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Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

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Abstract

Coarse-grained studies of CH3SH, CH3CHO and CHCl3 liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

Comparison of vdW intermolecular interaction energies calculated from the CG and all-atom simulations for CH3SH homo-dimers

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References

  1. Nilsson L, Karplus M (1986) J Comput Chem 7:591–616

    Article  CAS  Google Scholar 

  2. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL, Evansek JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B III, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  3. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P (1984) J Am Chem Soc 106:765–784

    Article  CAS  Google Scholar 

  4. Cornell WD, Cieplak P, Bayly CI, Gould IR Jr, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179–5197

    Article  CAS  Google Scholar 

  5. Jorgensen WL, Tirado-Rives J (1988) J Am Chem Soc 110:1657–1671

    Article  CAS  Google Scholar 

  6. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225–11236

    Article  CAS  Google Scholar 

  7. Hermans J, Berendsen HJC, van Gunsteren WF, Postma JPM (1984) Biopolymers 23:1513–1518

    Article  CAS  Google Scholar 

  8. Daura X, Mark AE, van Gunsteren WF (1998) J Comput Chem 19:535–547

    Article  CAS  Google Scholar 

  9. Onuchic J, Luthey-Schulten Z, Wolynes PG (1997) Annu Rev Phys Chem 48:545–600

    Article  CAS  Google Scholar 

  10. Dobson CM, Šali A, Karplus M (1998) Angew Chem Int Ed 37:868–893

    Article  Google Scholar 

  11. Shakhnovich EI (2006) Chem Rev 106:1559–1588

    Article  CAS  Google Scholar 

  12. Halgren TA, Damm W (2001) Curr Opin Struct Biol 11:236–242

    Article  CAS  Google Scholar 

  13. Finney JL (2001) J Mol Liq 90:303–312

    Article  CAS  Google Scholar 

  14. Rick SW, Stuart SJ (2002) Rev Comput Chem 18:89–146

    CAS  Google Scholar 

  15. Ren PY, Ponder JW (2003) J Phys Chem B 107:5933–5947

    Article  CAS  Google Scholar 

  16. Ponder JW, Case DA (2003) Adv Protein Chem 66:27–85

    Article  CAS  Google Scholar 

  17. Yang ZZ, Wang CS (2003) J Theor Comput Chem 2:273–300

    Article  CAS  Google Scholar 

  18. Gresh N, Guo H, Salahub DR, Roques BP, Kafafi SA (1999) J Am Chem Soc 121:7885–7894

    Article  CAS  Google Scholar 

  19. Patel S, Mackerell AD Jr, Brooks CL III (2004) J Comput Chem 25:1504–1514

    Article  CAS  Google Scholar 

  20. Banks JL, Kaminski GA, Zhou RH, Mainz DT, Berne BJ, Friesner RA (1999) J Chem Phys 110:741–754

    Article  CAS  Google Scholar 

  21. Akkermans RLC, Briels WJ (2001) J Chem Phys 114:1020–1031

    Article  CAS  Google Scholar 

  22. Marrink SJ, de Vries AH, Mark AE (2004) J Phys Chem B 108:750–760

    Article  CAS  Google Scholar 

  23. Zacharopoulos N, Vergadou N, Theodorou DN (2005) J Chem Phys 122:244111

    Article  Google Scholar 

  24. Chu JW, Izvekov S, Voth GA (2006) Mol Simul 32:211–218

    Article  CAS  Google Scholar 

  25. Girard S, Müller-Plathe F (2004) Lect Notes Phys 640:327–356

    Article  CAS  Google Scholar 

  26. Han W, Wu YD (2007) J Chem Theory Comput 3:2146–2161

    Article  CAS  Google Scholar 

  27. van den Noort A, den Otter WK, Briels WJ (2007) Europhys Lett 80:28003

    Article  Google Scholar 

  28. Hills RD, Brooks CL III (2009) Int J Mol Sci 10:889–905

    Article  CAS  Google Scholar 

  29. Tozzini V (2005) Curr Opin Struct Biol 15:144–150

    Article  CAS  Google Scholar 

  30. Voth GA (ed) (2009) Coarse-graining of condensed phase and biomolecular systems. CRC, Boca Raton

    Google Scholar 

  31. Golubkov PA, Ren PY (2006) J Chem Phys 125:064103

    Article  Google Scholar 

  32. Gay JG, Berne BJ (1981) J Chem Phys 74:3316–3319

    Article  CAS  Google Scholar 

  33. Cleaver DJ, Care CM, Allen MP, Neal MP (1996) Phys Rev E 54:559–567

    Article  CAS  Google Scholar 

  34. Golubkov PA, Wu JC, Ren PY (2008) Phys Chem Chem Phys 10:2050–2057

    Article  CAS  Google Scholar 

  35. Wu JC, Zhen X, Shen HJ, Li GH, Ren PY (2011) J Chem Phys 135:155104

    Article  Google Scholar 

  36. Xu PJ, Tang YY, Zhang J, Zhang ZB, Wang K, Shao Y, Shen HJ, Mao YC (2011) Acta Phys Chim Sin 27:1839–1846 (in Chinese)

    CAS  Google Scholar 

  37. Dennington R, Keith T, Millam J (2009) Semichem Inc, Shawnee Mission KS

  38. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR Jr, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03. Gaussian Inc, Wallingford

    Google Scholar 

  39. Stone AJ (2005) J Chem Theory Comput 1:1128–1132

    Article  CAS  Google Scholar 

  40. Pedretti A, Villa L, Vistoli G (2003) Theory Chem Acc 109:229–232

    Article  CAS  Google Scholar 

  41. Wu C, Siddiq M, Bo SQ, Chen TL (1996) Macromolecules 29:3157–3160

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work is supported by the National High-tech Research and Development Program (2009AA01A137), the National Natural Science Foundation of China (31070641/ C050101), and “Hundred Talents Program of the Chinese Academy Sciences”. The work of Y. S. is also supported by the Fundamental Research Funds for the Central Universities of China (2011QN151).

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Authors and Affiliations

  1. Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning Province, People’s Republic of China

    Peijun Xu, Hujun Shen, Lu Yang, Yang Ding, Beibei Li & Guohui Li

  2. School of Physics and Electronic Technology, Liaoning Normal University, Dalian, 116029, Liaoning Province, People’s Republic of China

    Peijun Xu, Lu Yang, Yang Ding, Beibei Li & Yingchen Mao

  3. Physics of Department, Dalian Maritime University, Dalian, 116026, Liaoning Province, People’s Republic of China

    Ying Shao

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  1. Peijun Xu
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  2. Hujun Shen
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  3. Lu Yang
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  4. Yang Ding
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  5. Beibei Li
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  6. Ying Shao
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  7. Yingchen Mao
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  8. Guohui Li
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Corresponding authors

Correspondence to Yingchen Mao or Guohui Li.

Additional information

Peijun Xu and Hujun Shen contributed equally to this work

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Xu, P., Shen, H., Yang, L. et al. Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials. J Mol Model 19, 551–558 (2013). https://doi.org/10.1007/s00894-012-1562-5

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  • DOI: https://doi.org/10.1007/s00894-012-1562-5

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