of localized π\textendashπ* transition, fragments related to larger volume and surface area of dyes along with hydrophobicity resulting in poor adhesion, fragment RC = N causing dye hydrolysis, steric hindrance for π electronic mobility, fragments enhancing polarity, etc. The identified features from the best QSPR model of the coumarin dataset was employed in designing of ten more efficient coumarin dyes (predicted %PCE ranging from 8.93 to 10.62) than the existing ones.},
keywords = {Chemometrics, DSSC, Dye, PCE, QSPR, Solar cell},
pubstate = {published},
tppubtype = {article}
}
@article{Afantitis2020,
title = {NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment},
author = {Antreas Afantitis, Georgia Melagraki, Panagiotis Isigonis, Andreas Tsoumanis, …. Jerzy Leszczynski, Christine Ogilvie Hendren, Mark Wiesner, David Winkler, Noriyuki Suzuki, Tae Hyun Yoon, Jang-Sik Choi, Natasha Sanabria, Mary Gulumian, Iseult Lynch},
doi = {https://doi.org/10.1016/j.csbj.2020.02.023},
year  = {2020},
date = {2020-03-20},
journal = {Comput Struc Biotechnol},
volume = {18},
pages = {583\textendash602},
abstract = {Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals. Here, the available NM libraries are analyzed for their suitability for integration with novel nanoinformatics approaches and for the development of NM specific Integrated Approaches to Testing and Assessment (IATA) for human and environmental risk assessment, all within the NanoSolveIT cloud-platform. These established and well-characterized NM libraries (e.g. NanoMILE, NanoSolutions, NANoREG, NanoFASE, caLIBRAte, NanoTEST and the Nanomaterial Registry (>2000 NMs)) contain physicochemical characterization data as well as data for several relevant biological endpoints, assessed in part using harmonized Organisation for Economic Co-operation and Development (OECD) methods and test guidelines. Integration of such extensive NM information sources with the latest nanoinformatics methods will allow NanoSolveIT to model the relationships between NM structure (morphology), properties and their adverse effects and to predict the effects of other NMs for which less data is available. The project specifically addresses the needs of regulatory agencies and industry to effectively and rapidly evaluate the exposure, NM hazard and risk from nanomaterials and nano-enabled products, enabling implementation of computational ‘safe-by-design’ approaches to facilitate NM commercialization.},
keywords = {Nanoinformatics; Computational toxicology; Hazard assessment; Engineered nanomaterials; QSAR; Integrated approach for testing and assessment; Safe-by-design; Machine learning},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2020b,
title = {The index of ideality of correlation: models of the flash points of ternary mixtures},
author = {Alla P. Toropova, Andrey A. Toropov, Danuta Leszczynskab and Jerzy Leszczynski},
doi = {https://doi.org/10.1039/D0NJ00121J},
year  = {2020},
date = {2020-02-17},
journal = {New J Chem},
volume = {44},
pages = {4858-4868},
abstract = {Reliable information related to the flash point of ternary mixtures assists in the rational classification of different ternary mixtures of liquids. Hence, dependable computational models for the predictions of the above-mentioned endpoint can be useful. A simplified molecular input-line entry system (SMILES) is the representation of the molecular structure. Quasi-SMILES is the expansion of traditional SMILES by means of additional symbols that reflect “eclectic”, which are able to influence the physicochemical behaviour of substances. The application of quasi-SMILES to build up a model for the flammability of ternary liquid mixtures has indicated that the approach provides a very good model for the flash points of the ternary mixtures of organic substances. The index of ideality of correlation (IIC) is a criterion of the predictive potential of the QSPR/QSAR models. The attempts of applying IIC to improve models for the flammability of ternary liquid mixtures confirm the applicability of this criterion to improve the predictive potential of the above-mentioned models.},
keywords = {Index of ideality of correlation, QSPR/QSAR models, Quasi-SMILES, Ternary mixtures of liquids},
pubstate = {published},
tppubtype = {article}
}
@article{Portis2020,
title = {Cleft-Induced Ditopic Binding of Spherical Halides with a Hexaurea Receptor},
author = {Bobby Portis, Ali Mirchi, Mohammad H. Hasan, Maryam Emami Khansari, Corey R. Johnson, Jerzy Leszczynski, Ritesh Tandon, and Md. Alamgir Hossain},
doi = {https://doi.org/10.1002/slct.201903950},
year  = {2020},
date = {2020-01-31},
journal = {Chem. Select},
volume = {5},
number = {4},
pages = {1401-1409},
abstract = {A tripodal-based hexaurea receptor with two clefts (inner cleft and outer cleft) has been studied for spherical halides by 1H NMR, UV-Vis titrations, and theoretical calculations using density functional theory (DFT). As demonstrated from experimental and computational results, the receptor exhibits cleft-induced binding for halides in a 1 : 2 binding mode, showing the binding strength in the order of fluoride > chloride > bromide > iodide. The strongest affinity for fluoride is attributed due to the best fit of two fluoride anions at the two clefts within the host‘s cavity. This is also supported by DFT calculations, suggesting that each anion is stabilized by six NH⋅⋅⋅F bonds - one at the inner cleft and other at the outer cleft. In addition, the synthesized receptor, as examined on HeLa cells, has been found to show good biocompatibility.},
keywords = {Binding of Spherical Halides, DFT calculations, Tripodal-based hexaurea receptor, UV-Vis titrations},
pubstate = {published},
tppubtype = {article}
}
@inbook{Ghosh2020b,
title = {Chapter: Ecotoxicity Databases for QSAR Modeling},
author = {Shinjita Ghosh, Supratik Kar, Jerzy Leszczynski},
editor = {Kunal Roy, (ed.)},
doi = {https://doi.org/10.1007/978-1-0716-0150-1_29},
year  = {2020},
date = {2020-01-28},
volume = {Ecotoxicological QSARs},
pages = {709-758},
publisher = {Springer Science+Business Media, LLC, part of Springer Nature},
edition = {1},
chapter = {29},
series = {Methods In Pharmacology and Toxicology},
abstract = {Industrial chemicals, pharmaceuticals along with illicit drugs (IDs), as well as day-to-day personal care products (PCPs) are documented as contaminants of emerging concerns (CECs). They are environmental pollutants due to their substantial detrimental impacts on the environment through their frequent presence, persistence, and peril to the species living in aquatic, terrestrial, and soil compartments as well as to humans. Although the toxic effects and occurrence concentration of pharmaceuticals and chemicals have been studied and reported for the last three decades, PCPs and IDs are quite neglected substances along with the mixtures and transformation products (TPs) or metabolites of all CECs, in the context of their ecotoxicological risk evaluation. Among various compartments, the effects of CECs are largely documented for aquatic species where often very little information is available with regard to terrestrial and soil toxicity. This deficiency of knowledge has led to greater effort to create new methods and approaches which would measure their occurrence, metabolism, bioaccumulation, and biodegradability followed by the mechanism of action (MOA) behind toxicity to individual living species and ecosystem. This information is very important for risk assessment and risk management along with regulatory decision-making followed by in silico or computational modeling for future ecotoxicity. Thus, the obtained information needs to be documented under a system called “database” based on different categories including chemical class, toxicity testing, test species, environmental compartment-specific, toxicity MOA specific as well as country. Ecotoxicity has a number of open-access and commercial databases which are implemented for risk profiling, regulatory decision-making followed by ecotoxicity prediction of new and untested substances over the years. The present chapter deals with the most commonly used ecotoxicity databases followed by their detailed information so that one can use these databases efficiently in experimental as well as computational research.},
keywords = {Database, Ecotoxicity, in silico, QSAR, Risk assessment, Risk management},
pubstate = {published},
tppubtype = {inbook}
}
@article{Samanta2020,
title = {First-Principles Approach for Assessing Cold Electron Injection Efficiency of Dye-Sensitized Solar Cell: Elucidation of Mechanism of Charge Injection and Recombination},
author = {Pabitra Narayan Samanta, D. Majumdar, Szczepan Roszak, and Jerzy Leszczynski},
doi = {https://doi.org/10.1021/acs.jpcc.9b10616},
year  = {2020},
date = {2020-01-17},
journal = {J. Phys. Chem. C},
volume = {124},
number = {5},
pages = {2817\textendash2836},
abstract = {The adequacy of the inclusion of spacer units in the metal-free D−π\textendashA organic dyes concerning the augmentation of dye-sensitized solar cell (DSSC) efficiency has been examined through the excited-state simulations of the charge injection and recombination processes at the dye\textendashsemiconductor interface. Within the framework of the time-dependent density functional theory, the proposed computational studies focus on the precise evaluation of pivotal factors controlling the rates of photoinduced charge-transfer and energy-transfer processes, including electronic coupling, reorganization energy, and threshold energy barrier in the semiclassical Marcus formalism. The estimation of the fluorescent state appears to be the crucial step while explaining the ultrafast electron injection process and the charge recombination at the Marcus inverted region, as revealed by the obtained results. The retardation of charge recombination is facilitated by the insertion of a thiophene moiety between the π-bridge and the acceptor units. The estimated cold electron injection efficiencies deploying the Onsager\textendashBraun theory, which rely on the computations of cold electron injection lifetime and cold electron lifetime, show a linear correlation with the experimental photovoltaic parameters of the DSSC comprising short-circuit current density, open-circuit voltage, and power conversion efficiency. The outcomes of the present investigation establish a basis for unraveling the mechanism of intricate dynamical processes upon photoexcitation of the sensitizers, as well as devising plausible routes for functional DSSC materials.},
keywords = {Charge injection and recombination processes, Cold Electron Injection Efficiency, DSSC, Excited-state simulations},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2020c,
title = {Ecotoxicological assessment of pharmaceuticals and personal care products using predictive toxicology approaches},
author = {Supratik Kar, Hans Sanderson, Kunal Roy, Emilio Benfenati and Jerzy Leszczynski},
doi = {https://doi.org/10.1039/C9GC03265G},
year  = {2020},
date = {2020-01-09},
journal = {Green Chem.},
volume = {22},
pages = {1458-1516},
abstract = {The use of active pharmaceutical ingredients (APIs) and personal care products (PCPs) is growing day by day all over the world. Thus, these materials have appeared as contaminants of emerging concern (CEC) responsible for hazards and toxicity towards aquatic and terrestrial living systems as well as to humans. Regulatory agencies from all over the world have formulated multiple rules, guidelines and regulations for the risk assessment of pharmaceuticals and PCPs (PPCPs) to the ecosystem. As the generation of a huge amount of experimental data is time consuming and costly, and also requires sacrifice of a large number of animals, computational modeling or in silico approaches are proving to be an efficient technique for not only risk assessment, but also for risk management and data gap filling. The present review deals with the critical assessment of the hazardous potential of PPCPs in the environment. The importance of in silico modeling approaches for the environmental toxicity endpoints to diverse organisms covering all compartments of taxonomy, details of the most commonly employed endpoints, ecotoxicity databases and expert systems as rapid screening tools are discussed meticulously with complete mechanistic interpretations of in silico models reported over the years.},
keywords = {Ecotoxicological assessment, in silico modeling},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2019b,
title = {Is clay-polycation adsorbent future of the greener society? In silico modeling approach with comprehensive virtual screening},
author = {Kar, Supratik and Ghosh, Shinjita and Leszczynski, Jerzy},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653518325578},
doi = {10.1016/j.chemosphere.2018.12.215},
issn = {00456535},
year  = {2019},
date = {2019-04-01},
journal = {Chemosphere},
volume = {220},
pages = {1108--1117},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2019b,
title = {Semi-correlations combined with the index of ideality of correlation: a tool to build up model of mutagenic potential},
author = {Toropova, Alla P. and Toropov, Andrey A. and Veselinovi\'{c}, Aleksandar M. and Veselinovi\'{c}, Jovana B. and Leszczynska, Danuta and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/s11010-018-3419-4},
doi = {10.1007/s11010-018-3419-4},
issn = {0300-8177},
year  = {2019},
date = {2019-02-01},
journal = {Molecular and Cellular Biochemistry},
volume = {452},
number = {1-2},
pages = {133--140},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Roy2019b,
title = {Electronic Structure and Optical Properties of Designed Photo-Efficient Indoline-Based Dye-Sensitizers with D\textendashA−$pi$\textendashA Framework},
author = {Roy, Juganta K. and Kar, Supratik and Leszczynski, Jerzy},
url = {http://pubs.acs.org/doi/10.1021/acs.jpcc.8b10708},
doi = {10.1021/acs.jpcc.8b10708},
issn = {1932-7447},
year  = {2019},
date = {2019-02-01},
journal = {The Journal of Physical Chemistry C},
volume = {123},
number = {6},
pages = {3309--3320},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2019b,
title = {Predicting Thermal Conductivity Enhancement of Al2O3/Water and CuO/Water Nanofluids Using Quantitative Structure-Property Relationship Approach},
author = {Sizochenko, Natalia and Kar, Supratik and Syzochenko, Michael and Leszczynski, Jerzy},
url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/IJQSPR.2019010102},
doi = {10.4018/IJQSPR.2019010102},
issn = {2379-7487},
year  = {2019},
date = {2019-01-01},
journal = {International Journal of Quantitative Structure-Property Relationships},
volume = {4},
number = {1},
pages = {18--27},
abstract = {In the current contribution, the authors have applied a quantitative structure-property relationship (QSPR) approach to develop theoretical models of thermal conductivity enhancement in water-based nanofluids (Al2O3 and CuO). The developed models represent physical properties of nanofluids as functions of experimentally measured and calculated descriptors. The developed model for Al2O3 is characterized by determination coefficient R2= 0.876 (training) and R2= 0.826 (test); the model for CuO is characterized by R2 = 0.984 (training) and R2= 0.912 (test). The developed models are in good agreement with modern theories of nanofluids behavior. Size-dependent and concentration-dependent behavior of thermal conductivity of Al2O3 and CuO nanoparticles properties were discussed. The authors found that thermal conductivity increases with increase of weighted fraction-dependent parameters. The developed models have been compared with the existing models for thermal conductivity of Al2O3 and CuO water-based nanofluids.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kuzmin2019b,
title = {Combining Features of Metal Oxide Nanoparticles},
author = {Kuz'min, Victor E and Ognichenko, Liudmila N and Sizochenko, Natalia and Chapkin, Valery A. and Stelmakh, Sergii I. and Shyrykalova, Angela O. and Leszczynski, Jerzy},
url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/IJQSPR.2019010103},
doi = {10.4018/IJQSPR.2019010103},
issn = {2379-7487},
year  = {2019},
date = {2019-01-01},
journal = {International Journal of Quantitative Structure-Property Relationships},
volume = {4},
number = {1},
pages = {28--40},
abstract = {A poor applicability of classic 2D descriptors for representation of metal oxide nanoparticles is briefly discussed. The combination of 1D descriptors with previously calculated size-dependent descriptors is utilized to represent the structural features of nanoparticles in QSAR modeling. For this purpose, descriptors based on the fundamental characteristics of atoms (nuclear charge, oxidation level, electronegativity, ionic radius, ionic refraction etc.) were combined with those derived from structural formula (doublets \textendashA2, AB, \ldots; triplets \textendash A3, A2B, ABC, \ldots etc.) and “liquid drop model” derived size-dependent parameters. Nano-QSAR models are developed for cytotoxicity of metal oxide nanoparticles against E. coli and HaCaT cells. Two developed nano-QSAR models are discussed in terms of cluster analysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Roy2018,
title = {Insight into the optoelectronic properties of designed solar cells efficient tetrahydroquinoline dye-sensitizers on TiO2(101) surface: first principles approach},
author = { Juganta K. Roy and  Supratik Kar and  Jerzy Leszczynski},
url = {http://www.nature.com/articles/s41598-018-29368-9},
doi = {10.1038/s41598-018-29368-9},
issn = {2045-2322},
year  = {2018},
date = {2018-12-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
pages = {10997},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jean2018,
title = {QSAR modeling of adipose/blood partition coefficients of Alcohols, PCBs, PBDEs, PCDDs and PAHs: A data gap filling approach},
author = {Jean, Jephthe and Kar, Supratik and Leszczynski, Jerzy},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0160412018319858},
doi = {10.1016/j.envint.2018.10.037},
issn = {01604120},
year  = {2018},
date = {2018-12-01},
journal = {Environment International},
volume = {121},
pages = {1193--1203},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2018,
title = {Single or mixture halogenated chemicals? Risk assessment and developmental toxicity prediction on zebrafish embryos based on weighted descriptors approach},
author = { Supratik Kar and  Shinjita Ghosh and  Jerzy Leszczynski},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653518313092},
doi = {10.1016/j.chemosphere.2018.07.051},
issn = {00456535},
year  = {2018},
date = {2018-11-01},
journal = {Chemosphere},
volume = {210},
pages = {588--596},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mirchi2018b,
title = {Catalytic abiotic synthesis of uracil from cysteine and urea: Theoretical studies},
author = {Mirchi, Ali and Sizochenko, Natalia and Wang, Jing and Leszczynski, Jerzy},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0009261418306845},
doi = {10.1016/j.cplett.2018.08.057},
issn = {00092614},
year  = {2018},
date = {2018-10-01},
journal = {Chemical Physics Letters},
volume = {710},
pages = {16--25},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Chatterjee2018,
title = {Ultrasound cavitation intensified amine functionalization: A feasible strategy for enhancing CO 2 capture capacity of biochar},
author = { Riya Chatterjee and  Baharak Sajjadi and  Daniell L. Mattern and  Wei-Yin Chen and  Tetiana Zubatiuk and  Danuta Leszczynska and  Jerzy Leszczynski and  Nosa O. Egiebor and  Nathan Hammer},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0016236118305532 http://link.springer.com/10.1007/978-1-4939-7899-1_19},
doi = {10.1016/j.fuel.2018.03.145},
issn = {00162361},
year  = {2018},
date = {2018-08-01},
journal = {Fuel},
volume = {225},
pages = {287--298},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Zubatiuk2018,
title = {Insight into mechanism of iron-oxides reduction in atmospheres of CH 4 and CO},
author = { Tetiana Zubatiuk and  Glake Hill and  Danuta Leszczynska and  Maohong Fan and  Asif H. Rony and  Jerzy Leszczynski},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0009261418305724},
doi = {10.1016/j.cplett.2018.07.027},
issn = {00092614},
year  = {2018},
date = {2018-08-01},
journal = {Chemical Physics Letters},
volume = {706},
pages = {708--714},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2018,
title = {Prediction of antimicrobial activity of large pool of peptides using quasi-SMILES},
author = { Alla P. Toropova and  Andrey A. Toropov and  Emilio Benfenati and  Danuta Leszczynska and  Jerzy Leszczynski},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0303264718300960},
doi = {10.1016/j.biosystems.2018.05.003},
issn = {03032647},
year  = {2018},
date = {2018-07-01},
journal = {Biosystems},
volume = {169-170},
pages = {5--12},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mirchi2018,
title = {Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: a combined molecular docking, QSAR, and ONIOM approach},
author = { Ali Mirchi and  Natalia Sizochenko and  Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-018-1100-x},
doi = {10.1007/s11224-018-1100-x},
issn = {1040-0400},
year  = {2018},
date = {2018-06-01},
journal = {Structural Chemistry},
volume = {29},
number = {3},
pages = {765--775},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Golbamaki2018,
title = {Genotoxicity induced by metal oxide nanoparticles: a weight of evidence study and effect of particle surface and electronic properties},
author = { Azadi Golbamaki and  Nazanin Golbamaki and  Natalia Sizochenko and  Bakhtiyor Rasulev and  Jerzy Leszczynski and  Emilio Benfenati},
url = {https://www.tandfonline.com/doi/full/10.1080/17435390.2018.1478999},
doi = {10.1080/17435390.2018.1478999},
issn = {1743-5390},
year  = {2018},
date = {2018-06-01},
journal = {Nanotoxicology},
pages = {1--17},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{C.P.2018,
title = {Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition},
author = { Anju C.P. and  Sunitha Subhramanian and  Natalia Sizochenko and  Anu R. Melge and  Jerzy Leszczynski and  C. Gopi Mohan},
url = {https://www.tandfonline.com/doi/full/10.1080/07391102.2018.1462731},
doi = {10.1080/07391102.2018.1462731},
issn = {0739-1102},
year  = {2018},
date = {2018-05-01},
journal = {Journal of Biomolecular Structure and Dynamics},
pages = {1--15},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropov2018,
title = {Towards the Development of Global Nano-Quantitative Structure\textendashProperty Relationship Models: Zeta Potentials of Metal Oxide Nanoparticles},
author = { Andrey Toropov and  Natalia Sizochenko and  Alla Toropova and  Jerzy Leszczynski},
url = {http://www.mdpi.com/2079-4991/8/4/243},
doi = {10.3390/nano8040243},
issn = {2079-4991},
year  = {2018},
date = {2018-04-01},
journal = {Nanomaterials},
volume = {8},
number = {4},
pages = {243},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kapusta2018,
title = {QSPR modeling of optical rotation of amino acids using specific quantum chemical descriptors},
author = { Karina Kapusta and  Natalia Sizochenko and  Sedat Karabulut and  Sergiy Okovytyy and  Eugene Voronkov and  Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s00894-018-3593-z},
doi = {10.1007/s00894-018-3593-z},
issn = {1610-2940},
year  = {2018},
date = {2018-03-01},
journal = {Journal of Molecular Modeling},
volume = {24},
number = {3},
pages = {59},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Khan2018,
title = {Interactions of Substituted Nitroaromatics with Model Graphene Systems: Applicability of Hammett Substituent Constants To Predict Binding Energies},
author = { Mehedi H. Khan and  Danuta Leszczynska and  D. Majumdar and  Szczepan Roszak and  Jerzy Leszczynski},
url = {http://pubs.acs.org/doi/10.1021/acsomega.7b01912},
doi = {10.1021/acsomega.7b01912},
issn = {2470-1343},
year  = {2018},
date = {2018-03-01},
journal = {ACS Omega},
volume = {3},
number = {3},
pages = {2773--2785},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ivashchenko2018,
title = {Electronic, thermodynamics and mechanical properties of LaB 6 from first-principles},
author = { V.I. Ivashchenko and  P.E.A. Turchi and  V.I. Shevchenko and  N.R. Medukh and  Jerzy Leszczynski and  Leonid Gorb},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0921452617310372},
doi = {10.1016/j.physb.2017.12.044},
issn = {09214526},
year  = {2018},
date = {2018-02-01},
journal = {Physica B: Condensed Matter},
volume = {531},
pages = {216--222},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gu2018,
title = {Structure and Energetics of (111) Surface of $gamma$-Al 2 O 3 : Insights from DFT Including Periodic Boundary Approach},
author = { Jiande Gu and  Jing Wang and  Jerzy Leszczynski},
url = {http://pubs.acs.org/doi/10.1021/acsomega.7b01921},
doi = {10.1021/acsomega.7b01921},
issn = {2470-1343},
year  = {2018},
date = {2018-02-01},
journal = {ACS Omega},
volume = {3},
number = {2},
pages = {1881--1888},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2018,
title = {How the toxicity of nanomaterials towards different species could be simultaneously evaluated: a novel multi-nano-read-across approach},
author = { Natalia Sizochenko and  Alicja Mikolajczyk and  Karolina Jagiello and  Tomasz Puzyn and  Jerzy Leszczynski and  Bakhtiyor Rasulev},
url = {http://xlink.rsc.org/?DOI=C7NR05618D},
doi = {10.1039/C7NR05618D},
issn = {2040-3364},
year  = {2018},
date = {2018-01-01},
journal = {Nanoscale},
volume = {10},
number = {2},
pages = {582--591},
abstract = {Identification of hidden patterns for nanoparticle toxicity against different species could be used for the safe-by-design approach.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@inbook{Sizochenko2018a,
title = {Chapter: In Silico Methods for Nanotoxicity Evaluation: Opportunities and Challenges},
author = { Natalia Sizochenko and Alicja Mikolajczyk and Jerzy Leszczynski and Tomasz Puzyn},
editor = {Vineet Kumar and Dasgupta, Nandita and Ranjan, Shivendu},
isbn = {9781498799416},
year  = {2018},
date = {2018-01-01},
booktitle = {Nanotoxicology: Toxicity Evaluation, Risk Assessment and Management},
pages = {527--557},
publisher = {CRC Press Taylor & Francis Group},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
@article{Golius2018,
title = {Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations},
author = { Anastasiia Golius and  Leonid Gorb and  Olexander Isayev and  Jerzy Leszczynski},
url = {https://www.tandfonline.com/doi/full/10.1080/07391102.2018.1424037},
doi = {10.1080/07391102.2018.1424037},
issn = {0739-1102},
year  = {2018},
date = {2018-01-01},
journal = {Journal of Biomolecular Structure and Dynamics},
pages = {1--9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Samanta2018,
title = {High-temperature thermoelectric transport behavior of the Al/$gamma$-Al 2 O 3 interface: impact of electron and phonon scattering at nanoscale metal\textendashceramic contacts},
author = { Pabitra Narayan Samanta and  Jerzy Leszczynski},
url = {http://xlink.rsc.org/?DOI=C8CP01374H},
doi = {10.1039/C8CP01374H},
issn = {1463-9076},
year  = {2018},
date = {2018-01-01},
journal = {Physical Chemistry Chemical Physics},
volume = {20},
number = {21},
pages = {14513--14524},
abstract = {Thermoelectric transport properties of the Al/$gamma$-Al 2 O 3 interface have been assessed from the ballistic electron and phonon transmission at the nanoscale contacts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@inbook{Kar2018a,
title = {Impact of Pharmaceuticals on the Environment: Risk Assessment Using QSAR Modeling Approach},
author = { Supratik Kar and Kunal Roy and Jerzy Leszczynski},
editor = {Orazio Nicolotti },
url = {http://link.springer.com/10.1007/978-1-4939-7899-1_6 http://link.springer.com/10.1007/978-1-4939-7899-1_19},
doi = {10.1007/978-1-4939-7899-1_19},
year  = {2018},
date = {2018-01-01},
booktitle = {Computational Toxicology: Methods and Protocols, Methods in Molecular Biology},
volume = {1800},
pages = {395--443},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
@inbook{Kar2018b,
title = {Applicability Domain: A Step Toward Confident Predictions and Decidability for QSAR Modeling},
author = { Supratik Kar and Kunal Roy and Jerzy Leszczynski},
editor = {Orazio Nicolotti},
url = {http://link.springer.com/10.1007/978-1-4939-7899-1_6},
doi = {10.1007/978-1-4939-7899-1_6},
year  = {2018},
date = {2018-01-01},
booktitle = {Toxicology: Methods and Protocols, Methods in Molecular Biology},
volume = {1800},
pages = {141--169},
publisher = {Springer Nature },
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
@article{Kar2017b,
title = {In silico designing of power conversion efficient organic lead dyes for solar cells using todays innovative approaches to assure renewable energy for future},
author = {Kar, Supratik and Roy, Juganta K. and Leszczynski, Jerzy},
url = {http://www.nature.com/articles/s41524-017-0025-z},
doi = {10.1038/s41524-017-0025-z},
issn = {2057-3960},
year  = {2017},
date = {2017-12-01},
journal = {npj Computational Materials},
volume = {3},
number = {1},
pages = {22},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{EmamiKhansari2017,
title = {Remarkable hexafunctional anion receptor with operational urea-based inner cleft and thiourea-based outer cleft: Novel design with high-efficiency for sulfate binding},
author = { Maryam Emami Khansari and Ali Mirchi and Avijit Pramanik and Corey R. Johnson and Jerzy Leszczynski and Md. Alamgir Hossain},
url = {http://www.nature.com/articles/s41598-017-05831-x},
doi = {10.1038/s41598-017-05831-x},
issn = {2045-2322},
year  = {2017},
date = {2017-12-01},
journal = {Scientific Reports},
volume = {7},
number = {1},
pages = {6032},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2017a,
title = {Endocrine-disrupting activity of per- and polyfluoroalkyl substances: Exploring combined approaches of ligand and structure based modeling},
author = {Kar, Supratik and Sep\'{u}lveda, Maria S. and Roy, Kunal and Leszczynski, Jerzy},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0045653517309268},
doi = {10.1016/j.chemosphere.2017.06.024},
issn = {00456535},
year  = {2017},
date = {2017-10-01},
journal = {Chemosphere},
volume = {184},
pages = {514--523},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{etianaZubatiuk2017,
title = {Modeling radical edge-site reactions of biochar in CO2/water solution under ultrasonic treatment},
author = {Tetiana Zubatiuk, Baharak Sajjadi, Glake Hill, Danuta Leszczynska, Wei-Yin Chen, Jerzy Leszczynski},
url = {http://www.sciencedirect.com/science/article/pii/S0009261417309089?via%3Dihub},
doi = {10.1016/j.cplett.2017.09.058},
year  = {2017},
date = {2017-09-28},
journal = {Chemical Physics Letters },
volume = {689},
pages = {48-55},
abstract = {We report results of theoretical evaluation of the mechanisms of possible radical reactions on the edge site of biochar with CO2, OH, and H radicals in irradiated aqueous solution. The computational studies were performed for model polyaromatic systems. Obtained mechanisms reflect one of the routes of the oxygen loss accompanied by the increase of hydrogen content, as observed in a photochemical experiment. The reaction of CO2 radical with the edge site of biochar mainly leads to reduced rather than oxidized products. The mechanism of CO2 capturing is mapped by different routes of one-electron reduction and radical addition to the aromatic ring.},
keywords = {Antanthrene, Biochar, Carbon dioxide radical anion, CO2 capture, Density function theory, Electron transfer, Hydroxide radical, Radical addition},
pubstate = {published},
tppubtype = {article}
}
@article{Gorb2017,
title = {d(A)3d(T)3 and d(G)3d(C)3 B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics},
author = {Gorb Leonid,
Zubatiuk Tatiana,
Zubatyuk Roman,
Hovorun Dmytro,
Leszczynski Jerzy},
url = {http://link.springer.com/10.1007/s00894-017-3449-y},
doi = {10.1007/s00894-017-3449-y},
issn = {1610-2940},
year  = {2017},
date = {2017-09-26},
journal = {Journal of Molecular Modeling},
volume = {23},
number = {10},
pages = {289},
abstract = {We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra\textemdashmolecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)3d(T)3 and d(G)3d(C)3 duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.},
keywords = {DNA geometrical and energetic characteristics, DNA mini helixes, Geometrical counterpoise type correction},
pubstate = {published},
tppubtype = {article}
}
@article{Vargaljuk2017,
title = {Copper Crystallization from Aqueous Solution: Initiation and Evolution of the Polynuclear Clusters},
author = {Vargaljuk, Viktor and Okovytyy, Sergiy and Polonskyy, Volodymyr and Kramska, Olga and Shchukin, Anatoly and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/s10876-017-1239-4},
doi = {10.1007/s10876-017-1239-4},
issn = {1040-7278},
year  = {2017},
date = {2017-09-01},
journal = {Journal of Cluster Science},
volume = {28},
number = {5},
pages = {2517--2528},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Portis2017b,
title = {An Ideal C 3 -Symmetric Sulfate Complex: Molecular Recognition of Oxoanions by m -Nitrophenyl- and Pentafluorophenyl-Functionalized Hexaurea Receptors},
author = { Bobby Portis and Ali Mirchi and Maryam Emami Khansari and Avijit Pramanik and Corey R. Johnson and Douglas R. Powell and Jerzy Leszczynski and Md. Alamgir Hossain},
url = {http://pubs.acs.org/doi/abs/10.1021/acsomega.7b01115},
doi = {10.1021/acsomega.7b01115},
issn = {2470-1343},
year  = {2017},
date = {2017-09-01},
journal = {ACS Omega},
volume = {2},
number = {9},
pages = {5840--5849},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jagiello2017,
title = {Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS},
author = {Jagiello, Karolina and Sosnowska, Anita and Kar, Supratik and Demkowicz, Sebastian and Da\'{s}ko, Mateusz and Leszczynski, Jerzy and Rachon, Janusz and Puzyn, Tomasz},
url = {http://link.springer.com/10.1007/s11224-016-0903-x},
doi = {10.1007/s11224-016-0903-x},
issn = {1040-0400},
year  = {2017},
date = {2017-08-01},
journal = {Structural Chemistry},
volume = {28},
number = {4},
pages = {1017--1032},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gooch2017,
title = {In vivo toxicity of nitroaromatics: A comprehensive quantitative structure-activity relationship study},
author = {Gooch, Aminah and Sizochenko, Natalia and Rasulev, Bakhtiyor and Gorb, Leonid and Leszczynski, Jerzy},
url = {http://doi.wiley.com/10.1002/etc.3761},
doi = {10.1002/etc.3761},
issn = {07307268},
year  = {2017},
date = {2017-08-01},
journal = {Environmental Toxicology and Chemistry},
volume = {36},
number = {8},
pages = {2227--2233},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nhat2017a,
title = {Another look at structure of gold clusters Au n from perspective of phenomenological shell model},
author = {Nhat, Pham Vu and Si, Nguyen Thanh and Leszczynski, Jerzy and Nguyen, Minh Tho},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0301010417303543},
doi = {10.1016/j.chemphys.2017.06.009},
issn = {03010104},
year  = {2017},
date = {2017-08-01},
journal = {Chemical Physics},
volume = {493},
pages = {140--148},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kirilchuk2017,
title = {On structure and stability of pyrimidine ylidenes and their homologues},
author = {Kirilchuk, Andrey A. and Rozhenko, Alexander B. and Leszczynski, Jerzy},
url = {http://linkinghub.elsevier.com/retrieve/pii/S2210271X17300324},
doi = {10.1016/j.comptc.2017.01.024},
issn = {2210271X},
year  = {2017},
date = {2017-03-01},
journal = {Computational and Theoretical Chemistry},
volume = {1103},
pages = {83--91},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yilmaz2017,
title = {Novel Imprinted Polymer for the Preconcentration of Cadmium with Determination by Inductively Coupled Plasma Mass Spectrometry},
author = {Yilmaz, Vedat and Yilmaz, Hayriye and Arslan, Zikri and Leszczynski, Jerzy},
url = {https://www.tandfonline.com/doi/full/10.1080/00032719.2016.1182544},
doi = {10.1080/00032719.2016.1182544},
issn = {0003-2719},
year  = {2017},
date = {2017-02-01},
journal = {Analytical Letters},
volume = {50},
number = {3},
pages = {482--499},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Watkins2017,
title = {Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure\textendashproperty relationship analysis},
author = {Watkins, Marquita and Sizochenko, Natalia and Moore, Quentarius and Golebiowski, Marek and Leszczynska, Danuta and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/s00894-016-3204-9},
doi = {10.1007/s00894-016-3204-9},
issn = {1610-2940},
year  = {2017},
date = {2017-02-01},
journal = {Journal of Molecular Modeling},
volume = {23},
number = {2},
pages = {39},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@incollection{Nhat2017,
title = {Structural Evolution, Vibrational Signatures and Energetics of Niobium Clusters from Nb2 to Nb20},
author = {Nhat, Pham Vu and Majumdar, Devashis and Leszczynski, Jerzy and Nguyen, Minh Tho},
url = {http://link.springer.com/10.1007/978-3-319-48918-6_3},
doi = {10.1007/978-3-319-48918-6_3},
year  = {2017},
date = {2017-01-01},
pages = {87--135},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Sizochenko2017,
title = {Predicting Physical Properties of Nanofluids by Computational Modeling},
author = {Sizochenko, Natalia and Syzochenko, Michael and Gajewicz, Agnieszka and Leszczynski, Jerzy and Puzyn, Tomasz},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b08850},
doi = {10.1021/acs.jpcc.6b08850},
issn = {1932-7447},
year  = {2017},
date = {2017-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {121},
number = {3},
pages = {1910--1917},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gajewicz2017,
title = {Addressing a bottle neck for regulation of nanomaterials: quantitative read-across (Nano-QRA) algorithm for cases when only limited data is available},
author = {Gajewicz, A. and Jagiello, K. and Cronin, M. T. D. and Leszczynski, J. and Puzyn, T.},
url = {http://xlink.rsc.org/?DOI=C6EN00399K},
doi = {10.1039/C6EN00399K},
issn = {2051-8153},
year  = {2017},
date = {2017-01-01},
journal = {Environ. Sci.: Nano},
volume = {4},
number = {2},
pages = {346--358},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@incollection{Toropova2017,
title = {Quasi-SMILES as a Novel Tool for Prediction of Nanomaterials′ Endpoints},
author = {Toropova, A.P. and Toropov, A.A. and Veselinovi\'{c}, A.M. and Veselinovi\'{c}, J.B. and Leszczynska, D. and Leszczynski, J.},
url = {http://linkinghub.elsevier.com/retrieve/pii/B9780081011294000084},
doi = {10.1016/B978-0-08-101129-4.00008-4},
year  = {2017},
date = {2017-01-01},
booktitle = {Multi-Scale Approaches in Drug Discovery},
pages = {191--221},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@incollection{Kar2017,
title = {On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments},
author = {Kar, Supratik and Roy, Kunal and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/978-3-319-56850-8_7},
doi = {10.1007/978-3-319-56850-8_7},
year  = {2017},
date = {2017-01-01},
pages = {203--302},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Ahmed2017,
title = {Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose},
author = {Ahmed, Lucky and Rasulev, Bakhtiyor and Kar, Supratik and Krupa, Pawe\l and Mozolewska, Magdalena A. and Leszczynski, Jerzy},
url = {http://xlink.rsc.org/?DOI=C7NR00770A},
doi = {10.1039/C7NR00770A},
issn = {2040-3364},
year  = {2017},
date = {2017-01-01},
journal = {Nanoscale},
volume = {9},
number = {29},
pages = {10263--10276},
abstract = {Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2017b,
title = {Modeling of Interactions between the Zebrafish Hatching Enzyme ZHE1 and A Series of Metal Oxide Nanoparticles: Nano-QSAR and Causal Analysis of Inactivation Mechanisms},
author = { Natalia Sizochenko and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://www.mdpi.com/2079-4991/7/10/330},
doi = {10.3390/nano7100330},
issn = {2079-4991},
year  = {2017},
date = {2017-01-01},
journal = {Nanomaterials},
volume = {7},
number = {10},
pages = {330},
keywords = {causality, liquid drop model, Metal oxide nanoparticles, molecular descriptors, QSAR, regression tree, Toxicity, zebrafish},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2017a,
title = {Drug-Nanoparticle Composites},
author = { Natalia Sizochenko and Jerzy Leszczynski},
url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/JNN.2017010101},
doi = {10.4018/JNN.2017010101},
issn = {2379-7452},
year  = {2017},
date = {2017-01-01},
journal = {Journal of Nanotoxicology and Nanomedicine},
volume = {2},
number = {1},
pages = {1--10},
keywords = {classifie, descriptors, drug delivery, drug-polymer interactions, molecular docking, plga},
pubstate = {published},
tppubtype = {article}
}
@article{Mikolajczyk2017,
title = {Evaluating the toxicity of TiO2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach},
author = { Alicja Mikolajczyk and Natalia Sizochenko and Ewa Mulkiewicz and Anna Malankowska and Michal Nischk and Przemyslaw Jurczak and Seishiro Hirano and Grzegorz Nowaczyk and Adriana Zaleska-Medynska and Jerzy Leszczynski, 
 and Agnieszka Gajewicz and Tomasz Puzyn},
doi = {10.3762/bjnano.8.216},
issn = {2190-4286},
year  = {2017},
date = {2017-01-01},
journal = {Nanomaterials},
volume = {accepted},
pages = {2171--2180},
keywords = {2017, 2171, 2180, 8, au, beilstein j, bimetallic nanoparticles, Nano-QSAR, nanotechnol, nanotoxicity, pd, second-generation nanoparticles, tio 2 photocatalyst},
pubstate = {published},
tppubtype = {article}
}
@article{Gooch2017b,
title = {A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds},
author = { A. Gooch and N. Sizochenko and L. Sviatenko and L. Gorb and J. Leszczynski},
url = {http://dx.doi.org/10.1080/1062936X.2017.1286687},
doi = {10.1080/1062936X.2017.1286687},
issn = {1029046X},
year  = {2017},
date = {2017-01-01},
journal = {SAR and QSAR in Environmental Research},
volume = {28},
number = {2},
pages = {133--150},
publisher = {Taylor & Francis},
abstract = {Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches. All geometries were optimized with density functional theory (DFT) using the solvation model based on density (SMD) and polarizable continuum model (PCM) solvent model protocols. Quantitative structure-activity/property (QSAR/QSPR) models were developed using descriptors obtained from quantum chemical optimizations as well as the DRAGON software program. The QSAR/QSPR equations developed consist of two to four descriptors. Correlations have been identified between electron affinity (ELUMO) and hydrophobicity (log P).},
keywords = {hydrophobicity, LUMO energy, nitroaromatic, QSAR, reduction potential, Toxicity},
pubstate = {published},
tppubtype = {article}
}
@article{Mirchi2017,
title = {Binding of alkali metal ions with 1,3,5- Tri(phenyl)benzene and 1,3,5-Tris(naphthyl)benzene: The effect of phenyl and naphthyl rings substitution on cation-$pi$ interactions revealed by DFT study},
author = { Ali Mirchi and Natalia Sizochenko and Tandabany C. Dinadayalane and Jerzy Leszczynski},
year  = {2017},
date = {2017-01-01},
journal = {(Submitted for publication)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mirchi2017a,
title = {Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: A combination of molecular docking, QSAR and ONIOM approaches},
author = { Ali Mirchi and Natalia Sizochenko and Jerzy Leszczynski},
year  = {2017},
date = {2017-01-01},
journal = {(Submitted for publication)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2016b,
title = {Quantitative structure-property relationship model leading to virtual screening of fullerene derivatives: Exploring structural attributes critical for photoconversion efficiency of polymer solar cell acceptors},
author = { Supratik Kar and Natalia Sizochenko and Lucky Ahmed and Victor S. Batista and Jerzy Leszczynski},
url = {http://dx.doi.org/10.1016/j.nanoen.2016.06.011 http://linkinghub.elsevier.com/retrieve/pii/S2211285516301914},
doi = {10.1016/j.nanoen.2016.06.011},
issn = {22112855},
year  = {2016},
date = {2016-08-01},
journal = {Nano Energy},
volume = {26},
pages = {677--691},
abstract = {The power conversion efficiency (PCE) of pure polymer solar cells (PSCs) remains low, although significantly higher values could be achieved by using PSCs as carrier donors in conjunction with composite fullerene derivative (FD) acceptors. Significant resources, however, are required to experimentally develop and screen FDs that may serve as efficient acceptors in PSCs. Often, the materials are expensive, the methods are time consuming, and the production processes can generate toxic hazards. As an alternative approach, we introduce a quantitative structure-property relationship (QSPR) model for predicting the PCE of 59 FDs, including both C60 and C70 FDs. The QSPR model enables identification of the essential structural attributes necessary for quantifying the molecular prerequisites of diverse FDs, chiefly responsible for high PCE of PSC acceptors in composition with poly(3-hexylthiophene) (P3HT). The identified properties and structural fragments are particularly valuable for guiding future synthetic efforts for development of FDs with improved power conversion efficiency. Furthermore, a large number of FDs are collected to generate a database. Virtual screening of the database employing the developed QSPR model allows for identification of nine FDs with higher PCE than previously studied FDs},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kolodziejczyk2016,
title = {A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies},
author = { Wojciech Kolodziejczyk and Supratik Kar and Glake A. Hill and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-016-0779-9},
doi = {10.1007/s11224-016-0779-9},
issn = {1040-0400},
year  = {2016},
date = {2016-08-01},
journal = {Structural Chemistry},
volume = {27},
number = {4},
pages = {1291--1302},
abstract = {Conformers of the psychoactive compound of the Khat plant cathinone along with its amino alcohol metabolites norephedrine and norpseudoephedrine have been calculated using DFT (M062X/B3LYP) and MP2 levels of theory for gas and solution phases. Gas-phase studies revealed that cathinone has two, norephedrine has four and norpseudoephedrine has three low-energy conformations with all conformers connected by rotational transition states. To understand the solvent effect to the energetic profiles of the studied species, the conductor-like screening model is employed within aqueous medium. It explains lowering of energy of all studied conformers in solution. The molecular electrostatic potential surface data for each molecule revealed likely reaction sites for the studied molecules. The computed IR spectra for cathinone and its metabolites have been compared with experimental data and rotational transition states connecting all conformers have been reported. The natural bond orbital analyses for only ligands and separately for their complexes with amino acid residues in protein pockets from the docking results are also performed to corroborate the results obtained from the MP2 and DFT calculations. The comprehensive computational study explore important amino acid residues},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2016b,
title = {Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna},
author = { Alla P. Toropova and Andrey A. Toropov and Aleksandar M. Veselinovi\'{c} and Jovana B. Veselinovi\'{c} and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://doi.wiley.com/10.1002/etc.3466},
doi = {10.1002/etc.3466},
issn = {07307268},
year  = {2016},
date = {2016-07-01},
journal = {Environmental Toxicology and Chemistry},
abstract = {Quantitative structure\textendashactivity relationships (QSARs) for toxicity of a large set of 758 organic compounds to Daphnia magna were built up. The simplified molecular input-line entry system (SMILES) was used to represent the molecular structure. The Correlation and Logic (CORAL) software was utilized as a tool to develop the QSAR models. These models are built up using the Monte Carlo method and according to the principle “QSAR is a random event” if one checks a group of random distributions in the visible training set and the invisible validation set. Three distributions of the data into the visible training, calibration, and invisible validation sets are examined. The predictive potentials (i.e., statistical characteristics for the invisible validation set of the best model) are as follows: n ¼ 87, r 2 ¼ 0.8377, root mean square error ¼ 0.564. The mechanistic interpretations and the domain of applicability of built models are suggested and discussed},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2016,
title = {Can Toxicity for Different Species be Correlated?},
author = { Supratik Kar and Rudra Narayan Das and Kunal Roy and Jerzy Leszczynski},
url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/IJQSPR.2016070102},
doi = {10.4018/IJQSPR.2016070102},
issn = {2379-7487},
year  = {2016},
date = {2016-06-01},
journal = {International Journal of Quantitative Structure-Property Relationships},
volume = {1},
number = {2},
pages = {23--51},
abstract = {Experimental evaluation of the toxicity of a compound is an expensive practice, and it requires sacrifice of a large number of animals. As a consequence, in silico techniques for predictive toxicology are taking the central stage of attention of the scientific community. Interspecies quantitative structuretoxicity relationship (i-QSTR) modeling provides a tool for estimation of contaminant's sensitivity with known levels of uncertainty for a diverse pool of species. It is capable of extrapolating data for one toxicity endpoint to another toxicity endpoint when the data for the second species are unavailable. The emerging i-QSTR approach can overcome the cost of multiple toxicity tests, improve the understanding of the mechanism of toxic action (MOA) of chemicals for different organisms and endpoints and is very useful in order to fill the data gaps where toxicity value for a particular compound is absent for a specific endpoint.},
keywords = {Extrapolation, i-QSTR, Interspecies Correlation, Mode of Action, QSAR, REACH, Toxicity, US EPA},
pubstate = {published},
tppubtype = {article}
}
@article{Yilmaz2016,
title = {Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives},
author = { Hayriye Yilmaz and Lucky Ahmed and Bakhtiyor Rasulev and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11051-016-3429-7},
doi = {10.1007/s11051-016-3429-7},
issn = {1388-0764},
year  = {2016},
date = {2016-05-01},
journal = {Journal of Nanoparticle Research},
volume = {18},
number = {5},
pages = {123},
abstract = {Fullerene and its derivatives have potential to be utilized in many biomedical applications. In the present study, we investigated the role of fullerene derivatives as inhibitors of HIV-RT by combined protein\textendashligand docking approach and QSAR methods. The study shows the best predictive QSAR model that represents a two-variable model. It has a good ratio of the number of descriptors and predictive ability. The main contributions to the inhibitory activity are provided by signal JhetZ descriptor and l (dipole moment, as a measure of the polarity of a compound). The developed GA-MLRA-based model demonstrates a good performance, confirmed by statistics R2 training ¼ 0:867; Q2 ¼ 0:788; R2 test ¼ 0:902 : The structure\textendashactivity analysis of these fullerene analogues allowed us to design and suggest for synthesis a set of new potentially active fullerenes. Finally, the molecular docking analysis was carried out to understand the details of interactions between HIV-RT and fullerene-C60 derivatives.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Golius2016,
title = {Experimental and computational study of membrane affinity for selected energetic compounds},
author = { Anastasiia Golius and Leonid Gorb and Andrea Michalkova Scott and Frances C. Hill and Manoj Shukla and A. Benjamin Goins and David R. Johnson and Jerzy Leszczynski},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0045653516300108},
doi = {10.1016/j.chemosphere.2016.01.010},
issn = {00456535},
year  = {2016},
date = {2016-04-01},
journal = {Chemosphere},
volume = {148},
pages = {322--327},
abstract = {The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanolewater (log(Kow)) and liposomeewater (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2016a,
title = {Extrapolating between toxicity endpoints of metal oxide nanoparticles: Predicting toxicity to Escherichia coli and human keratinocyte cell line (HaCaT) with Nano-QTTR},
author = { Supratik Kar and Agnieszka Gajewicz and Kunal Roy and Jerzy Leszczynski and Tomasz Puzyn},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0147651315302219},
doi = {10.1016/j.ecoenv.2015.12.033},
issn = {01476513},
year  = {2016},
date = {2016-04-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {126},
pages = {238--244},
abstract = {Synthesis of novel nanoparticles should always be accompanied by a comprehensive assessment of risk to human health and to ecosystem. Application of in silico models is encouraged by regulatory authorities to fill the data gaps related to the properties of nanoparticles affecting the environment and human health. Interspecies toxicity correlations provide a tool for estimation of contaminant's sensitivity with known levels of uncertainty for a diverse pool of species. We propose here first interspecies cytotoxicity correlation models between Escherichia coli (prokaryotic system) and human keratinocyte cell line (HaCaT) (eukaryotic system) to assess the discriminatory features for cytotoxicity of metal oxide nanoparticles. The nano-QTTR models can be employed for extrapolating cytotoxicity to E. coli and human keratinocyte cell line (HaCaT) for metal nanoparticles when the data for the other species are available. Informative illustrations of the contributing mechanisms of toxic action of the metal oxide nanoparticles to the HaCaT cell line as well as to the E. coli are identified from the developed nano quantitative toxicity\textendash toxicity relationship (nano-QTTR) models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut2016,
title = {A new hybrid (experimental\textendashtheoretical) quantitative method for detection of relative anomer concentrations in water},
author = { Sedat Karabulut and Devran Uysal and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-015-0722-5},
doi = {10.1007/s11224-015-0722-5},
issn = {1040-0400},
year  = {2016},
date = {2016-04-01},
journal = {Structural Chemistry},
volume = {27},
number = {2},
pages = {449--455},
abstract = {A novel and inexpensive hybrid (combined experimental and theoretical) approach was used to quantitatively identify anomer proportions of D-glucose, Dgalactose and D-mannose in water. The study involves three parts: recording of experimental FT-IR spectra of monosaccharides in water, calculation of vibrational frequencies of all stable anomers of monosaccharides and regression analysis of theoretical and experimental intensities. No expensive experimental processes and high-level calculations were needed during the study. The results were compared with the data from pure experimental and molecular dynamic studies. It has been concluded that in water while D-glucose and D-mannose have two stable anomers, a-pyranose and b-pyranose, D-galactose has four stable anomers, a-pyranose, b-pyranose, a-furanose and b-furanose. Comparison of detected results with the literature data showed that the developed method is working for the quantitative detection of anomer proportions of monosaccharides in water.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko2016,
title = {Adsorption of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) on a soil organic matter. A DFT M05 computational study},
author = { Liudmyla K. Sviatenko and Leonid Gorb and Manoj K. Shukla and Jennifer M. Seiter and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://linkinghub.elsevier.com/retrieve/pii/S004565351630011X},
doi = {10.1016/j.chemosphere.2016.01.011},
issn = {00456535},
year  = {2016},
date = {2016-04-01},
journal = {Chemosphere},
volume = {148},
pages = {294--299},
abstract = {Adsorption of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) by soil organic matter considering the Leonardite Humic Acid (LHA) model at the M05/tzvp level of Density Functional Theory (DFT) applying cluster approximation has been investigated. Different orientations of CL-20 toward LHA surface were examined. It was found that deprotonation of LHA is required to obtain stable complexes with CL-20. Hydrogen bonds between CL-20 and deprotonated LHA were analyzed applying the atoms in molecules (AIM) theory. An attachment or removal of an electron with respect to the complex does not have significant effect on mutual orientation of the adsorbent in complexes. It was shown that adsorbed CL-20 does not undergo redox transformation and, therefore, adsorption on soil organic matter may be responsible for decrease of the degradation rate of CL-20 in soil.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2016a,
title = {Introduction of simplex-informational descriptors for QSPR analysis of fullerene derivatives},
author = { Natalia Sizochenko and Victor Kuz'min and Liudmila Ognichenko and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s10910-015-0581-8},
doi = {10.1007/s10910-015-0581-8},
issn = {0259-9791},
year  = {2016},
date = {2016-03-01},
journal = {Journal of Mathematical Chemistry},
volume = {54},
number = {3},
pages = {698--706},
abstract = {Rational approach towards the QSAR/QSPR modeling requires the selection of descriptors to be computationally efficient and physically and chemically meaningful. However, fullerenes and their derivatives represent challenging compounds in terms of QSPR modeling and there is a lack of efficient and comprehensible descriptors for them. Based on existing informational field model and simplex representation of molecular structure approach, an outline of descriptoral representation for fullerenes was developed. Solubility of fullerene derivatives was chosen as target property for the estimation of descriptors' efficacy. Developed model provides well-defined physical meanings and obtained results are interpreted in terms of basic molecular properties.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Wang2016,
title = {Theoretical Studies on Hydrogen Bonds in Anions Encapsulated by an Azamacrocyclic Receptor},
author = { Jing Wang and Jiande Gu and Md. Hossain and Jerzy Leszczynski},
url = {http://www.mdpi.com/2073-4352/6/3/31},
doi = {10.3390/cryst6030031},
issn = {2073-4352},
year  = {2016},
date = {2016-03-01},
journal = {Crystals},
volume = {6},
number = {3},
pages = {31},
abstract = {Hydrogen bonds in two halides encapsulated by an azamacrocyclic receptor were studied in detail by the density functional theory (DFT) approaches at B3LYP/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels. The atoms in molecules (AIM) theory and the electron density difference maps were applied for characterizing the hydrogen bond patterns. The results suggest that the fluoride complex has a unique binding pattern which shows a hydrogen bond augmented with ionic bond characteristics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Watkins2016,
title = {Estimation of melting points of large set of persistent organic pollutants utilizing QSPR approach},
author = { Marquita Watkins and Natalia Sizochenko and Bakhtiyor Rasulev and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s00894-016-2917-0},
doi = {10.1007/s00894-016-2917-0},
issn = {1610-2940},
year  = {2016},
date = {2016-03-01},
journal = {Journal of Molecular Modeling},
volume = {22},
number = {3},
pages = {55},
abstract = {The presence of polyhalogenated persistent organic pollutants (POPs), such as Cl/Br-substituted benzenes, biphenyls, diphenyl ethers, and naphthalenes has been identified in all environmental compartments. The exposure to these compounds can pose potential risk not only for ecological systems, but also for human health. Therefore, efficient tools for comprehensive environmental risk assessment for POPs are required. Among the factors vital for environmental transport and fate processes is melting point of a compound. In this study, we estimated the melting points of a large group (1419 compounds) of chloro- and bromo- derivatives of dibenzo-p-dioxins, dibenzofurans, biphenyls, naphthalenes, diphenylethers, and benzenes by utilizing quantitative structure\textemdashproperty relationship (QSPR) techniques. The compounds were classified by applying structure-based clustering methods followed by GA-PLS modeling. In addition, random forest method has been applied to develop more general models. Factors responsible for melting point behavior and predictive ability of each method were discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kuramshina2016,
title = {Conformations, vibrational spectra and force field of 1-methyl-2-(2′-pyridyl)benzimidazole: experimental data and density functional theory investigation in comparison with 2-(2′-pyridyl)benzimidazole},
author = { G. M. Kuramshina and O. A. Vakula and N. I. Vakula and A. G. Majouga and V. M. Senyavin and Leonid G. Gorb and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-015-0693-6},
doi = {10.1007/s11224-015-0693-6},
issn = {1040-0400},
year  = {2016},
date = {2016-02-01},
journal = {Structural Chemistry},
volume = {27},
number = {1},
pages = {209--219},
abstract = {The molecular structure, conformational equilibria, vibrational spectra and molecular force field of 1-methyl-2-(20 -pyridyl)benzimidazole have been determined at the HF, MP2 and DFT/(B3LYP, BVP86) levels with 6-31?G(d,p) and TZVP basis sets. The torsional potentials for the rotation around the C1\textendashC2 pivotal bond have been calculated at the B3LYP/6-31?G(d,p) and BVP86/TZVP levels of theory for gaseous and aqueous 1-methyl-2-(20 - pyridyl)benzimidazole. FT-Raman (3500\textendash10 cm-1 ) and FTIR (3900\textendash400 cm-1 ) spectra of solid 1-methyl-2-(20 - pyridyl)benzimidazole have been recorded and interpreted on a base of calculated potential energy distribution. The results of the experimental and theoretical study of vibrational spectra and molecular structure of 1-methyl 2-(20 - pyridyl)benzimidazole are considered in comparison with similar data for 2-(20 -pyridyl)benzimidazole.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tinkov2016,
title = {Computational assessment of environmental hazards of nitroaromatic compounds: influence of the type and position of aromatic ring substituents on toxicity},
author = { Oleg V. Tinkov and Luidmila N. Ognichenko and Victor E. Kuz'min and Leonid G. Gorb and Anna P. Kosinskaya and Nail N. Muratov and Eugene N. Muratov and Frances C. Hill and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-015-0715-4},
doi = {10.1007/s11224-015-0715-4},
issn = {1040-0400},
year  = {2016},
date = {2016-02-01},
journal = {Structural Chemistry},
volume = {27},
number = {1},
pages = {191--198},
abstract = {This study summarizes the results of our recent QSAR and QSPR investigations on prediction of numerous aspects of environmental behavior of nitro compounds. In this study, we applied the QSAR/QSPR models previously developed by our group for virtual screening of energetic compounds, their precursors and other compounds containing nitro groups. To make predictions on the environmental impact of nitro compounds, we analyzed the trends in the change of the experimentally obtained and QSAR/ QSPR-predicted values of aqueous solubility, lipophilicity, Ames mutagenicity, bioavailability, blood\textendashbrain barrier penetration, aquatic toxicity on T. pyriformis and acute oral toxicity on rats as a function of chemical structure of nitro compounds. All the models were developed using simplex descriptors in combination with random forest (RF) modeling techniques. We interpreted the possible environmental impact (different toxicological properties) in terms of dividing considered nitro compounds based on hydrophobic and hydrophilic characteristics and in terms of the influence of their molecular fragments that promote and interfere with toxicity. In particular, we found that, in general, the presence of amide or tertiary amine groups leads to an increase in toxicity. Also, it was predicted that compounds containing a NO2 group in the para-position of a benzene ring are more toxic than meta-isomers, which, in turn, are more toxic than ortho-isomers. In general, we concluded that hydrophobic nitroaromatic compounds, especially the ones with electron-accepting substituents, halogens and amino groups, are the most environmentally hazardous},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2016a,
title = {Nano-QSAR: Model of mutagenicity of fullerene as a mathematical function of different conditions},
author = { Alla P. Toropova and Andrey A. Toropov and Aleksandar M. Veselinovi\'{c} and Jovana B. Veselinovi\'{c} and Emilio Benfenati and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0147651315301135},
doi = {10.1016/j.ecoenv.2015.09.038},
issn = {01476513},
year  = {2016},
date = {2016-02-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {124},
pages = {32--36},
abstract = {The experimental data on the bacterial reverse mutation test (under various conditions) on C60 nanoparticles for the cases (i) TA100, and (ii) WP2uvrA/pkM101 are examined as endpoints. By means of the optimal descriptors calculated with the Monte Carlo method a mathematical model of these endpoints has been built up. The models are a mathematical function of eclectic data such as (i) dose (g/plate); (ii) metabolic activation (i.e. with mix S9 or without mix S9); and (iii) illumination (i.e. darkness or irradiation). The eclectic data on different conditions were represented by so-called quasi-SMILES. In contrast to the traditional SMILES which are representation of molecular structure, the quasi-SMILES are representation of conditions by sequence of symbols. The calculations were carried out with the CORAL software, available on the Internet at http://www.insilico.eu/coral. The main idea of the suggested descriptors is the accumulation of all available eclectic information in the role of logical and digital basis for building up a model. The computational experiments have shown that the described approach can be a tool to build up models of mutagenicity of fullerene under different conditions},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Omelchenko2016,
title = {Aromaticity and conformational flexibility of five-membered monoheterocycles: pyrrole-like and thiophene-like structures},
author = { Irina V. Omelchenko and Oleg V. Shishkin and Leonid Gorb and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s11224-015-0707-4},
doi = {10.1007/s11224-015-0707-4},
issn = {1040-0400},
year  = {2016},
date = {2016-02-01},
journal = {Structural Chemistry},
volume = {27},
number = {1},
pages = {101--109},
abstract = {Aromaticity and conformational flexibility of the series of five-membered monoheterocycles with group 14\textendash16 heteroatoms, having one or two lone pairs, were studied with ab initio methods using NICS, ASE and I5 indices. For non-planar molecules like phosphole, aromaticity of their planar transition states was also studied, and a special modification of ASE index was proposed to that end. It was found that the presence of two lone pairs is generally preferable for aromaticity of all heterocycles except CPD and silolyl dianions. Heterocycles with group 16 heteroatoms have consistently lower aromaticity compared to other groups. A lot of structures should be classified as moderate aromatic and non-aromatic. Energies of out-of-plane deformation do not correlate with other indices studied, but reveal the same qualitative trends. Generally, aromaticity of five-membered monoheterocycles depends strongly on both heteroatom type and number of lone pairs on it.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Li201696,
title = {Purification and characterization of polysaccharides degradases produced by Alteromonas sp. A321},
author = { Y. Li W. Zhang G. L\"{u} X. Hwang H. Aker W.G. Guan H. Wang P. Li},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955463831&partnerID=40&md5=df42512ef17241e19b222cfaef97e126},
doi = {10.1016/j.ijbiomac.2016.01.033},
year  = {2016},
date = {2016-01-01},
journal = {International Journal of Biological Macromolecules},
volume = {86},
pages = {96-104},
abstract = {Two different degradases from Alteromonas sp. A321for polysaccharides from Enteromorpha prolifera (DPE-L and DPE-P) were purified to homogeneity. The molecular weights of purified DPE-L and DPE-P were 75.2 and 102.5kDa, respectively, and their internal sequences were analysed by LC-MS-MS. The enzymes exhibited an optimum temperature of 30-40°C (DPE-L) and 35-45°C (DPE-P), an optimum pH of 7.0 (DPE-L) and 6.0 (DPE-P). DPE-P was highly stable in the presence of EDTA and 1,10-phenanthroline while DPE-L was inhibited by 1,10-phenanthroline. The Km values of DPE-L and DPE-P were 2.93mg/ml and 0.31mg/ml and the Vmax values were 6.11μmol/min/ml and 2.88μmol/min/ml, respectively. Results of HPLC and ESI-MS analyses showed that enzymatic products were: Rha1(SO3H)1, Rha1(SO3H)1Gluc1, Rha2(SO3H)2Gluc1, and Rha3(SO3H)3Gluc1Xyl1 by DPE-L, and Glu2, Glu3, plus Glu4 by DPE-P, respectively. Thus DPE-L and DPE-P can be used to produce oligosaccharides which potentially revealed more of structure of polysaccharides from E. prolifera. © 2016 Published by Elsevier B.V..},
keywords = {bacterial enzyme; polysaccharide degradase; rhamnose; unclassified drug},
pubstate = {published},
tppubtype = {article}
}
@article{Qiao20161307,
title = {Rheological properties, gelling behavior and texture characteristics of polysaccharide from Enteromorpha prolifera},
author = { L. Li Y. Chi Y. Ji Y. Gao Y. Hwang H. Aker W.G. Wang P. Qiao},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84945953910&partnerID=40&md5=1080c0a42dffd2a768ab15cd94607ef9},
doi = {10.1016/j.carbpol.2015.10.030},
year  = {2016},
date = {2016-01-01},
journal = {Carbohydrate Polymers},
volume = {136},
pages = {1307-1314},
abstract = {Polysaccharide from Enteromorpha prolifera (PE) which is the most common green algae is gradually becoming an attractive candidate with novel functions by virtue of its unique chemical and physicochemical properties. The infrared spectrum (FT-IR) of PE confirmed that it is a distinctive, sulfated heteropolysaccharide. Dynamic rheology was systematically conducted to investigate the effect of concentration, temperature, pH, and electrolytes on PE. The flow behavior testing verified its pseudoplastic character. A closed hysteresis loop was obtained when the PE concentration reached 10 g/L. For the phase angel (tan δ) was always less than 1, the solid-like behavior of PE is also found at 10-14 g/L PE in the linear viscoelastic region (LVR). Furthermore, study on its potential gelling behavior showed that 16 g/L PE could form a gel and had well textural properties. The unique functional groups and characteristics of PE provided the possibility to apply into food industry. © 2015 Elsevier Ltd. All rights reserved.},
keywords = {Algae, chemistry; flow kinetics; gel; pH; temperature; Ulva; viscosity, Enteromorpha prolifera; FTIR spectroscopy; Heteropolysaccharide; Linear viscoelastic regions; Physicochemical property; Rheological property; Texture analysis; Texture characteristics, gel; polysaccharide, Gelation; Rheology, Gels; Hydrogen-Ion Concentration; Polysaccharides; Rheology; Temperature; Ulva; Viscosity},
pubstate = {published},
tppubtype = {article}
}
@article{He201681,
title = {Assessment of nitrogen-fluorine-codoped TiO<inf>2</inf> under visible light for degradation of BPA: Implication for field remediation},
author = { X. Aker W.G. Pelaez M. Lin Y. Dionysiou D.D. Hwang H.-M. He},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940676087&amp;partnerID=40&amp;md5=c8d7a3122f77efa396a4b455a00ced39},
doi = {10.1016/j.jphotochem.2015.08.014},
year  = {2016},
date = {2016-01-01},
journal = {Journal of Photochemistry and Photobiology A: Chemistry},
volume = {314},
pages = {81-92},
abstract = {Synthesized nitrogen-fluorine-codoped-TiO<inf>2</inf> (N-F-TiO<inf>2</inf>) nanoparticles, in comparison to commercial Sigma TiO<inf>2</inf>, were used to investigate the photocatalytic degradation of bisphenol A (BPA) as a model pollutant in aqueous solutions responding to visible light. The photocatalytic activities were first evaluated by studying the degradation of BPA under simulated sunlight (SSL) and visible light (VL). The light absorption of N-F-TiO<inf>2</inf>, in relation to the undoped TiO<inf>2</inf>, shifted to the visible light region. The visible-light-driven-degradation of BPA with N-F-TiO<inf>2</inf> was much higher (61.2%) after 4 h of irradiation than that with Sigma TiO<inf>2</inf> (19.2%), (p < 0.01). Moreover, the role of reactive oxygen species (ROS) was also investigated. Superoxide (O<inf>2</inf>-) was recognized to be the major ROS in degrading BPA under visible light. The correlation between visible-light-driven photocatalytic degradation and the physicochemical properties of N-F-TiO<inf>2</inf> is discussed as well. In this study, enhanced catalytic activity under visible light was found to be strongly dependent on surface-area-to-volume-ratio, visible light absorption, and superoxide formation, induced by N- and F-doping. In addition, the potential field application of N-F-TiO<inf>2</inf> was investigated with river water. The results highly demonstrated the use of N-F-TiO<inf>2</inf> in environmental remediation as a green and sustainable alternative technology. © 2015 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@incollection{Dinadayalane2016b,
title = {Fundamental Structural, Electronic, and Chemical Properties of Carbon Nanostructures: Graphene, Fullerenes, Carbon Nanotubes, and Their Derivatives},
author = {Dinadayalane, Tandabany C. and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/978-94-007-6169-8_22-2},
doi = {10.1007/978-94-007-6169-8_22-2},
year  = {2016},
date = {2016-01-01},
booktitle = {Handbook of Computational Chemistry},
pages = {1--84},
publisher = {Springer Netherlands},
address = {Dordrecht},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@incollection{Sponer2016,
title = {Computational Modeling of DNA and RNA Fragments},
author = {\v{S}poner, Ji\v{r}\'{i} and Shukla, Manoj K. and Wang, Jing and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/978-94-007-6169-8_35-2},
doi = {10.1007/978-94-007-6169-8_35-2},
year  = {2016},
date = {2016-01-01},
booktitle = {Handbook of Computational Chemistry},
pages = {1--24},
publisher = {Springer Netherlands},
address = {Dordrecht},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@incollection{Sizochenko2016b,
title = {Application of Quantum Mechanics and Molecular Mechanics in Chemoinformatics},
author = {Sizochenko, Natalia and Majumdar, D. and Roszak, Szczepan and Leszczynski, Jerzy},
url = {http://link.springer.com/10.1007/978-94-007-6169-8_52-1},
doi = {10.1007/978-94-007-6169-8_52-1},
year  = {2016},
date = {2016-01-01},
booktitle = {Handbook of Computational Chemistry},
pages = {1--23},
publisher = {Springer Netherlands},
address = {Dordrecht},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@incollection{Dinadayalane2016,
title = {Chapter: Hydrogenated Graphene: Preparation, Properties, and Applications},
author = { Tandabany C. Dinadayalane and Jerzy Leszczynski},
editor = {Aliofkhazraei, In M. and Ali, N. and Milne, W. I. and Ozkan, C. S. and Mitura, S. and Gervasoni, Juana L.},
year  = {2016},
date = {2016-01-01},
booktitle = {Graphene Science Handbook: Fabrication Methods},
pages = {431--450},
publisher = {CRC Press (Taylor &amp; Francis Group)},
address = {Boca Raton},
abstract = {Graphene, a nanomaterial represented by a single atomic layer of planar carbons, continues to attract widespread research interest due to its remarkable electronic and structural properties. Chemical modification of graphene that includes attachment of atomic hydrogen to selected carbon sites or all carbon sites correspondingly produces partially hydrogenated graphene (PHG) or fully hydrogenated graphene (graphane). H chemisorption is accompanied by transformation of carbon from sp2 to sp3 hybridization, resulting in a relaxation of the carbon atom toward the hydrogen atom. In this chapter, we reveal different approaches used for hydrogenation of graphene, and various experimental techniques employed for the characterization of structures, dehydrogenation, and important properties of hydrogenated graphene. We outline four isomeric single-sheet graphanes. Theoretical and experimental studies focusing on the feasibility of single-sided hydrogenated graphene at both low and high hydrogen coverage are delineated. We discuss the electronic and mechanical properties of graphane and PHG. The results of vibrational spectra and nuclear magnetic resonance (NMR) data from computational studies are provided. We also highlight the recent studies of experimentally known fluorographene, partially hydrogenated graphene (C4H), graphane nanotubes, and bilayer graphane. As an emerging and important field, the fully hydrogenated derivative of graphene (called graphane) and PHG have many potential applications and deserve detailed review of their characteristics and further comprehensive studies.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Gu2016,
title = {Electron interaction with a DNA duplex: dCpdC:dGpdG},
author = { Jiande Gu and Jing Wang and Jerzy Leszczynski},
url = {http://xlink.rsc.org/?DOI=C6CP01408A},
doi = {10.1039/C6CP01408A},
issn = {1463-9076},
year  = {2016},
date = {2016-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {18},
number = {19},
pages = {13657--13665},
abstract = {Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 50 position (dCpdC:dGpdG) or at the 30 position (dCpdC:dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1HpdC:dG2-HpdG and dCpdC2H:dGpdG1-H. These distonic radical anions are found to be approximately 1 to 4 kcal mol1 more stable than the normal radical anions. Intra-strand cytosine p - p transition energies are below the electron detachment energy. Inter-strand p - p transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex. Introdu},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2016,
title = {Causation or only correlation? Application of causal inference graphs for evaluating causality in nano-QSAR models},
author = { Natalia Sizochenko and Agnieszka Gajewicz and Jerzy Leszczynski and Tomasz Puzyn},
url = {http://xlink.rsc.org/?DOI=C5NR08279J},
doi = {10.1039/C5NR08279J},
issn = {2040-3364},
year  = {2016},
date = {2016-01-01},
journal = {Nanoscale},
volume = {8},
number = {13},
pages = {7203--7208},
abstract = {In this paper, we suggest that causal inference methods could be efficiently used in Quantitative Structure\textendashActivity Relationships (QSAR) modeling as additional validation criteria within quality evaluation of the model. Verification of the relationships between descriptors and toxicity or other activity in the QSAR model has a vital role in understanding the mechanisms of action. The well-known phrase “correlation does not imply causation” reflects insight statistically correlated with the endpoint descriptor may not cause the emergence of this endpoint. Hence, paradigmatic shifts must be undertaken when moving from traditional statistical correlation analysis to causal analysis of multivariate data. Methods of causal discovery have been applied for broader physical insight into mechanisms of action and interpretation of the developed nano-QSAR models. Previously developed nano-QSAR models for toxicity of 17 nano-sized metal oxides towards E. coli bacteria have been validated by means of the causality criteria. Using the descriptors confirmed by the causal technique, we have developed new models consistent with the straightforward causal-reasoning account. It was proven that causal inference methods are able to provide a more robust mechanistic interpretation of the developed nano-QSAR models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2016b,
title = {Review of Current and Emerging Approaches for Quantitative Nanostructure-Activity Relationship Modeling},
author = { Natalia Sizochenko and Jerzy Leszczynski},
url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/JNN.2016010101},
doi = {10.4018/JNN.2016010101},
issn = {2379-7452},
year  = {2016},
date = {2016-01-01},
journal = {Journal of Nanotoxicology and Nanomedicine},
volume = {1},
number = {1},
pages = {1--16},
abstract = {Quantitative structure-activity/property relationships (QSAR/QSPR) approaches that have been applied with success in a number of studies are currently used as indispensable tools in the computational analysis of nanomaterials. Evolution of nano-QSAR methodology to the ranks of novel field of knowledge has resulted in the development of new so-called “nano-descriptors” and extension of the statistical approaches domain. This brief review focuses on the critical analysis of advantages and disadvantages of existing methods of nanoparticles' representation and their analysis in framework of structure-activity relationships. It summarizes recent QSAR/QSPR studies on inorganic nanomaterials. Here the authors describe practices for the QSAR modeling of inorganic nanoparticles, existing datasets, and discuss applicable descriptors and future perspectives of this field. About 50 different (Q)SAR/SPR models for inorganic nanomaterials have been developed during the past 5 years. An analysis of these peer reviewed publications shows that the most popular property of nanoparticles modeled via QSAR is their toxicity towards different bacteria, cell lines, and microorganisms. It has been clearly shown how nano-QSAR can contribute to the elucidation of toxicity mechanisms and different physical properties of inorganic nanomaterials.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@incollection{Toropov2016,
title = {Development of the Latest Tools for Building up “Nano-QSAR”: Quantitative Features\textemdashProperty/Activity Relationships (QFPRs/QFARs)},
author = { Andrey A. Toropov and Alla P. Toropova and Karel Nesmerak and Aleksandar M. Veselinovi\'{c} and Jovana B. Veselinovi\'{c} and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/978-1-4899-7699-4_12},
doi = {10.1007/978-1-4899-7699-4_12},
year  = {2016},
date = {2016-01-01},
booktitle = {Practical Aspects of Computational Chemistry IV},
pages = {353--396},
publisher = {Springer US},
address = {Boston, MA},
abstract = {Computational studies of common compounds are already standard ways of their investigations. However, modeling properties of nanomaterials has been always a challenging task. This chapter reveals important differences between approaches applied to these two groups of species. The development of an optimal descriptor provides one of the efficient ways for the computational techniques to estimate endpoints related to nanospecies. Notably, the optimal descriptor can represent a translator of eclectic information into the endpoint prediction. Development of the optimal descriptor could start with consideration of a hybrid of topological indices calculated with the adjacency matrix of the molecular graph and application of additive scheme where a physicochemical parameter is modeled as the summation of contributions of molecular fragments. Further, the optimal descriptor might be advanced by taking into account contributions of various physicochemical conditions. Such contributions include presence/absence of defined chemical elements and/or defined kinds of covalent bonds, as well as different kinds of rings in the molecular system\textemdashfactors which are able to modify the physicochemical (biochemical) behavior of a substance. Finally, the latest version of optimal descriptor involves the applications of eclectic data into building up model for endpoints related to nanomaterials. A recently acquired collection of models developed to predict various endpoints of nanomaterials is presented and discussed in this chapter.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Toropova2016,
title = {Nano-QSAR: Genotoxicity of Multi-Walled Carbon Nanotubes},
author = { A.P. Toropova and A.A. Toropov and R. Rallo and D. Leszczynska and J. and Leszczynski},
year  = {2016},
date = {2016-01-01},
journal = {Int. J. Environ. Res.},
volume = {10},
number = {1},
pages = {59--64},
abstract = {ABSTRACT: The study was carried out to develop an efficient approach for prediction the genotoxicity of carbon nanotubes. The experimental data on the bacterial reverse mutation test (TA100) on multi-walled carbon nanotubes (MWCNTs) was collected from the literature and examined as an endpoint. By means of the optimal descriptors calculated with the Monte Carlo method a mathematical model of the endpoint was built up. The model is represented by a function of: (i) dose (µg/plate); (ii) metabolic activation (i.e. with S9 mix or without S9 mix); and (iii) two types of MWCNTs. The above listed conditions were represented by so-called quasi-SMILES. Simplified molecular input-line entry system (SMILES) is a tool for representation of molecular structure. The quasi-SMILES is a tool to represent physicochemical and / or biochemical conditions for building up a predictive model. Thus, instead of well-known paradigm of predictive modeling “endpoint is a mathematical function of molecular structure” a fresh paradigm “endpoint is a mathematical function of available eclectic data (conditions) is suggested.},
keywords = {Bacterial reverse mutation test, CORAL software, MWCNT, Nano-QSAR},
pubstate = {published},
tppubtype = {article}
}
@incollection{Yuldasheva2016,
title = {Iodine Containing Drugs: Complexes of Molecular Iodine and Tri-iodide with Bioorganic Ligands and Lithium Halogenides in Aqueous Solutions},
author = { Gulnara A. Yuldasheva and Georgii M. Zhidomirov and Jerzy Leszczynski and Aleksandr I. Ilin},
url = {http://link.springer.com/10.1007/978-1-4899-7699-4_10},
doi = {10.1007/978-1-4899-7699-4_10},
year  = {2016},
date = {2016-01-01},
booktitle = {Practical Aspects of Computational Chemistry IV},
pages = {279--301},
publisher = {Springer US},
address = {Boston, MA},
abstract = {This chapter reviews the results of molecular modeling of iodine-containing drugs. They are active ingredients of mixtures that in aqueous solutions consist of molecular iodine, bio-organic ligands, and potassium and lithium halogenides. In these drugs molecular iodine is in such an active form that after oral administration it minimizes toxic effects in humans. Previously it was shown that the active complex (AC) of the drugs contains molecular iodine that is located inside $alpha$-helix of dextrin and is coordinated by lithium halides and polypeptides (LiI5-$alpha$-dextrin polypeptide). In these types of complexes the electronic structure of the I2 molecule is different from the electronic structure of I2 in complexes with organic ligands, or in its free state. Interestingly, in the AC the molecular iodine exhibits acceptor properties with respect to polypeptides, and donor properties with respect to lithium halide. Our group was the first to propose the molecular model of active complexes of the iodine-containing drugs. This was based on the results of calculations performed using the DFT-B3PW91/midi approach. Model system of the water-glycine KI3-LiCl-ethanol was considered in this study. The calculations of the spectral parameters of the proposed structures are in good agreement with the experimental data of UV and IR spectral investigations. We have shown that $alpha$-dextrins ensure the presence in the studied mixtures of the three active centers located within the $alpha$-dextrin helix: molecular iodine coordinated lithium halogenides and polypeptides, triiodide, and lithium halogenides. Using UV spectroscopy, the interaction of $alpha$-dextrin-LiCl(I)-I2-polypeptid with the AGA nucleotide triplet was investigated. Comparison of the quantum chemical calculations carried out for electronic transitions obtained for the structure that models the interaction of $alpha$-dextrin-LiCl(I)-I2-polypeptid with the nucleotide triplet indicates that the DNA nucleotides can displace polypeptide and form stable complexes with molecular iodine and lithium halogenides. In such structures, molecular iodine binds both the nucleotide triplet and lithium halogenides. We have shown that the presence of molecular iodine is vital for activity of compounds that inhibit the active site of HIV-1 integrase. Iodine prevents the active site of integrase from the formation of a complex with HIV DNA and inhibits the active complex of integrase and viral DNA, becoming the center of another nucleoprotein complex, and binding together the active site of integrase and viral DNA.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Li2016144,
title = {Optimization study on the hydrogen peroxide pretreatment and production of bioethanol from seaweed Ulva prolifera biomass},
author = { Cui J Zhang G Liu Z Guan H Hwang H Aker W G Wang P Li Y.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964523304&amp;partnerID=40&amp;md5=3e27aaaba1e71bd4165e1bc4185ffb4d},
doi = {10.1016/j.biortech.2016.04.090},
year  = {2016},
date = {2016-01-01},
journal = {Bioresource Technology},
volume = {214},
pages = {144--149},
abstract = {The seaweed Ulva prolifera, distributed in inter-tidal zones worldwide, contains a large percentage of cellulosic materials. The technical feasibility of using U. prolifera residue (UPR) obtained after extraction of polysaccharides as a renewable energy resource was investigated. An environment-friendly and economical pretreatment process was conducted using hydrogen peroxide. The hydrogen peroxide pretreatment improved the efficiency of enzymatic hydrolysis. The resulting yield of reducing sugar reached a maximum of 0.42 g/g UPR under the optimal pretreatment condition (hydrogen peroxide 0.2%, 50 °C, pH 4.0, 12 h). The rate of conversion of reducing sugar in the concentrated hydrolysates to bioethanol reached 31.4% by Saccharomyces cerevisiae fermentation, which corresponds to 61.7% of the theoretical maximum yield. Compared with other reported traditional processes on Ulva biomass, the reducing sugar and bioethanol yield are substantially higher. Thus, hydrogen peroxide pretreatment is an effective enhancement of the process of bioethanol production from the seaweed U. prolifera. textcopyright 2016 Elsevier Ltd.},
keywords = {Bio-ethanol production; Cellulosic material; Environment friendly; Optimization studies; Pre-Treatment; Pretreatment conditions; Pretreatment process; Ulva prolifera residue, Bioethanol; Energy resources; Ethanol; Hydrogen peroxide; Hydrolysis; Oxidation; Peroxides; Renewable energy resources; Seaweed; Yeast, Enzymatic hydrolysis, Saccharomyces cerevisiae; Ulva; Ulva prolifera},
pubstate = {published},
tppubtype = {article}
}
@article{He201650,
title = {Assessing the effects of surface-bound humic acid on the phototoxicity of anatase and rutile TiO2 nanoparticles in vitro},
author = { Sanders S Aker W G Lin Y Douglas J Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84951810597&amp;partnerID=40&amp;md5=a29f1eac0158a06d758a8496eda62f8b},
doi = {10.1016/j.jes.2015.05.028},
year  = {2016},
date = {2016-01-01},
journal = {Journal of Environmental Sciences (China)},
volume = {42},
pages = {50--60},
abstract = {In this study, the cytotoxicity of two different crystal phases of TiO2 nanoparticles, with surface modification by humic acid (HA), to Escherichia coli, was assessed. The physicochemical properties of TiO2 nanoparticles were thoroughly characterized. Three different initial concentrations, namely 50, 100, and 200 ppm, of HA were used for synthesis of HA coated TiO2 nanoparticles (denoted as A/RHA50, A/RHA100, and A/RHA200, respectively). Results indicate that rutile (LC50 (concentration that causes 50% mortality compared the control group) = 6.5) was more toxic than anatase (LC50 = 278.8) under simulated sunlight (SSL) irradiation, possibly due to an extremely narrow band gap. It is noted that HA coating increased the toxicity of anatase, but decreased that of rutile. Additionally, AHA50 and RHA50 had the biggest differences compared to uncoated anatase and rutile with LC50 of 201.9 and 21.6, respectively. We then investigated the formation of reactive oxygen species (ROS) by TiO2 nanoparticles in terms of hydroxyl radicals (textlesssup/textgreaterOH) and superoxide anions (O2 -). Data suggested that O2 - was the main ROS that accounted for the higher toxicity of rutile upon SSL irradiation. We also observed that HA coating decreased the generation of textlesssup/textgreaterOH and O2 - on rutile, but increased O2 - formation on anatase. Results from TEM analysis also indicated that HA coated rutile tended to be attached to the surface of E. coli more than anatase. textcopyright 2015.},
keywords = {Biological materials; Coatings; Energy gap; Escherichia coli; Irradiation; Nanoparticles; Organic acids; Oxide minerals; Oxygen; Surface treatment; Synthesis (chemical); Toxicity, Crystallinities; Humic acid; Initial concentration; Physicochemical property; Reactive oxygen species; Simulated sunlight; Surface coatings; TiO, Escherichia coli, Titanium dioxide},
pubstate = {published},
tppubtype = {article}
}
@article{He2016,
title = {Nanotechnology in food science: Functionality, applicability, and safety assessment},
author = { Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84979233689&amp;partnerID=40&amp;md5=c978c607900d27649f042d45a19cd1d5},
doi = {10.1016/j.jfda.2016.06.001},
year  = {2016},
date = {2016-01-01},
journal = {Journal of Food and Drug Analysis},
abstract = {Rapid development of nanotechnology is expected to transform many areas of food science and food industry with increasing investment and market share. In this article, current applications of nanotechnology in food systems are briefly reviewed. Functionality and applicability of food-related nanotechnology are highlighted in order to provide a comprehensive view on the development and safety assessment of nanotechnology in the food industry. While food nanotechnology offers great potential benefits, there are emerging concerns arising from its novel physicochemical properties. Therefore, the safety concerns and regulatory policies on its manufacturing, processing, packaging, and consumption are briefly addressed. At the end of this article, the perspectives of nanotechnology in active and intelligent packaging applications are highlighted. textcopyright 2016.},
keywords = {food industry; investment; market; nanotechnology; nutritional science; physical chemistry; risk assessment},
pubstate = {published},
tppubtype = {article}
}
@article{He2016b,
title = {Assessing the effect of different natural dissolved organic matters on the cytotoxicity of titanium dioxide nanoparticles with bacteria},
author = { McAlliser D Aker W G Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84966679986&amp;partnerID=40&amp;md5=d293421b017d8c065d772e7255f606c0},
doi = {10.1016/j.jes.2016.02.012},
year  = {2016},
date = {2016-01-01},
journal = {Journal of Environmental Sciences (China)},
abstract = {Titanium dioxide nanoparticles (TiO2 NPs) are among the most widely manufactured nanomaterials on a global scale. However, prudent and vigilant surveillance, incumbent upon the scientific community with the advent of new technologies, has revealed potentially undesirable effects of TiO2 NPs on biological systems and the natural environment during their application and discharge. Such effects are likely best evaluated by first assessing the fate of the TiO2 NPs in natural environments. In this study, the effects of terrestrial humic acid (HA) and tannic acid (TA), two major members of the collective: dissolved organic matter (DOM), on the cytotoxicity of TiO2 NPs to Escherichia coli were investigated in the presence and absence of natural sunlight. Qualitative (transmission electron microscopy (TEM)) and quantitative (LC50) analyses were employed in this study. In addition, the production of reactive oxygen species (ROS) in the form of OH was further assessed-as HA or TA increased the production of ROS decreased. The inhibition of bacterial viability in the light treatment groups, with respective treatment organics at concentrations of 10 ppm, was less in TA than in terrestrial HA. SAS was used to analyze the treatment effect of individual factors of light irradiation, DOM, and concentration of TiO2 NPs. textcopyright 2016.},
keywords = {Bacteria; Biogeochemistry; Biological materials; Cytotoxicity; Escherichia coli; Flavonoids; High resolution transmission electron microscopy; Nanoparticles; Organic acids; Organic compounds; Oxides; Tannins; Titanium; Transmission electron microscopy, Dissolved organic matters; Humic acid; Manufactured nanomaterials; Natural environments; Reactive oxygen species; Scientific community; Tannic acid; Titanium dioxide nanoparticles, Titanium dioxide},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2015b,
title = {Introduction of simplex-informational descriptors for QSPR analysis of fullerene derivatives},
author = { Natalia Sizochenko and Victor Kuz’min and Liudmila Ognichenko and Jerzy Leszczynski},
url = {http://link.springer.com/10.1007/s10910-015-0581-8},
doi = {10.1007/s10910-015-0581-8},
issn = {0259-9791},
year  = {2015},
date = {2015-12-01},
journal = {Journal of Mathematical Chemistry},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2015,
title = {How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure\textendashProperty Relationship Modeling of Nanofluids},
author = { Natalia Sizochenko and Karolina Jagiello and Jerzy Leszczynski and Tomasz Puzyn},
url = {http://pubs.acs.org/doi/10.1021/acs.jpcc.5b05759},
doi = {10.1021/acs.jpcc.5b05759},
issn = {1932-7447},
year  = {2015},
date = {2015-11-01},
journal = {The Journal of Physical Chemistry C},
volume = {119},
number = {45},
pages = {25542--25547},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yilmaz2015,
title = {Amino substituted nitrogen heterocycle ureas as kinase insert domain containing receptor (KDR) inhibitors: Performance of structure\textendashactivity relationship approaches},
author = { Hayriye Yilmaz and Natalia Sizochenko and Bakhtiyor Rasulev and Andrey Toropov and Yahya Guzel and Viktor Kuz'min and Danuta Leszczynska and Jerzy Leszczynski},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1021949815000435},
doi = {10.1016/j.jfda.2015.03.001},
issn = {10219498},
year  = {2015},
date = {2015-06-01},
journal = {Journal of Food and Drug Analysis},
volume = {23},
number = {2},
pages = {168--175},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{He20154908b,
title = {Trends in infant mortality in united states: A brief study of the Southeastern states from 2005\textendash2009},
author = { Akil L Aker W G Hwang H.-M. Ahmad H A He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929359063&amp;partnerID=40&amp;md5=6c69043f6cf8840258415537adb15bad},
doi = {10.3390/ijerph120504908},
year  = {2015},
date = {2015-01-01},
journal = {International Journal of Environmental Research and Public Health},
volume = {12},
number = {5},
pages = {4908--4920},
abstract = {While overall infant mortality rates have declined over the past several decades, the Southeastern states have remained the leading states in high infant death in the United States. In this study, we studied the differences in infant mortality in the southeastern United States from 2005 through 2009 according to mother's characteristics (age of mother, marital status, maternal race, maternal education), birth characteristics (month when maternal prenatal care began, birth weight), and infant's characteristics (age of infant at death). This paper illustrates the significance level of each characteristic of mothers and infants, as well as socioeconomic factors that contribute to significant infant mortality that impacts subgroups within the US population. Descriptive statistics and analysis of variance studies were performed and presented. Statistical analysis of the contribution of causes of infant death to infant mortality at the national and state level was elaborated. Data suggest that mothers with no prenatal care had a very high overall infant death rate (5281.83 and 4262.16 deaths per 100,000 births in Mississippi and Louisiana, respectively, whereas the US average was 3074.82 deaths (p textless 0.01)). It is suggested that better education and living quality should be available and improved for the residents in Alabama, Louisiana, and Mississippi. textcopyright 2015 by the authors; licensee MDPI, Basel, Switzerland.},
keywords = {Alabama; Florida [United States]; Georgia; Louisiana; Mississippi; United States, analysis of variance; Article; child death; controlled study; human; infant; infant mortality; marriage; maternal care; mother child relation; parenting education; prenatal care; race; retrospective study; socioeconomics; trend study; United States, educational attainment; infant mortality; public health; quality of life; socioeconomic impact; socioeconomic status},
pubstate = {published},
tppubtype = {article}
}
@article{Li2015799b,
title = {Purification and characterization of a novel enzyme produced by Catenovulum sp. LP and its application in the pre-treatment to Ulva prolifera for bio-ethanol production},
author = { Huang Z Qiao L Gao Y Guan H Hwang H Aker W G Wang P Li Y.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939951071&amp;partnerID=40&amp;md5=5e5a7f063b0a78f872035a1c7cc04d19},
doi = {10.1016/j.procbio.2015.02.013},
year  = {2015},
date = {2015-01-01},
journal = {Process Biochemistry},
volume = {50},
number = {5},
pages = {799--806},
abstract = {The high viscosity of polysaccharides from Ulva prolifera (PU) is one reason that impeded the high production of bio-ethanol by U. prolifera. A depolymerase with high specificity was first isolated from Catenovulum sp. LP. The 75.5 kDa depolymerase was purified 42.35-fold to homogeneity with 22.86 U/mg specific activity. The enzyme showed the highest activity at the optimal conditions of pH 6.0 and 35°C. It also showed high stability with a Half-life (t1/2) of 1386 min at 35°C. It retained 100% of its residual activity in 10 mM EDTA, 1,10-phenanthrolin, or Tween 80 after incubation of 2 h. The depolymerase showed high efficiency to PU for reducing sugar production, which reached 50.2% yield in 6 h. However, the commercial enzymes showed no hydrolysis to PU. The viscosity of 1.2% PU noticeable declined from initially 1127 to 7.2 mPa s in 95 min of hydrolysis even in the room temperature. The application of depolymerase with these unique properties could bring promising prospects for enzymatic pretreatment of the bio-ethanol production from U. prolifera biomass. textcopyright 2015 Elsevier Ltd. All rights reserved.},
keywords = {Bio-ethanol production; Bio-ethanols; Commercial enzymes; Depolymerase; Enzymatic pretreatment; Optimal conditions; Residual activity; Specific activity, Bioethanol; Characterization; Enzymes; Ethanol; Hydrolysis; Polysaccharides; Purification; Viscosity, Enzyme activity},
pubstate = {published},
tppubtype = {article}
}
@article{He2015564,
title = {Toxicity of engineered metal oxide nanomaterials mediated by nano-bio-eco-interactions: A review and perspective},
author = { Aker W G Fu P P Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948684955&amp;partnerID=40&amp;md5=6a431aa35fd69d4137d4b721565f32d7},
doi = {10.1039/c5en00094g},
year  = {2015},
date = {2015-01-01},
journal = {Environmental Science: Nano},
volume = {2},
number = {6},
pages = {564--582},
abstract = {Along with the expanding use of engineered metal oxide nanomaterials (MONMs), there is a growing concern over their unintentional adverse toxicological effects on human health and the environment upon release and exposure. It is inevitable that biota will be exposed to nanomaterials, through intentional administration or inadvertent contact under such circumstances. Therefore, a thorough investigation of the potential nanotoxicity of MONMs at the nano-bio-eco interface is urgently needed. In general, nanomaterials interact with their surrounding environments, biotic and abiotic, immediately upon introduction into the environment. The behavior and fate of MONMs are influenced by the dynamics of the environment. Thus, understanding the interactions at the nano-bio-eco interface is necessary for selecting and designing MONMs with minimum adverse impacts. Despite the limitations of currently available techniques, careful characterization of nanomaterials and the choosing of methodologies that promote further risk assessment promise more reliable and accurate data output. Conventional toxicological analysis techniques lack the power to handle the large datasets generated from in vitro/in vivo observations. This paper provides a comprehensive review of the recent experimental and theoretical studies on the toxicity of MONMs mediated by two-way or three-way interactions. In the Perspectives, we also call for more open collaborations between industry, academia, and research labs to facilitate nanotoxicological studies focused specifically on interactions at the nano-bio-eco interface, leading to safe and effective nanotechnology for commercial, environmental, and medicinal use. textcopyright The Royal Society of Chemistry 2015.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{He20151887,
title = {Metal oxide nanomaterials in nanomedicine: Applications in photodynamic therapy and potential toxicity},
author = { Aker W G Huang M.-J. Watts J D Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84934784083&amp;partnerID=40&amp;md5=04d79c80eb87ce6b5687ba6665e5873c},
year  = {2015},
date = {2015-01-01},
journal = {Current Topics in Medicinal Chemistry},
volume = {15},
number = {18},
pages = {1887--1900},
abstract = {Metal oxide nanomaterials have exhibited excellent performance as nanomedicines in pho-todynamic therapy (PDT) for cancer and infection treatment. Their unique and tunable physicochemi-cal properties advance them as promising alternatives in drug delivery, early diagnosis, imaging, and treatment against various tumors and infectious diseases. Moreover, the implementation of nanopho-totherapy in deep tissue sites is enhanced by advancements in photosensitization technology. Notwithstanding the progress made in emerging metal oxide nanomaterials-derived PDT, the potential toxicity towards adjunct tissues associated with this approach remains challenging. Regulation and legislation have also been recommended and subsequently enacted in response to public concerns related to large-scale production, transportation, use, and disposal of those nanomaterials. Consequently, a quantitative structure-activity relationship (QSAR) paradigm has been adopted and is widely used in evaluating and predicting the side effects of nanomedicines, thus influencing their design and fabrication. This article briefly reviews the application of metal oxide nanomaterials in PDT and their associated adverse impacts as reported in recent publications. The future trends and implications of this platform in nanomedicine are also highlighted. However, more studies and efforts have to be carried out for developing novel nano-therapeutics with high selectivity, sensitivity, biocompatibility, and minimal side effects in PDT. textcopyright 2015 Bentham Science Publishers.},
keywords = {Bacteria; Fungi; Humans; Metals; Nanomedicine; Nanostructures; Neoplasms; Oxides; Parasitic Diseases; Photochemotherapy; Quantitative Structure-Activity Relationship},
pubstate = {published},
tppubtype = {article}
}
@article{Karahan20151,
title = {Experimental and theoretical investigation of a novel mononuclear copper(II) azido compound with tridentate (NNO) Schiff base},
author = { A.a Karahan and S.b Karabulut and H.c Dal and R.d Kurtaran and J.e Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84926217046&amp;partnerID=40&amp;md5=a719d3664d0b7ce9581055e2e173dd44},
doi = {10.1016/j.molstruc.2015.02.065},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Molecular Structure},
volume = {1093},
pages = {1-7},
abstract = {Abstract The tridentate (NNO) Schiff base (HL), has been prepared by the condensation of 2-(aminomethyl)pyridine with 5-chloro-salicylaldehyde. The mononuclear [N-(2-pyridylmethyl)-3-chloro-salicylaldiminato] (azido) copper(II) complex of general formula [Cu(L)(N<inf>3</inf>)] (1) has been synthesized by the treatment of HL and CuCl<inf>2</inf>·2H<inf>2</inf>O with sodium azide. The ligand and complex have been investigated by various methods including IR, TG-DTA and X-ray diffraction techniques. The complex crystallizes in monoclinic space group P2<inf>1/c</inf>, with unit cell dimensions a = 6.7369(4)},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko20158139,
title = {Structure and Redox Properties of 5-Amino-3-nitro-1 H -1,2,4-triazole (ANTA) Adsorbed on a Silica Surface: A DFT M05 Computational Study},
author = { L.K.a b Sviatenko and L.c Gorb and F.C.d Hill and D.e Leszczynska and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84937846562&amp;partnerID=40&amp;md5=c6da3e91fe7dbf113f9f0e4d8ec5aaf6},
doi = {10.1021/acs.jpca.5b03393},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry A},
volume = {119},
number = {29},
pages = {8139-8145},
abstract = {A cluster approximation was applied at the M05/tzvp level to model an adsorption of 5-amino-3-nitro-1H-1,2,4-triazole (ANTA) on the (001) surface of α-quartz. Structures of the obtained ANTA-silica complexes confirm a nearly parallel orientation of the nitro compound toward the surface. The atoms in molecules (AIM) method was applied to analyze binding between ANTA and the silica surface. Attachment or loss of an electron was found to lead to a significant deviation from coplanarity in the complexes and to a strengthening of a hydrogen bonding. Redox properties of the adsorbed ANTA were compared with those of gas-phase and hydrated species by calculation of the ionization potential, electron affinity, oxidation and reduction Gibbs free energies, and oxidation and reduction potentials. It was shown that the adsorbed ANTA has a lower ability to undergo redox transformations as compared to that of the hydrated one. (Figure Presented). © 2015 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Golius2015,
title = {Computational study of NTO (5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one) tautomeric properties in aqueous solution},
author = { A.a Golius and L.b Gorb and A.c Michalkova Scott and F.C.c Hill and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84930352756&amp;partnerID=40&amp;md5=c183c8a74b0a1fec80760aaee6ad32f5},
doi = {10.1007/s11224-014-0526-z},
year  = {2015},
date = {2015-01-01},
journal = {Structural Chemistry},
abstract = {This study focuses on elucidating the stable forms of a new energetic material that is a member of the class of insensitive munitions (IM), 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO), including its tautomers, and anions. The geometry and properties of all compounds were calculated using density functional theory (M06-2X) and MP2 quantum chemical approaches. Calculations were carried out in the gas phase and in aqueous solution. Chemical stability of these compounds was evaluated in terms of the Gibbs free energy change. Two different solvation models were applied (CPCM and PCM). Calculations showed that overall differences in the results obtained using these two solvation models are negligible for all compounds considered. All possible NTO tautomers were examined and the results are in good agreement with previous studies performed in the gas phase. The stability order was revealed to be slightly dependent on the method applied. In order to estimate acidic properties of NTO, anions of several NTO tautomers were analyzed. In addition, pK<inf>a</inf> values were calculated using different approaches. As compared with available experimental data it was found that the conductor-like screening model for real solvents approach leads to more accurate estimation of the pK<inf>a</inf> value than the CPCM and PCM approaches. The pK<inf>a</inf> value calculated using PCM and CPCM data showed large errors; however, it was proven that the pattern of deprotonation energy was correctly estimated. © 2015 Springer Science+Business Media New York},
note = {cited By 0; Article in Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko20151029,
title = {Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study},
author = { L.K.a b Sviatenko and O.c Isayev and L.d Gorb and F.C.e Hill and D.f Leszczynska and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84928495899&amp;partnerID=40&amp;md5=d4d52734dc1d365c787fd2c4c9fb92f5},
doi = {10.1002/jcc.23878},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Computational Chemistry},
volume = {36},
number = {14},
pages = {1029-1035},
abstract = {The reduction and oxidation properties of four nitrocompounds (trinitrotoluene [TNT], 2,4-dinitrotoluene, 2,4-dinitroanisole, and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one [NTO]) dissolved in water as compared with the same properties for compounds adsorbed on a silica surface were studied. To consider the influence of adsorption, cluster models were developed at the M05/tzvp level. A hydroxylated silica (001) surface was chosen to represent a key component of soil. The PCM(Pauling) and SMD solvation models were used to model water bulk influence. The following properties were analyzed: electron affinity, ionization potential, reduction Gibbs free energy, oxidation Gibbs free energy, and reduction and oxidation potentials. It was found that adsorption and solvation decrease gas phase electron affinity, ionization potential, and Gibbs free energy of reduction and oxidation, and thus, promote redox transformation of nitrocompounds. However, in case of solvation, the changes are more significant than for adsorption. This means that nitrocompounds dissolved in water are easier to transform by reduction or oxidation than adsorbed ones. Among the considered compounds, TNT was found to be the most reactive in an electron attachment process and the least reactive for an electron detachment transformation. During ionization, a deprotonation of adsorbed NTO was found to occur. © 2015 Wiley Periodicals, Inc.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yilmaz2015778,
title = {Modeling the dispersibility of single walled carbon nanotubes in organic solvents by quantitative structure-activity relationship approach},
author = { H.a b Yilmaz and B.b c Rasulev and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84937545945&amp;partnerID=40&amp;md5=7d454650f4e7df95e1f49db87c7c6fc1},
doi = {10.3390/nano5020778},
year  = {2015},
date = {2015-01-01},
journal = {Nanomaterials},
volume = {5},
number = {2},
pages = {778-791},
abstract = {The knowledge of physico-chemical properties of carbon nanotubes, including behavior in organic solvents is very important for design, manufacturing and utilizing of their counterparts with improved properties. In the present study a quantitative structure-activity/property relationship (QSAR/QSPR) approach was applied to predict the dispersibility of single walled carbon nanotubes (SWNTs) in various organic solvents. A number of additive descriptors and quantum-chemical descriptors were calculated and utilized to build QSAR models. The best predictability is shown by a 4-variable model. The model showed statistically good results (R2 <inf>training</inf> = 0.797},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mikolajczyk20152400,
title = {Zeta potential for metal oxide nanoparticles: A predictive model developed by a nano-quantitative structure-property relationship approach},
author = { A.a Mikolajczyk and A.a Gajewicz and B.b c Rasulev and N.d Schaeublin and E.d Maurer-Gardner and S.d Hussain and J.b Leszczynski and T.a Puzyn},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84927711807&amp;partnerID=40&amp;md5=f5a375c2c79c5b6f23cad1ce5b3d265e},
doi = {10.1021/cm504406a},
year  = {2015},
date = {2015-01-01},
journal = {Chemistry of Materials},
volume = {27},
number = {7},
pages = {2400-2407},
abstract = {Physico-chemical characterization of nanoparticles in the context of their transport and fate in the environment is an important challenge for risk assessment of nanomaterials. One of the main characteristics that defines the behavior of nanoparticles in solution is zeta potential (ζ). In this paper, we have demonstrated the relationship between zeta potential and a series of intrinsic physico-chemical features of 15 metal oxide nanoparticles revealed by computational study. The here-developed quantitative structure-property relationship model (nano-QSPR) was able to predict the ζ of metal oxide nanoparticles utilizing only two descriptors: (i) the spherical size of nanoparticles, a parameter from numerical analysis of transmission electron microscopy (TEM) images, and (ii) the energy of the highest occupied molecular orbital per metal atom, a theoretical descriptor calculated by quantum mechanics at semiempirical level of theory (PM6 method). The obtained consensus model is characterized by reasonably good predictivity (QEXT<inf>2</inf> = 0.87). Therefore, the developed model can be utilized for in silico evaluation of properties of novel engineered nanoparticles. This study is a first step in developing a comprehensive and computationally based system to predict physico-chemical properties that are responsible for aggregation phenomena in metal oxide nanoparticles. © 2015 American Chemical Society.},
note = {cited By 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jaro\'{n}20155689,
title = {Facile formation of thermodynamically unstable novel borohydride materials by a wet chemistry route},
author = { T.a Jaro\'{n} and W.b Wegner and K.J.a Fija\lkowski and P.J.a Leszczy\'{n}ski and W.a Grochala},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84925443691&amp;partnerID=40&amp;md5=2186f3ea2906b383a8acf4a5f960e57f},
doi = {10.1002/chem.201404968},
year  = {2015},
date = {2015-01-01},
journal = {Chemistry - A European Journal},
volume = {21},
number = {15},
pages = {5689-5692},
abstract = {A novel wet synthetic method utilizing weakly coordinating anions that yields LiCl-free Zn-based materials for hydrogen storage has recently been reported. Here we show that this method may also be applied for the synthesis of the pure yttrium derivatives, M[Y(BH4)4] (M=K, Rb, Cs). Moreover, it can be extended to the preparation of previously unknown thermodynamically unstable derivatives, Li[Y(BH4)4] and Na[Y(BH4)4]. Importantly, these two H-rich phases cannot be accessed by standard dry (mechanochemical) or solid/gas synthetic methods due to the thermodynamic obstacles. Here we describe their crystal structures and selected important physicochemical properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut20151815,
title = {Molecular structure of aurothioglucose: A comprehensive computational study},
author = { S.a Karabulut and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923629899&amp;partnerID=40&amp;md5=40a2d0a345c1ce5e14ba25b8ed871fde},
doi = {10.1016/j.tet.2015.02.007},
year  = {2015},
date = {2015-01-01},
journal = {Tetrahedron},
volume = {71},
number = {12},
pages = {1815-1821},
abstract = {In order to investigate the molecular structure of aurothioglucose (ATG), six stable, well-known conformations of glucopyranose (Gp) have been computed and compared with Gp, thioglucopyranose (TGp), monomeric aurothioglucose (MATG), and dimeric aurothioglucose (DATG) models. The study has been performed using two DFT approaches. It has been concluded that the 'β' anomer of ATG is more stable than the 'α' anomer for TGp, MATG, and DATG models. M06 and B3LYP levels molecular geometries have been compared for the TGp species. Though both methods provided similar results, B3LYP is slightly better than M06 for optimization of TGp, especially for accurate description of bond lengths and dihedral angles. © 2015 Elsevier Ltd. All rights reserved.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova20151223,
title = {QSAR model as a random event: A case of rat toxicity},
author = { A.P.a Toropova and A.A.a Toropov and E.a Benfenati and D.b Leszczynska and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923540970&amp;partnerID=40&amp;md5=e1bef8c80a6057260d55eddb4f2696d2},
doi = {10.1016/j.bmc.2015.01.055},
year  = {2015},
date = {2015-01-01},
journal = {Bioorganic and Medicinal Chemistry},
volume = {23},
number = {6},
pages = {1223-1230},
abstract = {Quantitative structure - property/activity relationships (QSPRs/QSARs) can be used to predict physicochemical and/or biochemical behavior of substances which were not studied experimentally. Typically predicted values for chemicals in the training set are accurate since they were used to build the model. QSPR/QSAR models must be validated before they are used in practice. Unfortunately, the majority of the suggested approaches of the validation of QSPR/QSAR models are based on consideration of geometrical features of clusters of data points in the plot of experimental versus calculated values of an endpoint. We believe these geometrical criteria can be more useful if they are analyzed for several splits into the training and test sets. In this way, one can estimate the reproducibility of the model with various splits and better evaluate model reliability. The probability of the correct prediction of an endpoint for external validation set (in the series of the above-mentioned splits) can provide an useful way to evaluate the domain of applicability of the model. © 2015 Elsevier Ltd. All rights reserved.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Paytakov20151190,
title = {Toward selection of efficient density functionals for van der waals molecular complexes: Comparative study of C-H···π and N-H···π Interactions},
author = { G.a Paytakov and T.b Dinadayalane and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923354385&amp;partnerID=40&amp;md5=c0807a5defd5c8ffde22ee39259a5b05},
doi = {10.1021/jp511450u},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry A},
volume = {119},
number = {7},
pages = {1190-1200},
abstract = {We have evaluated the performance of two of the recently developed density functionals (M06-2X and B2PLYP-D), which are widely used, by considering three important prototype systems, including benzene-acetylene, benzene-methane, and benzene-ammonia, possessing C-H···π or N-H···π interactions. Computational results are compared with the available experimental data. Considered density functionals are from two different classes: hybrid meta density functional (M06-2X) and double hybrid density functional (B2PLYP-D). The performance of a range of basis sets (6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311G(d,p), 6-311+G(d,p), aug-cc-pVXZ (X = D, T, Q)) with the above-mentioned two density functionals was evaluated. Comparison of the results includes Pople's basis sets versus Dunning's correlation consistent basis sets with the M06-2X and B2PLYP-D functionals considered in this study. The basis set effect on geometrical parameters, dissociation energies, and selected vibrational frequency shifts was thoroughly analyzed. We have addressed whether the counterpoise corrections with geometry optimizations and vibrational frequencies are important. Our computational study reveals that calculations carried out with smaller basis sets very well reproduce the reported experimental values of dissociation energies. The present study also shows that using the very large Dunning's correlation consistent basis set worsens the results. The necessity of including counterpoise correction for binding energies depends on the system and the type of method used. In general, vibrational frequency calculations using these DFT functionals generate characteristic red shifts for the C-H···π or N-H···π interactions in the complexes. © 2015 American Chemical Society.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gu20152454,
title = {Photoinduced electron detachment and proton transfer: The proposal for alternative path of formation of triplet states of guanine (G) and cytosine (C) pair},
author = { J.a Gu and J.b Wang and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84922818750&amp;partnerID=40&amp;md5=750f8db08ec59ed8cbe758eb3f1afe17},
doi = {10.1021/jp507385r},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry B},
volume = {119},
number = {6},
pages = {2454-2458},
abstract = {A viable pathway is proposed for the formation of the triplet state of the GC Watson-Crick base pair. It includes the following steps: (a) a low-energy electron is captured by cytosine in the GC pair, forming the cytosine base-centered radical anion GC-•; and (b) photoradiation with energy around 5 eV initiates the electron detachment from either cytosine (in the gas phase) or guanine (in aqueous solutions). This triggers interbase proton transfer from G to C, creating the triplet state of the GC pair. Double proton transfer involving the triplet state of GC pair leads to the formation of less stable tautomer G(N2-H)•C(O2H)•. Tautomerization is accomplished through a double proton transfer process in which one proton at the N3 of C(H)• migrates to the N1 of G(-H)•; meanwhile, the proton at the N2 of G transfers to the O2 of C. This process is energetically viable; the corresponding activation energy is around 12-13 kcal/mol. The base-pairing energy of the triplet is found to be ∼3-5 kcal/mol smaller than that of the singlet state. Thus, the formation of the triplet state GC pair in DNA double strand only slightly weakens its stability. The obtained highly reactive radicals are expected to cause serious damage in the DNA involved in biochemical processes, such as DNA replication where radicals are exposed in the single strands. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Shevchenko20151387,
title = {On the reaction of diaminocarbenes with aroylimines},
author = { I.V.a Shevchenko and K.V.a Turcheniuk and A.A.b Kirilchuk and J.c Leszczynski and A.B.b c Rozhenko},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84922666044&amp;partnerID=40&amp;md5=40d0f443dedb7a861041ed35dddca180},
doi = {10.1021/jo502155j},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Organic Chemistry},
volume = {80},
number = {3},
pages = {1387-1394},
abstract = {Several possible reaction pathways are analyzed for the recently studied experimental reaction of diaminocarbenes with aroylimines, where the carbene acted as an oxygen-abstracting agent. A number of structures corresponding to local minima and transition states are located by geometry optimization. In contrast to the more recent interpretation of the mechanism of this process, the reaction does not proceed via the direct formation of the corresponding carbonyl ylide resulted from the electrophilic addition of diaminocarbene to the carbonyl oxygen atom. Two other, more favorable pathways were predicted instead: the nucleophilic attack of the carbene lone pair on the imino nitrogen (pathway "a") or on the carbon atom in the C? - ?N moiety of aroylimine (pathway "b"), in agreement with predictions of the frontier molecular orbital (FMO) theory. Both intermediate adducts undergo a subsequent decomposition onto nitrile ylide and urea. Which of the two pathways becomes preferential depends on the nature of the substituents: pathway "a" is more favored for the experimentally studied species, whereas pathway "b" is thermodynamically preferable for the small-sized model structures. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yengui2015,
title = {Atomic scale study of corrugating and anticorrugating states on the bare Si(1 0 0) surface},
author = { M.a Yengui and H.P.b Pinto and J.b Leszczynski and D.a Riedel},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84921665809&amp;partnerID=40&amp;md5=7b2868cf9aa3dc9a30c8c840b30bcaa6},
doi = {10.1088/0953-8984/27/4/045001},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physics Condensed Matter},
volume = {27},
number = {4},
abstract = {In this article, we study the origin of the corrugating and anticorrugating states through the electronic properties of the Si(1 0 0) surface via a low-temperature (9 K) scanning tunneling microscope (STM). Our study is based on the analysis of the STM topographies corrugation variations when related to the shift of the local density of states (LDOS) maximum in the [1 1 0] direction. Our experimental results are correlated with numerical simulations using the density-functional theory with hybrid HeydScuseriaErnzerhof (HSE06) functional to simulate the STM topographies, the projected density of states variations at different depths in the silicon surface as well as the three dimensional partial charge density distributions in real-space. This work reveals that the Si(1 0 0) surface exhibits two anticorrugating states at +0.8 and +2.8V that are associated with a phase shift of the LDOS maximum in the unoccupied states STM topographies. By comparing the calculated data with our experimental results, we have been able to identify the link between the variations of the STM topographies corrugation and the shift of the LDOS maximum observed experimentally. Each surface voltage at which the STM topographies corrugation drops is defined as anticorrugating states. In addition, we have evidenced a sharp jump in the tunnel current when the second LDOS maximum shift is probed, whose origin is discussed and associated with the presence of Van Hove singularities. © 2015 IOP Publishing Ltd.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova201539,
title = {Optimal descriptor as a translator of eclectic data into prediction of cytotoxicity for metal oxide nanoparticles under different conditions},
author = { A.P.a Toropova and A.A.a Toropov and R.b Rallo and D.c Leszczynska and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84909979851&amp;partnerID=40&amp;md5=7c53deac17393d42639539c556f7582c},
doi = {10.1016/j.ecoenv.2014.10.003},
year  = {2015},
date = {2015-01-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {112},
pages = {39-45},
abstract = {The Monte Carlo technique has been used to build up quantitative structure-activity relationships (QSARs) for prediction of dark cytotoxicity and photo-induced cytotoxicity of metal oxide nanoparticles to bacteria Escherichia coli (minus logarithm of lethal concentration for 50% bacteria pLC50, LC50 in mol/L). The representation of nanoparticles include (i) in the case of the dark cytotoxicity a simplified molecular input-line entry system (SMILES), and (ii) in the case of photo-induced cytotoxicity a SMILES plus symbol '. ^. '. The predictability of the approach is checked up with six random distributions of available data into the visible training and calibration sets, and invisible validation set. The statistical characteristics of these models are correlation coefficient 0.90-0.94 (training set) and 0.73-0.98 (validation set). © 2014 Elsevier Inc.},
note = {cited By 4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Basaran2015657,
title = {Synthesis and anion binding properties of a urea-based molecular cleft},
author = { I.a b Basaran and X.a Wang and A.a Alamgir and J.a Wang and S.A.a Haque and Y.a Zhang and D.R.c Powell and J.a Leszczynski and M.A.a Hossain},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84920746876&amp;partnerID=40&amp;md5=dba19239462651acd46f3723a43999c8},
doi = {10.1016/j.tetlet.2014.12.015},
year  = {2015},
date = {2015-01-01},
journal = {Tetrahedron Letters},
volume = {56},
number = {5},
pages = {657-661},
abstract = {A new urea-based molecular cleft (L) derived from propylene-linked dipodal amine has been synthesized and its binding affinities for anions have been investigated by 1H NMR and UV-vis spectroscopic titrations in DMSO. The receptor has been shown to bind F-, HSO4 -, H2PO4 -, and AcO- in a 1:1 binding mode via hydrogen bonding interactions, providing the highest binding constant for F-. In addition, the new cleft shows a naked-eye color change in the presence of F- in DMSO. The interactions of L with fluoride have also been evaluated by theoretical calculations based on density functional theory (DFT), revealing that the cleft encapsulates a fluoride via four NH-F- and two CH-F- bonds. © 2014 Elsevier Ltd. All rights reserved.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nguyen201538,
title = {Borane and alane mediated hydrogen release from silane and methylsilane},
author = { H.T.a Nguyen and D.b Majumdar and J.b Leszczynski and M.T.a Nguyen},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84919949867&amp;partnerID=40&amp;md5=eabdf6481def7b0a6a795ce04b733c2b},
doi = {10.1016/j.cplett.2014.12.010},
year  = {2015},
date = {2015-01-01},
journal = {Chemical Physics Letters},
volume = {620},
pages = {38-42},
abstract = {The dehydrogenations of silanes SiH4 and CH3SiH3 in the presence of borane and alane were investigated using density functional (B3LYP) and coupled-cluster (CCSD(T)/aug-cc-pVnZ) theories. The calculated results showed that the hydrogen release reactions are more favorable in presence of BH3. Our theoretical analyses have further revealed that the addition of an extra BH3 can lead to several low energy barrier pathways. This observation is important to understand the catalytic role of BH3 in such reactions (depending on its release mechanism). Overall, silane and its alkyl derivatives can be used as effective starting materials for H2 production. © 2014 Elsevier B.V. All rights reserved.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jaro\'{n}20151236,
title = {Hydrogen storage materials: Room-temperature wet-chemistry approach toward mixed-metal borohydrides},
author = { T.a Jaro\'{n} and P.A.b Or\lowski and W.b Wegner and K.J.a Fija\lkowski and P.J.a Leszczy\'{n}ski and W.a Grochala},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84921029733&amp;partnerID=40&amp;md5=e41254b19961196e35bb03f390546be7},
doi = {10.1002/anie.201408456},
year  = {2015},
date = {2015-01-01},
journal = {Angewandte Chemie - International Edition},
volume = {54},
number = {4},
pages = {1236-1239},
abstract = {The poor kinetics of hydrogen evolution and the irreversibility of the hydrogen discharge hamper the use of transition metal borohydrides as hydrogen storage materials, and the drawbacks of current synthetic methods obstruct the exploration of these systems. A wet-chemistry approach, which is based on solvent-mediated metathesis reactions of precursors containing bulky organic cations and weakly coordinating anions, leads to mixed-metal borohydrides that contain only a small amount of "dead mass". The applicability of this method is exemplified by Li[Zn2(BH4)5] and M[Zn(BH4)3] salts (M = Na, K), and its extension to other systems is discussed. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ahmed2015383,
title = {Experimental and Theoretical Studies on Halide Binding with a p-Xylyl-Based Azamacrocycle},
author = { L.a Ahmed and M.M.a Rhaman and J.S.a Mendy and J.a Wang and F.R.b Fronczek and D.R.c Powell and J.a Leszczynski and M.A.a Hossain},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84927513991&amp;partnerID=40&amp;md5=258a29e2c6080aaf437341f14f4b7ec3},
doi = {10.1021/jp511040p},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry A},
volume = {119},
number = {2},
pages = {383-394},
abstract = {A p-xylyl-based macrocycle L has been synthesized and its binding properties with halides have been investigated by 1H NMR titrations, single crystal X-ray diffraction analysis, and density functional theory (DFT) calculations. As investigated by 1H NMR titrations, the ligand preferentially binds a halide in a 1:2 binding mode, with the association constants (in log K<inf>2</inf>) of 2.82, 2.70, 2.28, and 2.20 for fluoride, chloride, bromide, and iodide, respectively. The overall binding trend was found to be in the order of fluoride > chloride > bromide > iodide, reflecting that the binding strength correlates with the relative basicity and size of the respective halide. Crystallographic studies indicate that the ligand forms 1:2 complexes with chloride, bromide and iodide. In the chloride complex, the ligand is hexaprotonated and each chloride is held via three NH···Cl- bonds. The ligand is tetraprotonated for the other complexes, where each halide is H-bonded to two secondary ammonium NH+ groups via NH···X- bonds. The results of DFT calculations performed on [H<inf>6</inf>L]6+ at M062x/6-311G (d,p) level in both gas and solvent phases, suggest that the ligand binds halides with the binding energy in the order of F- > Cl- > Br- > I-, supporting the experimental data obtained from 1H NMR studies. Results from DFT calculations further indicate that a 1:2 binding is energetically more favorable than a 1:1 binding of the ligand. (Figure Presented). © 2014 American Chemical Society.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Zubatiuk2015381,
title = {Structural waters in the minor and major grooves of DNA - A major factor governing structural adjustments of the A-T mini-helix},
author = { T.a Zubatiuk and O.a b Shishkin and L.c Gorb and D.d e Hovorun and J.f Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84921032288&amp;partnerID=40&amp;md5=c7cc973e4fa36f0ae87bf51ff6f9b3c7},
doi = {10.1021/jp5075225},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry B},
volume = {119},
number = {2},
pages = {381-391},
abstract = {The role of microhydration in structural adjustments of the AT-tract in B-DNA was studied at the B97-D/def2-SV(P) level. The (dA:dT)5 complexes with 10 water molecules in minor and 15 water molecules in major grooves were studied. The obtained network of hydrogen bonds revealed the dependence between the groove width and the types of water patterns. In the minor groove, the following patterns were observed: interstrand one-water bridges similar to that of the Dickerson "water spine" and interstrand two-water bridges. The network of structural waters in the major groove is more diverse than that in the minor groove, which agrees with crystallographic data. As the major groove is wider, it is enriched by water molecules forming two- and three-water bridges. Results suggest the nucleobase-water interactions in both grooves prevent AT-tract twisting and its "collapse" along the minor groove. Whereby, a helix structure with narrow minor and wide major grooves is formed. The structural waters affect the polynucleotide conformation so that it becomes similar to poly(dA)·poly(dT) in fibers and acquires features of the A-tracts in DNA in solution. We suggest that formation of specific water patterns in both grooves is the factor responsible for stabilization of A-tracts with a narrowed minor groove, leading in turn to their strong intrinsic bending in DNA. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gajewicz2015,
title = {Novel approach for efficient predictions properties of large pool of nanomaterials based on limited set of species: Nano-read-across},
author = { A.a Gajewicz and M.T.D.b Cronin and B.c Rasulev and J.c Leszczynski and T.a Puzyn},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84916894750&amp;partnerID=40&amp;md5=3cfb06d8344513e3c9e30c96c8a6f03a},
doi = {10.1088/0957-4484/26/1/015701},
year  = {2015},
date = {2015-01-01},
journal = {Nanotechnology},
volume = {26},
number = {1},
abstract = {Creating suitable chemical categories and developing read-across methods, supported by quantum mechanical calculations, can be an effective solution to solving key problems related to current scarcity of data on the toxicity of various nanoparticles. This study has demonstrated that by applying a nano-read-across, the cytotoxicity of nano-sized metal oxides could be estimated with a similar level of accuracy as provided by quantitative structure-activity relationship for nanomaterials (nano-QSAR model(s)). The method presented is a suitable computational tool for the preliminary hazard assessment of nanomaterials. It also could be used for the identification of nanomaterials that may pose potential negative impact to human health and the environment. Such approaches are especially necessary when there is paucity of relevant and reliable data points to develop and validate nano-QSAR models.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mikolajczyk20151859,
title = {Ab Initio studies of anatase TiO<inf>2</inf> (101) surface-supported au<inf>8</inf> clusters},
author = { A. Mikolajczyk H.P. Pinto A. Gajewicz T. Puzyn J. Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84934760513&amp;partnerID=40&amp;md5=66884a4014218246fc1fa08b54eb2fbd},
year  = {2015},
date = {2015-01-01},
journal = {Current Topics in Medicinal Chemistry},
volume = {15},
number = {18},
pages = {1859-1867},
abstract = {Supported transition metals on TiO<inf>2</inf> surfaces have shown exceptional catalytic properties in many important process such as CO oxidation, selective propane oxidation, hydrogenation, water adsorption and other catalytic and photocatalytic oxidation reaction at low-temperature. Among the three polymorphs of TiO<inf>2</inf>, the anatase crystal is the more photoactive. The anatase (101) surface attracts more attention since it has lower surface energy relative to (001) and (100) surfaces and it is observed to adsorb small molecules on its surface. Using density-functional theory (DFT) with on-site Coulomb interactions corrections, we have computed the structural and electronic properties of selected Au<inf>8</inf> clusters interacting with clean and reduced anatase TiO<inf>2</inf>(101) surfaces. The computed adsorption energies are suggesting that the considered Au<inf>8</inf> clusters are only physisorbed onto pristine TiO<inf>2</inf>(101) surface. Oxygen vacancies are found to enhance the absorption of Au<inf>8</inf> on the TiO<inf>2</inf>(101) surface. Accurate simulations required spin polarized DFT since the ground state of Au<inf>8</inf> interacting with defective TiO<inf>2</inf>(101) shows magnetic solutions. The results show that Au<inf>8</inf> clusters are chemically bonded to the surface around the locality of the oxygen vacancy. The surface oxygen vacancy is found to be energetically more favorable than sub-surface oxygen vacancy configuration. These vacancy sites may act as nucleation sites for small Au clusters or Au atoms. Finally, the computed electronic structure of all the Au<inf>8</inf>/TiO<inf>2</inf>(101) configurations considered in this work are analyzed in the light of available experimental data. © 2015 Bentham Science Publishers.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Reis20151845,
title = {Reliable but timesaving: In search of an efficient quantum-chemical method for the description of functional fullerenes},
author = { H.a Reis and B.b c Rasulev and M.G.a Papadopoulos and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84934775057&amp;partnerID=40&amp;md5=7791cd13cbffe6cdabbd2fb3646eb461},
year  = {2015},
date = {2015-01-01},
journal = {Current Topics in Medicinal Chemistry},
volume = {15},
number = {18},
pages = {1845-1858},
abstract = {Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C<inf>60</inf> and C<inf>70</inf> fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans’ theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives. © 2015 Bentham Science Publishers.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Golbamaki20152154,
title = {Genotoxicity of metal oxide nanomaterials: Review of recent data and discussion of possible mechanisms},
author = { N.a Golbamaki and B.b d Rasulev and A.c Cassano and R.L.c Marchese Robinson and E.a Benfenati and J.b Leszczynski and M.T.D.c Cronin},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84922360946&amp;partnerID=40&amp;md5=9f7d55d1d237f1cf82a016157fb7ff7c},
doi = {10.1039/c4nr06670g},
year  = {2015},
date = {2015-01-01},
journal = {Nanoscale},
volume = {7},
number = {6},
pages = {2154-2198},
abstract = {Nanotechnology has rapidly entered into human society, revolutionized many areas, including technology, medicine and cosmetics. This progress is due to the many valuable and unique properties that nanomaterials possess. In turn, these properties might become an issue of concern when considering potentially uncontrolled release to the environment. The rapid development of new nanomaterials thus raises questions about their impact on the environment and human health. This review focuses on the potential of nanomaterials to cause genotoxicity and summarizes recent genotoxicity studies on metal oxide/silica nanomaterials. Though the number of genotoxicity studies on metal oxide/silica nanomaterials is still limited, this endpoint has recently received more attention for nanomaterials, and the number of related publications has increased. An analysis of these peer reviewed publications over nearly two decades shows that the test most employed to evaluate the genotoxicity of these nanomaterials is the comet assay, followed by micronucleus, Ames and chromosome aberration tests. Based on the data studied, we concluded that in the majority of the publications analysed in this review, the metal oxide (or silica) nanoparticles of the same core chemical composition did not show different genotoxicity study calls (i.e. positive or negative) in the same test, although some results are inconsistent and need to be confirmed by additional experiments. Where the results are conflicting, it may be due to the following reasons: (1) variation in size of the nanoparticles; (2) variations in size distribution; (3) various purities of nanomaterials; (4) variation in surface areas for nanomaterials with the same average size; (5) differences in coatings; (6) differences in crystal structures of the same types of nanomaterials; (7) differences in size of aggregates in solution/media; (8) differences in assays; (9) different concentrations of nanomaterials in assay tests. Indeed, due to the observed inconsistencies in the recent literature and the lack of adherence to appropriate, standardized test methods, reliable genotoxicity assessment of nanomaterials is still challenging. © The Royal Society of Chemistry 2015.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gajewicz2015313,
title = {Towards understanding mechanisms governing cytotoxicity of metal oxides nanoparticles: Hints from nano-QSAR studies},
author = { A.a Gajewicz and N.b Schaeublin and B.c Rasulev and S.b Hussain and D.d Leszczynska and T.a Puzyn and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84929663897&amp;partnerID=40&amp;md5=8caa23fac3de85bc7a3eb816b1097a7f},
doi = {10.3109/17435390.2014.930195},
year  = {2015},
date = {2015-01-01},
journal = {Nanotoxicology},
volume = {9},
number = {3},
pages = {313-325},
abstract = {The production of nanomaterials increases every year exponentially and therefore the probability these novel materials that they could cause adverse outcomes for human health and the environment also expands rapidly. We proposed two types of mechanisms of toxic action that are collectively applied in a nano-QSAR model, which provides governance over the toxicity of metal oxide nanoparticles to the human keratinocyte cell line (HaCaT). The combined experimental-theoretical studies allowed the development of an interpretative nano-QSAR model describing the toxicity of 18 nano-metal oxides to the HaCaT cell line, which is a common in vitro model for keratinocyte response during toxic dermal exposure. The comparison of the toxicity of metal oxide nanoparticles to bacteria Escherichia coli (prokaryotic system) and a human keratinocyte cell line (eukaryotic system), resulted in the hypothesis that different modes of toxic action occur between prokaryotic and eukaryotic systems. © 2014 Informa UK Ltd. All rights reserved: reproduction in whole or part not permitted.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko201531,
title = {Alkaline hydrolysis of hexahydro-1,3,5-trinitro-1,3,5-triazine: M06-2X investigation},
author = { L.K.a b Sviatenko and L.c Gorb and F.C.d Hill and D.e Leszczynska and S.I.b Okovytyy and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84930578852&amp;partnerID=40&amp;md5=c77de6be566414305291b945296dada6},
doi = {10.1016/j.chemosphere.2015.03.064},
year  = {2015},
date = {2015-01-01},
journal = {Chemosphere},
volume = {134},
pages = {31-38},
abstract = {Alkaline hydrolysis mechanism of possible environmental contaminant RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) was investigated computationally at the PCM(Pauling)/M06-2X/6-311++G(d,p) level of theory. Results obtained show that the initial deprotonation of RDX by hydroxide leads to nitrite elimination and formation of a denitrated cyclohexene intermediate. Further nucleophilic attack by hydroxide onto cyclic C. N double bond results in ring opening. It was shown that the presence of hydroxide is crucial for this stage of the reaction. The dominant decomposition pathway leading to a ring-opened intermediate was found to be formation of 4-nitro-2,4-diazabutanal. Hydrolytic transformation of its byproduct (methylene nitramine) leads to end products such as formaldehyde and nitrous oxide. Computational results are in a good agreement with experimental data on hydrolysis of RDX, suggesting that 4-nitro-2,4-diazabutanal, nitrite, formaldehyde, and nitrous oxide are main products for early stages of RDX decomposition under alkaline conditions. © 2015 Elsevier Ltd.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Micha\lowski2015324,
title = {Unexpectedly complex crystalline phases in the MSO3F-Ag(SO3F)2 phase diagram (M = Na, K, Rb, Cs)},
author = { T.a Micha\lowski and Z.b Mazej and A.c Budzianowski and Z.d Jagli\v{c}i\'{c} and P.J.c Leszczy\'{n}ski and W.c Grochala},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84921023640&amp;partnerID=40&amp;md5=81fe0a45bbb71bf8dd40b6e208159559},
doi = {10.1002/ejic.201402948},
year  = {2015},
date = {2015-01-01},
journal = {European Journal of Inorganic Chemistry},
volume = {2015},
number = {2},
pages = {324-332},
abstract = {The syntheses and characterizations of mixed-cation fluorosulfates containing AgII ions are reported and add to the moderately well-known chemistry of AgII compounds. The compounds synthesized mostly show different structures and compositions. The mixed sodium-silver fluorosulfate is isostructural with Ag3(SO3F)4 (monoclinic P21/c},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ivashchenko201583,
title = {First-principles quantum molecular calculations of structural and mechanical properties of TiN/SiNx heterostructures, and the achievable hardness of the nc-TiN/SiNx nanocomposites},
author = { V.I.a Ivashchenko and S.b Veprek and A.S.c Argon and P.E.A.d Turchi and L.e f Gorb and F.f Hill and J.g Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84925293182&amp;partnerID=40&amp;md5=62e3cfb80f458d2c2ce674a3bb110f8e},
doi = {10.1016/j.tsf.2015.02.013},
year  = {2015},
date = {2015-01-01},
journal = {Thin Solid Films},
volume = {578},
pages = {83-92},
abstract = {TiN/SiNx heterostructures with one monolayer of the interfacial SiNx have been investigated in the framework of first-principles molecular dynamics calculations in the temperature range of 0 to 1400 K with subsequent static relaxation. The atomic configurations, thermal stability and stress-strain relations have been calculated. Among the heterostructures studied, only the TiN(111)/SiN/TiN(111) and TiN(111)/Si2N3/TiN(111) ones are thermally stable. Upon tensile load, decohesion occurs between the TiN bonds adjacent to the SiNx interfacial layer for TiN(001)/SiN/TiN(001) and TiN(111)/Si2N3/TiN(111) heterostructures, and inside the TiN slab for TiN(001)/Si3N4/TiN(001) and TiN(110)/SiN/TiN(110) ones. Upon shear, failure occurs in TiN near the interfaces in all the heterostructures, except for the TiN(001)/Si3N4/TiN(001) one, for which the plastic flow occurs inside the TiN slab. Based on these results we estimate the maximum achievable hardness of nc-TiN/Si3N4 nanocomposites free of impurities to be about 170 GPa. © 2015 Elsevier B.V. All rights reserved.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropov2015376,
title = {The Monte Carlo method based on eclectic data as an efficient tool for predictions of endpoints for nanomaterials-two examples of application},
author = { A.A.a Toropov and A.P.a Toropova and A.M.b Veselinovi\'{c} and J.B.b Veselinovi\'{c} and K.c Nesmerak and I. Jr.d Raska and P.R.e Duchowicz and E.A.e Castro and V.O.f Kudyshkin and D.g Leszczynska and J.h Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84931263505&amp;partnerID=40&amp;md5=cb6ac26be8661a453c4539e4252ab8de},
year  = {2015},
date = {2015-01-01},
journal = {Combinatorial Chemistry and High Throughput Screening},
volume = {18},
number = {4},
pages = {376-386},
abstract = {The theoretical predictions of endpoints related to nanomaterials are attractive and more efficient alternatives for their experimental determinations. Such type of calculations for the "usual" substances (i.e. non nanomaterials) can be carried out with molecular graphs. However, in the case of nanomaterials, descriptors traditionally used for the quantitative structure-property/activity relationships (QSPRs/QSARs) do not provide reliable results since the molecular structure of nanomaterials, as a rule, cannot be expressed by the molecular graph. Innovative principles of computational prediction of endpoints related to nanomaterials extracted from available eclectic data (technological attributes, conditions of the synthesis, etc.) are suggested, applied to two different sets of data, and discussed in this work. © 2015 Bentham Science Publishers.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{EmamiKhansari201517606,
title = {Synthesis and anion binding studies of tris(3-aminopropyl)amine-based tripodal urea and thiourea receptors: Proton transfer-induced selectivity for hydrogen sulfate over sulfate},
author = { M.a Emami Khansari and C.R.a Johnson and I.a b Basaran and A.a Nafis and J.a Wang and J.a Leszczynski and M.A.a Hossain},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923233314&amp;partnerID=40&amp;md5=0ab7732e14f85b847f7daa0ce750b8df},
doi = {10.1039/c5ra01315a},
year  = {2015},
date = {2015-01-01},
journal = {RSC Advances},
volume = {5},
number = {23},
pages = {17606-17614},
abstract = {Tris(3-aminopropyl)amine-based tripodal urea and thiourea receptors, tris([(4-cyanophenyl)amino]propyl)urea (L1) and tris([(4-cyanophenyl)amino]propyl)thiourea (L2), have been synthesized and their anion binding properties have been investigated for halides and oxoanions. As investigated by 1H NMR titrations, each receptor binds an anion with a 1:1 stoichiometry via hydrogen-bonding interactions (NH⋯anion), showing the binding trend in the order of F- > H<inf>2</inf>PO<inf>4</inf>- > HCO<inf>3</inf>- > HSO<inf>4</inf>- > CH<inf>3</inf>COO- > SO<inf>4</inf>2- > Cl- > Br- > I in DMSO-d<inf>6</inf>. The interactions of the receptors were further studied by 2D NOESY, showing the loss of NOESY contacts of two NH resonances for the complexes of F-, H<inf>2</inf>PO<inf>4</inf>-, HCO<inf>3</inf>-, HSO<inf>4</inf>- or CH<inf>3</inf>COO- due to the strong NH⋯anion interactions. The observed higher binding affinity for HSO<inf>4</inf>- than SO<inf>4</inf>2- is attributed to the proton transfer from HSO<inf>4</inf>- to the central nitrogen of L1 or L2 which was also supported by the DFT calculations, leading to the secondary acid-base interactions. The thiourea receptor L2 has a general trend to show a higher affinity for an anion as compared to the urea receptor L1 for the corresponding anion in DMSO-d<inf>6</inf>. In addition, the compound L2 has been exploited for its extraction properties for fluoride in water using a liquid-liquid extraction technique, and the results indicate that the receptor effectively extracts fluoride from water showing ca. 99% efficiency (based on L2). This journal is © The Royal Society of Chemistry 2015.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jaro\'{n}2015,
title = {Facile Formation of Thermodynamically Unstable Novel Borohydride Materials by a Wet Chemistry Route},
author = { T.a Jaro\'{n} and W.b Wegner and K.J.a Fija\lkowski and P.J.a Leszczy\'{n}ski and W.a Grochala},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923011764&amp;partnerID=40&amp;md5=f924037af841d34daa432386ceca210a},
doi = {10.1002/chem.201404968},
year  = {2015},
date = {2015-01-01},
journal = {Chemistry - A European Journal},
abstract = {A novel wet synthetic method utilizing weakly coordinating anions that yields LiCl-free Zn-based materials for hydrogen storage has recently been reported. Here we show that this method may also be applied for the synthesis of the pure yttrium derivatives, M[Y(BH4)4] (M=K, Rb, Cs). Moreover, it can be extended to the preparation of previously unknown thermodynamically unstable derivatives, Li[Y(BH4)4] and Na[Y(BH4)4]. Importantly, these two H-rich phases cannot be accessed by standard dry (mechanochemical) or solid/gas synthetic methods due to the thermodynamic obstacles. Here we describe their crystal structures and selected important physicochemical properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
note = {cited By 0; Article in Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Nguyen20154524,
title = {Hydrogen release from ammonia alane-based materials: Formation of cyclotrialazane and alazine},
author = { V.S.a Nguyen and D.b Majumdar and J.b Leszczynski and M.T.a Nguyen},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84924152275&amp;partnerID=40&amp;md5=1abfe7f204236516c9505cf366a89ecb},
doi = {10.1021/jp511668z},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Physical Chemistry C},
volume = {119},
number = {9},
pages = {4524-4539},
abstract = {In previous papers (Nguyen et al. J. Phys. Chem. C 2008, 112, 5662-5667 and J. Phys. Chem. C 2009, 113, 18914-18926), formation of H2 molecules from ammonia alane monomer (AAl) and dimers (AAl)2 was shown to be facilitated by the addition of one or more alane or ammonia molecules that can play the role of efficient bifunctional catalyst. Ammonia alane emerges as a good starting compound for building up materials for chemical hydrogen storage (CHS). Further exploration of the products based on the H2 release from ammonia alane were carried out using coupled-cluster theory computations together with the aug-cc-pVTZ basis set (based on MP2/aug-cc-pVDZ optimized geometries). Our ab initio MO calculations for the first time led to the identification of cyclotrialazane [(H2AlNH2)3], alazine [(HAlNH)3], and its oligomer [H2Al(HNAlH)2NH2] that are produced along the multistep dehydrogenation processes from the reactions of ammonia alane and AlH3NH2AlH2NH3. The formation of alazine (homologue of borazine) as the final product in our H2 elimination reactions is an important feature because of its long-debated existence. The present reaction path analyses show that the formation of this compound is an important phenomenon for explaining the entire dehydrogenation process. © 2015 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Macioch201511,
title = {Hybrid treatment of the infected carotid-subclavian graft complicated by the septic haemorrhage},
author = { W.a Macioch and J.a Leszczynski and A.a Kosicki and T.a Ostrowski and T.a Brzezinski and R.b Maciag and M.a Skorski and Z.a Galazka},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84929315121&amp;partnerID=40&amp;md5=b65666bb7e34ea1ffb08b6175b896350},
doi = {10.5603/AA.2015.0003},
year  = {2015},
date = {2015-01-01},
journal = {Acta Angiologica},
volume = {21},
number = {1},
pages = {11-15},
abstract = {The paper presents combined method of treatment to 90-year-old female, admitted with the hemorrhage from the chronic purulent fistula in her left neck in the incision post left carotid to subclavian artery bypass in 1971. In the vascular center where she was operate on (outside of Poland) it was suggested, that she should undergo graft excision because of the possibility of graft blow and subsequent exsanguinations as the most severe complication but finally she gave up. In the new circumstances, in the face of no-indirect threat to life, there was urgent need for surgical treatment. Being aware of multiple risk factors from age, general condition and changes in local, developed the concept of radical, yet more saving, to-step procedure. At first by percutaneous means covered stents were implanted into the places of vascular anastomoses, followed by angioplasty of the narrowed origin of left subclavian artery. In the second phase, after a few days, the infected prosthesis was excised and the cavities in the arterial walls of the two arteries were provided. Before, during and after surgery targeted antibiotics were used with classic antiplatelet therapy regimen. Post-operative course was uneventful. The wound healed properly. Which currently consisting of 93 years, as for her age, she in excellent condition overall. There were no signs of infection recurrence observed. Copyright © 2015 Via Medica.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2015745,
title = {Optimal nano-descriptors as translators of eclectic data into prediction of the cell membrane damage by means of nano metal-oxides},
author = { A.P. Toropova and A.A. Toropov and E. Benfenati and R. Korenstein and D. Leszczynska and J. Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84933516264&amp;partnerID=40&amp;md5=a1829276c1e920c41d1401e8298603ed},
doi = {10.1007/s11356-014-3566-4},
year  = {2015},
date = {2015-01-01},
journal = {Environmental science and pollution research international},
volume = {22},
number = {1},
pages = {745-757},
abstract = {Systematization of knowledge on nanomaterials has become a necessity with the fast growth of applications of these species. Building up predictive models that describe properties (both beneficial and hazardous) of nanomaterials is vital for computational sciences. Classic quantitative structure-property/activity relationships (QSPR/QSAR) are not suitable for investigating nanomaterials because of the complexity of their molecular architecture. However, some characteristics such as size, concentration, and exposure time can influence endpoints (beneficial or hazardous) related to nanoparticles and they can therefore be involved in building a model. Application of the optimal descriptors calculated with the so-called correlation weights of various concentrations and different exposure times are suggested in order to build up a predictive model for cell membrane damage caused by a series of nano metal-oxides. The numerical data on correlation weights are calculated by the Monte Carlo method. The obtained results are in good agreement with the experimental data.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2015,
title = {QSAR model as a random event: A case of rat toxicity},
author = { A.P.a Toropova and A.A.a Toropov and E.a Benfenati and D.b Leszczynska and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923206293&amp;partnerID=40&amp;md5=ac31493f78e4ca1f3539af2d606d7a4e},
doi = {10.1016/j.bmc.2015.01.055},
year  = {2015},
date = {2015-01-01},
journal = {Bioorganic and Medicinal Chemistry},
abstract = {Quantitative structure-property/activity relationships (QSPRs/QSARs) can be used to predict physicochemical and/or biochemical behavior of substances which were not studied experimentally. Typically predicted values for chemicals in the training set are accurate since they were used to build the model. QSPR/QSAR models must be validated before they are used in practice. Unfortunately, the majority of the suggested approaches of the validation of QSPR/QSAR models are based on consideration of geometrical features of clusters of data points in the plot of experimental versus calculated values of an endpoint. We believe these geometrical criteria can be more useful if they are analyzed for several splits into the training and test sets. In this way, one can estimate the reproducibility of the model with various splits and better evaluate model reliability. The probability of the correct prediction of an endpoint for external validation set (in the series of the above-mentioned splits) can provide an useful way to evaluate the domain of applicability of the model. © 2015 Elsevier Ltd.},
note = {cited By 0; Article in Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut2015,
title = {Molecular structure of aurothioglucose: A comprehensive computational study},
author = { S.a Karabulut and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84922933991&amp;partnerID=40&amp;md5=58e454e733767f6b785a0bc73e643a01},
doi = {10.1016/j.tet.2015.02.007},
year  = {2015},
date = {2015-01-01},
journal = {Tetrahedron},
abstract = {In order to investigate the molecular structure of aurothioglucose (ATG), six stable, well-known conformations of glucopyranose (Gp) have been computed and compared with Gp, thioglucopyranose (TGp), monomeric aurothioglucose (MATG), and dimeric aurothioglucose (DATG) models. The study has been performed using two DFT approaches. It has been concluded that the 'β' anomer of ATG is more stable than the 'α' anomer for TGp, MATG, and DATG models. M06 and B3LYP levels molecular geometries have been compared for the TGp species. Though both methods provided similar results, B3LYP is slightly better than M06 for optimization of TGp, especially for accurate description of bond lengths and dihedral angles. © 2015 Elsevier Ltd.},
note = {cited By 0; Article in Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Blaszczuk2015,
title = {Simulation of mass balance behavior in a large-scale circulating fluidized bed reactor},
author = { A.a Blaszczuk and A.a Zylka and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84937239678&amp;partnerID=40&amp;md5=723c5129773e0cfde099f1bc7d9bacbb},
doi = {10.1016/j.partic.2015.04.003},
year  = {2015},
date = {2015-01-01},
journal = {Particuology},
abstract = {We determine using a compound model the influence of the mass of granular matter on the behavior of a supercritical circulating fluidized bed (CFB) reactor. Population balance enables a stationary-regime modeling of the mass flow of granular matter inside a CFB unit in a large-scale. The simulation includes some important dynamic processes of gas-particle flows in fluidized bed such as attrition, fragmentation, elutriation, and fuel combustion. Numerical calculations with full boiler loading were performed of operational parameters such as furnace temperature, furnace pressure, feeding materials mass flows, and excess air ratio. Furthermore, three bed inventory masses were adopted as experimental variables in the simulation model of mass balance. This approach enables a sensitivity study of mass flows of granular matter inside a CFB facility. Some computational results from this population balance model obtained for a supercritical CFB reactor are presented that show consistency with the operational data for large-scale CFB units. © 2015 Chinese Society of Particuology and Institute of Process Engineering, Chinese Academy of Sciences.},
note = {cited By 0; Article in Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2015745b,
title = {Optimal nano-descriptors as translators of eclectic data into prediction of the cell membrane damage by means of nano metal-oxides},
author = { A.P.a Toropova and A.A.a Toropov and E.a Benfenati and R.b Korenstein and D.c Leszczynska and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84925729852&amp;partnerID=40&amp;md5=4d95b66d621d6f71a7a1897c87f2a3e7},
doi = {10.1007/s11356-014-3566-4},
year  = {2015},
date = {2015-01-01},
journal = {Environmental Science and Pollution Research},
volume = {22},
number = {1},
pages = {745-757},
abstract = {Systematization of knowledge on nanomaterials has become a necessity with the fast growth of applications of these species. Building up predictive models that describe properties (both beneficial and hazardous) of nanomaterials is vital for computational sciences. Classic quantitative structure-property/activity relationships (QSPR/QSAR) are not suitable for investigating nanomaterials because of the comple xity of their molecular architecture. However, some characteristicssuch as size, concentration, and exposure time can influence endpoints (beneficial or hazardous) related to nanoparticles and they can therefore be involved in building a model. Application of the optimal descriptors calculated with the so-called correlation weights of various concentrations and different exposure times are suggested in order to build up a predictive model for cell membrane damage caused by a series of nano metal-oxides. The numerical data on correlation weights are calculated by the Monte Carlo method. The obtained results are in good agreement with the experimental data. © Springer-Verlag Berlin Heidelberg 2014.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{VirakaNellore201519210,
title = {Bio-Conjugated CNT-Bridged 3D Porous Graphene Oxide Membrane for Highly Efficient Disinfection of Pathogenic Bacteria and Removal of Toxic Metals from Water},
author = { B.P.a Viraka Nellore and R.a Kanchanapally and F.b Pedraza and S.S.a Sinha and A.a Pramanik and A.T.a Hamme and Z.a Arslan and D.b Sardar and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84940832068&amp;partnerID=40&amp;md5=3e384e99b9b2583c7a8433e02a08d062},
doi = {10.1021/acsami.5b05012},
issn = {19448244},
year  = {2015},
date = {2015-01-01},
journal = {ACS Applied Materials and Interfaces},
volume = {7},
number = {34},
pages = {19210-19218},
publisher = {American Chemical Society},
abstract = {More than a billion people lack access to safe drinking water that is free from pathogenic bacteria and toxic metals. The World Health Organization estimates several million people, mostly children, die every year due to the lack of good quality water. Driven by this need, we report the development of PGLa antimicrobial peptide and glutathione conjugated carbon nanotube (CNT) bridged three-dimensional (3D) porous graphene oxide membrane, which can be used for highly efficient disinfection of Escherichia coli O157:H7 bacteria and removal of As(III), As(V), and Pb(II) from water. Reported results demonstrate that versatile membrane has the capability to capture and completely disinfect pathogenic pathogenic E. coli O157:H7 bacteria from water. Experimentally observed disinfection data indicate that the PGLa attached membrane can dramatically enhance the possibility of destroying pathogenic E. coli bacteria via synergistic mechanism. Reported results show that glutathione attached CNT-bridged 3D graphene oxide membrane can be used to remove As(III), As(V), and Pb(II) from water sample at 10 ppm level. Our data demonstrated that PGLa and glutathione attached membrane has the capability for high efficient removal of E. coli O157:H7 bacteria, As(III), As(V), and Pb(II) simultaneously from Mississippi River water. © 2015 American Chemical Society.},
note = {cited By 0},
keywords = {Antimicrobial peptide; Bacteria removal; Escherichia coli O157:H7; Graphene oxides; Porous graphene; Synergistic mechanism; Threedimensional (3-d); World Health Organization, Bacteria; Carbon; Carbon nanotubes; Disinfection; Escherichia coli; Graphene; Lead removal (water treatment); Membranes; Peptides; Potable water; Water; Yarn, Water treatment},
pubstate = {published},
tppubtype = {article}
}
@article{Demeritte201513693,
title = {Hybrid Graphene Oxide Based Plasmonic-Magnetic Multifunctional Nanoplatform for Selective Separation and Label-Free Identification of Alzheimer's Disease Biomarkers},
author = { T. Demeritte and B.P. Viraka Nellore and R. Kanchanapally and S.S. Sinha and A. Pramanik and S.R. Chavva and P.C. Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84932631672&amp;partnerID=40&amp;md5=15de422ad8a401a1999e960e1cb706ab},
doi = {10.1021/acsami.5b03619},
issn = {19448244},
year  = {2015},
date = {2015-01-01},
journal = {ACS Applied Materials and Interfaces},
volume = {7},
number = {24},
pages = {13693-13700},
publisher = {American Chemical Society},
abstract = {Despite intense efforts, Alzheimer's disease (AD) is one of the top public health crisis for society even at 21st century. Since presently there is no cure for AD, early diagnosis of possible AD biomarkers is crucial for the society. Driven by the need, the current manuscript reports the development of magnetic core-plasmonic shell nanoparticle attached hybrid graphene oxide based multifunctional nanoplatform which has the capability for highly selective separation of AD biomarkers from whole blood sample, followed by label-free surface enhanced Raman spectroscopy (SERS) identification in femto gram level. Experimental ELISA data show that antibody-conjugated nanoplatform has the capability to capture more than 98% AD biomarkers from the whole blood sample. Reported result shows that nanoplatform can be used for SERS "fingerprint" identification of β-amyloid and tau protein after magnetic separation even at 100 fg/mL level. Experimental results indicate that very high sensitivity achieved is mainly due to the strong plasmon-coupling which generates huge amplified electromagnetic fields at the "hot spot". Experimental results with nontargeted HSA protein, which is one of the most abundant protein components in cerebrospinal fluid (CSF), show that multifunctional nanoplatform based AD biomarkers separation and identification is highly selective. (Graph Presented). © 2015 American Chemical Society.},
note = {cited By 0},
keywords = {Alzheimer's disease; Cerebro spinal fluids; Graphene oxides; plasmonic-magnetic multifunctional nanoplatform; Selective separation; Separation and identification; Shell nanoparticles; Tau proteins, Blood; Cerebrospinal fluid; Diagnosis; Electromagnetic fields; Glycoproteins; Magnetic separation; Magnetism; Nanomagnetics; Neurodegenerative diseases; Palmprint recognition; Plasmons; Proteins; Raman spectroscopy; Separation, Graphene},
pubstate = {published},
tppubtype = {article}
}
@article{Shi201510935,
title = {Multifunctional Biocompatible Graphene Oxide Quantum Dots Decorated Magnetic Nanoplatform for Efficient Capture and Two-Photon Imaging of Rare Tumor Cells},
author = { Y.a Shi and A.a Pramanik and C.a Tchounwou and F.b Pedraza and R.A.a Crouch and S.R.a Chavva and A.a Vangara and S.S.a Sinha and S.a Jones and D.b Sardar and C.c Hawker and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84930681705&amp;partnerID=40&amp;md5=b519c2cb892d24f0af7e7f4b62fcb667},
doi = {10.1021/acsami.5b02199},
issn = {19448244},
year  = {2015},
date = {2015-01-01},
journal = {ACS Applied Materials and Interfaces},
volume = {7},
number = {20},
pages = {10935-10943},
publisher = {American Chemical Society},
abstract = {Circulating tumor cells (CTCs) are extremely rare cells in blood containing billions of other cells. The selective capture and identification of rare cells with sufficient sensitivity is a real challenge. Driven by this need, this manuscript reports the development of a multifunctional biocompatible graphene oxide quantum dots (GOQDs) coated, high-luminescence magnetic nanoplatform for the selective separation and diagnosis of Glypican-3 (GPC3)-expressed Hep G2 liver cancer tumor CTCs from infected blood. Experimental data show that an anti-GPC3-antibody-attached multifunctional nanoplatform can be used for selective Hep G2 hepatocellular carcinoma tumor cell separation from infected blood containing 10 tumor cells/mL of blood in a 15 mL sample. Reported data indicate that, because of an extremely high two-photon absorption cross section (40530 GM), an anti-GPC3-antibody-attached GOQDs-coated magnetic nanoplatform can be used as a two-photon luminescence platform for selective and very bright imaging of a Hep G2 tumor cell in a biological transparency window using 960 nm light. Experimental results with nontargeted GPC3(-) and SK-BR-3 breast cancer cells show that multifunctional-nanoplatform-based cell separation, followed by two-photon imaging, is highly selective for Hep G2 hepatocellular carcinoma tumor cells. (Chemical Equation Presented). © 2015 American Chemical Society.},
note = {cited By 0},
keywords = {Absorbing materials; Graphene oxides; Liver cancer cells; luminescent magnetic nanoplatform; Two photon imaging, Antibodies; Biocompatibility; Blood; Cytology; Diagnosis; Diseases; Graphene; Image processing; Luminescence; Magnetism; Medical imaging; Photons; Quantum efficiency; Semiconductor quantum dots; Separation; Tumors; Two photon processes, Cells},
pubstate = {published},
tppubtype = {article}
}
@article{Sinha20152411,
title = {Long-range two-photon scattering spectroscopy ruler for screening prostate cancer cells},
author = { S.S. Sinha and D.K. Paul and R. Kanchanapally and A. Pramanik and S.R. Chavva and B.P. Viraka Nellore and S.J. Jones and P.C. Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84925002895&amp;partnerID=40&amp;md5=ad7d8033da152eabed7eae1e0175983b},
doi = {10.1039/c4sc03843f},
issn = {20416520},
year  = {2015},
date = {2015-01-01},
journal = {Chemical Science},
volume = {6},
number = {4},
pages = {2411-2418},
publisher = {Royal Society of Chemistry},
abstract = {Optical rulers have served as a key tool for scientists from different disciplines to address a wide range of biological activity. Since the optical window of state of the art FRET rulers is limited to a 10 nm distance, developing long range optical rulers is very important to monitor real life biological processes. Driven by this need, the current manuscript reports for the first time the design of long-range two-photon scattering (TPS) spectroscopy rulers using gold nano-antenna separated by a bifunctional rigid double strand DNA molecule, which controls the spectroscopy ruler length. Reported data demonstrate that the TPS spectroscopy ruler's working window is a within a 25 nm distance, which is more than twice that of well recognized FRET optical ruler. A possible mechanism for the two-photon spectroscopy ruler's long range capability have been discussed using angle-resolved TPS measurement and FDTD simulations. Solution-phase experimental data demonstrated that a long-range TPS ruler using A9 aptamer can be used for the screening of prostate-specific membrane antigen (PSMA) (+) prostate cancer cells even at 5 cells per mL level. Reported result with PSMA (-) normal skin HaCaT cells indicate that TPS ruler based assay has the capability to enable distinction from non-targeted cell lines. Ultimately, the long range TPS ruler can be used towards better understanding of chemical and biological processes. This journal is © The Royal Society of Chemistry.},
note = {cited By 1},
keywords = {Band structure; Bioactivity; Cell culture; Cytology; Diseases; Electromagnetic wave scattering; Nanoantennas; Photons; Urology, Biological process; Chemical and biologicals; Double-strand dnas; Possible mechanisms; Prostate cancer cells; Prostate-specific membrane antigens; Two-photon scattering; Two-photon spectroscopy, Cells},
pubstate = {published},
tppubtype = {article}
}
@article{VirakaNellore2015235,
title = {Aptamer-conjugated graphene oxide membranes for highly efficient capture and accurate identification of multiple types of circulating tumor cells},
author = { B.P. Viraka Nellore and R. Kanchanapally and A. Pramanik and S.S. Sinha and S.R. Chavva and A. Hamme and P.C. Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923263891&amp;partnerID=40&amp;md5=26267a80b20df2c7c40fccfc05a8cabe},
doi = {10.1021/bc500503e},
issn = {10431802},
year  = {2015},
date = {2015-01-01},
journal = {Bioconjugate Chemistry},
volume = {26},
number = {2},
pages = {235-242},
publisher = {American Chemical Society},
abstract = {Tumor metastasis is responsible for 1 in 4 deaths in the United States. Though it has been well-documented over past two decades that circulating tumor cells (CTCs) in blood can be used as a biomarker for metastatic cancer, there are enormous challenges in capturing and identifying CTCs with sufficient sensitivity and specificity. Because of the heterogeneous expression of CTC markers, it is now well understood that a single CTC marker is insufficient to capture all CTCs from the blood. Driven by the clear need, this study reports for the first time highly efficient capture and accurate identification of multiple types of CTCs from infected blood using aptamer-modified porous graphene oxide membranes. The results demonstrate that dye-modified S6, A9, and YJ-1 aptamers attached to 20-40 μm porous garphene oxide membranes are capable of capturing multiple types of tumor cells (SKBR3 breast cancer cells, LNCaP prostate cancer cells, and SW-948 colon cancer cells) selectively and simultaneously from infected blood. Our result shows that the capture efficiency of graphene oxide membranes is ∼95% for multiple types of tumor cells; for each tumor concentration, 10 cells are present per milliliter of blood sample. The selectivity of our assay for capturing targeted tumor cells has been demonstrated using membranes without an antibody. Blood infected with different cells also has been used to demonstrate the targeted tumor cell capturing ability of aptamer-conjugated membranes. Our data also demonstrate that accurate analysis of multiple types of captured CTCs can be performed using multicolor fluorescence imaging. Aptamer-conjugated membranes reported here have good potential for the early diagnosis of diseases that are currently being detected by means of cell capture technologies. © 2015 American Chemical Society.},
note = {cited By 4},
keywords = {1 (3 dimethylaminopropyl) 3 ethylcarbodiimide; aptamer; graphene oxide},
pubstate = {published},
tppubtype = {article}
}
@article{Kanchanapally201518881,
title = {Antimicrobial peptide-conjugated graphene oxide membrane for efficient removal and effective killing of multiple drug resistant bacteria},
author = { R.a Kanchanapally and B.P.V.a Nellore and S.S.a Sinha and F.b Pedraza and S.J.a Jones and A.a Pramanik and S.R.a Chavva and C.a Tchounwou and Y.a Shi and A.a Vangara and D.b Sardar and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84923368988&amp;partnerID=40&amp;md5=a729313d4eb08b48def171d49a86799d},
doi = {10.1039/c5ra01321f},
issn = {20462069},
year  = {2015},
date = {2015-01-01},
journal = {RSC Advances},
volume = {5},
number = {24},
pages = {18881-18887},
publisher = {Royal Society of Chemistry},
abstract = {According to the World Health Organization (WHO), multiple drug-resistant (MDR) bacterial infection is a top threat to human health. Since bacteria evolve to resist antibiotics faster than scientists can develop new classes of drugs, the development of new materials which can be used, not only for separation, but also for effective disinfection of drug resistant pathogens is urgent. Driven by this need, we report for the first time the development of a nisin antimicrobial peptide conjugated, three dimensional (3D) porous graphene oxide membrane for identification, effective separation, and complete disinfection of MDR methicillin-resistant Staphylococcus aureus (MRSA) pathogens from water. Experimental data show that due to the size differences, MRSA is captured by the porous membrane, allowing only water to pass through. SEM, TEM, and fluorescence images confirm that pathogens are captured by the membrane. RT-PCR data with colony counting indicate that almost 100% of MRSA can be removed and destroyed from the water sample using the developed membrane. Comparison of MDR killing data between nisin alone, the graphene oxide membrane and the nisin attached graphene oxide membrane demonstrate that the nisin antimicrobial peptide attached graphene oxide membrane can dramatically enhance the possibility of destroying MRSA via a synergistic effect due to the multimodal mechanism. © The Royal Society of Chemistry 2015.},
note = {cited By 1},
keywords = {Antibiotics; Bacteria; Disinfection; Health risks; Membranes; Microorganisms; Peptides, Antimicrobial peptide; Bacterial infections; Drug-resistant pathogens; Methicillin-resistant staphylococcus aureus; Multiple-drug-resistant bacterium; Synergistic effect; Threedimensional (3-d); World Health Organization, Graphene},
pubstate = {published},
tppubtype = {article}
}
@article{Hughes201537,
title = {Meisenheimer complex between 2,4,6-trinitrotoluene and 3-aminopropyltriethoxysilane and its use for a paper-based sensor},
author = { S. Hughes and S.S.R. Dasary and S. Begum and N. Williams and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84932634567&amp;partnerID=40&amp;md5=90a606dd69836b9349c886e3de041a71},
doi = {10.1016/j.sbsr.2015.06.003},
issn = {22141804},
year  = {2015},
date = {2015-01-01},
journal = {Sensing and Bio-Sensing Research},
volume = {5},
pages = {37-41},
publisher = {Elsevier},
abstract = {2,4,6-Trinitrotoluene (TNT) forms a red-colored Meisenheimer complex with 3-aminopropyltrienthoxysilane (APTES) both in solution and on solid phase. The TNT-APTES complex is unique since it forms yellow-colored complexes with 2,4,6-trinitrophenol and 4-nitrophenol, and no complex with 2,4-dinitrotoluene. The absorption spectrum of TNT-APTES has two absorption bands at 530 and 650nm, while APTES complexes with 2,4,6-trinitrophenol and 4-nitrophenol have absorption maxima at around 420nm, and no absorption change for 2,4-dinitrotoluene. The TNT-APTES complex facilitates the exchange of the TNT-CH<inf>3</inf> proton/deuteron with solvent molecules. The red color of TNT-APTES is immediately visible at 1μM of TNT. © 2015 The Authors.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Zhang2015762,
title = {Cytotoxicity of organic surface coating agents used for nanoparticles synthesis and stability},
author = { Y.a Zhang and B.a Newton and E.a Lewis and P.P.b Fu and R.c Kafoury and P.C.a Ray and H.a Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84924855864&amp;partnerID=40&amp;md5=c97192808259d6e3a5e994cf7691a0aa},
doi = {10.1016/j.tiv.2015.01.017},
issn = {08872333},
year  = {2015},
date = {2015-01-01},
journal = {Toxicology in Vitro},
volume = {29},
number = {4},
pages = {762-768},
publisher = {Elsevier Ltd},
abstract = {Impact on health by nanomaterials has become a public concern with the great advances of nanomaterials for various applications. Surface coating agents are an integral part of nanoparticles, but not enough attention has been paid during toxicity tests of nanoparticles. As a result, there are inconsistent toxicity results for certain nanomaterials. In this study, we explored the cytotoxicity of eleven commonly used surface coating agents in two cell lines, human epidermal keratinocyte (HaCaT) and lung fibroblast (CRL-1490) cells, at surface coating agent concentrations of 3, 10, 30, and 100. μM. Two exposure time points, 2. h and 24. h, were employed for the study. Six of the eleven surface coating agents are cytotoxic, especially those surfactants with long aliphatic chains, both cationic (cetyltrimethylammonium bromide, oleylamine, tetraoctylammonium bromide, and hexadecylamine) and anionic (sodium dodecylsulfate). In addition, exposure time and the use of different cell lines also affect the cytotoxicity results. Therefore, factors such as cell lines used and exposure times must be considered when conducting toxicity tests or comparing cytotoxicity results. © 2015 Elsevier Ltd.},
note = {cited By 2},
keywords = {Article; cell viability; concentration response; controlled study; drug cytotoxicity; human; human cell; keratinocyte; lung fibroblast, cetrimide; dodecyl sulfate sodium; hexadecylamine; nanoparticle; oleylamine; surface coating agent; surfactant; tetraoctylammonium bromide; unclassified drug},
pubstate = {published},
tppubtype = {article}
}
@article{McShan2015369,
title = {Synergistic Antibacterial Effect of Silver Nanoparticles Combined with Ineffective Antibiotics on Drug Resistant Salmonella typhimurium DT104},
author = { D. McShan and Y. Zhang and H. Deng and P.C. Ray and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84938856217&amp;partnerID=40&amp;md5=8e39814178862e5c4e484a233fdd0501},
doi = {10.1080/10590501.2015.1055165},
issn = {10590501},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Environmental Science and Health - Part C Environmental Carcinogenesis and Ecotoxicology Reviews},
volume = {33},
number = {3},
pages = {369-384},
publisher = {Taylor and Francis Inc.},
abstract = {Synergistic antibacterial activity of combined silver nanoparticles (AgNPs) with tetracycline (polykeptide), neomycin (aminoglycoside), and penicillin (β-lactam) was tested against the multidrug resistant bacterium Salmonella typhimurium DT104. Dose-dependent inhibition of Salmonella typhimurium DT104 growth is observed for tetracycline-AgNPs and neomycin-AgNPs combination with IC<inf>50</inf> of 0.07 μg/mL and 0.43 μg/mL, respectively. There is no inhibition by the penicillin-AgNPs combination. These results suggest that the combination of the ineffective tetracycline or neomycin with AgNPs effectively inhibits the growth of this bacterium. The synergistic antibacterial effect is likely due to enhanced bacterial binding by AgNPs assisted by tetracycline or neomycin, but not by penicillin. Copyright © Taylor & Francis Group, LLC.},
note = {cited By 1},
keywords = {ampicillin; antibiotic agent; chloramphenicol; neomycin; penicillin derivative; penicillin G sodium; silver nanoparticle; streptomycin; sulfonamide; tetracycline; tetracycline derivative, Anti-bacterial activity; Antibacterial effects; Multidrug resistants; neomycin penicillin; Salmonella typhimurium; Silver nanoparticles; Silver nanoparticles (AgNps); tetracycline, Antibiotics; Bacteria; Metal nanoparticles; Nanoparticles; Salmonella, Bacteria (microorganisms); Salmonella typhimurium, Silver},
pubstate = {published},
tppubtype = {article}
}
@article{Zhang2015286,
title = {Antimicrobial Activity of Gold Nanoparticles and Ionic Gold},
author = { Y. Zhang and T.P. Shareena Dasari and H. Deng and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84938847951&amp;partnerID=40&amp;md5=640b2a8f9a4f1b98004a2c61580018e0},
doi = {10.1080/10590501.2015.1055161},
issn = {10590501},
year  = {2015},
date = {2015-01-01},
journal = {Journal of Environmental Science and Health - Part C Environmental Carcinogenesis and Ecotoxicology Reviews},
volume = {33},
number = {3},
pages = {286-327},
publisher = {Taylor and Francis Inc.},
abstract = {Gold, in both nanoparticle (AuNPs) and ionic forms, has been studied for antibiotic activities. Some of the organic complexes of Au (I & III) ions are antibacterial. AuNPs are antifungal, but with conflicting results on their antibacterial activity. We summarized these publications and found that AuNPs are generally not bactericidal, or only weakly at high concentrations. However, the reason AuNPs appear to be bactericidal is possibly due to the bactericidal activity of co-existing chemicals not completely removed from AuNPs: gold ions, surface coating agents, and chemicals involved in the synthesis. AuNPs can also act as carriers or delivery vehicles of antibiotics, thus enhancing the bactericidal effect of the antibiotics. Copyright © Taylor & Francis Group, LLC.},
note = {cited By 1},
keywords = {Agents; Amphibious vehicles; Antibiotics; Bactericides; Fiber optic sensors; Gold; Ions; Metal nanoparticles; Microorganisms; Nanoparticles, Anti-bacterial activity; Anti-microbial activity; antibacterial; antimicrobial; Bactericidal activity; Gold ions; Gold Nanoparticles; Surface coating agents, antibiotic agent; antifungal agent; ceftriaxone; ciprofloxacin; gentamicin; gold complex; gold ion; gold nanoparticle; metal ion; nanocarrier; nanocoating; neomycin; reducing agent; streptomycin; unclassified drug; vancomycin, Gold coatings},
pubstate = {published},
tppubtype = {article}
}
@article{He20154908,
title = {Trends in infant mortality in united states: A brief study of the Southeastern states from 2005\textendash2009},
author = { X.a b He and L.a Akil and W.G.a Aker and H.-M.a Hwang and H.A.a Ahmad},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84929359063&amp;partnerID=40&amp;md5=6c69043f6cf8840258415537adb15bad},
doi = {10.3390/ijerph120504908},
issn = {16617827},
year  = {2015},
date = {2015-01-01},
journal = {International Journal of Environmental Research and Public Health},
volume = {12},
number = {5},
pages = {4908-4920},
publisher = {MDPI AG},
abstract = {While overall infant mortality rates have declined over the past several decades, the Southeastern states have remained the leading states in high infant death in the United States. In this study, we studied the differences in infant mortality in the southeastern United States from 2005 through 2009 according to mother’s characteristics (age of mother, marital status, maternal race, maternal education), birth characteristics (month when maternal prenatal care began, birth weight), and infant’s characteristics (age of infant at death). This paper illustrates the significance level of each characteristic of mothers and infants, as well as socioeconomic factors that contribute to significant infant mortality that impacts subgroups within the US population. Descriptive statistics and analysis of variance studies were performed and presented. Statistical analysis of the contribution of causes of infant death to infant mortality at the national and state level was elaborated. Data suggest that mothers with no prenatal care had a very high overall infant death rate (5281.83 and 4262.16 deaths per 100,000 births in Mississippi and Louisiana, respectively, whereas the US average was 3074.82 deaths (p < 0.01)). It is suggested that better education and living quality should be available and improved for the residents in Alabama, Louisiana, and Mississippi. © 2015 by the authors; licensee MDPI, Basel, Switzerland.},
note = {cited By 0},
keywords = {Alabama; Florida [United States]; Georgia; Louisiana; Mississippi; United States, analysis of variance; Article; child death; controlled study; human; infant; infant mortality; marriage; maternal care; mother child relation; parenting education; prenatal care; race; retrospective study; socioeconomics; trend study; United States, educational attainment; infant mortality; public health; quality of life; socioeconomic impact; socioeconomic status},
pubstate = {published},
tppubtype = {article}
}
@article{Li2015799,
title = {Purification and characterization of a novel enzyme produced by Catenovulum sp. LP and its application in the pre-treatment to Ulva prolifera for bio-ethanol production},
author = { Y. Li and Z. Huang and L. Qiao and Y. Gao and H. Guan and H. Hwang and W.G. Aker and P. Wang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84939951071&amp;partnerID=40&amp;md5=5e5a7f063b0a78f872035a1c7cc04d19},
doi = {10.1016/j.procbio.2015.02.013},
issn = {13595113},
year  = {2015},
date = {2015-01-01},
journal = {Process Biochemistry},
volume = {50},
number = {5},
pages = {799-806},
publisher = {Elsevier Ltd},
abstract = {The high viscosity of polysaccharides from Ulva prolifera (PU) is one reason that impeded the high production of bio-ethanol by U. prolifera. A depolymerase with high specificity was first isolated from Catenovulum sp. LP. The 75.5 kDa depolymerase was purified 42.35-fold to homogeneity with 22.86 U/mg specific activity. The enzyme showed the highest activity at the optimal conditions of pH 6.0 and 35°C. It also showed high stability with a Half-life (t<inf>1/2</inf>) of 1386 min at 35°C. It retained 100% of its residual activity in 10 mM EDTA, 1,10-phenanthrolin, or Tween 80 after incubation of 2 h. The depolymerase showed high efficiency to PU for reducing sugar production, which reached 50.2% yield in 6 h. However, the commercial enzymes showed no hydrolysis to PU. The viscosity of 1.2% PU noticeable declined from initially 1127 to 7.2 mPa s in 95 min of hydrolysis even in the room temperature. The application of depolymerase with these unique properties could bring promising prospects for enzymatic pretreatment of the bio-ethanol production from U. prolifera biomass. © 2015 Elsevier Ltd. All rights reserved.},
note = {cited By 0},
keywords = {Bio-ethanol production; Bio-ethanols; Commercial enzymes; Depolymerase; Enzymatic pretreatment; Optimal conditions; Residual activity; Specific activity, Bioethanol; Characterization; Enzymes; Ethanol; Hydrolysis; Polysaccharides; Purification; Viscosity, Enzyme activity},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2015a,
title = {Causal inference methods to assist in mechanistic interpretation of classification nano-SAR models},
author = { Natalia Sizochenko and Bakhtiyor Rasulev and Agnieszka Gajewicz and Elena Mokshyna and Victor E. Kuz'min and Jerzy Leszczynski and Tomasz Puzyn},
url = {http://xlink.rsc.org/?DOI=C5RA11399G},
doi = {10.1039/C5RA11399G},
issn = {2046-2069},
year  = {2015},
date = {2015-01-01},
journal = {RSC Adv.},
volume = {5},
number = {95},
pages = {77739--77745},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{bartlett2015integral,
title = {the integral packages MOLECULE (Alml\"{o}f, J.; Taylor, PR), PROPS (Taylor, PR), ABACUS (Helgaker, T.; Jensen, HJ Aa.; J\orgensen, P.; Olsen, J.), and ECP routines by Mitin, AV; van W\"{u}llen, C},
author = { R J Bartlett, U Benedikt, C Berger, D E Bernholdt, Y J Bomble, L Cheng, O Christiansen, M Heckert, O Heun, C Huber, JD Watts and Others},
url = {http://www.cfour.de/},
year  = {2015},
date = {2015-01-01},
journal = {Coupled-Cluster techniques for Computational Chemistry},
abstract = {CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on M\oller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{He2015,
title = {Metal Oxide Nanomaterials in Nanomedicine: Applications in Photodynamic Therapy and Potential Toxicity},
author = { Xiaojia; He and G. Aker and Winfred; and Ming-Ju; Huang and John; D. Watts and Huey-Min Hwang},
url = {http://www.ingentaconnect.com/content/ben/ctmc/2015/00000015/00000018/art00012},
year  = {2015},
date = {2015-01-01},
journal = {Current Topics in Medicinal Chemistry},
volume = {15},
number = {18},
pages = {1887--1900(14)},
abstract = {Metal oxide nanomaterials have exhibited excellent performance as nanomedicines in photodynamic therapy (PDT) for cancer and infection treatment. Their unique and tunable physicochemical properties advance them as promising alternatives in drug delivery, early diagnosis, imaging, and treatment against various tumors and infectious diseases. Moreover, the implementation of nanophototherapy in deep tissue sites is enhanced by advancements in photosensitization technology. Notwithstanding the progress made in emerging metal oxide nanomaterials-derived PDT, the potential toxicity towards adjunct tissues associated with this approach remains challenging. Regulation and legislation have also been recommended and subsequently enacted in response to public concerns related to large-scale production, transportation, use, and disposal of those nanomaterials. Consequently, a quantitative structure-activity relationship (QSAR) paradigm has been adopted and is widely used in evaluating and predicting the side effects of nanomedicines, thus influencing their design and fabrication. This article briefly reviews the application of metal oxide nanomaterials in PDT and their associated adverse impacts as reported in recent publications. The future trends and implications of this platform in nanomedicine are also highlighted. However, more studies and efforts have to be carried out for developing novel nano-therapeutics with high selectivity, sensitivity, biocompatibility, and minimal side effects in PDT.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sizochenko2014,
title = {From basic physics to mechanisms of toxicity: the “liquid drop” approach applied to develop predictive classification models for toxicity of metal oxide nanoparticles},
author = { Natalia Sizochenko and Bakhtiyor Rasulev and Agnieszka Gajewicz and Victor Kuz'min and Tomasz Puzyn and Jerzy Leszczynski},
url = {http://xlink.rsc.org/?DOI=C4NR03487B},
doi = {10.1039/C4NR03487B},
issn = {2040-3364},
year  = {2014},
date = {2014-09-01},
journal = {Nanoscale},
volume = {6},
number = {22},
pages = {13986--13993},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Liao2014b,
title = {Theoretical Comparative Study of Oxygen Adsorption on Neutral and Anionic Ag n and Au n Clusters ( n = 2\textendash25)},
author = { Meng-Sheng Liao and John D. Watts and Ming-Ju Huang},
url = {http://pubs.acs.org/doi/abs/10.1021/jp501701f},
doi = {10.1021/jp501701f},
issn = {1932-7447},
year  = {2014},
date = {2014-09-01},
journal = {The Journal of Physical Chemistry C},
volume = {118},
number = {38},
pages = {21911--21927},
abstract = {Using density functional theory, we performed a theoretical comparative study of oxygen adsorption on neutral and anionic Agn and Aun clusters in a large size range of n = 2\textendash25. Ionization potentials (IPs) and electron affinities (EAs) of the pure clusters and the Mnq\textendashO2 binding energies Ebind(Mnq\textendashO2) in the (MnO2)q complexes (M = Ag, Au; q = 0, −1) were determined. Three density functionals, namely, BP86, revPBE, and B3LYP, were used in the calculations, among which the BP86 functional gave the best results for IPs and EAs, while B3LYP gave the best results for Ebind(Mnq\textendashO2). A number of differences between the silver and gold clusters and their reactivities toward O2 adsorption are accounted for by the calculations. One interesting result is that the calculated Aun\textendash\textendashO2 binding energies are in good, quantitative agreement with the measured relative reactivities of the Aun\textendash cluster anions toward O2 adsorption.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@book{He20141,
title = {Engineered TIO2 nanoparticles: Their fate and effects in natural aquatic environments},
author = { Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940639957&amp;partnerID=40&amp;md5=6c4a636c46c6300cd06e0b9695408cd4},
year  = {2014},
date = {2014-01-01},
booktitle = {Titanium Dioxide: Chemical Properties, Applications and Environmental Effects},
pages = {1--20},
abstract = {Engineered nanomaterials (ENMs) have greatly impacted human society as well as natural environments over the past decade, in consequence of their production on a massive scale to support the emerging market for nanotechnology. Among these ENMs, TIO2 nanoparticles have been extensively employed in the development of novel solutions for photocatalytic applications in environmental remediation. Inevitably, TIO2 nanoparticles will be released into natural aquatic environments via discharges from sewage treatment, factory releases, and leaks or spills during transportation or use. Thus, they pose potential risks to living organisms in aquatic ecosystems, creating the urgent need for assessing and understanding the consequent environmental hazards. In this chapter, we critically reviewed the physicochemical properties and the fate of TIO2 nanoparticles in aquatic environments and the subsequent impact on aquatic biota. Their intimate interactions with biotic and abiotic compartments in aquatic ecosystems, also known as nano-bio-eco interfaces, are noted and discussed. On the basis of literature reviewed, the proper assessment of their effects on specific model organisms could provide precise predictions of their adverse effects, as well as concepts for the design of sustainable-use, green nanoparticles. textcopyright 2014 Nova Science Publishers, Inc.},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
@article{Pathakoti2014234,
title = {Using experimental data of Escherichia coli to develop a QSAR model for predicting the photo-induced cytotoxicity of metal oxide nanoparticles},
author = { Huang M.-J. Watts J D He X Hwang H.-M. Pathakoti K.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84890823294&amp;partnerID=40&amp;md5=2795be0e1e7e6812d95e50bb5dd9935f},
doi = {10.1016/j.jphotobiol.2013.11.023},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Photochemistry and Photobiology B: Biology},
volume = {130},
pages = {234--240},
abstract = {A quantitative structure-activity relationship (QSAR) study of seventeen metal oxide nanoparticles (MNPs), in regard to their photo-induced toxicity to bacteria Escherichia coli, was developed by using quantum chemical methods. A simple and statistically significant QSAR model (F = 33.83},
keywords = {aluminum oxide; antimony; bismuth; chromium; cobalt; copper oxide; indium tin oxide; iron oxide; lanthanum oxide; metal oxide; nanoparticle; nickel; silicon; tin oxide; vanadium; yttrium; zinc oxide; zirconium oxide, article; bacterial cell; controlled study; cytotoxicity; energy; Escherichia coli; heat; nonhuman; phototoxicity; priority journal; quantitative structure activity relation, Bacteria; Electronegativity; LUMO energy; Metal oxide nanoparticles; Phototoxicity, Escherichia coli; Metal Nanoparticles; Models, Theoretical; Oxides; Quantitative Structure-Activity Relationship; Ultraviolet Rays},
pubstate = {published},
tppubtype = {article}
}
@article{Li201440b,
title = {The optimization of saccharification of desulfurated red seaweed-derived polysaccharides and analysis of their composition},
author = { Li Y Mou H Gao Y Hwang H Wang P Li X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886534321&amp;partnerID=40&amp;md5=4f2fb93fe586e43a2dfb625d0afbd564},
doi = {10.1080/10826068.2013.791628},
year  = {2014},
date = {2014-01-01},
journal = {Preparative Biochemistry and Biotechnology},
volume = {44},
number = {1},
pages = {40--55},
abstract = {Currently processes of ethanol production from desulfurated red seaweed derived polysaccharides (De-RSDP) are well established. However, the optimization of the enzymatic saccharification process has not been reported. In this study, De-RSDP from Kappaphycus alvarezii was subjected to saccharification by different enzymes, including pectinase, cellobiase, cellulase, and hemicellulase. The best saccharification enzyme was determined as pectinase. In order to obtain more reducing sugar (RS), the single-factor experiment followed by central composite rotatable design (CCD) was used to optimize the parameters for enzymatic hydrolysis. The optimal saccharification parameters of De-RSDP were 4400 U/g pectinase dosage, 96 hr, and 55.5°C, respectively, and the yield of RS reached 81.3%. Subsequently, the saccharification liquids of De-RSDP were isolated and purified with gel permeation chromatography (GPC) to separate saccharides with different molecular weights. Simultaneously, the composition of saccharification liquids was analyzed by 1-phenyl-3-methyl-5-pyrazolone high-pressure liquid chromatography (PMP-HPLC) and mass spectroscopy (MS). The result showed that the content is mainly composed of galactose (65.2%) with the average molecular mass in the fourth peak 181.1 Da. The saccharification liquids of De-RSDP inoculated with Saccharomyces cerevisiae L-4 for ethanol fermentation produced 0.3 g ethanol/g De-RSDP, which corresponded to 71.8% of the theoretical yield (0.38 g ethanol/g). Copyright textcopyright Taylor and Francis Group, LLC.},
keywords = {alcohol; glucosidase; polysaccharide; vegetable protein, article; chemistry; growth, development and aging; metabolism; red alga; Saccharomyces cerevisiae, Ethanol; Glucosidases; Plant Proteins; Polysaccharides; Rhodophyta; Saccharomyces cerevisiae},
pubstate = {published},
tppubtype = {article}
}
@article{He2014185b,
title = {An in vivo study on the photo-enhanced toxicities of S-doped TiO 2 nanoparticles to zebrafish embryos (Danio rerio) in terms of malformation, mortality, rheotaxis dysfunction, and DNA damage},
author = { Aker W G Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905976063&amp;partnerID=40&amp;md5=6c85db88907922f3bf36e6084494d264},
doi = {10.3109/17435390.2013.874050},
year  = {2014},
date = {2014-01-01},
journal = {Nanotoxicology},
volume = {8},
number = {SUPPL. 1},
pages = {185--195},
abstract = {The role of light on the acute toxicities of S-doped and Sigma TiO 2 nanoparticles in zebrafish was studied. Metrics included mortality for both, and rheotaxis dysfunction and DNA damage for S-doped only. It was found that the acute toxicity of S-TiO2 nanoparticles was enhanced by simulated sunlight (SSL) irradiation (96-h LC50 of 116.56 ppm) and exceeded that of Sigma TiO2, which was essentially non-toxic. Behavioral disorder, in terms of rheotaxis, was significantly increased by treatment with S-TiO2 nanoparticles under SSL irradiation. In order to further understand its toxicity mechanism, we investigated hair cells in neuromasts of the posterior lateral line (PLL) using DASPEI staining. Significant hair cell damage was observed in the treated larvae. The Comet assay was employed to investigate the DNA damage, which might be responsible for the loss of hair cells. Production of the superoxide anion (O textperiodcentered- 2), a major ROS generated by TiO2 nanoparticles, was assayed and used to postulate causative factors to account for these damages. Oxidative effects were most severe in the liver, heart, intestine, pancreatic duct, and pancreatic islet-results consistent with our earlier findings in the investigation of embryonic malformation. TEM micrographs, used to further investigate the fate of S-TiO2 nanoparticles at the cellular level, suggested receptor-mediated autophagy and vacuolization. Our findings validate the benefit of using the transparent zebrafish embryo as an in vivo model for evaluating photo-induced nanotoxicity. These results highlight the importance of conducting a systematic risk assessment in connection with the use of doped TiO2 nanoparticles in aquatic ecosystems. textcopyright 2014 Informa UK Ltd. All rights reserved.},
keywords = {Animals; DNA Damage; Embryo, Electron, nanoparticle; reactive oxygen metabolite; superoxide; titanium dioxide; titanium oxide nanoparticle; unclassified drug; metal nanoparticle; titanium; titanium dioxide, Nonmammalian; Metal Nanoparticles; Microscopy, Transmission; Spectrophotometry, Ultraviolet; Titanium; Zebrafish},
pubstate = {published},
tppubtype = {article}
}
@article{He2014128b,
title = {Using a holistic approach to assess the impact of engineered nanomaterials inducing toxicity in aquatic systems},
author = { Aker W G Leszczynski J Hwang H.-M. He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901620492&amp;partnerID=40&amp;md5=a43a691da14e7beefa584920e345ee96},
doi = {10.1016/j.jfda.2014.01.011},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {128--146},
abstract = {In this report, we critically reviewed selected intrinsic physicochemical properties of engineered nanomaterials (ENMs) and their role in the interaction of the ENMs with the immediate surroundings in representative aquatic environments. The behavior of ENMs with respect to dynamic microenvironments at the nanoebioeeco interface level, and the resulting impact on their toxicity, fate, and exposure potential are elaborated. Based on this literature review, we conclude that a holistic approach is urgently needed to fulfill our knowledge gap regarding the safety of discharged ENMs. This comparative approach affords the capability to recognize and understand the potential hazards of ENMs and their toxicity mechanisms, and ultimately to establish a quantitative and reliable system to predict such outcomes. Copyright textcopyright 2014, Food and Drug Administration, Taiwan.},
keywords = {Animals; Humans; Nanostructures; Oxidative Stress; Reactive Oxygen Species; Toxicology, glutathione; lactate dehydrogenase; metal ion; nanomaterial; reactive oxygen metabolite; nanomaterial; reactive oxygen metabolite},
pubstate = {published},
tppubtype = {article}
}
@article{Li2014b,
title = {Red seaweed derived polysaccharides, a novel marine resource for bio-ethanol production},
author = { Li Y.-P. Mou H.-J. Hwang H.-M. Wang P Li X.-L.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901649756&amp;partnerID=40&amp;md5=9cdc6902915951501a3ce17af37e8c8b},
doi = {10.1063/1.4880515},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Renewable and Sustainable Energy},
volume = {6},
number = {3},
abstract = {Seaweed biomass could be a renewable feed stock source for bio-ethanol production. Kappaphycus alvarezii is a promising alternative feedstock for the production of renewable energy sources because of its high content of red seaweed derived polysaccharides (RSDP) and its abundance nationwide. Based on the success of the production of bio-ethanol from seaweed cellulose biomass, the purpose of this study was to verify the feasibility of converting RSDP (mainly composed of sulfated galactan) to fermentable reducing sugar for bio-ethanol production. In this study, RSDP, pretreated with methanolysis to remove sulfate radicals, had a better desulfuration effect than the method of organic solvolytic desulfation. The results of single factor and orthogonal experiments were conducted, and the optimal parameters for the methanolysis of RSDP were: 0.5% of substrate concentration, 1.0M HCl-methanol, temperature of 80 °C, and 20 h. The desulfuration rate and the total-sugars yield reached 93% and 91%, respectively. Using Infrared Spectra, it was proven that the sulfate radical content was reduced sharply and that the 3, 6-anhydro bond was broken. Above all, saccharification liquids of desulfurated RSDP inoculated with Saccharomyces cerevisiae L4 for ethanol fermentation could produce 0.27 g ethanol/g RSDP. The results could bring bright prospects of bio-ethanol conversion from red seaweed biomass. textcopyright 2014 AIP Publishing LLC.},
keywords = {Alternative feedstocks; Bio-ethanol production; Ethanol fermentation; Kappaphycus alvarezii; Orthogonal experiment; Renewable energy source; Substrate concentrations; Sulfated galactans, Bioethanol, Biomass; Marine biology; Natural resources; Polysaccharides; Renewable energy resources; Saccharification; Seaweed; Yeast},
pubstate = {published},
tppubtype = {article}
}
@article{Fu201464b,
title = {Mechanisms of nanotoxicity: Generation of reactive oxygen species},
author = { Xia Q Hwang H.-M. Ray P C Yu H Fu P.P.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901621691&amp;partnerID=40&amp;md5=87b6d168c775ae66fdc6767a8313bfbb},
doi = {10.1016/j.jfda.2014.01.005},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {64--75},
abstract = {Nanotechnology is a rapidly developing field in the 21st century, and the commercial use of nanomaterials for novel applications is increasing exponentially. To date, the scientific basis for the cytotoxicity and genotoxicity of most manufactured nanomaterials are not understood. The mechanisms underlying the toxicity of nanomaterials have recently been studied intensively. An important mechanism of nanotoxicity is the generation of reactive oxygen species (ROS). Overproduction of ROS can induce oxidative stress, resulting in cells failing to maintain normal physiological redox-regulated functions. This in turn leads to DNA damage, unregulated cell signaling, change in cell motility, cytotoxicity, apoptosis, and cancer initiation. There are critical determinants that can affect the generation of ROS. These critical determinants, discussed briefly here, include: size, shape, particle surface, surface positive charges, surface-containing groups, particle dissolution, metal ion release from nanometals and nanometal oxides, UV light activation, aggregation, mode of interaction with cells, inflammation, and pH of the medium. Copyright textcopyright 2014, Food and Drug Administration, Taiwan. Published by Elsevier Taiwan LLC. All rights reserved.},
keywords = {Animals; DNA Damage; Humans; Nanostructures; Nanotechnology; Oxidation-Reduction; Oxidative Stress; Reactive Oxygen Species, free radical; hydroxyl radical; metal ion; metal oxide; nanomaterial; reactive oxygen metabolite; superoxide; nanomaterial; reactive oxygen metabolite},
pubstate = {published},
tppubtype = {article}
}
@article{Quinones2014374b,
title = {Effects of light energy and reducing agents on C60-mediated photosensitizing reactions},
author = { Zhang Y Riascos P Hwang H.-M. Aker W G He X Gao R Quinones M.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896399009&amp;partnerID=40&amp;md5=b2cea6ee8b7840724cacec37d3aeef9f},
doi = {10.1111/php.12206},
year  = {2014},
date = {2014-01-01},
journal = {Photochemistry and Photobiology},
volume = {90},
number = {2},
pages = {374--379},
abstract = {Many biomolecules contain photoactive reducing agents, such as reduced nicotinamide adenine dinucleotide (NADH) and 6-thioguanine (6-TG) incorporated into DNA through drug metabolism. These reducing agents may produce reactive oxygen species under UVA irradiation or act as electron donors in various media. The interactions of C60 fullerenes with biological reductants and light energy, especially via the Type-I electron-transfer mechanism, are not fully understood although these factors are often involved in toxicity assessments. The two reductants employed in this work were NADH for aqueous solutions and 6-TG for organic solvents. Using steady-state photolysis and electrochemical techniques, we showed that under visible light irradiation, the presence of reducing agents enhanced C60-mediated Type-I reactions that generate superoxide anion (O2.-) at the expense of singlet oxygen (1O2) production. The quantum yield of O2.- production upon visible light irradiation of C 60 is estimated below 0.2 in dipolar aprotic media, indicating that the majority of triplet C60 deactivate via Type-II pathway. Upon UVA irradiation, however, both C60 and NADH undergo photochemical reactions to produce O2.-, which could lead to a possible synergistic toxicity effects. C60 photosensitization via Type-I pathway is not observed in the absence of reducing agents. The photosensitization pathways of C60 vary with the irradiation energy and reducing agents. C60/visible light-initiated Type-I reactions take place only in the presence of electron donors with the formation yield of superoxide anions below 0.2 in dipolar aprotic solvents. Under UVA irradiation, both C60 and UVA-active reducing agents may produce reactive oxygen species, leading to a synergistic toxicity. textcopyright 2013 The American Society of Photobiology.},
keywords = {chemistry; proton nuclear magnetic resonance; ultraviolet radiation, DNA; fullerene C60; fullerene derivative; nicotinamide adenine dinucleotide; photosensitizing agent; reducing agent, DNA; Fullerenes; NAD; Photosensitizing Agents; Proton Magnetic Resonance Spectroscopy; Reducing Agents; Ultraviolet Rays},
pubstate = {published},
tppubtype = {article}
}
@article{He2014759b,
title = {Synergistic combination of marine oligosaccharides and azithromycin against Pseudomonas aeruginosa},
author = { Hwang H.-M. Aker W G Wang P Lin Y Jiang X He X He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904730527&amp;partnerID=40&amp;md5=7a9b2ae75de712bea703d565dd34f1f3},
doi = {10.1016/j.micres.2014.01.001},
year  = {2014},
date = {2014-01-01},
journal = {Microbiological Research},
volume = {169},
number = {9-10},
pages = {759--767},
abstract = {In this paper we describe how utilization of low molecular weight alginate-derived oligosaccharide (ADO) and chito-oligosaccharide (COS) in conjunction with antibiotics, could more effectively inhibit the growth of wild-type and resistant Pseudomonas aeruginosa. Inhibition is effected by modulating the bacteria's quorum sensing (QS) system, thus regulating biofilm formation and reducing resistance to antibiotic treatment. This can be demonstrated by using conventional MIC screening. COS showed synergistic effects with azithromycin, whereas ADO indicated additive effects against wild-type P. aeruginosa. Using electrospray-ionization mass spectroscopy (ESI-MS), matrix-assisted laser desorption/ionization-time of flightmass spectroscopy (MALDI-TOF-MS) and nuclear magnetic resonance (NMR), the chemical structure of ADO and of COS was characterized. The wild-type and resistant strains were identified by 16S rRNA sequence analysis. This report demonstrates the feasibility of attenuating the tolerance of P. aeruginosa to azithromycin by using specific marine oligosaccharides. textcopyright 2014 Elsevier GmbH.},
keywords = {16S; Sequence Analysis, Alginate, Anti-Bacterial Agents; Azithromycin; Biofilms; DNA, Antibiotics; Bacteria; Electrospray ionization; Mass spectrometry; Nuclear magnetic resonance spectroscopy; Oligosaccharides; RNA, antiinfective agent; azithromycin; bacterial DNA; oligosaccharide; ribosome DNA; RNA 16S, Bacteria (microorganisms); Pseudomonas aeruginosa, Bacterial; DNA, biofilm; chemical structure; chemistry; classification; DNA sequence; drug effects; drug potentiation; electrospray mass spectrometry; genetics; growth, Chito-oligosaccharides; Low molecular weight; Matrix assisted laser desorption; Nuclear magnetic resonance(NMR); Pseudomonas aeruginosa; Quorum-sensing; Resistance to antibiotics; Synergistic combinations, development and aging; mass spectrometry; microbial sensitivity test; molecular genetics; nuclear magnetic resonance spectroscopy; physiological stress; physiology; Pseudomonas aeruginosa; quorum sensing, DNA; Spectrometry, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Stress, Physiological, Ribosomal, Ribosomal; Drug Synergism; Magnetic Resonance Spectroscopy; Microbial Sensitivity Tests; Molecular Sequence Data; Molecular Structure; Oligosaccharides; Pseudomonas aeruginosa; Quorum Sensing; RNA},
pubstate = {published},
tppubtype = {article}
}
@article{Soinski2014,
title = {Nanocrystalline block cores for high-frequency chokes},
author = { M.a Soinski and J.b Leszczynski and C.b c Swieboda and M.c Kwiecien},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84915747217&amp;partnerID=40&amp;md5=f96191459311bc47350b8b29526f58d5},
doi = {10.1109/TMAG.2014.2332035},
year  = {2014},
date = {2014-01-01},
journal = {IEEE Transactions on Magnetics},
volume = {50},
number = {11},
abstract = {Nanocrystalline Fe-based soft magnetic materials are more and more common not only in power electronic, but also in power energy conversion systems. The use of different treatments (the methods of stacking and annealing at/without magnetic field presence) on magnetic cores allow to achieve their predefined magnetic properties. This fact increases the level of the applicability such magnetic cores. Different concepts of nanocrystalline magnetic block cores were discussed in this paper. Obtained results were compared with magnetic cores used up to nowadays (made of amorphous and Fe-Si steel). © 2014 IEEE.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karwowska2014304,
title = {Influence of electrolyte composition and temperature on behaviour of AB5 hydrogen storage alloy used as negative electrode in Ni-MH batteries},
author = { M.a Karwowska and T.b Jaron and K.J.b Fijalkowski and P.J.b Leszczynski and Z.a b b Rogulski and A.a b b Czerwinski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84899991573&amp;partnerID=40&amp;md5=fabb801edb4071f4e8896caf4ebd1ad0},
doi = {10.1016/j.jpowsour.2014.04.050},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Power Sources},
volume = {263},
pages = {304-309},
abstract = {The AB5-type metal alloy (Mm-Ni4.1Al 0.2Mn0.4Co0.45) has been investigated in different electrolytes (LiOH, NaOH, KOH, RbOH, CsOH). All of the electrochemical measurements have been performed using limited volume electrode technique (LVE). Thickness of the working electrode is nearly equal to the diameter of the grain (ca. 50 μm). Hydrogen diffusion coefficient has been determined using chronoamperometry. Hydrogen diffusion coefficient calculated for 100% state of charge reaches maximum value in KOH (DH = 4.65·10-10 cm2 s-1). We have obtained the highest value of capacity for the electrode in KOH and the lowest - in CsOH. The temperature influence on alloy capacity has been also tested. The alloy has been also characterised with SEM coupled with EDS, TGA/DSC and powder XRD. The unit cell of MmNi4.1Al0.2Mn 0.4Co0.45 have been refined in the Cu5.4Yb 0.8 structure type (a modified LaNi5 structure); the structure is unaffected by the electrochemical treatment. © 2014 Published by Elsevier B.V.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Fijalkowski201423340,
title = {M(BH3NH2BH2NH2BH3)-the missing link in the mechanism of the thermal decomposition of light alkali metal amidoboranes},
author = { K.J.a Fijalkowski and T.a Jaro\'{n} and P.J.a Leszczy\'{n}ski and E.b Magos-Palasyuk and T.b Palasyuk and M.K.c Cyra\'{n}ski and W.a Grochala},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84908065129&amp;partnerID=40&amp;md5=ef825ece4c5d3689178ebfa76bc6bf86},
doi = {10.1039/c4cp03296a},
year  = {2014},
date = {2014-01-01},
journal = {Physical Chemistry Chemical Physics},
volume = {16},
number = {42},
pages = {23340-23346},
abstract = {We report a novel family of hydrogen-rich materials-alkali metal di(amidoborane)borohydrides, M(BH3NH2BH2NH2BH3). The title compounds are related to metal amidoboranes (amidotrihydroborates) but have higher gravimetric H content. Li salt contains 15.1 wt% H and discharges very pure H2 gas. Differences in thermal stability between amidoboranes and respective oligoamidoboranes explain the release of the ammonia impurity (along with H2) during the thermal decomposition of light alkali amidoboranes, LiNH2BH3, NaNH2BH3 and NaLi(NH2BH3)2, and confirm the mechanism of the side decomposition reaction. This journal is © the Partner Organisations 2014.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko201410465,
title = {Comprehensive investigations of kinetics of alkaline hydrolysis of TNT (2,4,6-trinitrotoluene), DNT (2,4-dinitrotoluene), and DNAN (2,4-dinitroanisole)},
author = { L.a b Sviatenko and C.c Kinney and L.d Gorb and F.C.e Hill and A.J.e Bednar and S.f Okovytyy and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84906874824&amp;partnerID=40&amp;md5=8482144ac6a0ba0770ecff9e94907362},
doi = {10.1021/es5026678},
year  = {2014},
date = {2014-01-01},
journal = {Environmental Science and Technology},
volume = {48},
number = {17},
pages = {10465-10474},
abstract = {Combined experimental and computational techniques were used to analyze multistep chemical reactions in the alkaline hydrolysis of three nitroaromatic compounds: 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), and 2,4-dinitroanisole (DNAN). The study reveals common features and differences in the kinetic behavior of these compounds. The analysis of the predicted pathways includes modeling of the reactions, along with simulation of UV-vis spectra, experimental monitoring of reactions using LC/MS techniques, development of the kinetic model by designing and solving the system of differential equations, and obtaining computationally predicted kinetics for decay and accumulation of reactants and products. Obtained results suggest that DNT and DNAN are more resistant to alkaline hydrolysis than TNT. The direct substitution of a nitro group by a hydroxide represents the most favorable pathway for all considered compounds. The formation of Meisenheimer complexes leads to the kinetic first-step intermediates in the hydrolysis of TNT. Janovsky complexes can also be formed during hydrolysis of TNT and DNT but in small quantities. Methyl group abstraction is one of the suggested pathways of DNAN transformation during alkaline hydrolysis. © 2014 American Chemical Society.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ivashchenko2014284,
title = {First-principles molecular dynamics investigation of thermal and mechanical stability of the TiN(001)/AlN and ZrN(001)/AlN heterostructures},
author = { V.I.a Ivashchenko and S.b Veprek and P.E.A.c Turchi and V.I.a Shevchenko and J.d Leszczynski and L.d e Gorb and F.e Hill},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904045623&amp;partnerID=40&amp;md5=11400efb3f462a0f00ae88716ad61064},
doi = {10.1016/j.tsf.2014.05.036},
year  = {2014},
date = {2014-01-01},
journal = {Thin Solid Films},
volume = {564},
pages = {284-293},
abstract = {First-principles quantum molecular dynamics investigations of TiN(001)/AlN and ZrN(001)/AlN heterostructures with one and two monolayers (1 ML and 2 ML) of AlN interfacial layers were carried out in the temperature range of 0-1400 K with subsequent static relaxation. It is shown that the epitaxially stabilized cubic B1-AlN interfacial layers are preserved in all TiN(001)/AlN heterostructures over the whole temperature range. In the ZrN(001)/AlN heterostructures, the B1-AlN(001) interfacial layer exists at 0 K, but it transforms into a distorted one at 10 K consisting of tetrahedral AlN 4, octahedral AlN6, and AlN5 units. The thermal stability of the interfaces was investigated by studying the phonon dynamic stability of the B1-AlN phase with different lattice parameters. The calculations showed that the B1-AlN interface should be unstable in ZrN(001)/AlN heterostructures and nanocomposites, and in those based on transition metal nitrides with lattice parameters larger than 4.4 r{A}. Electronic band structure calculations showed that energy gap forms around the Fermi energy for all interfaces. The formation of the interfacial AlN layer in TiN and ZrN crystals reduces their ideal tensile and shear strengths. Upon tensile load, decohesion occurs between Ti (Zr) and N atoms adjacent to the 1 ML AlN interfacial layer, whereas in the case of 2 ML AlN it occurs inside the TiN and ZrN slabs. The experimentally reported strength enhancement in the TiN/AlN and ZrN/AlN heterostructures is attributed to impeding effect of the interfacial layer on the plastic flow. © 2014 Elsevier B.V.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Roszak20145727,
title = {Unique bonding nature of carbon-substituted Be2 dimer inside the carbon (sp2) network},
author = { R.a b Roszak and S.a b Roszak and D.a Majumdar and L.c Firlej and B.d Kuchta and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84905399739&amp;partnerID=40&amp;md5=74920d8301638f4e5c0dfa41f24858bd},
doi = {10.1021/jp504618h},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry A},
volume = {118},
number = {30},
pages = {5727-5733},
abstract = {Controlled doping of active carbon materials (viz., graphenes, carbon nanotubes etc.) may lead to the enhancement of their desired properties. The least studied case of C/Be substitution offers an attractive possibility in this respect. The interactions of Be2 with Be or C atoms are dominated by the large repulsive Pauli exchange contributions, which in turn offsets the attractive interactions leading to relatively small binding energies. The Be2 dimer, e.g., after being doped inside a planar carbon network, undergoes orbital adjustments due to charge transfer and unusual intermolecular interactions and is oriented perpendicular to the plane of the carbon network with the Be-Be bond center located inside the plane. The present theoretical investigation on the nature of bonding in C/Be2 exchange complexes, using state of the art quantum chemical techniques, reveals a sp2 carbon-like bonding scheme in Be2 arising due to the molecular hybridization of σ and two π orbitals. The perturbations imposed by doped Be2 dimers exhibit a local character of the structural and electronic properties of the complexes, and the separation by two carbon atoms between beryllium active centers is sufficient to consider these centers as independent sites. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko2014981,
title = {In Silico kinetics and mechanism of interaction of cis-2-butene-1,4-dial with 2′-deoxycytidine},
author = { L.K.a b Sviatenko and L.a c d Gorb and D.c d Hovorun and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84902470284&amp;partnerID=40&amp;md5=4ca0db7deb89c01ae3df8df57a2f75dd},
doi = {10.1021/tx5000427},
year  = {2014},
date = {2014-01-01},
journal = {Chemical Research in Toxicology},
volume = {27},
number = {6},
pages = {981-989},
abstract = {Newly proposed approach involving computational analysis of multistep chemical reactions has been successfully applied to study the interaction between 2′-deoxycytidine and cis-2-butene-1,4-dial, a metabolite of furan. The new method comprises a combination of few steps. They include the prediction of the reaction mechanism, calculation of Gibbs free energies for the reaction pathway, and conversion of barrier energies to rate constants. On the basis of the results of previous steps, corresponding kinetic equations are constructed and solved. Such a procedure allows one to indicate the definite concentration of reaction species (reactants, intermediates, and products) at any moment in time. Obtained results show that 2′-deoxycytidine reacts with cis-2-butene-1,4-dial to form primary products, which are represented by four polycyclic diastereomers. These primary products further transform to more stable secondary product by dehydration, which is catalyzed by acid. The obtained data demonstrate that cis-2-butene-1,4-dial plays a key role in furan-induced carcinogenesis. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rossikhin2014689,
title = {Accurate calculations of dynamic first hyperpolarizability: Construction of physically justified slater-type basis sets},
author = { V.a Rossikhin and E.b Voronkov and S.c d Okovytyy and T.c d Sergeieva and K.c Kapusta and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84898997418&amp;partnerID=40&amp;md5=dea8fee936cca5592d0d739b1f0c502a},
doi = {10.1002/qua.24617},
year  = {2014},
date = {2014-01-01},
journal = {International Journal of Quantum Chemistry},
volume = {114},
number = {11},
pages = {689-695},
abstract = {An efficient procedure for construction of physically rationalized Slater-type basis sets for calculations of dynamic hyperpolarizability is proposed. Their performance is evaluated for the DFT level calculations for model molecules, carried out with a series of functionals. Advantages of new basis sets over standard d-aug-cc-pVTZ and recently developed LPOL-(FL,FS) Gaussian-type basis sets are discussed. © 2014 Wiley Periodicals, Inc.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Chomicz20146568,
title = {Electron induced single strand break and cyclization: A DFT study on the radiosensitization mechanism of the nucleotide of 8-bromoguanine},
author = { L.a Chomicz and A.b c Furmanchuk and J.b Leszczynski and J.a Rak},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896369621&amp;partnerID=40&amp;md5=2f6925ff6cb805a8b5e356dc472324a2},
doi = {10.1039/c3cp55411b},
year  = {2014},
date = {2014-01-01},
journal = {Physical Chemistry Chemical Physics},
volume = {16},
number = {14},
pages = {6568-6574},
abstract = {Cleavage of the O-P bond in 8-bromo-2′-deoxyguanosine-3′, 5′-diphosphate (BrdGDP), considered as a model of single strand break (SSB) in labelled double-stranded DNA (ds DNA), is investigated at the B3LYP/6-31++G(d,p) level. The thermodynamic and kinetic characteristics of the formation of SSB are compared to those related to the 5′,8-cycloguanosine lesion. The first reaction step, common to both damage types, which is the formation of the reactive guanyl radical, proceeds with a barrier-free or low-barrier release of the bromide anion. The guanyl radical is then stabilized by hydrogen atom transfer from the C3′ or C5′ sites of the 2′-deoxyribose moiety to its C8 center. The C3′ path, via the O-P bond cleavage, leads to a ketone derivative (the SSB model), while the C5′ path is more likely to yield 5′,8-cycloguanosine. © 2014 the Partner Organisations.},
note = {cited By 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rhaman20142045,
title = {Encapsulation and selectivity of sulfate with a furan-based hexaazamacrocyclic receptor in water},
author = { Md.M.a Rhaman and L.a Ahmed and J.a Wang and D.R.b Powell and J.a Leszczynski and Md.A.a Hossain},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897704507&amp;partnerID=40&amp;md5=ea6eb8918d888498e30ea4281f2b2784},
doi = {10.1039/c4ob00116h},
year  = {2014},
date = {2014-01-01},
journal = {Organic and Biomolecular Chemistry},
volume = {12},
number = {13},
pages = {2045-2048},
abstract = {A furan-based hexaazamacrocycle encapsulates a sulfate anion in its cavity showing strong affinity and selectivity for sulfate in water over a wide range of inorganic anions. The DFT calculations demonstrate that the receptor provides binding sites as hydrogen bonding donors and electrostatic positive charges for the strong binding of sulfate. © 2014 The Royal Society of Chemistry.},
note = {cited By 4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Turabekova20143488,
title = {Immunotoxicity of nanoparticles: A computational study suggests that CNTs and C60 fullerenes might be recognized as pathogens by Toll-like receptors},
author = { M.a b Turabekova and B.a Rasulev and M.c Theodore and J.c Jackman and D.b Leszczynska and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896348692&amp;partnerID=40&amp;md5=d9b654ce601d6015d35cdc39a276a30d},
doi = {10.1039/c3nr05772k},
year  = {2014},
date = {2014-01-01},
journal = {Nanoscale},
volume = {6},
number = {7},
pages = {3488-3495},
abstract = {Over the last decade, a great deal of attention has been devoted to study the inflammatory response upon exposure to multi/single-walled carbon nanotubes (CNTs) and different fullerene derivatives. In particular, carbon nanoparticles are reported to provoke substantial inflammation in alveolar and bronchial epithelial cells, epidermal keratinocytes, cultured monocyte-macrophage cells, etc. We suggest a hypothetical model providing the potential mechanistic explanation for immune and inflammatory responses observed upon exposure to carbon nanoparticles. Specifically, we performed a theoretical study to analyze CNT and C60 fullerene interactions with the available X-ray structures of Toll-like receptors (TLRs) homo- and hetero-dimer extracellular domains. This assumption was based on the fact that similar to the known TLR ligands both CNTs and fullerenes induce, in cells, the secretion of certain inflammatory protein mediators, such as interleukins and chemokines. These proteins are observed within inflammation downstream processes resulted from the ligand molecule dependent inhibition or activation of TLR-induced signal transduction. Our computational studies have shown that the internal hydrophobic pockets of some TLRs might be capable of binding small-sized carbon nanostructures (5,5 armchair SWCNTs containing 11 carbon atom layers and C 60 fullerene). High binding scores and minor structural alterations induced in TLR ectodomains upon binding C60 and CNTs further supported our hypothesis. Additionally, the proposed hypothesis is strengthened by the indirect experimental findings indicating that CNTs and fullerenes induce an excessive expression of specific cytokines and chemokines (i.e. IL-8 and MCP1). This journal is © the Partner Organisations 2014.},
note = {cited By 10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Pinto20146110,
title = {First-principles studies of paramagnetic vivianite Fe3(PO 4)2·8H2O surfaces},
author = { H.P. Pinto and A. Michalkova and J. Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897470626&amp;partnerID=40&amp;md5=1f316964d16397bfda758eec7d4dbf0c},
doi = {10.1021/jp404896q},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry C},
volume = {118},
number = {12},
pages = {6110-6121},
abstract = {Using density-functional theory, we have computed the structural and electronic properties of paramagnetic vivianite crystal Fe3(PO 4)2·8H2O and its (010)-(1 × 1) and (100)-(1 × 1) surfaces. The properties of bulk vivianite are studied with a set of functionals: HSE06, PBE, AM05, PBEsol, and PBE with on-site Coulomb repulsions corrections (PBE+U). The appropriate U parameter is estimated by considering the HSE06 results, and it is used to study the vivianite surfaces. The computed surface energy predicts the (010) surface to be the most stable. The less stable (100) surface is observed to have important reconstructions with the spontaneous formation of a water molecule at the surface and two hydroxide hydrate anions per unit cell. Using thermodynamical considerations within DFT, we have calculated the phase diagram of the (010) surface in equilibrium with hydrogen gas. The results suggest that under ultralow hydrogen pressure, the (010) surface with two hydrogen vacancies is stable. The electronic structure calculations for the surfaces are complemented with the computed scanning tunneling microscopy (STM) images for constant-current mode. The topology is dominated by the surface Fe-3d states that protrude into the vacuum. © 2014 American Chemical Society.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sergeieva20141895,
title = {Hydrazinolysis of 3-R-[1,2,4]Triazino[2,3-c]quinazolin-2-ones. Synthetic and theoretical aspects},
author = { T.Y.a e Sergeieva and O.Y.b Voskoboynik and S.I.a e Okovytyy and S.I.b Kovalenko and S.V.c Shishkina and O.V.c d Shishkin and J.e Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896284821&amp;partnerID=40&amp;md5=d0ae918f4c68182b655b755bd804ee1b},
doi = {10.1021/jp4052616},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry A},
volume = {118},
number = {10},
pages = {1895-1905},
abstract = {It has been shown that heating of 3-R-[1,2,4]triazino[2,3-c]quinazolin-2- ones with 5-fold excess of hydrazine hydrate in propanol-2 gave the corresponding 3-(2-aminophenyl)-6-R-1,2,4-triazin-5-ones with high yields. The mechanism of the reaction has been proposed based on the results of theoretical investigation at B3LYP and MP2 levels of theory. According to calculations, an attack of the hydrazine molecule on the C6\^{i} - ?N7 double bond leads to ring-opening with N5-C6 bond cleavage. The process continues by addition of the second nucleophile molecule and elimination of the formazan fragment through a series of transformations that yield the target product. © 2014 American Chemical Society.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Xu20142462,
title = {Expedient access to substituted 3-amino-2-cyclopentenones by dirhodium-catalyzed [3+2]-annulation of silylated ketene imines and enoldiazoacetates},
author = { X. Xu and J.S. Leszczynski and S.M. Mason and P.Y. Zavalij and M.P. Doyle},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893857278&amp;partnerID=40&amp;md5=197a32dbe81a079106c081c416323f77},
doi = {10.1039/c3cc48993k},
year  = {2014},
date = {2014-01-01},
journal = {Chemical Communications},
volume = {50},
number = {19},
pages = {2462-2464},
abstract = {In a reaction that proceeds under mild conditions with remarkable functional group tolerance, structurally diverse 3-amino-2-cyclopentenones bearing a quaternary carbon at the 4-position have been synthesized through a formal [3+2]-cycloaddition reaction of silylated ketene imines (SKIs) and enoldiazoaceates by dirhodium catalysis. © 2014 The Royal Society of Chemistry.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Scott20144774,
title = {Toward accurate and efficient predictions of entropy and gibbs free energy of adsorption of high nitrogen compounds on carbonaceous materials},
author = { A.M.a Scott and L.b Gorb and E.A.b Burns and S.N.c Yashkin and F.C.a Hill and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897714081&amp;partnerID=40&amp;md5=3cc5bb2605b52a96de0a4e3de92855f9},
doi = {10.1021/jp4121832},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry C},
volume = {118},
number = {9},
pages = {4774-4783},
abstract = {The adsorption of high nitrogen compounds (HNCs) on the selected adsorption sites of carbonaceous materials from the gas phase has been investigated by ab initio quantum chemical methods at the density functional level applying both periodic and cluster approaches with M06-2X and BLYP functionals including dispersion forces (BLYP-D2). Among the possible structures of the adsorption complexes, the most stable systems possess nitrogen-containing heterocycles in a parallel orientation toward the modeled carbon surface. The adsorption enthalpies, calculated using the rigid rotor-harmonic oscillator approach (RRHO), were in good agreement with available experimental data. This approach was shown to provide sufficiently accurate adsorption enthalpies from the gas phase for the HNC-carbon systems. The vibrational, rotational, and translation contributions to the adsorption entropy were also analyzed by the approach extended beyond the RRHO scheme. The effects of anharmonic vibrations and internal rotations of the adsorbate on the adsorption sites of the modeled carbon surface were estimated. The Gibbs free energies calculated using the RRHO approach were adjusted to take into account the heterogeneity of the carbon surfaces and underestimation of the adsorption enthalpies at the BLYP-D2(PBC) level. The corrected Gibbs free energy values of adsorption are negative for all of the investigated HNC-carbon systems, and they agree well with available experimental data. This suggests an effective adsorption of selected high nitrogen compounds on carbonaceous materials from the gas phase at 298.15 K. Partition coefficients for distribution of high nitrogen compounds on modeled carbon surfaces were also predicted in good agreement with the experimental results. © 2014 American Chemical Society.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut20141,
title = {Modeling the intermolecular interactions: Molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide},
author = { S.a Karabulut and H.a Namli and R.b Kurtaran and L.T.c Yildirim and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84890817730&amp;partnerID=40&amp;md5=14850302b9d127bddf0050611f0d998e},
doi = {10.1016/j.jmgm.2013.11.001},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {48},
pages = {1-8},
abstract = {The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by 1H NMR, 13C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2 1/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. © 2013 Elsevier Inc.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rozhenko20141479,
title = {On the stability of perfluoroalkyl-substituted singlet carbenes: A coupled-cluster quantum chemical study},
author = { A.B.a b c Rozhenko and W.W.c Schoeller and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897610082&amp;partnerID=40&amp;md5=390a1a094051240ad52e8d2564a7bf78},
doi = {10.1021/jp408778x},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry A},
volume = {118},
number = {8},
pages = {1479-1488},
abstract = {A series of trifluoromethyl-substituted carbenes R-C(:)-CF3 (R = NMe2, OMe, F, PMe2, P(NMe2)2, P(N(Pr-i)2)2, SMe, Cl); (dimethylamino)(perfluoroalkyl) carbenes Me2N-C(:)-R (R = CF3, C2F5, n-C3F7, i-C3F7, and t-C 4F9) and symmetrically substituted carbenes R-C(:)-R (R = NMe2, OMe, F, PMe2, SMe, Cl) have been investigated by means of quantum chemistry methods. Different levels of approximation were used, including the CCSD(T) approach also known in quantum chemistry as the "golden standard", in combination with three different basis sets (TZVP, cc-pVDZ, cc-pVTZ). Relative stabilities of carbenes have been estimated using the differences between the singlet and triplet ground state energies (ΔEST) and energies of the hydrogenation reaction for the singlet and triplet ground states of the carbenes. The latter seem to correlate better with stability of carbenes than the ΔEST values. The 13C NMR chemical shifts of the methylidene carbon indicate the more high-field chemical shift values in the known, isolable carbenes compared to the unstable ones. This is the first report on the expected chemical shifts in the highly unstable singlet carbenes. Using these criteria, some carbene structures from the studied series (as, for instance, Me2N-C(:)-CF3, Me2N-C(:)-C3F7-i) are proposed as good candidates for the experimental preparation. © 2014 American Chemical Society.},
note = {cited By 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Rozhenko2014241,
title = {Intermediate carbene formation in the reaction of thioamides with phosphorus (III) derivatives: Quantum chemical investigation},
author = { A.B.a b c Rozhenko and S.S.a Mykhaylychenko and N.V.a Pikun and Y.G.a Shermolovich and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84891610333&amp;partnerID=40&amp;md5=76ae9324715cc86243a8efa8ddadf5e9},
doi = {10.1002/qua.24546},
year  = {2014},
date = {2014-01-01},
journal = {International Journal of Quantum Chemistry},
volume = {114},
number = {4},
pages = {241-248},
abstract = {The reactions of perfluoroalkyl thioamides with trimethyl phosphine, trimethyl phosphite, and tris(dimethylamino)phosphine have been analyzed by means of quantum chemical (DFT and MP2) calculations. The reaction seems to proceed via the nucleophilic attack of the electrophilic carbon atom by the phosphorus lone pair with the formation of cyclic or acyclic adducts. The latter releases the thiophosphate molecule forming perfluoroalkylaminocarbene as the short-lived intermediate. The reaction of the carbene with the second molecule of trialkyl phosphite yields phosphorus ylide. The ylide undergoes a migration of fluorine from carbon to phosphorus. The reactions of perfluoroalkyl thioamides with phosphines and tris(dimethylamino)phosphine probably proceeds differently. Using alkyl thioamides or amides instead of perfluoroalkyl thioamides also makes the reaction less favorable. The only combination of perfluoroalkyl thioamides with trialkyl phosphite fulfills both the kinetic requirements (moderate activation energies and relative energies for intermediates) and the thermodynamic aspects (higher stabilities of the reaction products compared with the starting materials). © 2013 Wiley Periodicals, Inc. Theoretical methods are valuable for the study of highly reactive intermediaries in reactions. This work studies the mechanism of the recently reported reaction of (perfluoro)alkyl (thio)amides with phosphorus(III) derivatives. The formation of short-lived perfluoroalkyl carbenes is predicted as a probable intermediate in the reaction of perfluoroalkyl thioamides with trimethyl phosphites and tris(dimethylamino)phosphine. Adding the second mole of the phosphorus(III) derivative to the carbene is thermodynamically favored. The formed phosphorus ylides undergo further transformations. Copyright © 2013 Wiley Periodicals, Inc.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Tsendra20143023,
title = {Adsorption of nitrogen-containing compounds on the (100) α-quartz surface: Ab initio cluster approach},
author = { O.a b Tsendra and A.M.c Scott and L.d Gorb and A.D.e Boese and F.C.c Hill and M.M.f Ilchenko and D.g Leszczynska and J.a c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84894102370&amp;partnerID=40&amp;md5=f4f0c1108c7632cf90236984827c21b1},
doi = {10.1021/jp406827h},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry C},
volume = {118},
number = {6},
pages = {3023-3034},
abstract = {A cluster approach extended to the ONIOM methodology has been applied using several density functionals and M\oller-Plesset perturbation theory (MP2) to simulate the adsorption of selected nitrogen-containing compounds [NCCs, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazole-5-one (NTO)] on the hydroxyated (100) surface of α-quartz. The structural properties were calculated using the M06-2X functional and 6-31G(d,p) basis set. The M06-2X-D3, PBE-D3, and MP2 methods were used to calculate the adsorption energies. Results have been compared with the data from other studies of adsorption of compounds of similar nature on silica. Effect of deformation of the silica surface and adsorbates on the binding energy values was also studied. The atoms in molecules (AIM) analysis was employed to characterize the adsorbate-adsorbent binding and to calculate the bond energies. The silica surface shows different sorption affinity toward the chemicals considered depending on their electronic structure. All target NCCs are physisorbed on the modeled silica surface. Adsorption occurs due to the formation of multiple hydrogen bonds between the functional groups of NCCs and surface silanol groups. Parallel orientation of NCCs interacting with the silica surface was found to be favorable when compared with perpendicularly oriented NCCs. NTO was found to be the most strongly adsorbed on the silica surface among all of the considered compounds. Dispersion correction was shown to play an important role in the DFT calculations of the adsorption energies of silica-NCC systems. © 2014 American Chemical Society.},
note = {cited By 6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropov201420,
title = {Comprehension of drug toxicity: Software and databases},
author = { A.A.a Toropov and A.P.a Toropova and I.b Raska and D.c Leszczynska and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84890016373&amp;partnerID=40&amp;md5=8a93fb0e4feb486cc61820841b735ed4},
doi = {10.1016/j.compbiomed.2013.11.013},
year  = {2014},
date = {2014-01-01},
journal = {Computers in Biology and Medicine},
volume = {45},
number = {1},
pages = {20-25},
abstract = {Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool (in silico) to rapidly predict various endpoints in general, and drug toxicity in particular. However, this dynamic evolution of experimental data (expansion of existing experimental data on drugs toxicity) leads to the problem of critical estimation of the data. The carcinogenicity, mutagenicity, liver effects and cardiac toxicity should be evaluated as the most important aspects of the drug toxicity. The toxicity is a multidimensional phenomenon. It is apparent that the main reasons for the increase in applications of in silico prediction of toxicity include the following: (i) the need to reduce animal testing; (ii) computational models provide reliable toxicity prediction; (iii) development of legislation that is related to use of new substances; (iv) filling data gaps; (v) reduction of cost and time; (vi) designing of new compounds; (vii) advancement of understanding of biology and chemistry. This mini-review provides analysis of existing databases and software which are necessary for use of robust computational assessments and robust prediction of potential drug toxicities by means of in silico methods. © 2013 Elsevier Ltd.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gu2014915,
title = {Electron interaction with phosphate cytidine oligomer dCpdC: Base-centered radical anions and their electronic spectra},
author = { J.a Gu and J.b Wang and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893435294&amp;partnerID=40&amp;md5=b917021fcf221c157240d8debf050d09},
doi = {10.1021/jp409247d},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Physical Chemistry B},
volume = {118},
number = {4},
pages = {915-920},
abstract = {Computational chemistry approach was applied to explore the nature of electron attachment to cytosine-rich DNA single strands. An oligomer dinucleoside phosphate deoxycytidylyl-3′,5′-deoxycytidine (dCpdC) was selected as a model system for investigations by density functional theory. Electron distribution patterns for the radical anions of dCpdC in aqueous solution were explored. The excess electron may reside on the nucleobase at the 5′ position (dC•-pdC) or at the 3′ position (dCpdC•-). From comparison with electron attachment to the cytosine related DNA fragments, the electron affinity for the formation of the cytosine-centered radical anion in DNA is estimated to be around 2.2 eV. Electron attachment to cytosine sites in DNA single strands might cause perturbations of local structural characteristics. Visible absorption spectroscopy may be applied to validate computational results and determine experimentally the existence of the base-centered radical anion. The time-dependent DFT study shows the absorption around 550-600 nm for the cytosine-centered radical anions of DNA oligomers. This indicates that if such species are detected experimentally they would be characterized by a distinctive color. © 2014 American Chemical Society.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Szymanek2014687,
title = {Modelling and analysis of heat transfer through 1D complex granular system},
author = { E.a Szymanek and T.b Blaszczyk and M.R.c Hall and P.K.d Dehdezi and J.S.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84920282375&amp;partnerID=40&amp;md5=cef9ff6bf839125c6b052b5f3e6e0921},
doi = {10.1007/s10035-014-0517-1},
year  = {2014},
date = {2014-01-01},
journal = {Granular Matter},
volume = {16},
number = {5},
pages = {687-694},
abstract = {This article demonstrates the solution to the problem of the passage of air through the external wall barrier and the influence of the materials type and its layer arrangement on heat conductivity, in respect of building heat losses. It shows how the temperature changes inside the wall barriers and in a room while the external temperature changes. Also, this article presents the mathematical model based on fractional differential equation describing the analysed phenomenon. © 2014, The Author(s).},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Macioch201425,
title = {Original method of treatment applied to the patent with rupturing thoracoabdominal aortic aneurysm, multi-organ insufficiency and advance limb ischemia [Oryginalny spos\'{o}b leczenia chorego z pȩkaja̧cym tȩtniakiem aorty piersiowo-brzusznej, niewydolno\'{s}cia̧ wielonarza̧dowa̧ i zaawansowanym niedokrwieniem ko\'{n}czyn dolnych]},
author = { W. Macioch and J. Leszczy\'{n}ski and M. Szostek and W. Jakuczun and T. Ostrowski and A. Kosicki and T. Brzezi\'{n}ski and R. Pogorzelski and M. Sk\'{o}rski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901818195&amp;partnerID=40&amp;md5=5745bcb06cdfdeebff9d4d0683c163a6},
year  = {2014},
date = {2014-01-01},
journal = {Acta Angiologica},
volume = {20},
number = {1},
pages = {25-31},
abstract = {Presented is nonconventional method of treatment of patent with rupturing thoracoabdominal aortic aneurysm (Crawford type II), with multi-organ insufficiency and critical ischemia lower extremities due to dissection and thrombosis in the infra-renal part of an aneurysm. Due to high risk for surgery the patient was previously disqualified from the surgical treatment. On the new circumstances, that is the rupturing of an aneurysm and rest pain extremities forced us to try, to give it a chance for original method of treatment. From several vascular prostheses a special system of branches was constructed, it was then anastomosed by one and into coagulated sack of infra-renal part of an aneurysm. The branches of this system were then anastomosed with the renal arteries, mesenteric superior artery and with both common femoral arteries. In the second step through the technical branch of the system (conduit), the multi-segmented stent-graft was forced through the occluded aneurysm, thus restoring the blood flow to the kidneys, abdominal viscera and lower extremities. At end of the procedure there was a need for additional mesenteric to celiac anastomoses. In postoperative period transient functional renal impairment was observed, with no other adverse complications. After 12 months follow up the patient was found in the satisfactory condition. In bibliography there is a lack of description of the similar case.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut20141b,
title = {Combining ab initio calculations and Fourier-transform infrared (FT-IR) spectroscopy for quantitative analysis of multicomponent systems in solution: Tautomer proportions of ethyl acetoacetate},
author = { S.a Karabulut and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904725515&amp;partnerID=40&amp;md5=a27b9973c465a4a8257292046f7600aa},
doi = {10.1016/j.vibspec.2014.06.006},
year  = {2014},
date = {2014-01-01},
journal = {Vibrational Spectroscopy},
volume = {74},
pages = {1-5},
abstract = {A quantitative analysis method, combined experimental-computational approach (CECA), has been developed and applied for the detection of tautomer ratios of ethyl acetoacetate (eaa) in three organic solvents (acetonitrile, methanol, and chloroform). In order to obtain the relative concentrations of tautomers of eaa, IR intensities of both tautomers have been calculated at three different calculation levels (B3LYP/6-311++G(2d,2p), MP2/cc-pVDZ, and MP2/cc-pVTZ), augmented by the data obtained using basis set extrapolation technique. Experimental absorption bands were recorded at specific wavenumbers with FT-IR spectrophotometer and combined with calculated IR intensities in Lambert-Beer equation. Though the pure computational approach does not provide accurate values of the tautomers' ratio, yet the results obtained using the CECA method are very close to the experimental data. © 2014 Elsevier Ltd. All rights reserved.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{Nowak2014699,
title = {Influence of PSD of make-up material on CFB boiler operation burning biomass},
author = { W.a Nowak and J.b Leszczynski and M.c Niedzielska and M.b Wesolowska},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84902687742&amp;partnerID=40&amp;md5=bbd04d540ada982aa7e200e323964282},
year  = {2014},
date = {2014-01-01},
journal = {CFB-11: Proceedings of the 11th International Conference on Fluidized Bed Technology},
pages = {699-704},
abstract = {Particle size distribution of the make-up material is crucial to proper operation of any kind of CFB boilers. Particle size distribution forming circulating material in a CFB boiler mainly depends on the separation efficiency, the ability of combusted coal for thermal fragmentation and the ash content in the fuel. In this paper analysis of influence of particle size distribution (PSD) of sand particles on CFB boiler operation is reported. Experiments were carried out in the Foster Wheeler Compact CFB boiler in CHP Fortum Czestochowa, Poland. Power Plant of 120 MW and 64 MW thermal power produces 550 GWh of electricity and 450 GWh of heat consumption. Live steam parameters are (boiler) 77.1 kg/s, 515C, 111bar. Main fuels are hard coal/bio - 70/30%, forest biomass - max 30%, agro biomass - max 20%. The results of the mass balance model for the CFB that takes into account the following physical processes (i.e. attrition, segregation, fragmentation, coagulation) and chemical processes (i.e. fuel combustion) that occur in the CFB boiler were also presented.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@article{Sizochenko201413986,
title = {From basic physics to mechanisms of toxicity: The "liquid drop" approach applied to develop predictive classification models for toxicity of metal oxide nanoparticles},
author = { N.a b Sizochenko and B.b Rasulev and A.c Gajewicz and V.a d Kuz'Min and T.c Puzyn and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84911447644&amp;partnerID=40&amp;md5=87f6cb2b74f049cc41ca01082da74b62},
doi = {10.1039/c4nr03487b},
year  = {2014},
date = {2014-01-01},
journal = {Nanoscale},
volume = {6},
number = {22},
pages = {13986-13993},
abstract = {Many metal oxide nanoparticles are able to cause persistent stress to live organisms, including humans, when discharged to the environment. To understand the mechanism of metal oxide nanoparticles' toxicity and reduce the number of experiments, the development of predictive toxicity models is important. In this study, performed on a series of nanoparticles, the comparative quantitative-structure activity relationship (nano-QSAR) analyses of their toxicity towards E. coli and HaCaT cells were established. A new approach for representation of nanoparticles' structure is presented. For description of the supramolecular structure of nanoparticles the "liquid drop" model was applied. It is expected that a novel, proposed approach could be of general use for predictions related to nanomaterials. In addition, in our study fragmental simplex descriptors and several ligand-metal binding characteristics were calculated. The developed nano-QSAR models were validated and reliably predict the toxicity of all studied metal oxide nanoparticles. Based on the comparative analysis of contributed properties in both models the LDM-based descriptors were revealed to have an almost similar level of contribution to toxicity in both cases, while other parameters (van der Waals interactions, electronegativity and metal-ligand binding characteristics) have unequal contribution levels. In addition, the models developed here suggest different mechanisms of nanotoxicity for these two types of cells. This journal is © The Royal Society of Chemistry.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko2014311,
title = {Theoretical study of one-electron reduction and oxidation potentials of N-Heterocyclic compounds},
author = { L.K.a b Sviatenko and L.c Gorb and F.C.d Hill and D.e Leszczynska and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904363611&amp;partnerID=40&amp;md5=14a1bbb35b7d50fcb1ecfa7fdff904fb},
doi = {10.1007/s10593-014-1484-5},
year  = {2014},
date = {2014-01-01},
journal = {Chemistry of Heterocyclic Compounds},
volume = {50},
number = {3},
pages = {311-318},
abstract = {Computational protocols that successfully predict standard reduction potentials of N-heterocyclic compounds in dimethyl formamide and their standard oxidation potentials in acetonitrile were developed. Different solvation models were verified in conjunction with the MPWB1K/6-31+G(d) level of density functional theory. For reduction potentials calculations, the PCM(UA0) and SMD(Bondi) models were used to compute solvation energies of neutral forms and anion-radical forms, respectively. For oxidation potential calculations, the best results were obtained by a combination of SMD(UAHF) and PCM(Bondi) models to compute solvation energies of neutral forms and cation-radical forms, respectively. The mean absolute deviations (MAD) and root mean square errors (RMSE) of the current theoretical models for reduction potentials were found to be 0.09 V and 0.10, respectively, and for oxidation potentials MAD = 0.12 V and RMSE = 0.16. © 2014 Springer Science+Business Media New York.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Turabekova2014213,
title = {Aconitum and delphinium diterpenoid alkaloids of local anesthetic activity: Comparative QSAR analysis based on GA-MLRA/PLS and optimal descriptors approach},
author = { M.A.a b c Turabekova and B.F.a b Rasulev and F.N.b Dzhakhangirov and A.A.d Toropov and D.a c Leszczynska and J.a d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84907557729&amp;partnerID=40&amp;md5=8bd3154083b1f371a5633cb713bac8e1},
doi = {10.1080/10590501.2014.938886},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Environmental Science and Health - Part C Environmental Carcinogenesis and Ecotoxicology Reviews},
volume = {32},
number = {3},
pages = {213-238},
abstract = {The duration of anesthesia (related to protein binding of a drug) and the onset time (determined by the pKa) are important characteristics in assessment of local anesthetic agents. They are known to be affected by a number of factors. Early studies of antiarrhythmic diterpenoid alkaloids from plants Aconitum and Delphinium suggested that they possess local anesthetic activity due to their ability to suppress sodium currents of excited membranes.In this study we utilized toxicity, duration, and onset of action as endpoints to construct Quantitative Structure-Activity Relationship (QSAR) models for the series of 34 diterpenoid alkaloids characterized by local anesthetic activity using genetic algorithm-based multiple linear regression analysis/partial least squares and simplified molecular input line entry system (SMILES)-based optimal descriptors approach. The developed QSAR models correctly reflected factors that determine three endpoints of interest. Toxicity correlates with descriptors describing partition and reactivity of compounds. The duration of anesthesia was encoded by the parameters defining the ability of a compound to bind at the receptor site. The size and number of H-bond acceptor atoms were found not to favor the speed of onset, while topographic electronic descriptor demonstrated strong positive effect on it. SMILES-based optimal descriptors approach resulted in overall improvement of models. This approach was shown to be more sensitive to structural peculiarities of molecules than regression methods.The results clearly indicate that obtained QSARs are able to provide distinct rationales for compounds optimization with respect to particular endpoint. © 2014 Copyright © Taylor & Francis Group, LLC.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Ivashchenko2014381,
title = {Comparative investigation of NbN and Nb-Si-N films: Experiment and theory},
author = { V.I.a Ivashchenko and P.L.a Scrynskyy and O.S.b Lytvyn and O.O.a Butenko and O.K.a Sinelnichenko and L.c d Gorb and F.e Hill and J.c Leszczynski and A.O.a Kozak},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84919909079&amp;partnerID=40&amp;md5=67ec339906a1b2b7eb58091f7fa98b80},
doi = {10.3103/S1063457614060033},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Superhard Materials},
volume = {36},
number = {6},
pages = {381-392},
abstract = {NbN and Nb-Si-N films have been deposited by magnetron sputtering of the Nb and Si targets on silicon wafers at various powers supplied to the Nb target. The films have been investigated by an atomic force microscope, X-ray diffraction, X-ray photoelectron spectroscopy, nanoindentaion and microindentation. The NbN films were nanostructured, and the Nb-Si-N films represented an aggregation of δ-NbNx nanocrystallites embedded into the amorphous Si3N4 matrix (nc-δ-NbNx/a-Si3N4). The annealing of the films in vacuum showed that their intensive oxidation occurred at annealing temperature higher than 600°C. To explain the experimental results on the Nb-Si-N films, first-principles molecular dynamics simulations of the NbN(001)/Si3N4 heterostructures have been carried out. © 2014, Allerton Press, Inc.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sheng2014667,
title = {Thermal racemization of spiropyrans: Implication of substituent and solvent effects revealed by computational study},
author = { Y.a Sheng and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897109949&amp;partnerID=40&amp;md5=18499f6b3a35de923144f5bad92e7923},
doi = {10.1007/s11224-013-0374-2},
year  = {2014},
date = {2014-01-01},
journal = {Structural Chemistry},
volume = {25},
number = {2},
pages = {667-677},
abstract = {The thermal racemization of spiropyrans has been investigated by computational study at the density functional theory and MP2 levels. Two possible reaction mechanisms for the thermal racemization of spiropyrans were found. One reaction mechanism is a three-step reaction, the other represents a four-step reaction. The competition between these two mechanisms is dependent on the strengths of the substituents, as well as the polarities of the solvents. Different substituents and solvents change the rate-determining step and lead to various pathways. The solvent effect is found more pronounced on the electron-withdrawing substituted spiropyrans. In addition, bond length alternation (BLA), a structural parameter, has been employed in this study. It has been proven that BLA is a useful parameter to correlate the effect of substituents and solvents with the racemization mechanism of spiropyrans. The relationship between BLA and activation energies clearly explains the origin of the competition between the two reaction mechanisms. The results from this work would be valuable for selecting substituents and solvents for development of desired optical properties of spiropyrans. © 2013 Springer Science+Business Media New York.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Shishkin2014327,
title = {A theoretical investigation of the relative stability of isomeric dihydropyridines},
author = { O.V.a b Shishkin and R.I.a Zubatyuk and S.M.a Desenko and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904315132&amp;partnerID=40&amp;md5=11eff9e43826e863639a0a06dd2e267e},
doi = {10.1007/s10593-014-1480-9},
year  = {2014},
date = {2014-01-01},
journal = {Chemistry of Heterocyclic Compounds},
volume = {50},
number = {3},
pages = {327-335},
abstract = {The molecular structure and relative stability of isomeric dihydropyridines have been calculated using the density functional theory and the Moller-VPlesset second-order perturbation theory. The results of the calculations demonstrate that 3,4- and 2,3-dihydropyridines are the most stable species despite the presence of a 4π-electron conjugated system within the ring. A comparison of the relative energy of acyclic analogs of dihydropyridines indicates that this is caused by the internal properties of the conjugated system. The remaining dihydropyridines are strongly destabilized by the formation of antiaromatic conjugated (or quasi-conjugated) systems due to the interaction of pz atomic orbitals of the carbon and nitrogen atoms with the pseudo-π fragment orbital of the methylene group. Application of the more accurate CCSD(T)/CBS method results in considerable stabilization of 1,4-dihydropyridine. However, the order of stability of other isomers remains the same as it was found at the MP2 level of theory. © 2014 Springer Science+Business Media New York.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Jagiello2014997,
title = {Direct QSPR: The most efficient way of predicting organic carbon/water partition coefficient (log K OC) for polyhalogenated POPs},
author = { K.a Jagiello and A.a Sosnowska and S.b Walker and M.c Haranczyk and A.a Gajewicz and T.d Kawai and N.d Suzuki and J.b Leszczynski and T.a Puzyn},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84900496189&amp;partnerID=40&amp;md5=a70dc4b742411e99e9b6e893039b3e26},
doi = {10.1007/s11224-014-0419-1},
year  = {2014},
date = {2014-01-01},
journal = {Structural Chemistry},
volume = {25},
number = {3},
pages = {997-1004},
abstract = {The organic carbon/water partition coefficient (K OC) is one of the most important parameters describing partitioning of chemicals in soil/water system and measuring their relative potential mobility in soils. Because of a large number of possible compounds entering the environment, the experimental measurements of the soil sorption coefficient for all of them are virtually impossible. The alternative methods, such as quantitative structure-property relationship (QSPR techniques) have been applied to predict this important physical/chemical parameter. Most available QSPR models have been based on correlations with the n-octanol/water partition coefficient (K OW), which enforces the requirement to conduct experiments for obtaining the K OW values. In our study, we have developed a QSPR model that allows predicting logarithmic values of the organic carbon/water partition coefficient (log K OC) for 1,436 chlorinated and brominated congeners of persistent organic pollutants based on the computationally calculated descriptors. Appling such approach not only reduces time, cost, and the amount of waste but also allows obtaining more realistic results. © 2014 The Author(s).},
note = {cited By 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Kar2014162,
title = {Periodic table-based descriptors to encode cytotoxicity profile of metal oxide nanoparticles: A mechanistic QSTR approach},
author = { S.a b Kar and A.b Gajewicz and T.b Puzyn and K.a Roy and J.c Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84902524573&amp;partnerID=40&amp;md5=dcbe0f80414a592266a31fe219f41c2a},
doi = {10.1016/j.ecoenv.2014.05.026},
year  = {2014},
date = {2014-01-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {107},
pages = {162-169},
abstract = {Nanotechnology has evolved as a frontrunner in the development of modern science. Current studies have established toxicity of some nanoparticles to human and environment. Lack of sufficient data and low adequacy of experimental protocols hinder comprehensive risk assessment of nanoparticles (NPs). In the present work, metal electronegativity (χ), the charge of the metal cation corresponding to a given oxide (χox), atomic number and valence electron number of the metal have been used as simple molecular descriptors to build up quantitative structure-toxicity relationship (QSTR) models for prediction of cytotoxicity of metal oxide NPs to bacteria Escherichia coli. These descriptors can be easily obtained from molecular formula and information acquired from periodic table in no time. It has been shown that a simple molecular descriptor χox can efficiently encode cytotoxicity of metal oxides leading to models with high statistical quality as well as interpretability. Based on this model and previously published experimental results, we have hypothesized the most probable mechanism of the cytotoxicity of metal oxide nanoparticles to E. coli. Moreover, the required information for descriptor calculation is independent of size range of NPs, nullifying a significant problem that various physical properties of NPs change for different size ranges. © 2014 Elsevier Inc.},
note = {cited By 5},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Paytakov20142115,
title = {Homodimers of cytosine and 1-methylcytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents.},
author = { G. Paytakov and L. Gorb and A. Stepanyugin and S. Samiylenko and D. Hovorun and J. Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84908118911&amp;partnerID=40&amp;md5=c2346c90a1db90891af36f73ec424643},
doi = {10.1007/s00894-014-2115-x},
year  = {2014},
date = {2014-01-01},
journal = {Journal of molecular modeling},
volume = {20},
number = {3},
pages = {2115},
abstract = {Dimers of cytosine and its N1-methylated counterpart were investigated in gas-phase and in various solvents including chloroform, dimethylsulfoxide, and water. The studies were performed at DFT/M06-2X/6-31+G(d,p) level of theory. Relative stabilities of tautomers of cytosine solvated explicitly by a small number of solvent molecules were evaluated. Further solvation effect calculations for homodimers were carried out with conductor-like polarizable continuum model (CPCM). H-NMR shifts and IR frequencies for optimized structures were calculated and compared with available experimental data.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sk\'{o}rski201419,
title = {Fulminant course of visceral malperfusion due to type B aortic dissection [Piorunuja̧ce niedokrwienie trzewi w przebiegu ostrego rozwarstwienia aorty typu B]},
author = { M. Sk\'{o}rski and T. Brzezi\'{n}ski and M. Szostek and T. Ostrowski and J. Leszczy\'{n}ski and R. Tworus and P. Kabala and W. Macioch},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901850414&amp;partnerID=40&amp;md5=e4cfaabd4e154f158f191cef41ac80cb},
year  = {2014},
date = {2014-01-01},
journal = {Acta Angiologica},
volume = {20},
number = {1},
pages = {19-24},
abstract = {Aortic type B dissection can be treated conservatively in up to 90% of uncomplicated cases. Additional symptoms comprising of the pain in the thorax and abdominal cavity may suggest vascular complications. Visceral ischemia is observed in about 30% of aortic dissections. Synchronous symptoms in the thorax and abdomen are very rare situation. A 54-year old male patient was admitted to the clinic on duty with diagnosis of aortic dissection. Angiotomography proved a dissection starting just below the origin of the left subclavian artery and running along the aorta to the external iliac arteries. The patient presented also with very high systemic pressure and abdominal symptoms of diffuse peritonitis. Plain abdominal x-ray proved perforation of his gastroalimentary tract. Emergency laparotomy was performed disclosing a vast defect of gastric walls in the prepyloric region and visible ischemia of mucosa with patches of necrosis reaching up to the half of the stomach. B II resection was performed with anastomosis of the stomach stump to the small intestine on so-called Lahey loop. Histological evaluation did not prove the existence of peptic ulcer. In the postoperative period ischemia of the intestines was observed again. The afferent loop of gastrointestinal anastomosis was shrunken due to this fact. Patient received wide spectrum antibiotics and was maintained on total parenteral nutrition. Apart from this treatment the state of the patient did not change. It was decided that closure of the entry tear in the thoracic aorta was the only way to restore a proper blood flow in it. Aortic stent-graft was implanted to the thoracic aorta descending to the level of the celiac trunk despite the symptoms of septicemia. This endovascular procedure changed the blood flow in the thoracic aorta and improved the inflow to visceral arteries but the patient was operated two more times because of progressing necrosis in the vicinity of intestinal anastomoses with fistulae formation. Finally the patient recovered within three months since admission. He also experienced stroke during his hospital stay. Type B aortic dissection complicated with visceral ischemia requires an urgent surgical treatment. Aortic stent-graft placement seems to be the gold standard in such cases. This treatment should precede formation of intestine necrosis with fistulae and subsequent septic complications. It seems that regaining of the true channel below the stent-graft may require certain time for the shrinking of the false one filled with thrombi does not appear just after the endovascular procedure. Copyright © 2014 Via Medica.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Karabulut20143134,
title = {Reduction of aflatoxin B1 to aflatoxicol: A comprehensive DFT study provides clues to its toxicity},
author = { S.a Karabulut and G.b Paytakov and J.b Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84911808393&amp;partnerID=40&amp;md5=952ba53abb687c80cf21ea0cd3003da5},
doi = {10.1002/jsfa.6663},
year  = {2014},
date = {2014-01-01},
journal = {Journal of the Science of Food and Agriculture},
volume = {94},
number = {15},
pages = {3134-3140},
abstract = {BACKGROUND: Aflatoxicol (AFL) is one of most the important metabolites of aflatoxin B1 (AFB1). AFL can be formed through enzymatic or synthetic reduction of AFB1. Various experimental and theoretical studies have been focused on the AFB1 due to its high toxicity and carcinogenicity. RESULTS: The selective reduction of AFB1 carbonyls, molecular structure of AFL and its effect on toxicity has been studied here by the density functional theory (DFT) method. Although the toxicity of AFL is 18 times lower than that of AFB1, it has been concluded that both molecular structures have similar potency to form an exo-epoxide (AFEP) analogue which can bind to DNA. CONCLUSION: Calculations revealed that only one of the three possible tautomers of AFL is stable, both in the gas phase and water. The electronic properties of aflatoxicol are calculated as similar to aflatoxin B1 and this may be an explanation of similar carcinogenicity and toxicity of these compounds, which has been proved by experimental results. © 2014 Society of Chemical Industry.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{He2014128,
title = {Using a holistic approach to assess the impact of engineered nanomaterials inducing toxicity in aquatic systems},
author = { X.a He and W.G.b Aker and J.c Leszczynski and H.-M.a b Hwang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901620492&amp;partnerID=40&amp;md5=a43a691da14e7beefa584920e345ee96},
doi = {10.1016/j.jfda.2014.01.011},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {128-146},
abstract = {In this report, we critically reviewed selected intrinsic physicochemical properties of engineered nanomaterials (ENMs) and their role in the interaction of the ENMs with the immediate surroundings in representative aquatic environments. The behavior of ENMs with respect to dynamic microenvironments at the nanoebioeeco interface level, and the resulting impact on their toxicity, fate, and exposure potential are elaborated. Based on this literature review, we conclude that a holistic approach is urgently needed to fulfill our knowledge gap regarding the safety of discharged ENMs. This comparative approach affords the capability to recognize and understand the potential hazards of ENMs and their toxicity mechanisms, and ultimately to establish a quantitative and reliable system to predict such outcomes. Copyright © 2014, Food and Drug Administration, Taiwan.},
note = {cited By 6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2014203,
title = {Optimal descriptor as a translator of eclectic information into the prediction of membrane damage: The case of a group of ZnO and TiO2 nanoparticles},
author = { A.P.a Toropova and A.A.a Toropov and E.a Benfenati and T.b Puzyn and D.c Leszczynska and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84905248676&amp;partnerID=40&amp;md5=4c57fa88bb47624b5e8787040fe3b450},
doi = {10.1016/j.ecoenv.2014.07.005},
year  = {2014},
date = {2014-01-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {108},
pages = {203-209},
abstract = {The development of quantitative structure-activity relationships for nanomaterials needs representation of molecular structure of extremely complex molecular systems. Obviously, various characteristics of nanomaterial could impact associated biochemical endpoints. Following features of TiO2 and ZnO nanoparticles (n=42) are considered here: (i) engineered size (nm); (ii) size in water suspension (nm); (iii) size in phosphate buffered saline (PBS, nm); (iv) concentration (mg/L); and (v) zeta potential (mV). The damage to cellular membranes (units/L) is selected as an endpoint. Quantitative features-activity relationships (QFARs) are calculated by the Monte Carlo technique for three distributions of data representing values associated with membrane damage into the training and validation sets. The obtained models are characterized by the following average statistics: 0.78&lt;r2 training&lt;0.92 and 0.67&lt;r2 validation&lt;0.83. •Nanoparticles (NPs) are represented by codes of physicochemical features.•Two kinds of NPs are examined TiO2 and ZnO.•Optimal descriptors were used to build up a predictive model for membrane damage.•The optimal descriptor is a mathematical function of physicochemical NPs features.•The statistical quality of the model is quite good. © 2014 Elsevier Inc.},
note = {cited By 4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova20141171,
title = {Optimal descriptors as a tool to predict the thermal decomposition of polymers},
author = { A.P.a Toropova and A.A.a Toropov and V.O.b Kudyshkin and D.c Leszczynska and J.d Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897443954&amp;partnerID=40&amp;md5=b6c8bd17b53cc9104a316258a74a18ab},
doi = {10.1007/s10910-014-0323-3},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Mathematical Chemistry},
volume = {52},
number = {5},
pages = {1171-1181},
abstract = {Quantitative structure-property relationship for the thermal decomposition of polymers is suggested. The data on architecture of monomers is used to represent polymers. The structures of monomers are represented by simplified molecular input-line entry system. The average statistical quality of the suggested quantitative structure-property relationships for prediction of molar thermal decomposition function Yd,1/2 is the following: r2 = 0.970 ± 0.01 and RMSE = 4.71 ± 1.01 (K × kg × mol-1). © 2014 Springer International Publishing Switzerland.},
note = {cited By 2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Paytakov2014,
title = {Homodimers of cytosine and 1-methylcytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents},
author = { G.a Paytakov and L.b Gorb and A.b Stepanyugin and S.b Samiylenko and D.b Hovorun and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893864841&amp;partnerID=40&amp;md5=576ea549ee803e97183a516865f4c995},
doi = {10.1007/s00894-014-2115-x},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Molecular Modeling},
volume = {20},
number = {3},
abstract = {Dimers of cytosine and its N1-methylated counterpart were investigated in gas-phase and in various solvents including chloroform, dimethylsulfoxide, and water. The studies were performed at DFT/M06-2X/6-31+G(d, p) level of theory. Relative stabilities of tautomers of cytosine solvated explicitly by a small number of solvent molecules were evaluated. Further solvation effect calculations for homodimers were carried out with conductor-like polarizable continuum model (CPCM). H-NMR shifts and IR frequencies for optimized structures were calculated and compared with available experimental data. © 2014 Springer-Verlag.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Leszczynski2014283,
title = {Shutting down a working vivarium for decontamination},
author = { J. Leszczynski and M. Wallace and J. Tackett and U. Jiron and J. Collins and C. Warder and L. Richardson and L. Bell and C. Russell},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904884188&amp;partnerID=40&amp;md5=374bb70fac77f9a66c8dbd20cda3bc30},
doi = {10.1038/laban.567},
year  = {2014},
date = {2014-01-01},
journal = {Lab Animal},
volume = {43},
number = {8},
pages = {283-290},
abstract = {Handling a rodent disease outbreak in a facility can be a challenge. After the University of Colorado Denver Office of Laboratory Animal Resources enhanced its sentinel monitoring program, > 90% of the animal colonies housed in a vivarium at the Anschutz Medical Campus (with an area of 50,000 net ft 2), serving the labs of > 250 principal investigators, tested positive for multiple infective agents including mouse parvovirus, fur mites, pinworms and epizootic diarrhea of infant mice. The authors detail the process by which they planned and executed a shutdown and a decontamination of the facility, which involved the rederivation or cryopreservation of > 400 unique genetically modified mouse lines. The authors discuss the aspects of the project that were successful as well as those that could have been improved.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Sviatenko2014239,
title = {Interaction of 2'-deoxyguanosine with cis-2-butene-1,4-dial: Computational approach to analysis of multistep chemical reactions},
author = { L.K.a b Sviatenko and L.G.a c Gorb and D.M.c Hovorun and J.a Leszczynski},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84903581849&amp;partnerID=40&amp;md5=f3548d3b7e48d5e7a65160916e9a32f0},
doi = {10.7124/bc.00089C},
year  = {2014},
date = {2014-01-01},
journal = {Biopolymers and Cell},
volume = {30},
number = {3},
pages = {239-246},
abstract = {cis-2-Butene-1,4-dial represents a microsomal metabolite of furan, an industrially important chemical found in cigarette smoke, air pollution, and also in canned or jarred food. It is expected to be a human carcinogen. Aim. Investigation of an effect of cis-2-butene-1,4-dial on the 2'-deoxyguanosine which is a model of DNA site. Methods. Optimization of reaction species molecular structures, spectral parameters and Gibbs free energy calculations were performed using Gaussian09 program. Systems of differential equations for kinetics generation were solved using Mathcad15 program. Results. The predicted mechanism of the reaction of cis-2-butene-1,4- dial with 2'-deoxyguanosine consists of four-step process formation of four diastereomeric primary adducts and further base-mediated five-step transformation of the primary adducts to the secondary one. The reaction kinetics, which allows defining the concentration change of any reaction species was calculated. Conclusions. Under physiological conditions the interaction between cis-2-butene-1,4-dial and 2'-deoxyguanosine leads to the formation of a stable adduct which could be responsible for the furan genotoxicity. © Institute of Molecular Biology and Genetics, NAS of Ukraine, 2014.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Turabekova2014,
title = {Immunotoxicity of nanoparticles: a computational study suggests that CNTs and C60 fullerenes might be recognized as pathogens by Toll-like receptors.},
author = { M Turabekova and B Rasulev and M Theodore and J Jackman and D Leszczynska and J Leszczynski},
url = {http://pubs.rsc.org/en/content/articlehtml/2014/nr/c3nr05772k},
doi = {10.1039/c3nr05772k},
issn = {2040-3372},
year  = {2014},
date = {2014-01-01},
journal = {Nanoscale},
volume = {6},
number = {7},
pages = {3488--95},
abstract = {Over the last decade, a great deal of attention has been devoted to study the inflammatory response upon exposure to multi/single-walled carbon nanotubes (CNTs) and different fullerene derivatives. In particular, carbon nanoparticles are reported to provoke substantial inflammation in alveolar and bronchial epithelial cells, epidermal keratinocytes, cultured monocyte-macrophage cells, etc. We suggest a hypothetical model providing the potential mechanistic explanation for immune and inflammatory responses observed upon exposure to carbon nanoparticles. Specifically, we performed a theoretical study to analyze CNT and C60 fullerene interactions with the available X-ray structures of Toll-like receptors (TLRs) homo- and hetero-dimer extracellular domains. This assumption was based on the fact that similar to the known TLR ligands both CNTs and fullerenes induce, in cells, the secretion of certain inflammatory protein mediators, such as interleukins and chemokines. These proteins are observed within inflammation downstream processes resulted from the ligand molecule dependent inhibition or activation of TLR-induced signal transduction. Our computational studies have shown that the internal hydrophobic pockets of some TLRs might be capable of binding small-sized carbon nanostructures (5,5 armchair SWCNTs containing 11 carbon atom layers and C60 fullerene). High binding scores and minor structural alterations induced in TLR ectodomains upon binding C60 and CNTs further supported our hypothesis. Additionally, the proposed hypothesis is strengthened by the indirect experimental findings indicating that CNTs and fullerenes induce an excessive expression of specific cytokines and chemokines (i.e. IL-8 and MCP1).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2014,
title = {Optimal descriptors as a tool to predict the thermal decomposition of polymers},
author = { Alla P. Toropova and Andrey A. Toropov and Valentin O. Kudyshkin and Danuta Leszczynska and Jerzy Leszczynski},
doi = {10.1007/s10910-014-0323-3},
issn = {02599791},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Mathematical Chemistry},
volume = {52},
number = {5},
pages = {1171--1181},
keywords = {Monte Carlo method, Polymer, QSPR, Thermal decomposition},
pubstate = {published},
tppubtype = {article}
}
@article{Toropov2014,
title = {Comprehension of drug toxicity: Software and databases},
author = { Andrey A. Toropov and Alla P. Toropova and Ivan Raska and Danuta Leszczynska and Jerzy Leszczynski},
doi = {10.1016/j.compbiomed.2013.11.013},
issn = {00104825},
year  = {2014},
date = {2014-01-01},
journal = {Computers in Biology and Medicine},
volume = {45},
number = {1},
pages = {20--25},
abstract = {Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool (in silico) to rapidly predict various endpoints in general, and drug toxicity in particular. However, this dynamic evolution of experimental data (expansion of existing experimental data on drugs toxicity) leads to the problem of critical estimation of the data. The carcinogenicity, mutagenicity, liver effects and cardiac toxicity should be evaluated as the most important aspects of the drug toxicity. The toxicity is a multidimensional phenomenon. It is apparent that the main reasons for the increase in applications of in silico prediction of toxicity include the following: (i) the need to reduce animal testing; (ii) computational models provide reliable toxicity prediction; (iii) development of legislation that is related to use of new substances; (iv) filling data gaps; (v) reduction of cost and time; (vi) designing of new compounds; (vii) advancement of understanding of biology and chemistry. This mini-review provides analysis of existing databases and software which are necessary for use of robust computational assessments and robust prediction of potential drug toxicities by means of in silico methods. © 2013 Elsevier Ltd.},
keywords = {Computational toxicology, Drug toxicity, In silico methods, In silico toxicology, QSAR},
pubstate = {published},
tppubtype = {article}
}
@article{Toropova2014a,
title = {Optimal descriptor as a translator of eclectic information into the prediction of membrane damage: The case of a group of ZnO and TiO2 nanoparticles},
author = { Alla P. Toropova and Andrey A. Toropov and Emilio Benfenati and Tomasz Puzyn and Danuta Leszczynska and Jerzy Leszczynski},
doi = {10.1016/j.ecoenv.2014.07.005},
issn = {10902414},
year  = {2014},
date = {2014-01-01},
journal = {Ecotoxicology and Environmental Safety},
volume = {108},
pages = {203--209},
abstract = {The development of quantitative structure-activity relationships for nanomaterials needs representation of molecular structure of extremely complex molecular systems. Obviously, various characteristics of nanomaterial could impact associated biochemical endpoints. Following features of TiO2 and ZnO nanoparticles (n=42) are considered here: (i) engineered size (nm); (ii) size in water suspension (nm); (iii) size in phosphate buffered saline (PBS, nm); (iv) concentration (mg/L); and (v) zeta potential (mV). The damage to cellular membranes (units/L) is selected as an endpoint. Quantitative features-activity relationships (QFARs) are calculated by the Monte Carlo technique for three distributions of data representing values associated with membrane damage into the training and validation sets. The obtained models are characterized by the following average statistics: 0.78<r2 training<0.92 and 0.67<r2 validation<0.83. •Nanoparticles (NPs) are represented by codes of physicochemical features.•Two kinds of NPs are examined TiO2 and ZnO.•Optimal descriptors were used to build up a predictive model for membrane damage.•The optimal descriptor is a mathematical function of physicochemical NPs features.•The statistical quality of the model is quite good. © 2014 Elsevier Inc.},
keywords = {Membrane damage, Monte Carlo method, Nanoparticle, QFAR, QSAR},
pubstate = {published},
tppubtype = {article}
}
@article{Velizhanin2014,
title = {Exciton-plasmaritons in graphene/semiconductor structures},
author = { Kirill A. Velizhanin and Tigran V. Shahbazyan},
doi = {10.1103/PhysRevB.90.085403},
issn = {1550235X},
year  = {2014},
date = {2014-01-01},
journal = {Physical Review B - Condensed Matter and Materials Physics},
volume = {90},
number = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Goupalov2014,
title = {Crystal structure anisotropy explains anomalous elastic properties of nanorods},
author = { Serguei V. Goupalov},
doi = {10.1021/nl404837e},
issn = {15306992},
year  = {2014},
date = {2014-01-01},
journal = {Nano Letters},
volume = {14},
number = {3},
pages = {1590--1595},
abstract = {It is demonstrated that the frequency of the extensional vibrational mode of a nanorod made of an elastically anisotropic crystalline material deviates widely from the predictions of the theories based on the analysis of the long-wavelength limit. The dispersion relation for the fundamental extensional mode of a gold rod grown in the [100] direction is calculated and found to be in excellent agreement with experimental data obtained from the transient optical absorption measurements on gold nanorods. This explains an anomaly in the elastic properties of nanorods which was previously attributed to a 26% decrease in Young's modulus for nanorods compared to its bulk value. The developed approach allows one to investigate the role of the crystal structure anisotropy for acoustic phonons in nanorods and nanowires made of any metal or semiconductor material having cubic crystal structure.},
keywords = {acoustic vibrations, anisotropy, gold nanoparticles, Nanorods},
pubstate = {published},
tppubtype = {article}
}
@article{Fan20141109,
title = {Enhancing targeted tumor treatment by near IR light-activatable photodynamic-photothermal synergistic therapy},
author = { Z.a Fan and X.a Dai and Y.b Lu and E.a Yu and N.a Brahmbatt and N.a Carter and C.a Tchouwou and A.K.a Singh and Y.c Jones and H.a Yu and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897994827&amp;partnerID=40&amp;md5=c0bbaa8ffa96504172a783ccf84dc14b},
doi = {10.1021/mp4002816},
issn = {15438384},
year  = {2014},
date = {2014-01-01},
journal = {Molecular Pharmaceutics},
volume = {11},
number = {4},
pages = {1109-1116},
publisher = {American Chemical Society},
abstract = {For several decades, cancer has been one of the most life-threatening diseases. For enhancing anticancer efficiency with minimum side effects, combination therapy is envisioned. The current manuscript reports for the first time the development of a methylene blue (MB) bound nanoplatform, which is capable of delivering targeted diagnostic and combined synergistic photothermal and photodynamic treatment of cancer. Experimental data found that, once the nanoparticle binds with the target cell surface, it can detect LNCaP human prostate cancer cell selectively using fluorescence imaging. Our result shows that the therapeutic actions can be controlled with external NIR light. No cytotoxicity was observed in the absence of NIR light. Targeted photodynamic and photothermal treatment using 785 nm NIR light indicates that the multimodal treatment enhances the possibility of destroying LNCaP prostate cancer cells in vitro dramatically. We discuss the operating principle for the targeted imaging and possible mechanisms for combined therapeutic actions. Our experimental data show that NIR light activated combined therapy for cancer may become a highly effective treatment procedure in clinical settings. © 2014 American Chemical Society.},
note = {cited By 3},
keywords = {Cell Line, methylene blue; nanoparticle; methylene blue; nanomaterial; reactive oxygen metabolite, Tumor; Combined Modality Therapy; Humans; Male; Methylene Blue; Molecular Targeted Therapy; Nanostructures; Photochemotherapy; Phototherapy; Prostatic Neoplasms; Reactive Oxygen Species},
pubstate = {published},
tppubtype = {article}
}
@article{Demeritte20141017,
title = {Gold nanocage assemblies for selective second harmonic generation imaging of cancer cell},
author = { T.a Demeritte and Z.a Fan and S.S.a Sinha and J.b Duan and R.b Pachter and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84892610770&amp;partnerID=40&amp;md5=f05bc07fe5a3d77bc573375a1fa264d7},
doi = {10.1002/chem.201303306},
issn = {09476539},
year  = {2014},
date = {2014-01-01},
journal = {Chemistry - A European Journal},
volume = {20},
number = {4},
pages = {1017-1022},
abstract = {Second harmonic generation (SHG) imaging using near infrared laser light is the key to improving penetration depths, leading to biological understanding. Unfortunately, currently SHG imaging techniques have limited capability due to the poor signal-to-noise ratio, resulting from the low SHG efficiency of available dyes. Targeted tumor imaging over nontargeted tissues is also a challenge that needs to be overcome. Driven by this need, in this study, the development of two-photon SHG imaging of live cancer cell lines selectively by enhancement of the nonlinear optical response of gold nanocage assemblies is reported. Experimental results show that two-photon scattering intensity can be increased by few orders of magnitude by just developing nanoparticle self-assembly. Theoretical modeling indicates that the field enhancement values for the nanocage assemblies can explain, in part, the enhanced nonlinear optical properties. Our experimental data also show that A9 RNA aptamer conjugated gold nanocage assemblies can be used for targeted SHG imaging of the LNCaP prostate cancer cell line. Experimental results with the HaCaT normal skin cell lines show that bioconjugated nanocage-based assemblies demonstrate SHG imaging that is highly selective and will be able to distinguish targeted cancer cell lines from other nontargeted cell types. After optimization, this reported SHG imaging assay could have considerable application for biology. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
note = {cited By 6},
keywords = {article; chemistry; first hyperpolarizability; fluorescence microscopy; human; imaging agents; male; methodology; pathology; prostate; prostate tumor; self-assembly; SHG imaging; theoretical modeling; tumor cell line; ultrastructure, Cell culture; Gold; Imaging techniques; Infrared lasers; Nonlinear optics; Self assembly, Cell Line, Cells, diagnostic agent; gold; nanomaterial, First hyperpolarizabilities; Imaging agent; Nanoparticle self-assembly; Non-linear optical properties; Nonlinear optical response; Prostate cancer cells; Theoretical modeling; Two-photon scattering, first hyperpolarizability; imaging agents; self-assembly; SHG imaging; theoretical modeling, Fluorescence; Nanostructures; Prostate; Prostatic Neoplasms, Tumor; Gold; Humans; Male; Microscopy},
pubstate = {published},
tppubtype = {article}
}
@article{VirakaNellore2014257,
title = {Aptamer-conjugated theranostic hybrid graphene oxide with highly selective biosensing and combined therapy capability},
author = { B.P. Viraka Nellore and A. Pramanik and S.R. Chavva and S.S. Sinha and C. Robinson and Z. Fan and R. Kanchanapally and J. Grennell and I. Weaver and A.T. Hamme and P.C. Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84920950952&amp;partnerID=40&amp;md5=e9d4aba00ad2c20bcc0076b0dc178512},
doi = {10.1039/c4fd00074a},
issn = {13596640},
year  = {2014},
date = {2014-01-01},
journal = {Faraday discussions},
volume = {175},
pages = {257-271},
abstract = {Cancer is a life-threatening disease, which is rapidly becoming a global pandemic. Driven by this need, here we report for the first time an aptamer-conjugated theranostic magnetic hybrid graphene oxide-based assay for highly sensitive tumor cell detection from blood samples with combined therapy capability. AGE-aptamer-conjugated theranostic magnetic nanoparticle-attached hybrid graphene oxide was developed for highly selective detection of tumor cells from infected blood samples. Experimental data indicate that hybrid graphene can be used as a multicolor luminescence platform for selective imaging of G361 human malignant melanoma cancer cells. The reported results have also shown that indocyanine green (ICG)-bound AGE-aptamer-attached hybrid graphene oxide is capable of combined synergistic photothermal and photodynamic treatment of cancer. Targeted combined therapeutic treatment using 785 nm near-infrared (NIR) light indicates that the multimodal therapeutic treatment is highly effective for malignant melanoma cancer therapy. The reported data show that this aptamer-conjugated theranostic graphene oxide-based assay has exciting potential for improving cancer diagnosis and treatment.},
note = {cited By 1},
keywords = {aptamer; graphite; indocyanine green; oxide; photosensitizing agent, Aptamers, chemical structure; chemistry; diagnostic use; genetic procedures; human; Neoplasms; particle size; photochemotherapy; procedures; surface property; tumor cell line, Nucleotide; Biosensing Techniques; Cell Line, Tumor; Graphite; Humans; Indocyanine Green; Molecular Structure; Neoplasms; Oxides; Particle Size; Photochemotherapy; Photosensitizing Agents; Surface Properties},
pubstate = {published},
tppubtype = {article}
}
@article{Chavva20141252,
title = {Theranostic graphene oxide for prostate cancer detection and treatment},
author = { S.R.a Chavva and A.a Pramanik and B.P.V.a Nellore and S.S.a Sinha and B.b Yust and R.a Kanchanapally and Z.a Fan and R.A.a Crouch and A.K.c Singh and B.a Neyland and K.a Robinson and X.d Dai and D.b Sardar and Y.d Lu and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84918785359&amp;partnerID=40&amp;md5=fc5f44a48abca9f4da64b0c225b07be4},
doi = {10.1002/ppsc.201400143},
issn = {09340866},
year  = {2014},
date = {2014-01-01},
journal = {Particle and Particle Systems Characterization},
volume = {31},
number = {12},
pages = {1252-1259},
publisher = {Wiley-VCH Verlag},
abstract = {Although prostate cancer has been known for thousands of years, it is a major public health issue for men even in the 21st century. As the understanding of cancer biology and the signaling pathways advances, it is now well understood that the detection of prostate cancer circulating tumor cells (CTCs) is an invaluable tool for monitoring the progression and finding possible therapies. Driven by this need, in this article, the development of magnetic-nanoparticleattached theranostic graphene oxide (GO) is reported for targeted capture of prostate CTCs, accurate diagnosis, and combined therapeutic action of prostate cancer. Reported results show that anti-epithelial cell adhesion molecule (EpCAM) antibody and A9-aptamer-attached fl ower-shaped magnetic nanoparticle- bound 2D graphene can be used for selective capture and label-free multicolor luminescence imaging of LNCaP prostate cancer cell from infected blood. Experimental data demonstrate that indocyanine green (ICG)-bound A9-aptamer-attached theranostic GO is capable of external near IR 785 nm light-driven combined synergistic photothermal and photodynamic treatment of prostate cancer. Possible mechanisms for targeted capture, accurate analysis, and combined therapeutic actions have been discussed. Experimental results show that the theranostic GO can have enormous potential for real-life applications, once optimized properly in clinical settings. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
note = {cited By 1},
keywords = {Cell adhesion; Cell signaling; Cells; Diagnosis; Graphene; Nanomagnetics; Nanoparticles; Photodynamic therapy; Urology, Circulating tumor cells; Epithelial cell adhesion molecules; Magnetic nano-particles; Multicolor luminescences; Photodynamic treatments; Prostate cancer cells; Prostate cancer detection; Real-life applications, Diseases},
pubstate = {published},
tppubtype = {article}
}
@article{Fan2014357,
title = {Theranostic nanoplatforms for MRSA detection and destruction from whole blood},
author = { Z.a Fan and S.A.a Khan and X.a Dai and C.a Tchouwou and Y.b Lu and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896405309&amp;partnerID=40&amp;md5=269e8ccb57e16cb72cb1bcf41f6aa7b5},
doi = {10.1002/ppsc.201300169},
issn = {09340866},
year  = {2014},
date = {2014-01-01},
journal = {Particle and Particle Systems Characterization},
volume = {31},
number = {3},
pages = {357-364},
publisher = {Wiley-VCH Verlag},
abstract = {Bloodstream infection with methicillin-resistant Staphylococcus aureus (MRSA) and other drug-resistant bacteria kill several million people in the world every year. Detection of drug-resistant bacteria in the blood stream is clinically important to save lives. Driven by this need, multifunctional theranostic nanoplatforms have been developed for simultaneous targeted imaging and multimodal photodestruction of MRSA in a whole-blood sample. Experimental data for the whole-blood sample spiked with MRSA show that the theranostic nanoplatform can be used for fluorescence imaging after magnetic separation even in a 10-5:1 ratio. A targeted photodynamic and photothermal combined treatment shows that the multimodal treatment regime can dramatically enhance the possibility of destroying MRSA in vitro. Therefore, our developed theranostic nanoplatform have a great potential as a fluorescent marker and as a light absorber for combined therapy in clinical settings. The possible mechanisms and operating principles are discussed for targeted imaging and combined therapeutic actions using theranostic nanoplatform. Theranostic nanoplatforms have been developed that simultaneously deliver separation, enrichment, and diagnosis of methicillin-resistant Staphylococcus aureus (MRSA) from blood samples. They are capable of combined treatment in a single procedure. © 2013 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.},
note = {cited By 0},
keywords = {Bacteria; Fluorescence; Magnetic separation; Photodynamic therapy, Blood, combined therapeutic actions; Drug-resistant bacteria; Fluorescence imaging; Methicillin-resistant staphylococcus aureus; Operating principles; Photo-thermal; Photodynamic treatments; theranostic nanoplatform},
pubstate = {published},
tppubtype = {article}
}
@article{Yu201415763,
title = {Highly dispersible and charge-tunable magnetic Fe3O4nanoparticles: Facile fabrication and reversible binding to GO for efficient removal of dye pollutants},
author = { H.a Yu and Y.a Li and X.a Li and L.a Fan and S.b Yang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84907153074&amp;partnerID=40&amp;md5=70040d58b298359f2cc88c8461ab75df},
doi = {10.1039/c4ta03476g},
issn = {20507488},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Materials Chemistry A},
volume = {2},
number = {38},
pages = {15763-15767},
publisher = {Royal Society of Chemistry},
abstract = {The surface charge-tunable Fe3O4nanoparticles with high dispersibility and high superparamagnetism are fabricated by a facile electrochemical method in acetonitrile. These nanoparticles can reversibly bind to graphene oxides, which could be recycled and continually used for high-efficient removal of dye pollutants from water. This journal is © the Partner Organisations 2014.},
note = {cited By 0},
keywords = {Dispersibilities; Dye pollutants; ELectrochemical methods; Facile fabrication; Graphene oxides; Reversible binding, Nanoparticles, Water pollution},
pubstate = {published},
tppubtype = {article}
}
@article{Zhao201446,
title = {Fabrication of atomic single layer graphitic-C3N4 and its high performance of photocatalytic disinfection under visible light irradiation},
author = { H. Zhao and H. Yu and X. Quan and S. Chen and Y. Zhang and H. Zhao and H. Wang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893488799&amp;partnerID=40&amp;md5=3784d2855188e0576b295adc4c00700a},
doi = {10.1016/j.apcatb.2014.01.023},
issn = {09263373},
year  = {2014},
date = {2014-01-01},
journal = {Applied Catalysis B: Environmental},
volume = {152-153},
pages = {46-50},
abstract = {Photocatalytic disinfection over a high performance metal-free photocatalyst under visible light irradiation was studied. An atomic single layer g-C3N4 (SL g-C3N4) with the thickness of 0.5nm was fabricated by a two-step approach including thermal etching of bulk g-C3N4 into g-C3N4 nanosheets (g-C3N4 NS) and followed by an ultrasonic exfoliation of g-C3N4 NS. The performance of photocatalytic disinfection was investigated by inactivation of Escherichia coli. Under the visible light irradiation, 2×107cfumL-1 of E. coli could be killed completely over the SL g-C3N4 within 4h, whereas only about 3log and 5log of E. coli could be killed on bulk g-C3N4 and g-C3N4 NS under the same condition, respectively. Especially, the direct destruction of the E. coli cell wall was observed by TEM. The enhancement of photocatalytic efficiency of SL g-C3N4 was attributed to the low charge transfer resistance and efficient charge separation which were confirmed by electrochemical impedance spectroscopy and photo-current measurements. Owing to the excellent performance of SL g-C3N4, a visible light response and environmental friendly photocatalyst for disinfection was achieved. © 2014 Elsevier B.V.},
note = {cited By 20},
keywords = {Disinfection, Electrochemical impedance spectroscopy; Escherichia coli, G-C&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;N&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;; Metal free; Photocatalytic disinfections; Single layer; Visible light},
pubstate = {published},
tppubtype = {article}
}
@article{Zhao2014419,
title = {Preparation and characterization of vertically columnar boron doped diamond array electrode},
author = { Y. Zhao and H. Yu and X. Quan and S. Chen and H. Zhao and Y. Zhang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84898015804&amp;partnerID=40&amp;md5=4b7f3b7f57dce567c99267774105d862},
doi = {10.1016/j.apsusc.2014.03.017},
issn = {01694332},
year  = {2014},
date = {2014-01-01},
journal = {Applied Surface Science},
volume = {303},
pages = {419-424},
publisher = {Elsevier},
abstract = {A vertically columnar boron doped diamond (BDD) array electrode was fabricated by microwave plasma chemical vapor deposition. Observed by scanning electron microscopy, the fabricated samples were structured with aligned columns whose diameter and height was 8 μm and 12 μm, respectively, and the minimum interval of neighboring columns was 2 μm. The results of electrochemistry measurement showed that the columnar BDD array electrode possessed high oxygen evolution potential and low background current. Besides that, comparing with flat BDD electrode, the columnar BDD array electrode showed higher electrochemical activity (due to its inner active surface being up to 4.25 cm2), lower impedance of electric double layer, and especially enhanced electrical response signal (2.12 μA/μM, 4 times of flat BDD in glucose detection as a sample). These excellent performances may open the door for the BDD materials to be applied in wide areas including electrochemical detection, electrochemistry degradation, electrochemical synthesis, and so on. © 2014 Elsevier B.V.},
note = {cited By 2},
keywords = {Array-electrode; Electric double layer; Electrical response; Electrochemical activities; ELectrochemical detection; Electrochemical synthesis; Electrochemistry measurements; Microwave plasma chemical vapor depositions, Chemical vapor deposition; Electrochemistry; Scanning electron microscopy, Electrochemical electrodes},
pubstate = {published},
tppubtype = {article}
}
@article{Shu2014630,
title = {Selective catalytic reaction of NOx with NH3 over Ce-Fe/TiO2-loaded wire-mesh honeycomb: Resistance to SO2 poisoning},
author = { Y.a b Shu and T.a b Aikebaier and X.a b Quan and S.a b Chen and H.a b Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893188375&amp;partnerID=40&amp;md5=6a5292be1df67edeea728df23aa4327c},
doi = {10.1016/j.apcatb.2014.01.008},
issn = {09263373},
year  = {2014},
date = {2014-01-01},
journal = {Applied Catalysis B: Environmental},
volume = {150-151},
pages = {630-635},
abstract = {Ce-Fe/TiO2/Al2O3/wire-mesh honeycomb catalyst (Ce-Fe/WMH) exhibited a high activity for the selective catalytic reduction (SCR) of NOx in SO2-containing gases. Analysis of fresh and spent catalysts by XRD, BET, XPS, TG and FTIR indicated that Ce sites were sulfated preferentially over Ce-Fe/WMH during the SCR reaction in the presence of SO2, which could increase the amount of surface active oxygen species. On the other hand, the formation of surface hydroxyls due to the hydration of SO4 2- could supply more Br\onsted acid sites to adsorb NH3 in the form of NH4 +. These two factors played significant roles in the good SO2 durability of Ce-Fe/WMH. In addition, the sulfation of CeO2 on catalyst surface might approach a stable state upon certain amount of SO2 in reactant gas. The reaction mechanism study showed that only Eley-Rideal reaction pathway between ionic NH4 +, coordinated NH3 and gaseous NO dominated in the reaction; the Langmuir-Hinshelwood reaction pathway was cut off by the sulfation, resulting in the rapid decrease of NOx conversion in the early period of SCR reaction in the presence of SO2. © 2014 Elsevier B.V.},
note = {cited By 6},
keywords = {Catalysis; Catalysts; Coordination reactions; Honeycomb structures; Ionization of gases; Sulfur dioxide; Thyristors; Wire, Catalyst surfaces; Honeycomb catalysts; Langmuir-Hinshelwood; Reaction mechanism; Reaction pathways; Resistance to SO; Selective catalytic reactions; Wire-mesh honeycomb, Selective catalytic reduction},
pubstate = {published},
tppubtype = {article}
}
@article{Fan20141109b,
title = {Enhancing targeted tumor treatment by near IR light-activatable photodynamic-photothermal synergistic therapy},
author = { Z.a Fan and X.a Dai and Y.b Lu and E.a Yu and N.a Brahmbatt and N.a Carter and C.a Tchouwou and A.K.a Singh and Y.c Jones and H.a Yu and P.C.a Ray},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897994827&amp;partnerID=40&amp;md5=c0bbaa8ffa96504172a783ccf84dc14b},
doi = {10.1021/mp4002816},
issn = {15438384},
year  = {2014},
date = {2014-01-01},
journal = {Molecular Pharmaceutics},
volume = {11},
number = {4},
pages = {1109-1116},
publisher = {American Chemical Society},
abstract = {For several decades, cancer has been one of the most life-threatening diseases. For enhancing anticancer efficiency with minimum side effects, combination therapy is envisioned. The current manuscript reports for the first time the development of a methylene blue (MB) bound nanoplatform, which is capable of delivering targeted diagnostic and combined synergistic photothermal and photodynamic treatment of cancer. Experimental data found that, once the nanoparticle binds with the target cell surface, it can detect LNCaP human prostate cancer cell selectively using fluorescence imaging. Our result shows that the therapeutic actions can be controlled with external NIR light. No cytotoxicity was observed in the absence of NIR light. Targeted photodynamic and photothermal treatment using 785 nm NIR light indicates that the multimodal treatment enhances the possibility of destroying LNCaP prostate cancer cells in vitro dramatically. We discuss the operating principle for the targeted imaging and possible mechanisms for combined therapeutic actions. Our experimental data show that NIR light activated combined therapy for cancer may become a highly effective treatment procedure in clinical settings. © 2014 American Chemical Society.},
note = {cited By 3},
keywords = {Cell Line, methylene blue; nanoparticle; methylene blue; nanomaterial; reactive oxygen metabolite, Tumor; Combined Modality Therapy; Humans; Male; Methylene Blue; Molecular Targeted Therapy; Nanostructures; Photochemotherapy; Phototherapy; Prostatic Neoplasms; Reactive Oxygen Species},
pubstate = {published},
tppubtype = {article}
}
@article{Yu2014180,
title = {Electrocatalytic debromination of BDE-47 at palladized graphene electrode},
author = { H. Yu and B. Ma and S. Chen and Q. Zhao and X. Quan and S. Afzal},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84892434968&amp;partnerID=40&amp;md5=daced96c91f32230aef3cb59dd9b52ea},
doi = {10.1007/s11783-013-0552-x},
issn = {20952201},
year  = {2014},
date = {2014-01-01},
journal = {Frontiers of Environmental Science and Engineering},
volume = {8},
number = {2},
pages = {180-187},
abstract = {Graphene electrodes (Ti/Gr) were prepared by depositing Gr sheets on Ti substrate, followed by an annealing process for enhancing the adhesion strength. Electrochemical impedance spectroscopies and X-ray diffraction patterns displayed that the electrochemical behavior of Ti/Gr electrodes can be improved due to the generation of TiO2 layer at Ti-Gr interface during the annealing process. The palladized Gr electrodes (Ti/Gr/Pd) were prepared by electrochemical depositing Pd nanoparticles on Gr sheets. The debromination ability of Ti/Gr/Pd electrodes was investigated using BDE-47 as a target pollutant with various bias potentials. The results indicated that the BDE-47 degradation rates on Ti/Gr/Pd electrodes increased with the negative bias potentials from 0 V to -0.5 V (vs. SCE). Almost all of the BDE-47 was removed in the debromination reaction on the Ti/Gr/Pd electrode at -0.5 V for 3 h, and the main product was diphenyl ethers, meaning it is promising to debrominate completely using the Ti/Gr/Pd electrode. Although the debromination rate was slightly slower at -0.3 V than that under -0.5 V, the current efficiency at -0.3 V was higher, because the electrical current acted mostly on BDE-47 rather than on water. © 2014 Higher Education Press and Springer-Verlag Berlin Heidelberg.},
note = {cited By 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Yu20143457,
title = {Electrochemical preparation of N-doped cobalt oxide nanoparticles with high electrocatalytic activity for the oxygen-reduction reaction},
author = { H.a Yu and Y.a Li and X.a Li and L.a Fan and S.b Yang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896402435&amp;partnerID=40&amp;md5=32d522993b3531eb61ca91cce32dafe9},
doi = {10.1002/chem.201303814},
issn = {09476539},
year  = {2014},
date = {2014-01-01},
journal = {Chemistry - A European Journal},
volume = {20},
number = {12},
pages = {3457-3462},
publisher = {Wiley-VCH Verlag},
abstract = {Nitrogen-doped CoO (N-CoO) nanoparticles with high electrocatalytic activity for the oxygen-reduction reaction (ORR) were fabricated by electrochemical reduction of CoCl2 in acetonitrile solution at cathodic potentials. The initially generated, highly reactive nitrogen-doped Co nanoparticles were readily oxidized to N-CoO nanoparticles in air. In contrast to their N-free counterparts (CoO or Co3O4), N-CoO nanoparticles with a N content of about 4.6 % exhibit remarkable ORR electrocatalytic activity, stability, and immunity to methanol crossover in an alkaline medium. The Co-Nx active sites in the CoO nanoparticles are held responsible for the high ORR activity. This work opens a new path for the preparation of nitrogen-doped transition metal oxide nanomaterials, which are promising electrocatalysts for fuel cells. © 2014 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.},
note = {cited By 4},
keywords = {Acetonitrile solutions; Cathodic potentials; Cobalt oxide nanoparticles; Electrocatalytic activity; Electrochemical preparation; Electrochemical reductions; Oxygen reduction reaction; Transition-metal oxides, Cobalt compounds; Doping (additives); Electrocatalysis; Electrocatalysts; Electrochemistry; Electrolytic reduction; Oxygen, Nanoparticles},
pubstate = {published},
tppubtype = {article}
}
@article{Li20142888,
title = {Fabrication of graphene wrapped ZnIn2S4 microspheres heterojunction with enhanced interfacial contact and its improved photocatalytic performance},
author = { H. Li and H. Yu and S. Chen and H. Zhao and Y. Zhang and X. Quan},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84892908148&amp;partnerID=40&amp;md5=5ad9df2eb49114f9a2c0b36456bfc687},
doi = {10.1039/c3dt52820k},
issn = {14779226},
year  = {2014},
date = {2014-01-01},
journal = {Dalton Transactions},
volume = {43},
number = {7},
pages = {2888-2894},
abstract = {Due to their build-in electric fields locating at interfaces of different materials, heterojunctions have shown excellent carrier separation ability and received wide attention in photocatalysis and photovoltaics. In general, larger interface area and smoother carrier transfer pathway are favorable for heterojunctions to achieve larger active area of build-in electric fields and longer photogenerated charge lifetime, respectively, and sequentially the heterojunctions may show optimized separation ability. However, there is hardly any report about this topic. In this paper, we design a new heterojunction material where a graphene (Gr) layer is close-fitting as the surface of the ZnIn2S4 microspheres (ZnIn2S4@Gr) in virtue of the electrostatic interaction between the functional groups of GO and the amino groups of ZnIn2S4 microspheres. Benefiting from the effective contact of Gr and ZnIn2S4 at their interface as well as the superior charge transfer ability of Gr, this structure displays good photocatalytic capability. The kinetic constant of phenol degradation on ZnIn2S4@Gr was 3.03 h-1, which was 8.4-fold and 1.5-fold higher than those on ZnIn2S4 and ZnIn2S4-Gr composites, respectively. Furthermore, the excellent performance was stable according to the result of the consecutive cycling experiment. These experimental results demonstrated that the large interface area and smooth carrier transfer pathway were significant for heterojunction materials to provide better photogenerated charge separation properties. © 2014 The Royal Society of Chemistry.},
note = {cited By 8},
keywords = {Biodegradation; Electric fields; Functional groups; Graphene; Interfaces (materials); Microspheres, Carrier separation; Carrier transfer; Effective contact; Interfacial contact; Phenol degradation; Photocatalytic performance; Photogenerated charge; Separation ability, Heterojunctions},
pubstate = {published},
tppubtype = {article}
}
@article{Li2014227,
title = {Electrochemical preparation of color-tunable fluorescent carbon quantum dots},
author = { T. Li and Y. Li and L. Xiao and H. Yu and L. Fan},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84894739528&amp;partnerID=40&amp;md5=ab8b37cb3c8cd3bf56409acbe878cc1f},
doi = {10.6023/A13101036},
issn = {05677351},
year  = {2014},
date = {2014-01-01},
journal = {Acta Chimica Sinica},
volume = {72},
number = {2},
pages = {227-232},
abstract = {Carbon quantum dots have attracted much attention in the fields of bioimaging, biolabeling and drug delivery. Theoretical and experimental studies have shown that carbon quantum dots are expected to show unique optical properties due to their quantum confinement and edge effect. In this report, water-soluble and color-tunable fluorescent carbon dots were prepared by cyclic voltammetry (CV) in alkaline condition. The structure of the carbon dots was confirmed by means of transmission electron microscope (TEM), Raman spectrum and atomic force microscope (AFM). The finding shows that the carbon quantum dots have a uniform diameter around 19 nm, and are mainly consist of 1 to 4 layers of graphene with a mass of oxygen-containing functional groups. Their features and properties were characterized by photoluminescence spectra (PL), UV-visible spectroscopy (UV-vis), fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). The results indicated that the carbon quantum dots have two fluorescent emission peaks at 400 nm and 525 nm. The former peak was associated with the π-π conjugated system of carbon dots, which showed an excitation-wavelength dependent feature, while the latter peak was associated with n-π conjugated system of oxygen-containing functional groups, which remained unshifted when excited by different excitation wavelengths, suggesting a novel kind of fluorescent feature and mechanism different from those of previously reported carbon quantum dots depending on excitation wavelengths. The fluorescent color of carbon quantum dots could be controlled by the cycles of CV. As the increase of CV cycles, the relative content of oxygen-containing functional groups increased, leading to the decrease of the relative intensity of fluorescent peaks at 400 nm and the increase of the relative intensity of fluorescent peak at 525 nm; and the color of the fluorescent changes from blue to yellow. The color-tunable fluorescent carbon quantum dots showed a high water solubility and good photostability, which indicates that the carbon quantum dots might be used as a bioimaging marker in cell imaging. © 2014 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Zhang2014185,
title = {Nitrogen-doped diamond electrode shows high performance for electrochemical reduction of nitrobenzene},
author = { Q. Zhang and Y. Liu and S. Chen and X. Quan and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84890778710&amp;partnerID=40&amp;md5=c2d26365c0251b916e173b661a13a236},
doi = {10.1016/j.jhazmat.2013.11.065},
issn = {03043894},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Hazardous Materials},
volume = {265},
pages = {185-190},
publisher = {Elsevier},
abstract = {Effective electrode materials are critical to electrochemical reduction, which is a promising method to pre-treat anti-oxidative and bio-refractory wastewater. Herein, nitrogen-doped diamond (NDD) electrodes that possess superior electrocatalytic properties for reduction were fabricated by microwave-plasma-enhanced chemical vapor deposition technology. Nitrobenzene (NB) was chosen as the probe compound to investigate the material's electro-reduction activity. The effects of potential, electrolyte concentration and pH on NB reduction and aniline (AN) formation efficiencies were studied. NDD exhibited high electrocatalytic activity and selectivity for reduction of NB to AN. The NB removal efficiency and AN formation efficiency were 96.5% and 88.4% under optimal conditions, respectively; these values were 1.13 and 3.38 times higher than those of graphite electrodes. Coulombic efficiencies for NB removal and AN formation were 27.7% and 26.1%, respectively; these values were 4.70 and 16.6 times higher than those of graphite electrodes under identical conditions. LC-MS analysis revealed that the dominant reduction pathway on the NDD electrode was NB to phenylhydroxylamine (PHA) to AN. © 2013 Elsevier B.V.},
note = {cited By 1},
keywords = {analytic method; article; catalysis; concentration (parameters); electrochemical analysis; electrode; liquid chromatography; mass spectrometry; microwave plasma enhanced chemical vapor deposition technology; pH; surface property, Aniline formation; Electrocatalysis; Nitrobenzene reduction; Nitrogen-doped diamond, aniline; diamond; graphite; hydroxylamine; nitrobenzene; nitrogen; nitrogen doped diamond; unclassified drug, Aniline; Doping (additives); Efficiency; Electrocatalysis; Electrolytic reduction; Graphite electrodes; Nitrobenzene; Plasma enhanced chemical vapor deposition; Wastewater treatment, benzene; catalysis; diamond; electrochemistry; electrode; nitrogen; organic nitrogen compound; pollutant removal; reduction; wastewater, Catalysis; Diamond; Electrochemistry; Electrodes; Graphite; Nitrobenzenes; Nitrogen; Oxidation-Reduction; Waste Disposal, Chemical, Coulombic efficiency; Electrocatalytic activity; Electrocatalytic properties; Electrochemical reductions; Electrolyte concentration; Microwave plasma-enhanced chemical vapor deposition; Nitrogen-doped diamond; Removal efficiencies, Fluid; Water Pollutants, Niobium compounds},
pubstate = {published},
tppubtype = {article}
}
@article{Zou2014566,
title = {Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides},
author = { Y.a Zou and A.M.a Spokoyny and C.a Zhang and M.D.a Simon and H.b Yu and Y.-S.b Lin and B.L.a Pentelute},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84890815500&amp;partnerID=40&amp;md5=b56f1e124cd54e5be70728a11e48e05d},
doi = {10.1039/c3ob42168f},
issn = {14770520},
year  = {2014},
date = {2014-01-01},
journal = {Organic and Biomolecular Chemistry},
volume = {12},
number = {4},
pages = {566-573},
abstract = {Here we describe a general synthetic platform for side-chain macrocyclization of an unprotected peptide library based on the SNAr reaction between cysteine thiolates and a new generation of highly reactive perfluoroaromatic small molecule linkers. This strategy enabled us to simultaneously "scan" two cysteine residues positioned from i, i + 1 to i, i + 14 sites in a polypeptide, producing 98 macrocyclic products from reactions of 14 peptides with 7 linkers. A complementary reverse strategy was developed; cysteine residues within the polypeptide were first modified with non-bridging perfluoroaryl moieties and then commercially available dithiol linkers were used for macrocyclization. The highly convergent, site-independent, and modular nature of these two strategies coupled with the unique chemoselectivity of a SNAr transformation allows for the rapid diversity-oriented synthesis of hybrid macrocyclic peptide libraries with varied chemical and structural complexities. This journal is © The Royal Society of Chemistry.},
note = {cited By 11},
keywords = {Amino acids; Chains; Peptides, article; chemical structure; chemistry; cyclization; peptide library; synthesis, Chemo-selectivity; Cysteine residues; Dithiol linkers; Diversity-oriented synthesis; Macro-cyclization; Macrocyclic products; Peptide library; Structural complexity, Cyclization; Macrocyclic Compounds; Molecular Structure; Peptide Library; Peptides, macrocyclic compound; peptide, Polypeptides},
pubstate = {published},
tppubtype = {article}
}
@article{Fu201464,
title = {Mechanisms of nanotoxicity: Generation of reactive oxygen species},
author = { P.P.a Fu and Q.a Xia and H.-M.b Hwang and P.C.c Ray and H.c Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901621691&amp;partnerID=40&amp;md5=87b6d168c775ae66fdc6767a8313bfbb},
doi = {10.1016/j.jfda.2014.01.005},
issn = {10219498},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {64-75},
publisher = {National Laboratories of Foods and Drugs},
abstract = {Nanotechnology is a rapidly developing field in the 21st century, and the commercial use of nanomaterials for novel applications is increasing exponentially. To date, the scientific basis for the cytotoxicity and genotoxicity of most manufactured nanomaterials are not understood. The mechanisms underlying the toxicity of nanomaterials have recently been studied intensively. An important mechanism of nanotoxicity is the generation of reactive oxygen species (ROS). Overproduction of ROS can induce oxidative stress, resulting in cells failing to maintain normal physiological redox-regulated functions. This in turn leads to DNA damage, unregulated cell signaling, change in cell motility, cytotoxicity, apoptosis, and cancer initiation. There are critical determinants that can affect the generation of ROS. These critical determinants, discussed briefly here, include: size, shape, particle surface, surface positive charges, surface-containing groups, particle dissolution, metal ion release from nanometals and nanometal oxides, UV light activation, aggregation, mode of interaction with cells, inflammation, and pH of the medium. Copyright © 2014, Food and Drug Administration, Taiwan. Published by Elsevier Taiwan LLC. All rights reserved.},
note = {cited By 16},
keywords = {Animals; DNA Damage; Humans; Nanostructures; Nanotechnology; Oxidation-Reduction; Oxidative Stress; Reactive Oxygen Species, free radical; hydroxyl radical; metal ion; metal oxide; nanomaterial; reactive oxygen metabolite; superoxide; nanomaterial; reactive oxygen metabolite},
pubstate = {published},
tppubtype = {article}
}
@article{Yedjou2014605,
title = {Basic apoptotic and necrotic cell death in human liver carcinoma (HepG2) cells induced by synthetic azamacrocycle},
author = { C.G.a Yedjou and M.A.b Saeed and M.A.b Hossain and W.a Dorsey and H.b Yu and P.B.a Tchounwou},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84898849314&amp;partnerID=40&amp;md5=5f0e0ba288d181413b1d1f7ead0ab6f8},
doi = {10.1002/tox.21786},
issn = {15204081},
year  = {2014},
date = {2014-01-01},
journal = {Environmental Toxicology},
volume = {29},
number = {6},
pages = {605-611},
publisher = {John Wiley and Sons Inc.},
abstract = {Treatment of diseases with synthetic materials has been an aspiration of mankind since the dawn of human development. In this research, three complex compounds of azamacrocycle (TD1, TD2, and TD3) were synthesized, and experiments were conducted to determine whether their toxicity to human liver carcinoma (HepG2) cells is associated with apoptotic and/or necrotic cell death. Cell survival was determined by MTT assay. Apoptosis and necrosis were measured by annexin V FITC/PI assay using the flow cytometry and by propidium iodide (PI) assay using the cellometer vision. HepG2 cells were treated with different concentrations of azamacrocycles for 48 h. Results from MTT assay indicated that all the three azamacrocycles significantly (p &lt; 0.05) reduce cell viability in a dose-dependent manner, showing 48 h-LD50 values of about 37.97, 33.60, and 19.29 μM, for TD3, TD1 and TD2, respectively. Among the three compounds tested, TD2 showed the most pronounced cytotoxic activity against HepG2 cells, being about twofold more potent than TD3. The order of toxicity was TD2 &gt; TD1 &gt; TD3. Because TD2 exerted the most cytotoxic activity against HepG2 cells, it was used in the subsequent apoptosis and necrosis-related experiments. The flow cytometry assessment showed a strong dose-response relationship with regard to TD2 exposure and annexin V/PI positive cells. PI assay data indicated that TD2 exposure increased the proportion of fluorescence positive cells. Overall, our results indicate that azamacrocycle toxicity to HepG2 cells is associated with apoptotic and necrotic cell death resulting from phosphatidylserine externalization and loss of membrane integrity. © 2012 Wiley Periodicals, Inc.},
note = {cited By 1},
keywords = {Antibiotics; Cytotoxicity; Experiments; Flow cytometry; Toxicity, Antineoplastic Agents; Apoptosis; Carcinoma, apoptosis; azamacrocycle; cytotoxicity; HepG2 cells; necrosis, Azamacrocycle; Cytotoxic activities; Dose response relationships; Dose-dependent manner; Membrane integrity; Necrosis; Necrotic cell deaths; Synthetic materials, Cell death, Hepatocellular; Cell Survival; Flow Cytometry; Hep G2 Cells; Humans; Liver Neoplasms; Macrocyclic Compounds; Necrosis},
pubstate = {published},
tppubtype = {article}
}
@article{Wang201448912,
title = {Porous metal-organic framework MIL-100(Fe) as an efficient catalyst for the selective catalytic reduction of NOx with NH3},
author = { P.a Wang and H.a Zhao and H.b Sun and H.a Yu and S.a Chen and X.a Quan},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84907979400&amp;partnerID=40&amp;md5=89ac403a29e04151c0c4ee9d65bc0c1e},
doi = {10.1039/c4ra07028c},
issn = {20462069},
year  = {2014},
date = {2014-01-01},
journal = {RSC Advances},
volume = {4},
number = {90},
pages = {48912-48919},
publisher = {Royal Society of Chemistry},
abstract = {The development of an efficient catalyst with excellent catalytic activity and high SO2 resistance at low temperatures (&lt;300 °C) remains a challenge for the selective catalytic reduction (SCR) reaction. In this study, we report that MIL-100(Fe) is an alternative catalyst for the SCR of NOx with NH3, and it exhibits higher NOx conversion than the conventional V2O5-WO3/TiO2 catalyst below 300°C. In addition, the effect of H2O and SO2 on the catalytic activity is reversible, and NOx conversions are recovered after ceasing the flow of SO2 and H2O. In situ diffuse reflectance infrared Fourier transform spectroscopy results indicate that both ionic NH4 + and coordinated NH3 existed on MIL-100(Fe) and that the reaction primarily followed the Langmuir-Hinshelwood mechanism, in which NH4 + reacts with NO2 formed from NO oxidation over iron sites. Furthermore, the redox properties of the iron species (Fe3+ + e- 虠 Fe2+) could play a significant role in activating the reactants. © the Partner Organisations 2014.},
note = {cited By 0},
keywords = {Efficient catalysts; Metal organic framework; Mil 100(Fe); Selective catalytic reduction of NO},
pubstate = {published},
tppubtype = {article}
}
@article{McShan2014116,
title = {Molecular toxicity mechanism of nanosilver},
author = { D. McShan and P.C. Ray and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901604308&amp;partnerID=40&amp;md5=3920f0d07cd1fea44cf52f720fbdea46},
doi = {10.1016/j.jfda.2014.01.010},
issn = {10219498},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {116-127},
publisher = {National Laboratories of Foods and Drugs},
abstract = {Silver is an ancient antibiotic that has found many new uses due to its unique properties on the nanoscale. Due to its presence in many consumer products, the toxicity of nanosilver has become a hot topic. This review summarizes recent advances, particularly the molecular mechanism of nanosilver toxicity. The surface of nanosilver can easily be oxidized by O2 and other molecules in the environmental and biological systems leading to the release of Ag+, a known toxic ion. Therefore, nanosilver toxicity is closely related to the release of Ag+. In fact, it is difficult to determine what portion of the toxicity is from the nano-form and what is from the ionic form. The surface oxidation rate is closely related to the nanosilver surface coating, coexisting molecules, especially thiol-containing compounds, lighting conditions, and the interaction of nanosilver with nucleic acids, lipid molecules, and proteins in a biological system. Nanosilver has been shown to penetrate the cell and become internalized. Thus, nanosilver often acts as a source of Ag+ inside the cell. One of the main mechanisms of toxicity is that it causes oxidative stress through the generation of reactive oxygen species and causes damage to cellular components including DNA damage, activation of antioxidant enzymes, depletion of antioxidant molecules (e.g., glutathione), binding and disabling of proteins, and damage to the cell membrane. Several major questions remain to be answered: (1) the toxic contribution from the ionic form versus the nano-form; (2) key enzymes and signaling pathways responsible for the toxicity; and (3) effect of coexisting molecules on the toxicity and its relationship to surface coating. Copyright © 2014, Food and Drug Administration, Taiwan.},
note = {cited By 21},
keywords = {Animals; Cell Membrane; DNA Damage; DNA Repair; Humans; Metal Nanoparticles; Oxidation-Reduction; Oxidative Stress; Reactive Oxygen Species; Silver, glutathione; lipid; nanomaterial; nucleic acid; reactive oxygen metabolite; silver; silver nanoparticle; thiol derivative; metal nanoparticle; reactive oxygen metabolite; silver},
pubstate = {published},
tppubtype = {article}
}
@article{McShan2014489,
title = {DNA damage in human skin keratinocytes caused by multiwalled carbon nanotubes with carboxylate functionalization},
author = { D. McShan and H. Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84903547010&amp;partnerID=40&amp;md5=ff059910d5ae431da734e9953be740dd},
doi = {10.1177/0748233712459914},
issn = {07482337},
year  = {2014},
date = {2014-01-01},
journal = {Toxicology and Industrial Health},
volume = {30},
number = {6},
pages = {489-498},
publisher = {SAGE Publications Ltd},
abstract = {Water-soluble carbon nanotubes have been found to be one of the most promising nanomaterials in biological- and biomedical-based applications. However, there have been major concerns on their ability to cause cellular and DNA damages upon exposure. In this work, we explore the toxic effects of three multiwalled carbon nanotubes (MWCNTs: nonpurified, purified and carboxylate-functionalized) on human skin keratinocytes (HaCaT). Cytotoxicity tests using the conventional thiazolyl blue tetrazolium bromide (MTT) and the water-soluble tetrazolium (WST-1) assays for 0.5 or 24 h exposure to 20 μg/mL of MWCNTs show that all three caused minimum cytotoxicity that is generally not statistically significant. Assessment of direct and oxidative DNA damages using both alkaline Comet assay and formamidopyrimidine DNA glycosylase-modified Comet assay reveals that the treatment with 20 μg/mL of MWCNTs does not cause significant direct DNA damages, but causes great amount of oxidative DNA damages in HaCaT cells. The oxidative DNA damage reaches the maximum amount at 4 h of incubation in Dulbecco's minimum essential medium, but decreases to the minimum at 8 and 24 h of incubation, indicating repair of the oxidative damages by the intrinsic DNA repair mechanism of the cells. © The Author(s) 2012.},
note = {cited By 1},
keywords = {3 (4, 5 dimethyl 2 thiazolyl) 2, 5 diphenyltetrazolium bromide; carboxylic acid; DNA formamidopyrimidine glycosylase; multi walled nanotube, article; cell membrane; cell viability; comet assay; controlled study; DNA damage; DNA repair; drug cytotoxicity; human; human cell; human tissue; keratinocyte; oxidative stress; statistical significance},
pubstate = {published},
tppubtype = {article}
}
@article{Gardner2014347,
title = {Theoretical study of tautomeric and ionizing effects of guanine, cytosine, and their methyl derivatives},
author = { N.a Gardner and D.b Magers and G.a Hill Jr.},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84897663338&amp;partnerID=40&amp;md5=00abc8befc602b1e8b7c761ee7b9e110},
doi = {10.1007/s11224-013-0301-6},
issn = {10400400},
year  = {2014},
date = {2014-01-01},
journal = {Structural Chemistry},
volume = {25},
number = {1},
pages = {347-353},
abstract = {The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of guanine and cytosine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre- and post-translational effects of guanine and cytosine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory B3LYP functional accompanied with 6-311G (d,p), 6-311+G (d,p), and 6-311++G (df,pd) basis sets. Our results reveal that the cytosine tautomer has a higher EA and IP than the guanine tautomers. The higher EA suggest that an electron that attaches to the GC base pair would predominately attach to the cytosine instead of guanine. The higher IP would suggest that an electron that is removed from the GC base pair would be predominately removed from the guanine within the base pair. Understanding how tautomerization, ionization, and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases. © 2013 Springer Science+Business Media New York.},
note = {cited By 4},
keywords = {Ips},
pubstate = {published},
tppubtype = {article}
}
@article{Lewis20141678,
title = {One-electron redox properties of DNA nucleobases and common tautomers},
author = { K. Lewis and K. Copeland and G. Hill},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84912003742&amp;partnerID=40&amp;md5=962efd048090d734a1998a454a153dcd},
doi = {10.1002/qua.24745},
issn = {00207608},
year  = {2014},
date = {2014-01-01},
journal = {International Journal of Quantum Chemistry},
volume = {114},
number = {24},
pages = {1678-1684},
publisher = {John Wiley and Sons Inc.},
abstract = {The redox properties of DNA play an influential role in several important processes such as DNA mutation and the interaction of DNA with drugs. Structural changes in DNA nucleobases from its canonical form to its tautomeric forms can alter these properties and may lead to DNA mutation due to altered base-pairing properties. Experimental results for the standard value of DNA redox properties vary due to choice of methodology and solvent. Theoretical determination of these properties is helpful in pinpointing standard values but still vary depending on methodology and chosen experimental benchmark. However, it is of importance to identify the overall trend of electron mobility within DNA while providing reliable standard values for redox reactions. In this work, we present the results of theoretical calculations for redox properties. Using the thermodynamic cycle, we can approximate reliable values. We report the electron affinities, ionization potentials, and redox potential for the canonical DNA nucleobases and their rare tautomers. For each of these properties, we evaluate its overall trend to gain a greater understanding of the role that electron attachment and electron mobility have within the DNA strand. All calculations are computed at the M06-2X/ 6-3111G(d,p) level of theory. © 2014 Wiley Periodicals, Inc.},
note = {cited By 0},
keywords = {DNA, DNA mutation; Enol; Imine; In-silico; Keto; Oxidation potentials; Reduction potential; Tautomerizations, Electron affinity; Electron mobility; Electrons; Ionization potential; Nucleic acids; Redox reactions; Thermodynamic properties},
pubstate = {published},
tppubtype = {article}
}
@article{Li201440,
title = {The optimization of saccharification of desulfurated red seaweed-derived polysaccharides and analysis of their composition},
author = { X.a Li and Y.a Li and H.a Mou and Y.b Gao and H.c Hwang and P.a Wang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84886534321&amp;partnerID=40&amp;md5=4f2fb93fe586e43a2dfb625d0afbd564},
doi = {10.1080/10826068.2013.791628},
issn = {10826068},
year  = {2014},
date = {2014-01-01},
journal = {Preparative Biochemistry and Biotechnology},
volume = {44},
number = {1},
pages = {40-55},
abstract = {Currently processes of ethanol production from desulfurated red seaweed derived polysaccharides (De-RSDP) are well established. However, the optimization of the enzymatic saccharification process has not been reported. In this study, De-RSDP from Kappaphycus alvarezii was subjected to saccharification by different enzymes, including pectinase, cellobiase, cellulase, and hemicellulase. The best saccharification enzyme was determined as pectinase. In order to obtain more reducing sugar (RS), the single-factor experiment followed by central composite rotatable design (CCD) was used to optimize the parameters for enzymatic hydrolysis. The optimal saccharification parameters of De-RSDP were 4400 U/g pectinase dosage, 96 hr, and 55.5°C, respectively, and the yield of RS reached 81.3%. Subsequently, the saccharification liquids of De-RSDP were isolated and purified with gel permeation chromatography (GPC) to separate saccharides with different molecular weights. Simultaneously, the composition of saccharification liquids was analyzed by 1-phenyl-3-methyl-5-pyrazolone high-pressure liquid chromatography (PMP-HPLC) and mass spectroscopy (MS). The result showed that the content is mainly composed of galactose (65.2%) with the average molecular mass in the fourth peak 181.1 Da. The saccharification liquids of De-RSDP inoculated with Saccharomyces cerevisiae L-4 for ethanol fermentation produced 0.3 g ethanol/g De-RSDP, which corresponded to 71.8% of the theoretical yield (0.38 g ethanol/g). Copyright © Taylor and Francis Group, LLC.},
note = {cited By 0},
keywords = {alcohol; glucosidase; polysaccharide; vegetable protein, article; chemistry; growth, development and aging; metabolism; red alga; Saccharomyces cerevisiae, Ethanol; Glucosidases; Plant Proteins; Polysaccharides; Rhodophyta; Saccharomyces cerevisiae},
pubstate = {published},
tppubtype = {article}
}
@article{Fu201464b,
title = {Mechanisms of nanotoxicity: Generation of reactive oxygen species},
author = { P.P.a Fu and Q.a Xia and H.-M.b Hwang and P.C.c Ray and H.c Yu},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901621691&amp;partnerID=40&amp;md5=87b6d168c775ae66fdc6767a8313bfbb},
doi = {10.1016/j.jfda.2014.01.005},
issn = {10219498},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {64-75},
publisher = {National Laboratories of Foods and Drugs},
abstract = {Nanotechnology is a rapidly developing field in the 21st century, and the commercial use of nanomaterials for novel applications is increasing exponentially. To date, the scientific basis for the cytotoxicity and genotoxicity of most manufactured nanomaterials are not understood. The mechanisms underlying the toxicity of nanomaterials have recently been studied intensively. An important mechanism of nanotoxicity is the generation of reactive oxygen species (ROS). Overproduction of ROS can induce oxidative stress, resulting in cells failing to maintain normal physiological redox-regulated functions. This in turn leads to DNA damage, unregulated cell signaling, change in cell motility, cytotoxicity, apoptosis, and cancer initiation. There are critical determinants that can affect the generation of ROS. These critical determinants, discussed briefly here, include: size, shape, particle surface, surface positive charges, surface-containing groups, particle dissolution, metal ion release from nanometals and nanometal oxides, UV light activation, aggregation, mode of interaction with cells, inflammation, and pH of the medium. Copyright © 2014, Food and Drug Administration, Taiwan. Published by Elsevier Taiwan LLC. All rights reserved.},
note = {cited By 16},
keywords = {Animals; DNA Damage; Humans; Nanostructures; Nanotechnology; Oxidation-Reduction; Oxidative Stress; Reactive Oxygen Species, free radical; hydroxyl radical; metal ion; metal oxide; nanomaterial; reactive oxygen metabolite; superoxide; nanomaterial; reactive oxygen metabolite},
pubstate = {published},
tppubtype = {article}
}
@article{He2014185,
title = {An in vivo study on the photo-enhanced toxicities of S-doped TiO 2 nanoparticles to zebrafish embryos (Danio rerio) in terms of malformation, mortality, rheotaxis dysfunction, and DNA damage},
author = { X.a He and W.G.a b Aker and H.-M.a Hwang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84905976063&amp;partnerID=40&amp;md5=6c85db88907922f3bf36e6084494d264},
doi = {10.3109/17435390.2013.874050},
issn = {17435390},
year  = {2014},
date = {2014-01-01},
journal = {Nanotoxicology},
volume = {8},
number = {SUPPL. 1},
pages = {185-195},
publisher = {Informa Healthcare},
abstract = {The role of light on the acute toxicities of S-doped and Sigma TiO 2 nanoparticles in zebrafish was studied. Metrics included mortality for both, and rheotaxis dysfunction and DNA damage for S-doped only. It was found that the acute toxicity of S-TiO2 nanoparticles was enhanced by simulated sunlight (SSL) irradiation (96-h LC50 of 116.56 ppm) and exceeded that of Sigma TiO2, which was essentially non-toxic. Behavioral disorder, in terms of rheotaxis, was significantly increased by treatment with S-TiO2 nanoparticles under SSL irradiation. In order to further understand its toxicity mechanism, we investigated hair cells in neuromasts of the posterior lateral line (PLL) using DASPEI staining. Significant hair cell damage was observed in the treated larvae. The Comet assay was employed to investigate the DNA damage, which might be responsible for the loss of hair cells. Production of the superoxide anion (O ·- 2), a major ROS generated by TiO2 nanoparticles, was assayed and used to postulate causative factors to account for these damages. Oxidative effects were most severe in the liver, heart, intestine, pancreatic duct, and pancreatic islet-results consistent with our earlier findings in the investigation of embryonic malformation. TEM micrographs, used to further investigate the fate of S-TiO2 nanoparticles at the cellular level, suggested receptor-mediated autophagy and vacuolization. Our findings validate the benefit of using the transparent zebrafish embryo as an in vivo model for evaluating photo-induced nanotoxicity. These results highlight the importance of conducting a systematic risk assessment in connection with the use of doped TiO2 nanoparticles in aquatic ecosystems. © 2014 Informa UK Ltd. All rights reserved.},
note = {cited By 3},
keywords = {Animals; DNA Damage; Embryo, Electron, nanoparticle; reactive oxygen metabolite; superoxide; titanium dioxide; titanium oxide nanoparticle; unclassified drug; metal nanoparticle; titanium; titanium dioxide, Nonmammalian; Metal Nanoparticles; Microscopy, Transmission; Spectrophotometry, Ultraviolet; Titanium; Zebrafish},
pubstate = {published},
tppubtype = {article}
}
@article{Quinones2014374,
title = {Effects of light energy and reducing agents on C60-mediated photosensitizing reactions},
author = { M.a Quinones and Y.b Zhang and P.a Riascos and H.-M.c Hwang and W.G.c Aker and X.c He and R.a b Gao},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896399009&amp;partnerID=40&amp;md5=b2cea6ee8b7840724cacec37d3aeef9f},
doi = {10.1111/php.12206},
issn = {00318655},
year  = {2014},
date = {2014-01-01},
journal = {Photochemistry and Photobiology},
volume = {90},
number = {2},
pages = {374-379},
publisher = {Blackwell Publishing Inc.},
abstract = {Many biomolecules contain photoactive reducing agents, such as reduced nicotinamide adenine dinucleotide (NADH) and 6-thioguanine (6-TG) incorporated into DNA through drug metabolism. These reducing agents may produce reactive oxygen species under UVA irradiation or act as electron donors in various media. The interactions of C60 fullerenes with biological reductants and light energy, especially via the Type-I electron-transfer mechanism, are not fully understood although these factors are often involved in toxicity assessments. The two reductants employed in this work were NADH for aqueous solutions and 6-TG for organic solvents. Using steady-state photolysis and electrochemical techniques, we showed that under visible light irradiation, the presence of reducing agents enhanced C60-mediated Type-I reactions that generate superoxide anion (O2 .-) at the expense of singlet oxygen (1O2) production. The quantum yield of O2 .- production upon visible light irradiation of C 60 is estimated below 0.2 in dipolar aprotic media, indicating that the majority of triplet C60 deactivate via Type-II pathway. Upon UVA irradiation, however, both C60 and NADH undergo photochemical reactions to produce O2 .-, which could lead to a possible synergistic toxicity effects. C60 photosensitization via Type-I pathway is not observed in the absence of reducing agents. The photosensitization pathways of C60 vary with the irradiation energy and reducing agents. C60/visible light-initiated Type-I reactions take place only in the presence of electron donors with the formation yield of superoxide anions below 0.2 in dipolar aprotic solvents. Under UVA irradiation, both C60 and UVA-active reducing agents may produce reactive oxygen species, leading to a synergistic toxicity. © 2013 The American Society of Photobiology.},
note = {cited By 0},
keywords = {chemistry; proton nuclear magnetic resonance; ultraviolet radiation, DNA; fullerene C60; fullerene derivative; nicotinamide adenine dinucleotide; photosensitizing agent; reducing agent, DNA; Fullerenes; NAD; Photosensitizing Agents; Proton Magnetic Resonance Spectroscopy; Reducing Agents; Ultraviolet Rays},
pubstate = {published},
tppubtype = {article}
}
@article{He2014759,
title = {Synergistic combination of marine oligosaccharides and azithromycin against Pseudomonas aeruginosa},
author = { X.a b He and H.-M.b Hwang and W.G.b Aker and P.a Wang and Y.c Lin and X.a Jiang and X.d He},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904730527&amp;partnerID=40&amp;md5=7a9b2ae75de712bea703d565dd34f1f3},
doi = {10.1016/j.micres.2014.01.001},
issn = {09445013},
year  = {2014},
date = {2014-01-01},
journal = {Microbiological Research},
volume = {169},
number = {9-10},
pages = {759-767},
publisher = {Urban und Fischer Verlag Jena},
abstract = {In this paper we describe how utilization of low molecular weight alginate-derived oligosaccharide (ADO) and chito-oligosaccharide (COS) in conjunction with antibiotics, could more effectively inhibit the growth of wild-type and resistant Pseudomonas aeruginosa. Inhibition is effected by modulating the bacteria's quorum sensing (QS) system, thus regulating biofilm formation and reducing resistance to antibiotic treatment. This can be demonstrated by using conventional MIC screening. COS showed synergistic effects with azithromycin, whereas ADO indicated additive effects against wild-type P. aeruginosa. Using electrospray-ionization mass spectroscopy (ESI-MS), matrix-assisted laser desorption/ionization-time of flightmass spectroscopy (MALDI-TOF-MS) and nuclear magnetic resonance (NMR), the chemical structure of ADO and of COS was characterized. The wild-type and resistant strains were identified by 16S rRNA sequence analysis. This report demonstrates the feasibility of attenuating the tolerance of P. aeruginosa to azithromycin by using specific marine oligosaccharides. © 2014 Elsevier GmbH.},
note = {cited By 1},
keywords = {16S; Sequence Analysis, Alginate, Anti-Bacterial Agents; Azithromycin; Biofilms; DNA, Antibiotics; Bacteria; Electrospray ionization; Mass spectrometry; Nuclear magnetic resonance spectroscopy; Oligosaccharides; RNA, antiinfective agent; azithromycin; bacterial DNA; oligosaccharide; ribosome DNA; RNA 16S, Bacteria (microorganisms); Pseudomonas aeruginosa, Bacterial; DNA, biofilm; chemical structure; chemistry; classification; DNA sequence; drug effects; drug potentiation; electrospray mass spectrometry; genetics; growth, Chito-oligosaccharides; Low molecular weight; Matrix assisted laser desorption; Nuclear magnetic resonance(NMR); Pseudomonas aeruginosa; Quorum-sensing; Resistance to antibiotics; Synergistic combinations, development and aging; mass spectrometry; microbial sensitivity test; molecular genetics; nuclear magnetic resonance spectroscopy; physiological stress; physiology; Pseudomonas aeruginosa; quorum sensing, DNA; Spectrometry, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Stress, Physiological, Ribosomal, Ribosomal; Drug Synergism; Magnetic Resonance Spectroscopy; Microbial Sensitivity Tests; Molecular Sequence Data; Molecular Structure; Oligosaccharides; Pseudomonas aeruginosa; Quorum Sensing; RNA},
pubstate = {published},
tppubtype = {article}
}
@article{Li2014,
title = {Red seaweed derived polysaccharides, a novel marine resource for bio-ethanol production},
author = { X.-L.a Li and Y.-P.a Li and H.-J.a Mou and H.-M.b Hwang and P.a Wang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901649756&amp;partnerID=40&amp;md5=9cdc6902915951501a3ce17af37e8c8b},
doi = {10.1063/1.4880515},
issn = {19417012},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Renewable and Sustainable Energy},
volume = {6},
number = {3},
publisher = {American Institute of Physics Inc.},
abstract = {Seaweed biomass could be a renewable feed stock source for bio-ethanol production. Kappaphycus alvarezii is a promising alternative feedstock for the production of renewable energy sources because of its high content of red seaweed derived polysaccharides (RSDP) and its abundance nationwide. Based on the success of the production of bio-ethanol from seaweed cellulose biomass, the purpose of this study was to verify the feasibility of converting RSDP (mainly composed of sulfated galactan) to fermentable reducing sugar for bio-ethanol production. In this study, RSDP, pretreated with methanolysis to remove sulfate radicals, had a better desulfuration effect than the method of organic solvolytic desulfation. The results of single factor and orthogonal experiments were conducted, and the optimal parameters for the methanolysis of RSDP were: 0.5% of substrate concentration, 1.0M HCl-methanol, temperature of 80 °C, and 20 h. The desulfuration rate and the total-sugars yield reached 93% and 91%, respectively. Using Infrared Spectra, it was proven that the sulfate radical content was reduced sharply and that the 3, 6-anhydro bond was broken. Above all, saccharification liquids of desulfurated RSDP inoculated with Saccharomyces cerevisiae L4 for ethanol fermentation could produce 0.27 g ethanol/g RSDP. The results could bring bright prospects of bio-ethanol conversion from red seaweed biomass. © 2014 AIP Publishing LLC.},
note = {cited By 0},
keywords = {Alternative feedstocks; Bio-ethanol production; Ethanol fermentation; Kappaphycus alvarezii; Orthogonal experiment; Renewable energy source; Substrate concentrations; Sulfated galactans, Bioethanol, Biomass; Marine biology; Natural resources; Polysaccharides; Renewable energy resources; Saccharification; Seaweed; Yeast},
pubstate = {published},
tppubtype = {article}
}
@article{He2014128b,
title = {Using a holistic approach to assess the impact of engineered nanomaterials inducing toxicity in aquatic systems},
author = { X.a He and W.G.b Aker and J.c Leszczynski and H.-M.a b Hwang},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84901620492&amp;partnerID=40&amp;md5=a43a691da14e7beefa584920e345ee96},
doi = {10.1016/j.jfda.2014.01.011},
issn = {10219498},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Food and Drug Analysis},
volume = {22},
number = {1},
pages = {128-146},
publisher = {National Laboratories of Foods and Drugs},
abstract = {In this report, we critically reviewed selected intrinsic physicochemical properties of engineered nanomaterials (ENMs) and their role in the interaction of the ENMs with the immediate surroundings in representative aquatic environments. The behavior of ENMs with respect to dynamic microenvironments at the nanoebioeeco interface level, and the resulting impact on their toxicity, fate, and exposure potential are elaborated. Based on this literature review, we conclude that a holistic approach is urgently needed to fulfill our knowledge gap regarding the safety of discharged ENMs. This comparative approach affords the capability to recognize and understand the potential hazards of ENMs and their toxicity mechanisms, and ultimately to establish a quantitative and reliable system to predict such outcomes. Copyright © 2014, Food and Drug Administration, Taiwan.},
note = {cited By 6},
keywords = {Animals; Humans; Nanostructures; Oxidative Stress; Reactive Oxygen Species; Toxicology, glutathione; lactate dehydrogenase; metal ion; nanomaterial; reactive oxygen metabolite; nanomaterial; reactive oxygen metabolite},
pubstate = {published},
tppubtype = {article}
}
@article{Pathakoti2014,
title = {Using experimental data of Escherichia coli to develop a QSAR model for predicting the photo-induced cytotoxicity of metal oxide nanoparticles},
author = { Kavitha Pathakoti and Ming-Ju Huang and John D. Watts and Xiaojia He and Huey-Min Hwang},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1011134413002753},
doi = {10.1016/j.jphotobiol.2013.11.023},
issn = {10111344},
year  = {2014},
date = {2014-01-01},
journal = {Journal of Photochemistry and Photobiology B: Biology},
volume = {130},
pages = {234--240},
abstract = {A quantitative structure\textendashactivity relationship (QSAR) study of seventeen metal oxide nanoparticles (MNPs), in regard to their photo-induced toxicity to bacteria Escherichia coli, was developed by using quantum chemical methods. A simple and statistically significant QSAR model (F = 33.83},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Liao2013b,
title = {Binding of O 2 and NO to Heme in Heme-Nitric Oxide/Oxygen-Binding (H-NOX) Proteins. A Theoretical Study},
author = { Meng-Sheng Liao and Ming-Ju Huang and John D. Watts},
url = {http://pubs.acs.org/doi/abs/10.1021/jp403998u},
doi = {10.1021/jp403998u},
issn = {1520-6106},
year  = {2013},
date = {2013-09-01},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {35},
pages = {10103--10114},
abstract = {The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron\textendashhistidine (Fe\textendashHis) binding. The Heme\textendashAB (AB = O2, NO) and Fe\textendashHis binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN, where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe\textendashHis binding strength, but a dispersion contribution to Ebind(Fe\textendashHis) may be significant, depending on the crystal structure used. We speculate that the Fe\textendashHis binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Liao2013a,
title = {Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies},
author = { Meng-Sheng Liao and Ming-Ju Huang and John D. Watts},
url = {http://link.springer.com/10.1007/s00894-013-1864-2},
doi = {10.1007/s00894-013-1864-2},
issn = {1610-2940},
year  = {2013},
date = {2013-08-01},
journal = {Journal of Molecular Modeling},
volume = {19},
number = {8},
pages = {3307--3323},
abstract = {The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Napolion2013,
title = {Accurate theoretical predictions for carbonyl diazide molecules: A coupled-cluster study of the potential energy surface and thermochemical properties},
author = { Brian Napolion and John D. Watts and Ming-Ju Huang and Frederick M. McFarland and Eric E. McClendon and Wilbur L. Walters and Quinton L. Williams},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009261413000080},
doi = {10.1016/j.cplett.2012.12.056},
issn = {00092614},
year  = {2013},
date = {2013-02-01},
journal = {Chemical Physics Letters},
volume = {559},
pages = {18--25},
abstract = {Enthalpies of formation (View the MathML source) of syn-syn (C2v), anti-syn (Cs), and the newly proposed C2 isomer of carbonyl diazide, OC(N3)2, at 298 K have been predicted using CCSD(T) theory in conjunction with a systematic basis set expansion that has been extrapolated to the complete basis set (CBS) limit. The View the MathML source has been calculated via three independent pathways and ‘chemical accuracy' has been obtained. The predicted CCSD(T)/CBS values are (kJ mol−1): syn-syn (C2v), 471.5; anti-syn (Cs), 479.5; C2, 517.4. These values deviate by 14.5 kJ mol−1 compared to prior G4 approximations. CCSD(T) torsional potential energy scan reveals a previously undiscovered conformer of OC(N3)2 possessing C2 symmetry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Hwang2013190,
title = {Toxicology of designer/engineered metallic nanoparticles},
author = { Ray P C Yu H He X Hwang H.-M.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84898726092&amp;partnerID=40&amp;md5=c80718c161443f6fa3f8e7a0b51c6294},
year  = {2013},
date = {2013-01-01},
journal = {RSC Green Chemistry},
pages = {190--212},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Pathakoti20131093,
title = {Photoinduced toxicity of CdSe/ZnS quantum dots with different surface coatings to Escherichia coli},
author = { Hwang H.-M. Wang X Aker W G Pathakoti K.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84892638438&amp;partnerID=40&amp;md5=89cfe8583356a6a0fcc158d593ab2775},
doi = {10.1504/IJNT.2013.058567},
year  = {2013},
date = {2013-01-01},
journal = {International Journal of Nanotechnology},
volume = {10},
number = {12},
pages = {1093--1108},
abstract = {Quantum dot (QD) nanoparticles are increasingly used for various biomedical applications. To increase their biocompatibility, QDs are frequently coated with different surface coatings. Since QDs are photoactive under UV irradiation and may lead to oxidative stress, in this study the photoinduced toxicities of CdSe/ZnS QDs with three different coatings at three different wavelengths (530, 580 and 620 nm), along with a reference sample, a non-cadmium based QD CuInS2/ZnS were tested with E. coli under solar irradiation and dark conditions. QEI QDs coated with polyethylenimine (PEI) were found to be highly phototoxic to E. coli, conversely, QSA QDs with polyethyleneglycol coating and QSH QDs with amphiphilic polymer coating did not show toxicity. LC50 values for QEI QDs are smaller in the light exposure groups than those in the dark exposure groups. CuInS2/ZnS was less toxic to E. coli both under the light and dark conditions. The release of cadmium ions from the QD core was found to be negligible. Instead, the primary mechanism of the phototoxicity of QDs is the oxidative stress via formation of hydroxyl radicals that leads to lipid peroxidation and a concomitant decrease in reduced glutathione. The results also indicated that CdSe/ZnS QDs with PEI coating are highly toxic to E. coli and the non-cadmium based QD CuInS2/ZnS have better biocompatibility. Copyright textcopyright 2013 Inderscience Enterprises Ltd.},
keywords = {Amphiphilic polymers; Biomedical applications; CdSe/ZnS quantum dots; E. coli; Lipid peroxidation; Photoinduced toxicity; Quantum dot nanoparticles; Reduced glutathione, Biocompatibility; Cadmium; Cadmium compounds; Coatings; Escherichia coli; Lipids; Medical applications; Oxidative stress; Peptides; Semiconductor quantum dots, Toxicity},
pubstate = {published},
tppubtype = {article}
}
@article{Li2013988,
title = {Production of enzymes by Alteromonas sp. A321 to degrade polysaccharides from Enteromorpha prolifera},
author = { Wang J Yu Y Li X Jiang X Hwang H Wang P Li Y.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84885146960&amp;partnerID=40&amp;md5=82f9464735241040bd8f950816f62359},
doi = {10.1016/j.carbpol.2013.07.016},
year  = {2013},
date = {2013-01-01},
journal = {Carbohydrate Polymers},
volume = {98},
number = {1},
pages = {988--994},
abstract = {Polysaccharides from Enteromorpha prolifera (PE) are becoming increasingly popular due to its bioactivity and abundant source. Screening novel microorganisms which could secrete enzymes to degrade PE efficiently for oligosaccharides production is a promising solution to improve its application. In this study, a marine bacterium that can produce enzymes to degrade PE specifically was selected. It was identified as Alteromonas sp. A321, based on the biochemical properties and 16S rDNA gene sequencing. In order to maximize the activity of degradase for polysaccharides from E. prolifera (DPE), the effects of medium composition and culture conditions were investigated. The highest DPE production was obtained in the medium consisting of K 2HPO4 0.15%, PE 0.9%, NaNO3 0.4%, NaCl 1.0% and MgSO4 0.05%. The degradase activity was enhanced from original 0.391 U/ml to 0.744 U/ml. DPE show high efficiency and substrate specificity to PE with 63.53% of reducing sugar production in the 7 h hydrolysis. Crown Copyright textcopyright 2013 Published by Elsevier Ltd. All rights reserved.},
keywords = {16S rDNA gene sequencing; Alteromonas sp. A321; Biochemical properties; Degradase; Enteromorpha prolifera; Prolifera; Response surface methodology; Substrate specificity, 16S; Ulva, Alteromonas sp. A321; Degradase; degrdase for polysaccharides from Enteromorpha prolifera; DPE; Enzymatic hydrolysis; Identification; PE; polysaccharides from Enteromorpha prolifera; Polysaccharides from Enteromorpha prolifera; Response surface methodology, Alteromonas; Alteromonas sp. A321; article; chemistry; culture technique; Degradase; degrdase for polysaccharides from Enteromorpha prolifera; enzymology; fermentation; genetics; growth, Alteromonas; Carbon; Culture Techniques; Fermentation; Hydrolases; Nitrogen; Polysaccharides; RNA, carbon; dipivefrine; hydrolase; nitrogen; polysaccharide; RNA 16S, development and aging; hydrolysis; identification; isolation and purification; metabolism; methodology; PE; Polysaccharides from Enteromorpha prolifera; response surface method; Ulva, Enzymatic hydrolysis; Identification (control systems); Polysaccharides, Ribosomal, Substrates},
pubstate = {published},
tppubtype = {article}
}
@article{Pathakoti20139988,
title = {Photoinactivation of Escherichia coli by sulfur-doped and nitrogen-fluorine-codoped TiO2 nanoparticles under solar simulated light and visible light irradiation},
author = { Morrow S Han C Pelaez M He X Dionysiou D D Hwang H.-M. Pathakoti K.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883515650&amp;partnerID=40&amp;md5=e99376f9e227f31be565eedccf960cf7},
doi = {10.1021/es401010g},
year  = {2013},
date = {2013-01-01},
journal = {Environmental Science and Technology},
volume = {47},
number = {17},
pages = {9988--9996},
abstract = {Titanium dioxide (TiO2) is one of the most widely used photocatalysts for the degradation of organic contaminants in water and air. Visible light (VL) activated sulfur-doped TiO2 (S-TiO2) and nitrogen-fluorine-codoped TiO2 (N-F-TiO2) were synthesized by sol-gel methods and characterized. Their photoinactivation performance was tested against Escherichia coli under solar simulated light (SSL) and VL irradiation with comparison to commercially available TiO 2. Undoped Degussa-Evonik P-25 (P-25) and Sigma-TiO2 showed the highest photocatalytic activity toward E coli inactivation under SSL irradiation, while S-TiO2 showed a moderate toxicity. After VL irradiation, Sigma-TiO2 showed higher photoinactivation, whereas S-TiO2 and P-25 showed moderate toxicity. Oxidative stress to E coli occurred via formation of hydroxyl radicals leading to lipid peroxidation as the primary mechanism of bacterial inactivation. Various other biological models, including human keratinocytes (HaCaT), zebrafish liver cells (ZFL), and zebrafish embryos were also used to study the toxicity of TiO2 NPs. In conclusion, N-F-TiO2 did not show any toxicity based on the assay results from all the biological models used in this study, whereas S-TiO 2 was toxic to zebrafish embryos under all the test conditions. These findings also demonstrate that the tested TiO2 nanoparticles do not show any adverse effects in HaCaT and ZFL cells. textcopyright 2013 American Chemical Society.},
keywords = {Animals; Embryo, Bacterial inactivation; Degradation of organic contaminants; Human keratinocytes; Hydroxyl radicals; Lipid peroxidation; Photocatalytic activities; Solar-simulated light; Visible-light irradiation, barium ion; cadmium; chromium; fluorine; hydroxyl radical; iron; manganese; nanoparticle; nitrogen; reactive oxygen metabolite; sulfur; titanium dioxide; zinc, bioassay; catalyst; coliform bacterium; cyprinid; embryo; light effect; organic pollutant; oxidation; oxide; particulate matter; radiation balance; toxicity; visible spectrum, Doping (additives); Escherichia coli; Fluorine; Irradiation; Light; Nanoparticles; Nitrogen; Photocatalysts; Sol-gel process; Sulfur; Toxicity, Electron, Nonmammalian; Escherichia coli; Fluorine; Keratinocytes; Light; Liver; Microscopy, Titanium dioxide, Transmission; Nanoparticles; Nitrogen; Photoelectron Spectroscopy; Photolysis; Reactive Oxygen Species; Sulfur; Sunlight; Titanium; X-Ray Diffraction; Zebrafish},
pubstate = {published},
tppubtype = {article}
}
@article{Dasari20131925,
title = {Effect of humic acids and sunlight on the cytotoxicity of engineered zinc oxide and titanium dioxide nanoparticles to a river bacterial assemblage},
author = { Hwang H.-M. Dasari T.P.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883767125&amp;partnerID=40&amp;md5=e2770cffb5521b7bf048284305c93c0a},
doi = {10.1016/S1001-0742(12)60271-X},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Environmental Sciences (China)},
volume = {25},
number = {9},
pages = {1925--1935},
abstract = {The effect of a terrestrial humic acid (HA) and Suwannee River HA on the cytotoxicity of engineered zinc oxide nanoparticles (ZnONPs) and titanium dioxide nanoparticles (TiO2NPs) to natural aquatic bacterial assemblages was measured with spread plate counting. The effect of HA (10 and 40 ppm) on the cytotoxicity of ZnONPs and TiO2NPs was tested factorially in the presence and absence of natural sunlight (light irradiation (LI)). The experiment was of full factorial, completely randomized design and the results were analyzed using the General Linear Model in SAS analytical software. The method of least squares means was used to separate the means or combinations of means. We determined the mechanism of toxicity via measurements of oxidative stress and metal ions. The toxicity of ZnONPs and TiO2NPs to natural aquatic bacterial assemblages appears to be concentration dependent. Moreover, the cytotoxicity of ZnONPs and TiO2NPs appeared to be affected by HA concentration, the presence of sunlight irradiation, and the dynamic multiple interactions among these factors. With respect to light versus darkness in the control group, the data indicate that bacterial viability was inhibited more in the light exposure than in the darkness exposure. The same was true in the HA treatment groups. With respect to terrestrial versus Suwanee River HA for a given nanoparticle, in light versus darkness, bacterial viability was more inhibited in the light treatment groups containing the terrestrial HA than in those containing Suwanee River HA. Differences in the extent of reactive oxygen species formation, adsorption/binding of ZnONPs/TiO2NPs by HA, and the levels of free metal ions were speculated to account for the observed cytotoxicity. TEM images indicate the attachment and binding of the tested nanoparticles to natural bacterial assemblages. Besides the individual parameter, significant effects on bacterial viability count were also observed in the following combined treatments: HA-ZnONPs, HA-LI, ZnONPs-LI, and HA-ZnONPs-LI. The main effects of all independent variables, plus interaction effects in all cases were significant with TiO2NPs. textcopyright 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences.},
keywords = {article; bacterium; chemistry; classification; humic substance; microbiology; oxidative stress; river; sunlight; transmission electron microscopy, Bacteria, Bacteria; Humic Substances; Metal Nanoparticles; Microscopy, Bacterial assemblages; Completely randomized designs; Humic acid; Median Lethal concentration; Method of least squares; Reactive oxygen species; Titanium dioxide nanoparticles; Zinc oxide nanoparticles, bacterium; concentration (composition); experimental study; humic acid; nanotechnology; oxidation; titanium; toxicity; zinc, Biological materials; Cytotoxicity; Enzyme immobilization; Irradiation; Least squares approximations; Metal ions; Nanoparticles; Organic acids; Oxides; Oxygen; Rivers; Titanium dioxide; Toxicity; Zinc oxide, Electron, metal nanoparticle; titanium; titanium dioxide, Suwannee River; United States, Transmission; Oxidative Stress; Rivers; Sunlight; Titanium; Water Microbiology},
pubstate = {published},
tppubtype = {article}
}
@article{Dasari2013882,
title = {Determination of the mechanism of photoinduced toxicity of selected metal oxide nanoparticles (ZnO, CuO, Co3O4 and TiO2) to E. coli bacteria},
author = { Pathakoti K Hwang H.-M. Dasari T.P.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84877823140&amp;partnerID=40&amp;md5=62c6a318e13dbe616498106017cff3e4},
doi = {10.1016/S1001-0742(12)60152-1},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Environmental Sciences (China)},
volume = {25},
number = {5},
pages = {882--888},
abstract = {Cytotoxicity of selected metal oxide nanoparticles (MNPs) (ZnO, CuO, Co3O4 and TiO2) was investigated in Escherichia coli both under light and dark conditions. Cytotoxicity experiments were conducted with spread plate counting and the LC50 values were calculated. We determined the mechanism of toxicity via measurements of oxidative stress, reduced glutathione, lipid peroxidation, and metal ions. The overall ranking of the LC50 values was in the order of ZnO textless CuO textless Co3O4 textless TiO2 under dark condition and ZnO textless CuO textless TiO2 textless Co3O4 under light condition. ZnO MNPs were the most toxic among the tested nanoparticles. Our results indicate depletion of reduced glutathione level and elevation of malondialdehyde level correlated with the increase in oxidative stress. Released metal ions were found to have partial effect on the toxicity of MNPs to E. coli. In summary, the dynamic interactions of multiple mechanisms lead to the toxicity of the tested MNPs to E. coli. textcopyright 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences.},
keywords = {article; drug effect; Escherichia coli; lipid peroxidation; metabolism; oxidative stress; radiation exposure; sunlight, coliform bacterium; lipid; oxidation; oxide; toxicity, Copper; Escherichia coli; Glutathione; Lipid Peroxidation; Metal Nanoparticles; Oxidative Stress; Oxides; Reactive Oxygen Species; Sunlight, copper; glutathione; metal nanoparticle; oxide; reactive oxygen metabolite, Escherichia coli; Lipids; Metal ions; Metallic compounds; Nanoparticles; Oxidative stress; Peptides; Titanium dioxide; Zinc oxide, Lipid peroxidation; Median Lethal concentration; Metal oxide nanoparticles; Reactive oxygen species; Reduced glutathione, Toxicity},
pubstate = {published},
tppubtype = {article}
}
@article{He2013858,
title = {Influence of marine oligosaccharides on the response of various biological systems to UV irradiation},
author = { Li R Huang G Hwang H.-M. Jiang X He X.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84876716478&amp;partnerID=40&amp;md5=d97541a972ebacc5e6f961c03bf697ff},
doi = {10.1016/j.jff.2013.01.035},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Functional Foods},
volume = {5},
number = {2},
pages = {858--868},
abstract = {Low molecular weight alginate-derived oligosaccharide (ADO) (373-571. Da) and chito-oligosaccharide (COS) (855-1671. Da) were purified from alginate and chitosan, and known as marine oligosaccharides with polyanionic and polycationic properties, respectively. We compared the effects of ADO and COS on cell regulation using several biological models (Candida albicans, Escherichia coli and Bacillus subtilis spore), cellular uptake determination, erythrocytes haemolysis inhibition and antioxidant capacity assay to investigate stress response under UV radiation. Our results further confirmed the anti-UVR potential of ADO and COS and their potential for commercial UVR protector application in the area of functional foods as food ingredients. textcopyright 2013 Elsevier Ltd.},
keywords = {Bacillus subtilis; Candida albicans; Escherichia coli},
pubstate = {published},
tppubtype = {article}
}
@article{Pathakoti2013163,
title = {In vitro cytotoxicity of CdSe/ZnS quantum dots with different surface coatings to human keratinocytes HaCaT cells},
author = { Hwang H.-M. Xu H Aguilar Z P Wang A Pathakoti K.},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872389332&amp;partnerID=40&amp;md5=e88378a9150ecf2e2202b4ba8d92a9ec},
doi = {10.1016/S1001-0742(12)60015-1},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Environmental Sciences (China)},
volume = {25},
number = {1},
pages = {163--171},
abstract = {Quantum dots (QD) nanoparticles have been widely used in biomedical and electronics fields, because of their novel optical properties. Consequently it confers enormous potential for human exposure and environmental release. To increase the biocompatibility of QDs, a variety of surface coatings or functional groups are added to increase their bioactivity and water solubility. Human adult low calcium high temperature (HaCaT) cells are the epithelial cells derived from adult human skin that exhibits normal differentiation capacity and a DNA fingerprint pattern that is unaffected by long-term cultivation, transformation, or the presence of multiple chromosomal alternations. Human keratinocytes, HaCaT cells were used to systematically evaluate the cytotoxicity of biocompatible QD made of CdSe metal core and ZnS shell with three different coatings and at three different wavelengths (530, 580 and 620 nm). In terms of halfmaximal inhibitory concentration, QSA-QDs with amine-polyethyleneglycol coating and QSH-QDs with amphiphilic polymer coating were not cytotoxic, while QEI-QDs with polyethylenimine coating were highly toxic to the HaCaT cells in comparison to a reference CuInS2/ZnS. QEI-QDs led to significant increase in reactive oxygen species, decrease in mitochondrial membrane potential and DNA damage in HaCaT cells. The mechanisms of toxicity of QEI-530 and QEI-580 can be attributed to the combination of intracellular reactive oxygen species production and loss of MMP. The QDs toxicity can be attributed to the polyethylemimine surface coating which was highly toxic to cells in comparison with amine-polyethyleneglycol, but not due to the release of cadmium ions. textcopyright 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences.},
keywords = {article; cell line; drug effect; human; keratinocyte, bioactivity; concentration (composition); DNA fingerprinting; genotoxicity; inhibitor; membrane; mitochondrion; quantum mechanics, Biocompatibility; Cadmium; Cadmium compounds; Cells; Cytology; Cytotoxicity; Nanoparticles; Optical properties; Organic compounds; Oxygen; Semiconductor quantum dots; Toxicity; Zinc sulfide, Cadmium Compounds; Cell Line; Humans; Keratinocytes; Quantum Dots; Selenium Compounds; Sulfides; Zinc Compounds, cadmium derivative; cadmium selenide; quantum dot; selenium derivative; sulfide; zinc derivative; zinc sulfide, Coatings},
pubstate = {published},
tppubtype = {article}
}
@incollection{Pustovit2013,
title = {Cooperative Effects in Plasmonics},
author = { Vitaliy N. Pustovit and Tigran V. Shahbazyan},
url = {http://link.springer.com/10.1007/978-94-007-7805-4_15},
doi = {10.1007/978-94-007-7805-4_15},
year  = {2013},
date = {2013-01-01},
booktitle = {Plasmonics: Theory and Applications},
pages = {525--565},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
@article{Smith20131681,
title = {Conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete},
author = { S.A.a Smith and Q.b Cheng and G.a Hill and D.H.b Magers},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84885177720&amp;partnerID=40&amp;md5=f30209bb1a027235517b7d40d7a7f4d6},
doi = {10.1007/s11224-012-0186-9},
issn = {10400400},
year  = {2013},
date = {2013-01-01},
journal = {Structural Chemistry},
volume = {24},
number = {5},
pages = {1681-1691},
abstract = {The conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory, and density functional theory and employing the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single-point fourth-order perturbation theory, CCSD, and CCSD(T) calculations employing the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectfully, to ascertain the contribution of higher order correlation. Three DFT functionals, B3LYP, wB97XD, and M06-2X, are employed to determine whether they can yield results similar to those obtained at the CCSD(T) level. © 2013 Springer Science+Business Media New York.},
note = {cited By 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gardner20133543,
title = {Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives},
author = { N.a Gardner and D.b Magers and G.a Hill Jr.},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84882979785&amp;partnerID=40&amp;md5=c3fa505dcf0279a8ab314d32cee4e1c8},
doi = {10.1007/s00894-013-1833-9},
issn = {16102940},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Molecular Modeling},
volume = {19},
number = {9},
pages = {3543-3549},
abstract = {The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of adenine and thymine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre-translational effects and post translational effects of adenine and thymine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory (DFT) B3LYP functional accompanied with 6-311G(d,p), 6-311+G(d,p) and 6-311++G(df,pd) basis sets. Our results reveal that the thymine tautomer has a higher EA and IP than the adenine tautomers. The higher EA suggests that an electron that attaches to the AT base pair would predominately attach to the thymine instead of adenine. The higher IP would suggest that an electron that is removed from the AT base pair would be predominately removed from the adenine within the base pair. Understanding how tautomerization, ionization and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases. © 2013 Springer-Verlag Berlin Heidelberg.},
note = {cited By 3},
keywords = {adenine; cytosine; cytosine derivative; DNA base; methyl group; thymine, Adenine; DNA; Electrons; Methylation; Models, article; chemical structure; density functional theory; electron; ionization; methylation; oxidation; priority journal; protein processing; tautomer; tautomerization; theoretical study, Theoretical; Thymine},
pubstate = {published},
tppubtype = {article}
}
@article{Smith2013558,
title = {Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results?},
author = { S.A.a Smith and K.E.b Hand and M.L.b Love and G.a Hill and D.H.b Magers},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84873741872&amp;partnerID=40&amp;md5=371483810d9ba25644e3354cbbd0252f},
doi = {10.1002/jcc.23165},
issn = {01928651},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Computational Chemistry},
volume = {34},
number = {7},
pages = {558-565},
abstract = {The conventional strain energies for azetidine and phosphetane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using self-consistent field theory, second-order perturbation theory, and density functional theory and using the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single point fourth-order perturbation theory, CCSD, and CCSD(T) calculations using the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectively, to ascertain the contribution of higher order correlation effects and to determine if the quadruple-zeta valence basis set is needed when higher order correlation is included. In the density functional theory study, eight different functionals are used including B3LYP, wB97XD, and M06-2X to determine if any functional can yield results similar to those obtained at the CCSD(T) level. © 2012 Wiley Periodicals, Inc.},
note = {cited By 3},
keywords = {article; chemical structure; chemistry; quantum theory, azetidine; azetidine derivative; phosphorus derivative, Azetidines; Molecular Structure; Phosphorus Compounds; Quantum Theory, Density functional theory; Mean field theory; Molecular orbitals; Organic compounds, Strain energy},
pubstate = {published},
tppubtype = {article}
}
@article{Kolodziejczyk20131451,
title = {Conformational analysis of flephedrone using quantum mechanical models},
author = { W.a Kolodziejczyk and J.a Jodkowski and T.M.b d Holmes and G.A.c Hill},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84877125462&amp;partnerID=40&amp;md5=f1c4be6ff3aceeca045e69cbc71be5c3},
doi = {10.1007/s00894-012-1673-z},
issn = {16102940},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Molecular Modeling},
volume = {19},
number = {3},
pages = {1451-1458},
abstract = {Flephedrone is an analogue of cathinone - chemically similar to ephedrine, cathine and other amphetamines. Conformations of all isomers of flephedrone have been studied at the quantum-chemical level. Calculations have been performed using DFT and MP2 methods with two basis sets - 6-31G and 6-31G(d,p). Results show that there are low energy conformers for the ortho, meta, and para isomers that are connected by way of low-barrier transition states. Boltzmann distribution of population predicts the highest population for the 1-meta conformer with a 10 % increase in solution. The molecular electrostatic potential surface data for each molecule has been calculated revealing likely reaction sites. © 2012 The Author(s).},
note = {cited By 1},
keywords = {2 fluoromethcathinone; 3 fluoromethcathinone; 4 fluoromethcathinone; cathinone; flephedrone; unclassified drug, Alkaloids; Amphetamines; Designer Drugs; Molecular Conformation; Propiophenones; Psychotropic Drugs; Static Electricity, article; chemical structure; conformational transition; crystal structure; density functional theory; isomerism; priority journal; quantum chemistry; quantum mechanics; static electricity; thermodynamics},
pubstate = {published},
tppubtype = {article}
}
@article{Saloni20131531,
title = {Theoretical investigation on monomer and solvent selection for molecular imprinting of nitrocompounds},
author = { J.a b Saloni and K.b Walker and G.b Hill Jr.},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84874121255&amp;partnerID=40&amp;md5=4b2cf9530d2cb513442008933a3be3cd},
doi = {10.1021/jp2124839},
issn = {10895639},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Physical Chemistry A},
volume = {117},
number = {7},
pages = {1531-1534},
abstract = {The aim of this work is to serve as a guideline for the initial selection of monomer and solvent for the synthesis of the nitrocompound-based molecularly imprinted polymers, MIPs. Reported data include evaluation of six systems with the ability to form noncovalently bonded monomer-template complexes. These systems are represented by the following aliphatic and aromatic molecules: acrolein, acrylonitrile, 2,6-bisacrylamide, 4-ethylenebenzoic acid, methyl methacrylate, and 2-vinylpyridine. Cave models for selected monomers are also presented and supported by binding energy analysis under various conditions. Solvent effects on monomer-template binding energy have been studied for four solvents: acetone, acetonitrile, chloroform, and methanol. Additionally, systems such as 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), pentachlorophenol (PCP), and 3,6-dichloro-2-methoxybenzoic acid (Dicamba) have been used to study selectivity of acrolein-based MIP toward TNT detection. The density functional theory, DFT, method has been used for all structural, vibrational frequency, and solvent calculations. © 2013 American Chemical Society.},
note = {cited By 1},
keywords = {2, 4-dinitrotoluene; 2, 4-DNT; 2, 6 dinitrotoluene (2, 6 dnt); 2-vinylpyridine; Aromatic molecules; Binding energy analysis; Dicamba; Methyl methacrylates; Molecular imprinting; Molecularly Imprinted Polymer; Nitro-compounds; Solvent effects; Solvent selection; Theoretical investigations, Acetone; Acetonitrile; Aldehydes; Binding energy; Density functional theory; Esters; Explosives detection; Herbicides; Methanol; Monomers; Phenols; Solvents, Organic solvents},
pubstate = {published},
tppubtype = {article}
}
@article{Liao2013,
title = {Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study},
author = { Meng-Sheng Liao and Ming-Ju Huang and John D. Watts},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0162013412002978},
doi = {10.1016/j.jinorgbio.2012.09.011},
issn = {01620134},
year  = {2013},
date = {2013-01-01},
journal = {Journal of Inorganic Biochemistry},
volume = {118},
pages = {28--38},
abstract = {Enthalpies of formation (View the MathML source) of syn-syn (C2v), anti-syn (Cs), and the newly proposed C2 isomer of carbonyl diazide, OC(N3)2, at 298 K have been predicted using CCSD(T) theory in conjunction with a systematic basis set expansion that has been extrapolated to the complete basis set (CBS) limit. The View the MathML source has been calculated via three independent pathways and ‘chemical accuracy' has been obtained. The predicted CCSD(T)/CBS values are (kJ mol−1): syn-syn (C2v), 471.5; anti-syn (Cs), 479.5; C2, 517.4. These values deviate by 14.5 kJ mol−1 compared to prior G4 approximations. CCSD(T) torsional potential energy scan reveals a previously undiscovered conformer of OC(N3)2 possessing C2 symmetry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Mirchi2007,
title = {Study of Nickel concentration in tri-cation Zinc Phosphate Process on automotive bodies},
author = { Ali Mirchi and A. Badiei and Y. Khanyani},
year  = {2007},
date = {2007-01-01},
journal = {Electroplating Industry Magazine},
volume = {44},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@inbook{Roy2021b,
title = {Chapter: Computational screening of organic dye-sensitizers for dye-sensitized solar cells: DFT/TDDFT approach},
author = {J. Roy, S. Kar, J. Leszczynski},
editor = {J. Roy, S. Kar, J. Leszczynski (eds.)},
doi = {https://doi.org/10.1007/978-3-030-69445-6_8},
isbn = {978-3-030-69445-6},
volume = {32},
pages = {187-206},
publisher = {Springer, Cham},
series = {Development of Solar Cells. Challenges and Advances in Computational Chemistry and Physics},
abstract = {Dye-sensitized solar cells (DSSCs) represent a promising third-generation photovoltaic technology due to their ease in fabrication, low cost, ability to operate in diffused light, flexibility, and being lightweight. Organic dye-sensitizers are vital components of the DSSCs. Comprehensive theoretical study of the dye’s spectroscopic properties, including excitation energies ground- and excited-state oxidation potential, allows to design and screen organic dye-sensitizers for an efficient DSSC. Density functional theory (DFT) and time-dependent DFT (TDDFT) approaches have been efficiently used to estimate different optoelectronic properties of sensitizers. This chapter outlined the use of the DFT and TDDFT framework to design organic dye-sensitizers for DSSCs to predict different photophysical properties. Prediction of essential factors such as short-circuit current density (JSC), open-circuit voltage (VOC), along with charge transfer phenomena, will help experimental groups to fabricate DSSCs with higher photoconversion efficiency (PCE). Besides, this chapter includes a basic understanding of the mechanism of DSSCs, based on the energetics of the various constituents of the heterogeneous device.},
keywords = {DFT, DSSC, Organic Sensitizer, TD-DFT},
pubstate = {published},
tppubtype = {inbook}
}
@article{Roy2022,
title = {Photophysical Properties of Donor-Acceptor-π Bridge-Acceptor Sensitizers with a Naphthobisthiadiazole Auxiliary Acceptor: Toward Longer-Wavelength Access in Dye-Sensitized Solar Cells.},
author = {Juganta K. Roy, Ravinder Kaur, Andrew Daniel, Alexandra Baumann, Qing Li, Jared H. Delcamp, and Jerzy Leszczynski},
doi = {10.1021/acs.jpcc.2c02117},
journal = {J. Phys. Chem. C },
volume = {126},
number = {29},
pages = {11875\textendash11888},
abstract = {Accessing longer-wavelength photons is a critical research direction in dye-sensitized solar cells (DSSCs). Currently, dye-sensitized solar cells are exceptional at generating high photovoltages with shorter wavelength photons, but few examples exist of DSSCs using photons in the shortwave infrared region (>1000 nm). New dye building blocks are critical toward accessing these longer-wavelength photons. With this in mind, five new triphenylamine-based metal-free dyes derived from a donor\textendashauxiliary acceptor−π bridge\textendashacceptor (D\textendashA′−π\textendashA) structure are characterized theoretically for application in dye-sensitized solar cells (DSSCs). The driving force of electron injection, the spontaneity of dye regeneration, charge-transfer length, and partial density of states of the isolated and TiO2-bound dyes, which are all critical to DSSC performance, are systematically investigated via first-principles calculations. We find that replacing the high-performing benzothiadiazole (BTD) auxiliary acceptor building block with a longer conjugation length and stronger electron-withdrawing building block, naphtho[1,2-c:5,6-c′]bis([1,2,5]thiadiazole) (NTz), is beneficial toward the kinetics of charge injection along with reducing the optical energy gap of the designed dyes. The obtained results imply that using the NTz unit extends the absorption spectrum toward longer wavelengths and improves charge separation due to the planarity and conjugation length extension that arises from the NTz fragment. The shift of the conduction band of TiO2 (ΔECB value) is higher for the designed NTz-based dyes than for the BTD-based dye on TiO2, suggesting that the open-circuit voltage (VOC) of a dye-sensitized solar cell device will also be higher. Concerning the photophysical properties of the dyes, the NTz-based dyes are promising as they possess a longer excited state and longer radiative lifetime than a BTD-based dye. We synthesize a model NTz-based dye and a BTD analogue for comparison with computational results. The optical properties of the NTz-based dye are computed to validate our computational approach, which agrees with the experimental observations. Our combined computational and experimental approach sheds light on the physical principle of molecular photogenerated charge transfer and provides valuable guidance for the further molecular synthesis of long-wavelength absorbing materials.},
note = {NSF EPSCoR CEMOs  OIA-1757220
Mississippi Center for Supercomputing Research 
},
keywords = {Dye-Sensitized Solar Cells},
pubstate = {published},
tppubtype = {article}
}