Citation: XU Pei-Jun, TANG Yuan-Yuan, ZHANG Jing, ZHANG Zhi-Bo, WANG Kun, SHAO Ying, SHEN Hu-Jun, MAO Ying-Chen. Molecular Dynamics Simulation of Organic Solvents Based on the Coarse-Grained Model[J]. Acta Physico-Chimica Sinica, ;2011, 27(08): 1839-1846. doi: 10.3866/PKU.WHXB20110811 shu

Molecular Dynamics Simulation of Organic Solvents Based on the Coarse-Grained Model

1.
1. School of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China;
2. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning Province, P. R. China;
3. Department of Physics, Dalian Maritime University, Dalian 116026, Liaoning Province, P. R. China

Received Date: 28 February 2011
Available Online: 14 June 2011
Fund Project: 中央高校专项资金优秀青年教师基金(2009QN069)资助项目 (2009QN069)

To obtain Gay-Berne (GB) parameters, we carried out Monte Carlo sampling of four reference configurations based on the Boltzmann distribution. After comparing with the van der Waals potential within the all-atom model we obtained the GB parameters. Also by fitting the charge, dipole, and quadrupole with the electric potential obtained from quantum chemical computations with Gaussian 03 we obtained the electric multipole potential (EMP) parameters. With the GB-EMP parameters we then carried out molecular dynamics simulations (MDS) for CHCl₃ and tetrahydrofuran (THF) based on the coarse- grained (CG) model. Compared with the all-atom model, the CG model can reproduce the simulation results on the whole, but there are some deviations in the simulations in some details. The reason is that we only take one interaction site into account in this work. Therefore, for more complicated molecules it is necessary to take the placement of the interaction sites into account. Additionally, the multi-sites situation is also considered in the MDS within the frame of the coarse-grained model.
- Coarse-grained model,
- Gay-Berne potential,
- Electric multipole potential,
- Radial distribution function,
- Molecular dynamics simulation
1. [1]
  
  (1) Dror, R. O.; Jensen, M. ?.; Borhani, D.W.; Shaw, D. E. J. Gen. Physiol. 2010, 135, 555.
2. [2]
  (2) Karplus, M.; McCammon, J. A. Nature Struct. Biol. 2002, 9, 646.
3. [3]
  (3) Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan Y. B.;Wriggers,W. Science 2010, 330, 341.
4. [4]
  (4) van Gunsteren,W. F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glättli, A.; Hünenberger, P. H.; Kastenholz, M. A.; Oostenbrink, C.; Schenk, M.; Trzesniak, D.; van der Vegt, N. F. A.; Yu, H. B. B. Angew. Chem. Int. Edit. 2006, 45, 4064.
5. [5]
  (5) Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Curr. Opin. Struct. Biol. 2009, 19, 120.
6. [6]
  (6) Freddolino, P. L.; Harrison, C. B.; Liu, Y. X.; Schulten. K. Nature Phys. 2010, 6, 751.
7. [7]
  (7) Xu, X. J.; Hou, T. J.; Qiao, X. B.; Zhang,W. Computer Aided Drug Design; Chemical Industry Press: Beijing, 2004; pp 169-172. [徐筱杰, 侯廷军, 乔学斌, 章威. 计算机辅助药物分子设计. 北京: 化学工业出版社, 2004, 169-172.]
8. [8]
  (8) Leach, A. P. Molecular Modeling, Principles and Application; Person Education Limited: England, 2001; pp165-245.
9. [9]
  (9) Schlick, T. Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd ed.; Springer: New York, 2010; pp 265-343.
10. [10]
  (10) Voth, G. A. Coarse-Graining Of Condensed Phase and Biomolecular Systems; CRC Press: England, 2009.
11. [11]
  (11) Chu, J.W.; Izvekov, S.; Voth, G. A. Mol. Sim. 2006, 32, 211.
12. [12]
  (12) Marrink, S. J.; de Vries, A. H.; Mark, A. E. J. Phys. Chem. B 2004, 108, 750.
13. [13]
  (13) Tozzini, V. Curr. Opin. Struc. Biol. 2005, 15, 114.
14. [14]
  (14) lubkov, P. A.; Ren, P. Y. J. Chem. Phys. 2006, 125, 064103.
15. [15]
  (15) Berne, B. J.; Pechukas, P. J. Chem. Phys. 1972, 56, 4213.
16. [16]
  (16) Gay, J. G.; Berne, B. J. J. Chem. Phys. 1981, 74, 3316.
17. [17]
  (17) Cleaver, D. J.; Care, C. M.; Allen, M. P.; Neal, M. P. Phys. Rev. E 1996, 54, 559.
18. [18]
  (18) Wilson, M. R. J. Chem. Phys. 1997, 107, 8654.
19. [19]
  (19) Care, C. M.; Cleaver, D. J. Rep. Prog. Phys. 2005, 68, 2665.
20. [20]
  (20) Paramonov, L.; Yaliraki, S. N. J. Chem. Phys. 2005, 123, 194111.
21. [21]
  (21) Kabadi, V. N.; Steele,W. A. Ber. Bunsenges. Phys. Chem. 1985, 89, 2.
22. [22]
  (22) Kabadi, V. N. Ber. Bunsenges. Phys. Chem. 1986, 90, 327.
23. [23]
  (23) Jackson, J. D. Classical Electrodynamics, 3rd ed; JohnWiley & Sons Inc.: New York, 1999; pp 145-150.
24. [24]
  (24) Applequist, J. J. Phys. A 1989, 22, 4303.
25. [25]
  (25) Ponder, J.W. TINKER Molecular Modeling, Package 5.1; Washington University Medical School.
26. [26]
  (26) Darden, T.; York, D.; Pedersen, L. G. J. Chem. Phys. 1993, 98, 10089.
27. [27]
  (27) Sagui, C.; Pedersen, L. G.; Darden, T. A. J. Chem. Phys. 2004, 120, 73.
28. [28]
  (28) Ren, P. Y.; Ponder, J.W. J. Phys. Chem. B 2003, 107, 5933.
29. [29]
  (29) Wang, J. M.;Wolf, R. M.; Caldwell,W. J.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157.
30. [30]
  (30) Yang, L. J.; Tan, C. H.; Hsieh, M. J.;Wang, J. M.; Duan, Y.; Cieplak, P.; Caldwell,W. J.; Kollman, P. A. Luo, R. J. Phys. Chem. B 2006, 110, 13166.
31. [31]
  (31) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03, Revision A.01; Gaussian Inc.: Pittsburgh, PA, 2003.
32. [32]
  (32) Stone, A. J. J. Chem. Theory Comput. 2005, 1, 1128.
33. [33]
  (33) lubkov, P. A.;Wu, J. C.; Ren, P. Y. Phys. Chem. Chem. Phys. 2008, 10, 2050.
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