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Chin. Phys. B, 2018, Vol. 27(8): 083103    DOI: 10.1088/1674-1056/27/8/083103
ATOMIC AND MOLECULAR PHYSICS Prev   Next  

A simulation study of water property changes using geometrical alteration in SPC/E

Ming-Ru Li(李明儒)1,2, Nan Zhang(张楠)1,2, Feng-Shou Zhang(张丰收)1,2,3
1 Key Laboratory of Beam Technology and Materials Modification of the Ministry of Education of China and College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China;
2 Beijing Radiation Center, Beijing 100875, China;
3 Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China
Abstract  We present a systematic investigation of the impact of changing the geometry structure of the SPC/E water model by performing a series of molecular dynamic simulations at 1 bar (1 bar=105 Pa) and 298.15 K. The geometric modification includes altering the H-O-H angle range from 90° to 115° and modifying the O-H length range from 0.90 Å to 1.10 Å in the SPC/E model. The former is achieved by keeping the dipole moment constant by modifying the O-H length, while in the latter only the O-H length is changed. With the larger bond length and angle, we find that the liquid shows a strong quadrupole interaction and high tetrahedral structure order parameter, resulting in the enhancement of the network structure of the liquid. When the bond length or angle is reduced, the hydrogen bond lifetime and self-diffusion constant decrease due to the weakening of the intermolecular interaction. We find that modifying the water molecular bond length leading to the variation of the intermolecular interaction strength is more intensive than changing the bond angle. Through calculating the average reduced density gradient and thermal fluctuation index, it is found that the scope of vdW interaction with neighbouring water molecules is inversely proportional to the change of the bond length and angle. The effect is mainly due to a significant change of the hydrogen bond network. To study the effect of water models as a solvent whose geometry has been modified, the solutions of ions in different solvent environments are examined by introducing NaCl. During the dissolving process, NaCl ions are ideally dissolved in SPC/E water and bond with natural water more easily than with other solvent models.
Keywords:  molecular dynamics simulation      geometric modification      intermolecular interaction      ion's solvation  
Received:  03 April 2018      Revised:  15 May 2018      Accepted manuscript online: 
PACS:  31.15.xv (Molecular dynamics and other numerical methods)  
  31.70.-f (Effects of atomic and molecular interactions on electronic structure)  
  61.25.Em (Molecular liquids)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11635003, 11025524, and 11161130520), the National Basic Research Program of China (Grant No. 2010CB832903), and the European Commission's 7th Framework Programme (Fp7-PEOPLE-2010-IRSES) (Grant Agreement Project No. 269131).
Corresponding Authors:  Feng-Shou Zhang     E-mail:  fszhang@bnu.edu.cn

Cite this article: 

Ming-Ru Li(李明儒), Nan Zhang(张楠), Feng-Shou Zhang(张丰收) A simulation study of water property changes using geometrical alteration in SPC/E 2018 Chin. Phys. B 27 083103

[1] Davis J G, Gierszal K P, Wang P and Ben-Amotz D 2012 Nature 491 582
[2] Stiopkin I V, Weeraman C, Pieniazek P A, Shalhout F Y, Skinner J L and Benderskii A V 2011 Nature 474 192
[3] Ji M, Odelius M and Gaffney K J 2010 Science 328 1003
[4] Chen B, Ivanov I, Klein M L and Parrinello M 2003 Phys. Rev. Lett. 91 215503
[5] Vega C, Sanz E and Abascal J L F 2005 J. Chem. Phys. 122 114507
[6] Harrington S, Poole P H, Sciortino F and Stanley H E 1997 J. Chem. Phys. 107 7443
[7] Horne R A and Johnson D S 1966 J. Phys. Chem. 70 2182
[8] Tan M L, Fischer J T, Chandra A, Brooks B R and Ichiye T 2003 Chem. Phys. Lett. 376 646
[9] Gu B, Zhang F S, Wang Z P and Zhou H Y 2008 Phys. Rev. Lett. 100 088104
[10] Shen X, Gu B, Che S A and Zhang F S 2011 J. Chem. Phys. 135 034509
[11] Shen H, Cheng W and Zhang F S 2015 RSC Adv. 5 9627
[12] Huang J, Lopes P E M, Roux B and MacKerell A D 2014 J. Phys. Chem. Lett. 5 3144
[13] Vedamuthu M, Singh S and Robinson G W 1994 J. Phys. Chem. 98 2222
[14] Yan Z, Buldyrev S V and Stanley H E 2008 Phys. Rev. E 78 051201
[15] Nilsson A and Pettersson L G M 2015 Nat. Commun. 6 8998
[16] Lynden-Bell R M, Giovambattista N, Debenedetti P G, Head-Gordon T and Rossky P 2011 Phys. Chem. Chem. Phys. 13 2748
[17] Bergman D L and Lynden-Bell R M 2001 Mol. Phys. 99 1011
[18] Lynden-Bell R M and Head-Gordon T 2006 Mol. Phys. 104 3593
[19] Lynden-Bell R M and Youngs T G A 2006 Mol. Simul. 32 1025
[20] Lynden-Bell R M and Debenedetti P G 2005 J. Phys. Chem. B 109 6527
[21] Zhang F S and Lynden-Bell R M 2005 Phys. Rev. E 71 021502
[22] Chatterjee S, Debenedetti P G, Stillinger F H and Lynden-Bell R M 2008 J. Chem. Phys. 128 124511
[23] Gu B, Zhang F S, Wang Z P and Zhou H Y 2008 J. Chem. Phys. 129 184505
[24] Berendsen H J C, Grigera J R and Straatsma T P 1987 J. Phys. Chem. 91 6269
[25] Weerasinghe S and Smith P E 2003 J. Chem. Phys. 119 11342
[26] Bussi G, Donadio D and Parrinello M 2007 J. Chem. Phys. 126 014101
[27] Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A D and Haak J R 1984 J. Chem. Phys. 81 3684
[28] Ryckaert J P, Ciccotti G and Berendsen H J C 1977 J. Comput. Phys. 23 327
[29] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
[30] Petersen H G 1995 J. Chem. Phys. 103 3668
[31] Hess B, Kutzner C, van der Spoel D and Lindahl E 2008 J. Chem. Theory Comput. 4 435
[32] Lu T and Chen F 2012 J. Comput. Chem. 33 580
[33] Humphrey W, Dalke A and Schulten K 1996 J. Mol. Graphics 14 33
[34] Kumar R, Schmidt J R and Skinner J L 2007 J. Chem. Phys. 126 204107
[35] Kalinichev A G and J D Bass 1994 Chem. Phys. Lett. 231 301
[36] Svishchev I M and Kusalik P G 1993 J. Chem. Phys. 99 3049
[37] Errington J R and Debenedetti P G 2001 J. Chem. Phys. 409 318
[38] Torquato S, Truskett T M and Debenedetti P G 2000 Phys. Rev. Lett. 84 2064
[39] Sharma R, Chakraborty S N and Chakravarty C 2006 J. Chem. Phys. 125 204501
[40] Truskett T M, Torquato S and Debenedetti P G 2000 Phys. Rev. E 62 993
[41] Abascal J L F and C Vega 2007 J. Phys. Chem. 111 15811
[42] Abascal J L F and Vega C 2007 Phys. Chem. Chem. Phys. 9 2775
[43] Jabes B S, Nayar D, Dhabal D, Molinero V and Chakravarty C 2012 J. Phys: Condens. Matter 24 284116
[44] Johnson E R, Keinan S, Snchez P M, Garca J C, Cohen A J and Yang W 2010 J. Am. Chem. Soc. 132 6498
[45] Contreras-Garcia J, Johnson E R, Keinan S, Chaudret R, Piquemal J. P, Beratan D N and Yang W 2011 J. Chem. Theory Comput. 7 625
[46] Garcia J C, Calatayud M, Piquemal J P and Recio J M 2012 Comput. Theor. Chem. 998 193
[47] Roza A O, Johnson E R and Garcia J C 2012 Phys. Chem. Chem. Phys. 14 12165
[48] Bartha F, Kapuy O, Kozmutza C and Van Alsenoy C 2003 J. Mol. Struct. (Theochem) 666 117
[49] Lyubartsev A P and Laaksonen A 1996 J. Phys. Chem. 100 16410
[50] Gu B, Zhang F S, Huang Y G and Fang X 2010 Chin. Phys. B 19 036101
[51] Kropman M F and Bakker H J 2001 Science 291 2118
[52] Hribar B, Southall N T, Vlachy V and Dill K A 2002 J. Am. Chem. Soc. 41 12302
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