Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

doi:10.1088/1674-1056/25/1/013104

中国物理B ›› 2016, Vol. 25 ›› Issue (1): 13104-013104.doi: 10.1088/1674-1056/25/1/013104

所属专题： TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics

• TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

Yexin Feng(冯页新), Ji Chen(陈基), Xin-Zheng Li(李新征), Enge Wang(王恩哥)

1. International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, China;
2. School of Physics, Peking University, Beijing 100871, China;
3. Collaborative Innovation Center of Quantum Matter, Beijing 100871, China

收稿日期:2015-05-21 出版日期:2016-01-05 发布日期:2016-01-05
通讯作者: Xin-Zheng Li E-mail:xzli@pku.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

Yexin Feng(冯页新)¹, Ji Chen(陈基)¹, Xin-Zheng Li(李新征)^2,3, Enge Wang(王恩哥)^1,3

1. International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, China;
2. School of Physics, Peking University, Beijing 100871, China;
3. Collaborative Innovation Center of Quantum Matter, Beijing 100871, China

Received:2015-05-21 Online:2016-01-05 Published:2016-01-05
Contact: Xin-Zheng Li E-mail:xzli@pku.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

摘要/Abstract

摘要：

The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice.

关键词: ab initio calculations, isotope, molecular dynamics, hydrogen bonds

Abstract:

Key words: ab initio calculations, isotope, molecular dynamics, hydrogen bonds

中图分类号: (Ab initio calculations)

31.15.A-

67.63.-r (Hydrogen and isotopes) 71.15.Pd (Molecular dynamics calculations (Car-Parrinello) and other numerical simulations) 82.30.Rs (Hydrogen bonding, hydrophilic effects)

冯页新, 陈基, 李新征, 王恩哥. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds[J]. 中国物理B, 2016, 25(1): 13104-013104.

Yexin Feng(冯页新), Ji Chen(陈基), Xin-Zheng Li(李新征), Enge Wang(王恩哥). Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds[J]. Chin. Phys. B, 2016, 25(1): 13104-013104.

参考文献 65

[1]	Marx D, Tuckerman M E, Hutter J and Parrinello M 1999 Nature 397 601
[2]	Marrone J A and Car R 2008 Phys. Rev. Lett. 101 017801
[3]	Fanourgakis G S, Schenter G K and Xantheas S S 2006 J. Chem. Phys. 125 141102
[4]	Habershon T E, Markland S and Manolopoulos D E 2009 J. Chem. Phys. 131 024501
[5]	Chen B, Ivanov I, Klein M L and Parrinello M 2003 Phys. Rev. Lett. 91 215503
[6]	Li X Z, Probert M I J, Alavi A and Michaelides A 2010 Phys. Rev. Lett. 104 066102
[7]	Li X Z, Walker B and Michaelides A 2011 Proc. Natl. Acad. Sci. USA 108 6369
[8]	Matsushita E and Matsubara T 1982 Prog. Theor. Phys. 67 1
[9]	Ubbelohde A R and Gallagher K J 1955 Acta. Crystallogr. 8 71
[10]	Marrone J A, Lin L and Car R 2009 J. Chem. Phys. 130 204511
[11]	Burnham C J, Anick D J, Mankoo P K and Reiter G F 2008 J. Chem. Phys. 128 154519
[12]	Meng X Z 2015 Nat. Phys. 11 235
[13]	Zhang D H, Collins M A and Lee S Y 2000 Science 290 961
[14]	Liu K 2001 Annu. Rev. Phys. Chem. 52 139
[15]	Collins M A 2002 Theo. Chem. Acc. 108 313
[16]	Althorpe S C and Clary D C 2003 Annu. Rev. Phys. Chem. 54 593
[17]	Qiu M H 2006 Science 311 1440
[18]	Feynman R P 1949 Phys. Rev. 76 769
[19]	Feynman R P 1953 Phys. Rev. 90 1116
[20]	Feynman R P 1953 Phys. Rev. 91 1291
[21]	Feynman R P 1953 Phys. Rev. 91 1301
[22]	Feynman R P and Hibbs A R 1965 Quantum Mechanics and Path Integrals (New York: McGraw-Hill Inc.)
[23]	Chandler D and Wolynes P G 1981 J. Chem. Phys. 74 4078
[24]	Parrinello M and Rahman A 1984 J. Chem. Phys. 80 860
[25]	Berne B J and Thirumalai D 1986 Annu. Rev. Phys. Chem. 37 401
[26]	Pollock E L and Ceperley D M 1984 Phys. Rev. B 30 2555
[27]	Ceperley D M and Pollock E L 1986 Phys. Rev. Lett. 56 351
[28]	Pollock E L and Ceperley D M 1987 Phys. Rev. B 36 8343
[29]	Ceperley D M 1995 Rev. Mod. Phys. 67 279
[30]	Tuckerman M E, Marx D, Klein M L and Parrinello M 1996 J. Chem. Phys. 104 5579
[31]	Marx D and Parrinello M 1996 J. Chem. Phys. 104 4077
[32]	Morales M A, Pierleoni C, Schwegler E and Ceperley D M 2010 Proc. Natl. Acad. Sci. USA 107 12799
[33]	Li X Z 2013 J. Phys.: Condens. Matter 25 085402
[34]	Chen J 2013 Nat. Commun. 4 2064
[35]	Morales M A, McMahon J M, Pierleoni C and Ceperley D M 2013 Phys. Rev. Lett. 110 065702
[36]	Morales M A, McMahon J M, Pierleoni C and Ceperley D M 2013 Phys. Rev. B 87 184107
[37]	Davidson E R M, Klimes J, Alf'e D and Michaelides A 2014 ACS Nano 8 9905
[38]	Tachikawa M and Shiga M 2005 J. Am. Chem. Soc. 127 11908
[39]	Kaczmarek A, Shiga M and Marx D 2009 J. Phys. Chem. A 113 1985
[40]	Tozzini V 2005 Curr. Opin. Struct. Biol. 15 144
[41]	Bartels C and Karplus M 1998 J. Phys. Chem. B 102 865
[42]	Sugita Y and Okamoto Y 1999 Chem. Phys. Lett. 314 141
[43]	Laio A and Parrinello M 2002 Proc. Natl. Acad. Sci. USA 99 12562
[44]	Gao Y Q, Yang L J, Fan Y B and Shao Q 2008 Int. Rev. Phys. Chem. 27 201
[45]	Pérez A and von Lilienfeld O A 2011 J. Chem. Theory Comput. 7 2358
[46]	Habershon S and Manolopoulos D E 2011 J. Chem. Phys. 135 224111
[47]	Li X Z and Wang E G 2014 Computer Simulations of Molecules and Condensed Matters: From Electronic Structures to Molecular Dynamics (Beijing: Peking University Press)
[48]	Stroobants A, Lekkerkerker H N W and Frenkel D 1987 Phys. Rev. A 36 2929
[49]	Frenkel D, Lekkerkerker H N W and Stroobants A 1988 Nature 332 822
[50]	Meijer E J, Frenkel D, LeSar R A and Ladd A J C 1990 J. Chem. Phys. 92 7570
[51]	Meijer E J and Frenkel D 1991 J. Chem. Phys. 94 2269
[52]	Eldridge M D, Madden P A and Frenkel D 1993 Nature 365 35
[53]	Perdew J P, Burke K and Ernzerhof M 1996 Phys. Rev. Lett. 77 3865
[54]	Clark S J 2005 Z. Kristallogr 220 567
[55]	Tuckerman M E, Berne B J, Martyna G J and Klein M L 1993 J. Chem. Phys. 99 2796
[56]	Feng Y X, Chen J, Alfé D, Li X Z, Wang E G, et al. 2015 J. Chem. Phys. 142 064506
[57]	Feng Y X et al. to be submitted
[58]	Andersen H C 1980 J. Chem. Phys. 72 2384
[59]	Raugei S and Klein M L 2003 J. Am. Chem. Soc. 125 8992
[60]	Gregory J K and Clary D C 1996 J. Phys. Chem. 100 18014
[61]	Clary D C, Benoit D M and van Mourik T 2000 Acc. Chem. Res. 33 441
[62]	Wendler K, Thar J, Zahn S and Kirchner B 2010 J. Phys. Chem. A 114 9529
[63]	Xantheas S S and Dunning T H 1993 J. Chem. Phys. 99 8774
[64]	Cubero E, Orozco M, Hobza P and Luque F J 1999 J. Phys. Chem. A 103 6394
[65]	Swalina C, Wang Q, Chakraborty A and Hammes-Schiffer S 2007 J. Phys. Chem. A 111 2206

Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

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