基于全极化连续介质模型计算溶液分子的第一原理电子结构理论方法的发展和应用

doi:10.3866/PKU.WHXB20110101

Abstract

Abstract:

This is a brief review of some recent progress in the development and application of firstprinciples electronic structure approaches for molecules in solution. In particular, it accounts for the background, theoretical features, and representative applications of a recently developed, truly accurate continuum solvation model which is known as Surface and Volume Polarization for Electrostatics (SVPE) or Fully Polarizable Continuum Model (FPCM) in literature. The FPCM-based first-principles electronic structure approaches have been widely employed to study a variety of chemical and biochemical problems and serve as an integrated part of various computational protocols for rational drug design. Some perspective of the future of the FPCM-based first-principles electronic structure approaches is also given.

Key words: Solvation, Solvent effect, Electronic structure theory, Continuum model

ZHAN Chang-Guo. Development and Application of First-Principles Electronic Structure Approach for Molecules in Solution Based on Fully Polarizable Continuum Model[J].Acta Phys. -Chim. Sin., 2011, 27(01): 1-10.

References

1. Rivail, J. L.; Rinaldi, D. Computational chemistry: reviews of current trends. Leszczynski, J. Ed. Singapore:World Scientific, 1996:Vol.1, p139
2. Orozco, M.; Luque, F. J. Chem. Rev., 2000, 100: 4187
3. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev., 2005, 105: 2999
4. Cramer, C. J.;Truhlar, D. G.Acc. Chem. Res., 2009, 42: 493
5. Bandyopadhyay, P.; Gordon, M. S. J. Chem. Phys., 2000, 113, 1104
6. Zhan, C. G.; Landry, D.W.; Ornstein, R. L. J. Am. Chem. Soc., 2000, 122: 1522
7. Zhan, C. G.; Landry, D.W.; Ornstein, R. L. J. Am. Chem. Soc., 2000, 122: 2621
8. Gronert, S.; Pratt, L. M.; Mogali, S. J. Am. Chem. Soc., 2001, 123: 3081
9. Clementi, E. Computational aspects of large chemical systems. Berlin: Springer, 1980
10. Gao, J.; Xia, X. F. Science, 1992, 258: 631
11. Vreven,T.; Morokuma, K. J. Chem. Phys., 2000, 113: 2969
12. Cui, Q.; Karplus, M. J. Chem. Phys., 2000, 112: 1133
13. Florian, J.;Warshel,A. J. Phys. Chem. B, 1997, 101: 5583
14. Broo,A.; Pearl, G.; Zerner, M. C. J. Phys. Chem.A, 1997, 101: 2478
15. Jung,Y.; Ho Choi, C. H.; Gordon, M. S. J. Phys. Chem. B, 2001, 105: 4039
16. Hori,T.;Takahashi, H.; Nakano, M.; Nitta,T.;Yang,W. Chem. Phys. Lett., 2006, 419: 240
17. Acevedo, O.; Jorgensen,W. L. Acc. Chem. Res., 2010, 43: 142
18. Tomasi, J.; Persico, M. Chem. Rev., 1994, 94: 2027
19. Cramer, C. J.;Truhlar, D. G. Chem. Rev., 1999, 99: 2161
20. Kinoshita, M.; Hirata, F. J. Chem. Phys., 1996, 104: 8807
21. Palmer, D. S.; Sergiievskyi,V. P.; Jensen, F.; Fedorov, M.V. J. Chem. Phys., 2010, 133: 044104
22. Miyata,T.; Ikuta,Y.; Hirata, F. J. Chem. Phys., 2010, 133: 044114
23. Chen,W.; Gordon, M. S. J. Chem. Phys., 1996, 105: 11081
24. Kerdcharoen,T.; Morokuma, K. Chem. Phys. Lett., 2002, 355: 257
25. Kerdcharoen,T.; Morokuma, K. J. Chem. Phys., 2003, 118: 8856
26. Hou, G.; Zhu, X.; Cui, Q. J. Chem. Theory Comput., 2010, 6: 2303
27. Heard, G. L.;Yates, B. F. J. Comput. Chem., 1996, 17: 1444
28. Cossi, M.; Barone,V.; Cammi, R.;Tomasi, J. Chem. Phys. Lett., 1996, 255: 327
29. Foresman, J. B.; Keith,T. A.;Wiberg, K. B.; Snoonian, J.; Frisch, M. J. J. Phys. Chem., 1996, 100: 16098
30. Cancès, E.; Mennucci, B.;Tomasi, J. J. Chem. Phys., 1997, 107: 3032
31. Tomasi, J.; Mennucci, B.; Cances, E. J. Mol. Struct. -Theochem, 1999, 464: 211
32. Klamt,A.; Jonas,V. J. Chem. Phys., 1996, 105: 9972
33. Barone,V.; Cossi, M., J. Phys. Chem.A, 1998, 102: 1995
34. Zhan, C. G.; Bentley, J.; Chipman, D. M. J. Chem. Phys., 1998, 108: 177
35. Zhan, C. G.; Chipman, D. M. J. Chem. Phys., 1998, 109: 10543
36. Zhan, C. G.; Chipman, D. M. J. Chem. Phys., 1999, 110: 1611
37. Zhan, C. G.; Landry, D.W.; Ornstein, R. L. J. Phys. Chem.A, 2000, 104: 7672
38. Zhan, C. G.; Norberto de Souza, O.; Rittenhouse, R.; Ornstein, R. L. J. Am. Chem. Soc., 1999, 121: 7279
39. Zhan, C. G.; Zheng, F. J. Am. Chem. Soc., 2001, 123: 2835
40. Zhan, C. G.; Landry, D.W. J. Phys. Chem.A, 2001, 105: 1296
41. Zhan, C. G.; Niu, S.; Ornstein, R. L. J. Chem. Soc. Perkin Trans. 2, 2001: 23
42. Zheng, F.; Zhan, C. G.; Ornstein, R. L. J. Chem. Soc. Perkin Trans. 2, 2001: 2355
43. Zhan, C. G.; Dixon, D.A. J. Phys. Chem.A, 2001, 105: 11534
44. Dixon, D.A.; Feller, D.; Zhan, C. G.; Francisco, J. S. J. Phys. Chem. A, 2002, 106: 3191
45. Zheng, F.; Zhan, C. G.; Ornstein, R. L. J. Phys. Chem. B, 2002, 106: 717
46. Zhan, C. G.; Dixon, D.A. J. Phys. Chem.A, 2002, 106: 9737
47. Zhan, C. G.; Dixon, D.A.; Sabri, M. I.; Kim, M. S.; Spencer, P. S. J. Am. Chem. Soc., 2002, 124: 2744
48. Zhan, C. G.; Dixon, D.A. J. Phys. Chem. B, 2003, 107: 4403
49. Dixon, D.A.; Feller, D.; Zhan, C. G.; Francisco, S. F. Int. J. Mass Spectrom., 2003, 227: 421
50. Zhan, C. G.; Dixon, D.A.; Spencer, P. S. J. Phys. Chem. B, 2003, 107: 2853
51. Chen, X.; Zhan, C. G. J. Phys. Chem.A, 2004, 108: 3789
52. Chen, X.; Zhan, C. G. J. Phys. Chem.A, 2004, 108: 6407
53. Zhan, C. G.; Spencer, P. S.; Dixon, D.A. J. Phys. Chem. B, 2004, 108: 6098
54. Zhan, C. G.; Dixon, D.A. J. Phys. Chem.A, 2004, 108: 2020
55. Zhan, C. G.; Deng, S. X.; Skiba, J. G.; Hayes, B.A.;Tschampel, S. M.; Shields, G. C.; Landry, D.W. J. Comput. Chem., 2005, 26: 980
56. Xiong,Y.; Zhan, C. G. J. Phys. Chem.A, 2006, 110: 12644
57. Lu, H.-T.; Chen, X.; Zhan, C. G. J. Phys. Chem. B, 2007, 111: 10599
58. Chen, X.; Zhan, C. G. J. Phys. Chem. B, 2008, 112: 16851
59. Zheng, F.; Dwoskin, L. P.; Crooks, P. A.; Zhan, C. G. Theo. Chem. Acc., 2009, 124: 269
60. Chipman, D. M. J. Chem. Phys., 1999, 110: 8012
61. Chipman, D. M. J. Chem. Phys., 2000, 112: 5558
62. Chipman, D. M. Theo. Chem. Acta, 2002, 107: 80
63. Chipman, D. M. Theo. Chem. Acta, 2004, 111: 61
64. Xiong,Y.; Zhan, C. G. J. Org. Chem., 2004, 69: 8451
65. Dejaegere, A.; Karplus, M. J. Am. Chem. Soc., 1993, 115: 5316
66. Schmidt, M.W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S.T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.;Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem., 1993, 14: 1347
67. Vilkas, M. J.; Zhan, C. G. J. Chem. Phys., 2008, 129: 194109
68. Frisch, M. J.;Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03. Revision C.02.Wallingford, CT: Gaussian Inc., 2004
69. Cramer, C. J.;Truhlar, D. G.Acc. Chem. Res., 2008, 41: 760
70. Liu, J.; Kelly, C. P.; Goren,A. C.; Marenich,A.V.; Cramer, C. J.; Truhlar, D. G.; Zhan, C. G. J. Chem. Theory Comput., 2010, 6: 1109
71. Kelly, C. P.; Cramer, C. J.;Truhlar, D. G. J. Chem. Theory Comput., 2005, 1: 1133
72. ?lebocka-Tilk,H.; Sauriol, F.;Monette,M.;Brown,R. S. Can. J. Chem., 2002, 80: 1343
73. Bolton, P. D.Aust. J. Chem., 1966, 19: 1013
74. Bolton, P. D.; Jackson, G. L. Aust. J. Chem., 1971, 24: 969
75. Guthrie, J. P. J. Am. Chem. Soc., 1974, 96: 3608
76. Conway, B. E. Ionic hydration in chemistry and biophysics. New York: Elsevier, 1981
77. Marcus,Y. Ion salvation. NewYork:Wiley, 1985
78. Hille, B. Ionic channels of excitable membranes. 2nd ed. Sunderland, MA: Sinauer, 1992
79. Franks, N. P.; Lieb,W. R. Nature, 1997, 389: 334
80. Gunshin, H.; Mackenzie, B.; Berger, U.V.; Gunshin,Y.; Romero, M. F.; Boron,W. F.; Nussberger, S.; Gollan, J. L.; Hediger, M.A. Nature, 1997, 388: 482
81. Doyle, D.A.; Cabral, J. M.; Pfuetzner, R.A.; Kuo,A.; Gulbis, J. M.; Cohen, S. L.; Chait, B.T.; MacKinnon, R. Science, 1998, 280: 69
82. MacKinnon, R.; Cohen, S. L.; Kuo,A.; Lee, A.; Chait, B.T. Science, 1998, 280: 106
83. Nakamura,T.;Akutagawa,T.; Honda, K.; Underhill,A. E.; Coomber,A.T.; Friend, R. H. Nature, 1998, 394: 159
84. Roux, B.; MacKinnon, R. Science, 1999, 285: 100
85. Wu, K.; Iedema, M. J.; Cowin, J. P. Science, 1999, 286: 2482
86. Anson, L. Nature, 1999, 402: 739
87. MacFarlane, D. R.; Huang, J.; Forsyth, M. Nature, 1999, 402: 792
88. Kolbe, M.; Besir, H.; Essen, L. O.; Oesterhelt, D. Science, 2000, 288: 1390
89. Weber, J. M.; Kelley, J. A.; Nielsen, S. B.;Ayotte, P.; Johnson, M.A. Science, 2000, 287: 2461
90. Aqvist, J.; Luzhkov,V. Nature, 2000, 404: 881
91. Williams, K.A. Nature, 2000, 403: 112
92. Pasquarello, A.; Petri, I.; Salmon, P. S.; Parisel, O.; Car, R.; Tóth, é.; Powell, D. H.; Fischer, H. E.; Helm, L.; Merbach,A. Science, 2001, 291: 856
93. Kielpinski, D.; Meyer,V.; Rowe, M.A.; Sackett, C.A.; Itano,W. M.; Monroe, C.;Wineland, D. J. Science, 2001, 291: 1013
94. Kropman, M. F.; Bakker, H. J. Science, 2001, 291: 2118
95. Mejias, J. A.; Lago, S. J. Chem. Phys., 2000, 113: 7306
96. Friedman, H. L.; Krishnan,V.V.Water:Acomprehensive treatise. NewYork: Plenum, 1973
97. Zhu,T.; Li, J.; Hawkins, G. D.; Cramer, C. J.;Truhlar, D. G. J. Chem. Phys. 1998, 109: 9117
98. Tissandier, M. D.; Cowen, K.A.; Feng,W.Y.; Gundlach, E.; Cohen, M. H.; Earhart,A. D.; Coe, J.V. J. Phys. Chem.A, 1998, 102: 7787; 1998, 102: 9308 (correction)
99. Mallard,W. G.; Linstrom, P. J. Eds. NIST chemistry webbook, NIST standard reference database number 69, February 2000. Gaithersburg, MD: National Institute of Standards andTechnology, 2000 (http://webbook.nist.gov)
100. Ruscic, B.; Feller, D.; Dixon, D.A.; Peterson, K.A.; Harding, L. B.;Asher, R. L.;Wagner,A. F. J. Phys. Chem.A, 2001, 105: 1
101. Ruscic, B.;Wagner,A. F.; Harding, L. B.;Asher, R. L.; Feller, D.; Dixon, D.A.; Peterson, K.A.; Song,Y.; Qian, X.; Ng, C.Y.; Liu, J.; Chen,W.; Schwenke, D.W. J. Phys. Chem.A, 2002, 106: 2727
102. Huang, X.; Zheng, F.; Crooks, P. A.; Dwoskin, L. P.; Zhan, C. G. J. Am. Chem. Soc., 2005, 127: 14401
103. Huang, X.; Zheng, F.; Chen, X.; Crooks, P. A.; Dwoskin, L. P.; Zhan, C. G. J. Med. Chem., 2006, 49: 7661
104. Huang, X.; Zheng, F.; Stokes, C.; Papke, R. L.; Zhan, C. G. J. Med. Chem., 2008, 51: 6293
105. Huang, X.; Zheng, F.; Zhan, C. G. J. Am. Chem. Soc., 2008, 130: 16691
106. Pan,Y.; Gao, D.; Zhan, C. G. J. Am. Chem. Soc., 2008, 130: 5140
107. Zhan, C. G.; Zheng, F.; Landry, D.W. J. Am. Chem. Soc., 2003, 125: 2462
108. Hamza,A.; Cho, H.;Tai, H. H.; Zhan, C. G. J. Phys. Chem. B, 2005, 109: 4776
109. Gao, D.; Zhan, C. G. J. Phys. Chem. B, 2005, 109: 23070
110. Zhan, C. G.; Gao, D. Biophysical Journal, 2005, 89: 3863
111. Liu, J.; Hamza,A.; Zhan, C. G. J. Am. Chem. Soc., 2009, 131: 11964
112. Gao, D.; Zhan, C. G. Proteins, 2006, 62: 99
113. Pan,Y.; Gao, D.;Yang,W.; Cho, H.;Yang, G. F.;Tai, H. H.; Zhan, C. G. Proc. Natl. Acad. Sci. U. S.A., 2005, 102: 16656
114. Gao, D.; Cho, H.;Yang,W.; Pan,Y.;Yang, G. F.;Tai, H. H.; Zhan, C. G.Angew. Chem. Int. Edit., 2006, 45: 653
115. Pan,Y.; Gao, D.;Yang,W.; Cho, H.; Zhan, C. G. J. Am. Chem. Soc., 2007, 129: 13537
116. Zheng, F.;Yang,W.; Ko, M. C.; Liu, J.; Cho, H.; Gao, D.;Tong, M.;Tai, H.-H.;Woods, J. H.; Zhan, C. G. J. Am. Chem. Soc., 2008, 130: 12148
117. Yang,W.; Pan,Y.; Fang, L.; Gao, D.; Zheng, F.; Zhan, C. G. J. Phys. Chem. B, 2010, 114: 10889
118. Yang,W.; Pan,Y.; Zheng, F.; Cho, H.;Tai, H. H.; Zhan, C. G. Biophysical Journal, 2009, 96: 1931
119. Zheng, F.; Zhan, C. G. Org. Biomol. Chem., 2008, 6: 836
120. Zheng, F.; Zhan, C. G. J. Computer-Aided Mol. Design, 2008, 22: 661
121. Brim, R. L.; Nance, M. R.;Youngstrom, D.W.; Narasimhan, D.; Zhan, C. G.;Tesmer, J. J. G.; Sunahara, R. K.;Woods, J. H. Mol. Pharmacol., 2010, 77: 593
122. Yang,W.; Xue, L.; Fang, L.; Zhan, C. G. Chemico-Biological Interactions, 2010, 187: 148
123. Gao, D.; Narasimhan, D. L.; Macdonald, J.; Ko, M. C.; Landry, D. W.;Woods, J. H.; Sunahara, R. K.; Zhan, C. G. Mol. Pharmacol., 2009, 75: 318
124. Zheng, F.; Zhan, C. G. Future Med. Chem., 2009, 1: 515
125. Collins, G.T.; Brim, R. L.; Narasimhan, D.; Ko, M. C.; Sunahara, R. K.; Zhan, C. G.;Woods, J. H. J. Pharm. Exp. Ther., 2009, 331: 445
126. Koca, J.; Zhan, C. G.; Rittenhouse, R.; Ornstein, R. L. J. Am. Chem. Soc., 2001, 123: 817
127. Xiong,Y.; Lu, H.; Li,Y.;Yang, G.; Zhan, C. G. Biophysical Journal, 2006, 91: 1858
128. Xiong,Y.; Lu, H.T.; Zhan, C. G. J. Comput. Chem., 2008, 29: 1259
129. Lu, H.; Goren,A. C.; Zhan, C. G. J. Phys. Chem. B, 2010, 114: 7022

[1]	Yae Qi, Yongyao Xia. Electrolyte Regulation Strategies for Improving the Electrochemical Performance of Aqueous Zinc-Ion Battery Cathodes [J]. Acta Phys. -Chim. Sin., 2023, 39(2): 2205045-0.
[2]	Aidi Han, Xiaohui Yan, Junren Chen, Xiaojing Cheng, Junliang Zhang. Effects of Dispersion Solvents on Proton Conduction Behavior of Ultrathin Nafion Films in the Catalyst Layers of Proton Exchange Membrane Fuel Cells [J]. Acta Phys. -Chim. Sin., 2022, 38(3): 1912052-.
[3]	Zixu He, Yawei Chen, Fanyang Huang, Yulin Jie, Xinpeng Li, Ruiguo Cao, Shuhong Jiao. Fluorinated Solvents for Lithium Metal Batteries [J]. Acta Phys. -Chim. Sin., 2022, 38(11): 2205005-.
[4]	Zhang Xin, Dengbao Han, Xiaomei Chen, Yu Chen, Shuai Chang, Haizheng Zhong. Effects of Solvent Coordination on Perovskite Crystallization [J]. Acta Phys. -Chim. Sin., 2021, 37(4): 2008055-.
[5]	Chen Wu, Ying Zhou, Xiaolong Zhu, Minzhi Zhan, Hanxi Yang, Jiangfeng Qian. Research Progress on High Concentration Electrolytes for Li Metal Batteries [J]. Acta Phys. -Chim. Sin., 2021, 37(2): 2008044-.
[6]	Yi Yang, Chong Yan, Jiaqi Huang. Research Progress of Solid Electrolyte Interphase in Lithium Batteries [J]. Acta Phys. -Chim. Sin., 2021, 37(11): 2010076-.
[7]	Kang YANG,Xiaorui SHUAI,Huachao YANG,Jianhua YAN,Kefa CEN. Electrochemical Performance of Activated Graphene Powder Supercapacitors Using a Room Temperature Ionic Liquid Electrolyte [J]. Acta Phys. -Chim. Sin., 2019, 35(7): 755-765.
[8]	Fuzhen BI,Xiao ZHENG,Chiyung YAM. First-Principles Study of Mixed Cation Methylammonium-Formamidinium Hybrid Perovskite [J]. Acta Phys. -Chim. Sin., 2019, 35(1): 69-75.
[9]	Hassan GOLMOHAMMADI,Zahra DASHTBOZORGI,Sajad KHOOSHECHIN. Developing a Support Vector Machine Based QSPR Model to PredictGas-to-Benzene Solvation Enthalpy of Organic Compounds [J]. Acta Phys. -Chim. Sin., 2017, 33(5): 918-926.
[10]	Yang WU,Li-Li YUE,Qiao-Zhen LIU,Xia WANG. A Theoretical Study of the Thermodynamic Properties of Imidazolium Acetate Ionic Liquids [J]. Acta Phys. -Chim. Sin., 2016, 32(8): 1960-1966.
[11]	Jing ZOU,Zhi-Lin FAN,Li-Sha JIANG,Dan-Hong ZHOU. Theoretical Study of the Solvent Adsorption on Ti-Peroxo Active Center in Ti-MWW Zeolite [J]. Acta Phys. -Chim. Sin., 2016, 32(4): 935-942.
[12]	Jun-Feng XIANG,Ping-Gui YI,Zhi-Yong REN,Xian-Yong YU,Jian CHEN,Wu LIU,Tao-Mei LI. Effect of Supra-Molecular Interaction on the Intramolecular Proton Transfer of 2-(2-Aminophenyl)benzothiazole [J]. Acta Phys. -Chim. Sin., 2016, 32(3): 624-630.
[13]	Dong ZHENG,Xiang-Ai YUAN,Jing MA. Rationalization of pH-Dependent Absorption Spectrum of o-Methyl Red in Aqueous Solutions: TD-DFT Calculation and Experiment Study [J]. Acta Phys. -Chim. Sin., 2016, 32(1): 290-300.
[14]	WU Ying-Xi, WANG Hong-Yan, LIN Yue-Xia. Aqueous Solution Effects on the Proton-Transfer Processes of GC and AT Base Pairs [J]. Acta Phys. -Chim. Sin., 2014, 30(2): 257-264.
[15]	ZHAO Cheng-Xiao, WANG Hai-Tao, LI Min. Research Progress in the Correlation between Gelation Properties and Solvent Parameters [J]. Acta Phys. -Chim. Sin., 2014, 30(12): 2197-2209.

Development and Application of First-Principles Electronic Structure Approach for Molecules in Solution Based on Fully Polarizable Continuum Model

PDF

Like

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Metrics

Recommended 0