用第一性原理方法获取周期体系中原子的部分电荷

doi:10.3866/PKU.WHXB20101009

Abstract

Abstract:

We calculated the electrostatic potential (ESP) and electric field (EF) of periodic liquid water systems using the quantum chemistry software package, Crystal. We proposea method to obtain atomic partial charges rapidly for periodic systems based on first-principles calculations. In this method, the average electrostatic potential φ^mean, which is introduced to meet the periodic boundary condition, is taken as a parameter during the least squares fitting of the ESP from first-principles calculations and used in the Ewald summation. A comparison of the two methods, i.e., ESP and EF fitting, reveals that the relative root mean-square deviation (RMS) of the former method is only 2%-3%, which is one order of magnitude smaller than that of the latter method. In addition, the distribution of the derived atomic partial charges and dipole moments for the water system are discussed using four charge restrained fits.

Key words: Atomic partial charge, Least square fitting, Electrostatic potential, Electrostatic field, Ewald summation

MSC2000:

O641

LI Ya-Na, Lü Yang, ZHOU Li-Chuan, CHEN Li, LI Shen-Min. Atomic Partial Charges for Periodic Systems from First -Principles Calculations[J].Acta Phys. -Chim. Sin., 2010, 26(10): 2793-2800.

References

1. Verstraelen, T.; Speybroeck, V. V.; Waroquier, M. J. Chem. Phys., 2009, 131: 044127
2. Mulliken, R. S. J. Chem. Phys., 1955, 23: 1833
3. Bader, R. F. W.; Matta, C. F. J. Phys. Chem. A, 2004, 108: 8385
4. Breneman, C. M.;Wiberg, K. B. J. Comput. Chem., 1990, 11: 361
5. Arroyo, S. T.; Martin, J. A. S.; Carcia, A. H. Chem. Phys. Lett., 2002, 357: 279
6. Besler, B. H.; Merz, K. M.; Kollman Jr., P. A. J. Comput. Chem., 1990, 11: 431
7. Singh, U. C.; Kollman, P. A. J. Comput. Chem., 1984, 5: 129
8. Wang, J.; Wolf, R. M.; Caklwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem., 2004, 25: 1157
9. Whitten, A. E.; Mckinnon, J. J.; Spackman, M. A. J. Comput. Chem., 2006, 27: 1063
10. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem., 2000, 21: 1049
11. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; CheathamIII, T. E.; Wang, J.; Ross,W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. AMBER 7 user's Manual. California: University of California, 2002
12. Gao, J.; Xia, X. Science, 1992, 258: 631
13. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem., 1990, 11: 700
14. Patel, S.; Brooks, C. L. J. Comput. Chem., 2004, 25: 1
15. Varekova, R. S.; Koca, J. J. Comput. Chem., 2006, 27: 396
16. Sanderson, R. T. Chemical bond and bond energies. NewYork: Academic Press, 1976
17. Sanderson, R. T. Polar covalence. NewYork: Academic Press, 1983
18. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem., 1987, 91: 6269
19. Jorgensen,W. L.; Madura, J. D. J. Am. Chem. Soc., 1983, 105: 1407
20. Mahoney, M.W.; Jorgensen, W. L. J. Chem. Phys., 2000, 112: 8910
21. Yang, Z. Z.; Wu, Y.; Zhao, D. X. J. Chem. Phys., 2004, 120: 2541
22. Zhang, Q.; Yang, Z. Z. Chem. Phys. Lett., 2005, 403: 242
23. Yang, Z. Z.; Zhang, Q. J. Comput. Chem., 2006, 27: 1
24. Yang, Z. Z.; Qian, P. J. Chem. Phys., 2006, 125: 064311
25. Wu, Y.; Yang, Z. Z. J. Phys. Chem. A, 2004, 108: 7563
26. Ewald, P. P. Ann. Phys., 1921, 64: 253
27. Dovesi, R.; Saunders, V. R.; Roetti, C.; Orlando, R.; Zicovich- Wilson, C. M.; Pascale, F.; Civalleri, B.; Doll, K.; Harrison, N. M.; Bush, I. J.; D'Arco, P.; Llunell, M. Crystal 06 user's manual. Torino: University of Torino, 2006
28. Spoel, D. v. d.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem., 2005, 26: 1701
29. Saunders, V. R.; Freyria-Fava, C.; Dovesi, R.; Salasco, L.; Roetti, C. Mol. Phys., 1992, 77: 629
30. Stewart, R. F. God Jugosl Cent Kristalogr, 1982, 17: 1
31. Campañá, C.; Mussard, B.; Woo, T. K. J. Chem. Theory Comput., 2009, 5: 2866
32. Shirono, K.; Daiguji, H. Chem. Phys. Lett., 2006, 417: 251

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Atomic Partial Charges for Periodic Systems from First -Principles Calculations

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