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Supratik Kar, Natalia Sizochenko, Lucky Ahmed, Victor S. Batista, Jerzy Leszczynski Nano Energy, 26 , pp. 677–691, 2016, ISSN: 22112855. (Abstract | Links | BibTeX | Tags: ) @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} } 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 |
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Wojciech Kolodziejczyk, Supratik Kar, Glake A. Hill, Jerzy Leszczynski A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies (Journal Article) Structural Chemistry, 27 (4), pp. 1291–1302, 2016, ISSN: 1040-0400. (Abstract | Links | BibTeX | Tags: ) @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} } 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 |
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Alla P. Toropova, Andrey A. Toropov, Aleksandar M. Veselinović, Jovana B. Veselinović, Danuta Leszczynska, Jerzy Leszczynski Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna (Journal Article) Environmental Toxicology and Chemistry, 2016, ISSN: 07307268. (Abstract | Links | BibTeX | Tags: ) @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. Veselinović and Jovana B. Veselinović 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–activity 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} } Quantitative structure–activity 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 |
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Supratik Kar, Rudra Narayan Das, Kunal Roy, Jerzy Leszczynski Can Toxicity for Different Species be Correlated? (Journal Article) International Journal of Quantitative Structure-Property Relationships, 1 (2), pp. 23–51, 2016, ISSN: 2379-7487. (Abstract | Links | BibTeX | Tags: Extrapolation, i-QSTR, Interspecies Correlation, Mode of Action, QSAR, REACH, Toxicity, US EPA) @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} } 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. |
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Hayriye Yilmaz, Lucky Ahmed, Bakhtiyor Rasulev, Jerzy Leszczynski Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives (Journal Article) Journal of Nanoparticle Research, 18 (5), pp. 123, 2016, ISSN: 1388-0764. (Abstract | Links | BibTeX | Tags: ) @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–ligand 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–activity 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} } 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–ligand 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–activity 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. |
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Anastasiia Golius, Leonid Gorb, Andrea Michalkova Scott, Frances C. Hill, Manoj Shukla, A. Benjamin Goins, David R. Johnson, Jerzy Leszczynski Experimental and computational study of membrane affinity for selected energetic compounds (Journal Article) Chemosphere, 148 , pp. 322–327, 2016, ISSN: 00456535. (Abstract | Links | BibTeX | Tags: ) @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} } 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). |
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Supratik Kar, Agnieszka Gajewicz, Kunal Roy, Jerzy Leszczynski, Tomasz Puzyn Ecotoxicology and Environmental Safety, 126 , pp. 238–244, 2016, ISSN: 01476513. (Abstract | Links | BibTeX | Tags: ) @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– toxicity relationship (nano-QTTR) models.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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– toxicity relationship (nano-QTTR) models. |
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Sedat Karabulut, Devran Uysal, Jerzy Leszczynski A new hybrid (experimental–theoretical) quantitative method for detection of relative anomer concentrations in water (Journal Article) Structural Chemistry, 27 (2), pp. 449–455, 2016, ISSN: 1040-0400. (Abstract | Links | BibTeX | Tags: ) @article{Karabulut2016, title = {A new hybrid (experimental–theoretical) 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} } 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. |
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Liudmyla K. Sviatenko, Leonid Gorb, Manoj K. Shukla, Jennifer M. Seiter, Danuta Leszczynska, Jerzy Leszczynski 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 (Journal Article) Chemosphere, 148 , pp. 294–299, 2016, ISSN: 00456535. (Abstract | Links | BibTeX | Tags: ) @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} } 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. |
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Natalia Sizochenko, Victor Kuz'min, Liudmila Ognichenko, Jerzy Leszczynski Introduction of simplex-informational descriptors for QSPR analysis of fullerene derivatives (Journal Article) Journal of Mathematical Chemistry, 54 (3), pp. 698–706, 2016, ISSN: 0259-9791. (Abstract | Links | BibTeX | Tags: ) @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} } 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. |
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Jing Wang, Jiande Gu, Md. Hossain, Jerzy Leszczynski Theoretical Studies on Hydrogen Bonds in Anions Encapsulated by an Azamacrocyclic Receptor (Journal Article) Crystals, 6 (3), pp. 31, 2016, ISSN: 2073-4352. (Abstract | Links | BibTeX | Tags: ) @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} } 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. |
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Marquita Watkins, Natalia Sizochenko, Bakhtiyor Rasulev, Jerzy Leszczynski Estimation of melting points of large set of persistent organic pollutants utilizing QSPR approach (Journal Article) Journal of Molecular Modeling, 22 (3), pp. 55, 2016, ISSN: 1610-2940. (Abstract | Links | BibTeX | Tags: ) @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—property 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} } 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—property 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. |
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G. M. Kuramshina, O. A. Vakula, N. I. Vakula, A. G. Majouga, V. M. Senyavin, Leonid G. Gorb, Jerzy Leszczynski Structural Chemistry, 27 (1), pp. 209–219, 2016, ISSN: 1040-0400. (Abstract | Links | BibTeX | Tags: ) @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–C2 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 (3500–10 cm-1 ) and FTIR (3900–400 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} } 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–C2 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 (3500–10 cm-1 ) and FTIR (3900–400 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. |
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Oleg V. Tinkov, Luidmila N. Ognichenko, Victor E. Kuz'min, Leonid G. Gorb, Anna P. Kosinskaya, Nail N. Muratov, Eugene N. Muratov, Frances C. Hill, Jerzy Leszczynski Computational assessment of environmental hazards of nitroaromatic compounds: influence of the type and position of aromatic ring substituents on toxicity (Journal Article) Structural Chemistry, 27 (1), pp. 191–198, 2016, ISSN: 1040-0400. (Abstract | Links | BibTeX | Tags: ) @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–brain 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} } 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–brain 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 |
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Alla P. Toropova, Andrey A. Toropov, Aleksandar M. Veselinović, Jovana B. Veselinović, Emilio Benfenati, Danuta Leszczynska, Jerzy Leszczynski Nano-QSAR: Model of mutagenicity of fullerene as a mathematical function of different conditions (Journal Article) Ecotoxicology and Environmental Safety, 124 , pp. 32–36, 2016, ISSN: 01476513. (Abstract | Links | BibTeX | Tags: ) @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. Veselinović and Jovana B. Veselinović 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} } 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 |
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