2018 |
| Anastasiia Golius, Leonid Gorb, Olexander Isayev, Jerzy Leszczynski Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations (Journal Article) Journal of Biomolecular Structure and Dynamics, pp. 1–9, 2018, ISSN: 0739-1102. (Links | BibTeX | Tags: ) @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}
}
|
| Pabitra Narayan Samanta, Jerzy Leszczynski High-temperature thermoelectric transport behavior of the Al/$gamma$-Al 2 O 3 interface: impact of electron and phonon scattering at nanoscale metal–ceramic contacts (Journal Article) Physical Chemistry Chemical Physics, 20 (21), pp. 14513–14524, 2018, ISSN: 1463-9076. (Abstract | Links | BibTeX | Tags: ) @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{\textendash}ceramic 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}
}
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. |
| Supratik Kar, Kunal Roy, Jerzy Leszczynski Impact of Pharmaceuticals on the Environment: Risk Assessment Using QSAR Modeling Approach (Book Chapter) Nicolotti, Orazio (Ed.): Computational Toxicology: Methods and Protocols, Methods in Molecular Biology, 1800 , pp. 395–443, 2018. (Links | BibTeX | Tags: ) @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}
}
|
| Supratik Kar, Kunal Roy, Jerzy Leszczynski Applicability Domain: A Step Toward Confident Predictions and Decidability for QSAR Modeling (Book Chapter) Nicolotti, Orazio (Ed.): Toxicology: Methods and Protocols, Methods in Molecular Biology, 1800 , pp. 141–169, Springer Nature , 2018. (Links | BibTeX | Tags: ) @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}
}
|
2017 |
| Kar, Supratik, Roy, Juganta K., Leszczynski, Jerzy In silico designing of power conversion efficient organic lead dyes for solar cells using todays innovative approaches to assure renewable energy for future (Journal Article) npj Computational Materials, 3 (1), pp. 22, 2017, ISSN: 2057-3960. (Links | BibTeX | Tags: ) @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}
}
|
| Maryam Emami Khansari, Ali Mirchi, Avijit Pramanik, Corey R. Johnson, Jerzy Leszczynski, Md. Alamgir Hossain Remarkable hexafunctional anion receptor with operational urea-based inner cleft and thiourea-based outer cleft: Novel design with high-efficiency for sulfate binding (Journal Article) Scientific Reports, 7 (1), pp. 6032, 2017, ISSN: 2045-2322. (Links | BibTeX | Tags: ) @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}
}
|
| Kar, Supratik, Sepúlveda, Maria S., Roy, Kunal, Leszczynski, Jerzy Endocrine-disrupting activity of per- and polyfluoroalkyl substances: Exploring combined approaches of ligand and structure based modeling (Journal Article) Chemosphere, 184 , pp. 514–523, 2017, ISSN: 00456535. (Links | BibTeX | Tags: ) @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}
}
|
| Tetiana Zubatiuk, Baharak Sajjadi, Glake Hill, Danuta Leszczynska, Wei-Yin Chen, Jerzy Leszczynski Modeling radical edge-site reactions of biochar in CO2/water solution under ultrasonic treatment (Journal Article) Chemical Physics Letters , 689 , pp. 48-55, 2017. (Abstract | Links | BibTeX | Tags: Antanthrene, Biochar, Carbon dioxide radical anion, CO2 capture, Density function theory, Electron transfer, Hydroxide radical, Radical addition) @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}
}
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. |
| Gorb Leonid,
Zubatiuk Tatiana,
Zubatyuk Roman,
Hovorun Dmytro,
Leszczynski Jerzy 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 (Journal Article) Journal of Molecular Modeling, 23 (10), pp. 289, 2017, ISSN: 1610-2940. (Abstract | Links | BibTeX | Tags: DNA geometrical and energetic characteristics, DNA mini helixes, Geometrical counterpoise type correction) @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{\textemdash}molecular 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}
}
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—molecular 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. |
| Vargaljuk, Viktor, Okovytyy, Sergiy, Polonskyy, Volodymyr, Kramska, Olga, Shchukin, Anatoly, Leszczynski, Jerzy Copper Crystallization from Aqueous Solution: Initiation and Evolution of the Polynuclear Clusters (Journal Article) Journal of Cluster Science, 28 (5), pp. 2517–2528, 2017, ISSN: 1040-7278. (Links | BibTeX | Tags: ) @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}
}
|
| Bobby Portis, Ali Mirchi, Maryam Emami Khansari, Avijit Pramanik, Corey R. Johnson, Douglas R. Powell, Jerzy Leszczynski, Md. Alamgir Hossain An Ideal C 3 -Symmetric Sulfate Complex: Molecular Recognition of Oxoanions by m -Nitrophenyl- and Pentafluorophenyl-Functionalized Hexaurea Receptors (Journal Article) ACS Omega, 2 (9), pp. 5840–5849, 2017, ISSN: 2470-1343. (Links | BibTeX | Tags: ) @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}
}
|
| Jagiello, Karolina, Sosnowska, Anita, Kar, Supratik, Demkowicz, Sebastian, Daśko, Mateusz, Leszczynski, Jerzy, Rachon, Janusz, Puzyn, Tomasz Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS (Journal Article) Structural Chemistry, 28 (4), pp. 1017–1032, 2017, ISSN: 1040-0400. (Links | BibTeX | Tags: ) @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}
}
|
| Gooch, Aminah, Sizochenko, Natalia, Rasulev, Bakhtiyor, Gorb, Leonid, Leszczynski, Jerzy In vivo toxicity of nitroaromatics: A comprehensive quantitative structure-activity relationship study (Journal Article) Environmental Toxicology and Chemistry, 36 (8), pp. 2227–2233, 2017, ISSN: 07307268. (Links | BibTeX | Tags: ) @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}
}
|
| Nhat, Pham Vu, Si, Nguyen Thanh, Leszczynski, Jerzy, Nguyen, Minh Tho Another look at structure of gold clusters Au n from perspective of phenomenological shell model (Journal Article) Chemical Physics, 493 , pp. 140–148, 2017, ISSN: 03010104. (Links | BibTeX | Tags: ) @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}
}
|
| Kirilchuk, Andrey A., Rozhenko, Alexander B., Leszczynski, Jerzy On structure and stability of pyrimidine ylidenes and their homologues (Journal Article) Computational and Theoretical Chemistry, 1103 , pp. 83–91, 2017, ISSN: 2210271X. (Links | BibTeX | Tags: ) @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}
}
|
