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Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations)
We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, me...
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Formato: | Texto |
Lenguaje: | English |
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Molecular Diversity Preservation International (MDPI)
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821004/ https://www.ncbi.nlm.nih.gov/pubmed/20162016 http://dx.doi.org/10.3390/ijms11010288 |
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author | Xue, Yong Mansoori, G. Ali |
author_facet | Xue, Yong Mansoori, G. Ali |
author_sort | Xue, Yong |
collection | PubMed |
description | We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives. |
format | Text |
id | pubmed-2821004 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-28210042010-02-16 Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) Xue, Yong Mansoori, G. Ali Int J Mol Sci Article We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives. Molecular Diversity Preservation International (MDPI) 2010-01-21 /pmc/articles/PMC2821004/ /pubmed/20162016 http://dx.doi.org/10.3390/ijms11010288 Text en © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Xue, Yong Mansoori, G. Ali Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title | Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title_full | Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title_fullStr | Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title_full_unstemmed | Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title_short | Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) |
title_sort | self-assembly of diamondoid molecules and derivatives (md simulations and dft calculations) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821004/ https://www.ncbi.nlm.nih.gov/pubmed/20162016 http://dx.doi.org/10.3390/ijms11010288 |
work_keys_str_mv | AT xueyong selfassemblyofdiamondoidmoleculesandderivativesmdsimulationsanddftcalculations AT mansoorigali selfassemblyofdiamondoidmoleculesandderivativesmdsimulationsanddftcalculations |