Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field
Nonbonding parameters of AMBER force field have been refined based on ab initio binding energies of CO2–[C7H5N2]− complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 for ε and σ parameters, respectively. Molecular dynamics simulations of CO2 molecules in rigid framework...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2013-01-01
|
| Series: | Journal of Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2013/415027 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832559744626196480 |
|---|---|
| author | W. Wongsinlatam T. Remsungnen |
| author_facet | W. Wongsinlatam T. Remsungnen |
| author_sort | W. Wongsinlatam |
| collection | DOAJ |
| description | Nonbonding parameters of AMBER force field have been refined based on ab initio binding energies of CO2–[C7H5N2]− complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 for ε and σ parameters, respectively. Molecular dynamics simulations of CO2 molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2 molecules. One slight but notable difference is that CO2 molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II. |
| format | Article |
| id | doaj-art-188d7b8bff4f4cd997b1a15888a41eec |
| institution | Kabale University |
| issn | 2090-9063 2090-9071 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Chemistry |
| spelling | doaj-art-188d7b8bff4f4cd997b1a15888a41eec2025-02-03T01:29:15ZengWileyJournal of Chemistry2090-90632090-90712013-01-01201310.1155/2013/415027415027Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force FieldW. Wongsinlatam0T. Remsungnen1The Applied Mathematics Research Group (AMRG), Department of Mathematics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, ThailandThe Applied Mathematics Research Group (AMRG), Department of Mathematics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, ThailandNonbonding parameters of AMBER force field have been refined based on ab initio binding energies of CO2–[C7H5N2]− complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 for ε and σ parameters, respectively. Molecular dynamics simulations of CO2 molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2 molecules. One slight but notable difference is that CO2 molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.http://dx.doi.org/10.1155/2013/415027 |
| spellingShingle | W. Wongsinlatam T. Remsungnen Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field Journal of Chemistry |
| title | Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field |
| title_full | Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field |
| title_fullStr | Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field |
| title_full_unstemmed | Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field |
| title_short | Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field |
| title_sort | molecular dynamics simulations of co2 molecules in zif 11 using refined amber force field |
| url | http://dx.doi.org/10.1155/2013/415027 |
| work_keys_str_mv | AT wwongsinlatam moleculardynamicssimulationsofco2moleculesinzif11usingrefinedamberforcefield AT tremsungnen moleculardynamicssimulationsofco2moleculesinzif11usingrefinedamberforcefield |