期刊文献+

有机小分子溶液的红外吸收光谱的分子动力学模拟 被引量:2

Molecular Dynamics Simulation of Infrared Absorption Spectrum of Small Organic Molecular Liquids
下载PDF
导出
摘要 在AMOEBA极化力场下对水、甲醇和乙醇溶液的红外吸收光谱进行了分子动力学模拟,与传统力场的计算结果相比,更好地符合了实验结果。这主要由于考虑了电多极矩效应和诱导偶极矩效应,AMOEBA力场对静电相互作用进行精确的描述,进而较好地模拟了化学键的弯曲振动和伸缩振动。 The aim of this paper is to study the infrared spectrum of water, methanol and ethanol liquids by molecular dynamics simulations. Compared with the results by the simulations based on the traditional force fields, the results from the simulations with the AMOEBA polarizable force field are more in line with the experiment results. The critical reason is that AMOEBA force field describes the electrostatic interaction much better than others force fields due to the electric multipole effects and the induced dipole effect considered in the field, and makes the bend vibration and the stretch vibration of molecular bonds more accurately determined in the simulation.
出处 《辽宁工业大学学报(自然科学版)》 2013年第1期38-42,共5页 Journal of Liaoning University of Technology(Natural Science Edition)
关键词 红外吸收光谱 可极化力场 分子动力学模拟 infrared absorption spectrum polarizable force field molecular dynamic simulation
  • 相关文献

参考文献18

  • 1Allinger N L, Yuh Y H, Lii J H. Molecular mechanics. The MM3 force field for hydrocarbon. 1 [J]. J Am Chem Soc, 1989, 111: 8551-8566.
  • 2Cornell W D, Cieplak P, Bayly C I, et al. A second generation force field for the simulation of protein, nucleic acids, and organic molecules, A[J]. J Am Chem Soc, 1995, 117: 5179-5197.
  • 3MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins[J]. J Phys Chem B, 1998, 102: 3586-3616.
  • 4Jorgensen W L, Miaxwell D S, Tirado-Rives J. Development and testing of the OPLS All-atom force field on conformational energetics and properties of organic liquids[J]. J Am Chem Soc, 1996, 118:11225-11236.
  • 5Oostenbrink C, Villa A, Mark A E, et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6[J]. J Comput Chem, 2004, 25: 1656-1676.
  • 6Ren ,: Y, Ponder J W. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations[J]. J Comput Chem, 2002, 23: 1497-1506.
  • 7Grossfield A, Ren P Y, Ponder J W. Ion solvation thermodynamics from simulation with a polarizable force field[J]. J Am Chem Soc, 2003, 125: 15671-15682.
  • 8Ren P, Ponder J W. Polarizable atomic multipole water model for molecular mechanics simulation[J]. J Phys Chem B, 2003, 107: 5933-5947.
  • 9Kaminski G A, Stem H A, Berne B J, et al. Development of an accurate and robust polarizable molecular mechanics force field form ab initio quantum chemistry[J]. J Phys Chem A, 2004, 108: 621-627.
  • 10Ren P, Ponder J W. Phys. Temperature and pressure dependence of the AMOEBA water model[J]. J Phys Chem B, 2004, 108: 13427-13437.

二级参考文献33

  • 1Dror, R. O.; Jensen, M. 0.; Borhani, D. W.; Shaw, D. E. J. Gen. Physiol. 2010, 135, 555.
  • 2Karplus, M.; McCammon, J. A. Nature Struct. Biol. 2002, 9, 646.
  • 3Shaw, D. E.; Maragakis, E; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. E; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y. B.; Wriggers, W. Science 2010, 330, 341.
  • 4van Gunsteren, W. F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glattli, A.; Hiinenberger, P. H.; Kastenholz, M. A.; Oostenbrink, C.; Schenk, M.; Trzesniak, D.; van der Vegt, N. E A.; Yu, H. B. B. Angew. Chem. Int. Edit. 2006, 45, 4064.
  • 5Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Curt. Opin. Struct. Biol. 2009, 19, 120.
  • 6Freddolino, E L.; Harrison, C. B.; Liu, Y. X.; Schulten, K. Nature Phys. 2010, 6, 751.
  • 7Xu, X. J.; Hou, T. J.; Qiao, X. B.; Zhang, W. Computer Aided Drug Design; Chemical Industry Press: Beijing, 2004; pp169-172.
  • 8Leach, A. P. Molecular Modeling, Principles and Application; Person Education Limited: England, 2001; pp 165-245.
  • 9Schlick, T. Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd ed.; Springer: New York, 2010; pp 265-343.
  • 10Voth, G. A. Coarse-Graining of Condensed Phase and Biomolecular Systems; CRC Press: England, 2009.

共引文献2

同被引文献27

引证文献2

二级引证文献11

相关作者

内容加载中请稍等...

相关机构

内容加载中请稍等...

相关主题

内容加载中请稍等...

浏览历史

内容加载中请稍等...
;
使用帮助 返回顶部