甘油对冰晶生长抑制作用的分子动力学模拟

doi:10.7503/cjcu20180744

高等学校化学学报 ›› 2019, Vol. 40 ›› Issue (4): 763.doi: 10.7503/cjcu20180744

甘油对冰晶生长抑制作用的分子动力学模拟

高洋¹, 李代禧¹(), 刘宝林¹, 郭柏松², 魏冬青³

1. 上海理工大学食品科学与工程研究所, 上海 200093
2. 上海东富龙科技股份有限公司注射剂实验室, 上海 201108
3. 上海交通大学微生物代谢国家重点实验室, 上海 200240

收稿日期:2018-11-02 出版日期:2019-04-10 发布日期:2019-02-25
作者简介:联系人简介: 李代禧, 男, 博士, 副教授, 主要从事计算生物学方面的研究. E-mail: dxli75@126.com
基金资助:
上海市自然科学基金(批准号: 12ZR1420400)和国家自然科学基金(批准号: 51776130)资助.

Inhibitory Mechanism of Glycerol on the Growth of Ice Crystals by Molecular Dynamics^†

GAO Yang¹, LI Daixi^1,^*(), LIU Baolin¹, GUO Baisong², WEI Dongqing³

1. Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
2. Injection Laboratory, Shanghai Tofflon Science and Technology Co., Ltd., Shanghai 201108, China
3. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China

Received:2018-11-02 Online:2019-04-10 Published:2019-02-25
Contact: LI Daixi E-mail:dxli75@126.com
Supported by:
† Supported by the Natural Science Foundation of Shanghai, China(No.12ZR1420400) and the National Natural Science Foundation of China(No.51776130).

摘要/Abstract

摘要：

采用分子模拟方法研究了正交晶系冰晶(020)生长面在不同浓度甘油水溶液中的生长情况. 通过统计分析氢键数、密度分布函数、均方根偏差和原子间径向分布函数研究了水分子和甘油分子的动态行为. 结果表明, 甘油分子在水溶液中可与水分子形成大量氢键, 这使水分子间的氢键作用受到抑制, 降低了水分子的扩散性, 致使冰晶不易成核和生长; 另外, 一些甘油分子可代替水分子吸附在晶面上, 甚至占据晶格位点, 这种行为打破了冰晶的对称性并且降低了冰晶的生长速率. 因此, 甘油可同时在晶面和液相中抑制冰晶的生长.

关键词: 抑制机理, 低温保护剂, 甘油, 冰晶生长, 分子动力学

Abstract:

The molecular simulations of the growth process of crystal face(020) of orthorhombic ice were performed in glycerol aqueous solutions at 225 K, 1×10⁵ Pa in order to investigate the inhibitory mechanism of glycerol for ice growth. Hydrogen bond number, density profile, root mean square deviation and intermolecular radial distribution functions were calculated to study the dynamic behavior of water and glycerol molecules. The result shows that the glycerol molecules can form numerous hydrogen bonds with water molecules. And water-water hydrogen bonds decreased with the increasing concentration of glycerol. Glycerol inhibits the interaction of hydrogen bonding between water molecules and makes nucleation of ice crystal difficult. Glycerol increases the viscosity of water solution and decreases the diffusivity of water molecule from solution to ice crystal face. More important, glycerol molecules have a competitive adsorption with water molecules on the crystal face, even occupy the surface lattice site and take place two or three water molecules. This behavior can break the symmetry of ice crystal face and prevent the further growth. Therefore, glycerol can play a role in inhibiting the growth of ice crystals in both aqueous solution and crystal face. So, the current research gives a better understanding for the inhibitory mechanism of glycerol on the growth of ice crystal and provide theoretical support for optimizing the protection prescriptions of biological tissues and protein medicine.

Key words: Inhibitory mechanism, Cryoprotective agent, Glycerol, Ice crystal growth, Molecular dynamics

中图分类号:

O641

TrendMD:

高洋, 李代禧, 刘宝林, 郭柏松, 魏冬青. 甘油对冰晶生长抑制作用的分子动力学模拟. 高等学校化学学报, 2019, 40(4): 763.

GAO Yang, LI Daixi, LIU Baolin, GUO Baisong, WEI Dongqing. Inhibitory Mechanism of Glycerol on the Growth of Ice Crystals by Molecular Dynamics^†. Chem. J. Chinese Universities, 2019, 40(4): 763.

图/表 9

Fig.1 Unit cell structure of orthorhombic ice Red sticks represent O atoms, white sticks represent H atoms.

Table 1 Detail component of ice, water and glycerol in each system*

System	N_G	N_W	N_I	X_G(%)	L_X,L_Y,L_Z/nm
B0	0	8040	432	0	4.38,2.65,22.90
B1	10	8030	432	0.12	4.41,2.65,23.13
B2	20	8020	432	0.25	4.42,2.62,23.18
B3	30	8010	432	0.37	4.40,2.63,23.34
B4	40	8000	432	0.50	4.39,2.64,23.44
B5	50	7990	432	0.62	4.39,2.63,23.47
B6	60	7980	432	0.75	4.39,2.62,23.56

Fig.2 Crystal morphology of ice unit cell in vacuum

Table 2 Crystal habit parameters of ice unit cell in vacuum

hkl	Multiplicity	d_hkl/nm	Total facet area/nm²	Total facet area(%)
(110)	4	0.389	32.3308	27.15
(020)	2	0.389	16.1668	13.58
(111)	4	0.344	15.7192	13.20
(11 $1 ˉ$ )	4	0.344	15.7192	13.20
(002)	1	0.366	11.7121	9.84
(00 $2 ˉ$ )	1	0.366	11.7121	9.84
(021)	2	0.344	7.8605	6.60
(02 $1 ˉ$ )	2	0.344	7.8605	6.60

Table 2 Crystal habit parameters of ice unit cell in vacuum

hkl	Multiplicity	d_hkl/nm	Total facet area/nm²	Total facet area(%)
(110)	4	0.389	32.3308	27.15
(020)	2	0.389	16.1668	13.58
(111)	4	0.344	15.7192	13.20
(11 $1 ˉ$ )	4	0.344	15.7192	13.20
(002)	1	0.366	11.7121	9.84
(00 $2 ˉ$ )	1	0.366	11.7121	9.84
(021)	2	0.344	7.8605	6.60
(02 $1 ˉ$ )	2	0.344	7.8605	6.60

Fig.3 Growing status of the facet (020) in each system after 200 ns(A) The H-bond number between water molecules in each system; (B) snapshots of each system at 200 ns.

Fig.4 H-bond number between water molecules and glycerol molecules in each system(A) The number of H-bond between water and glycerol molecule vs. XG; (B) the water-water H-bond average number(HW…OW/NW) and the glycerol-water H-bond percentage P vs. XG.

Fig.5 Competitive adsorption behavior of glycerol moleculeRed sticks represent O atoms, white sticks represent H atoms, and gray sticks represent C atoms. (A) A normal ice crystal layer; (B) an ice crystal layer which two water molecules are replaced by one glycerol molecules; (C) an ice crystal layer which three water molecules are replaced by one glycerol.

Fig.6 Dynamic adsorption process of glycerol molecule(A) The distance between initial crystal face and glycerols vs. time; (B) RMSD of Gly-free and Gly-bound vs. time. a. Gly-free; b. Gly-bound.

Fig.7 Snapshots of B1 system at 1 ns(A), 71 ns(B) and 141 ns(C)Red sticks represent O atoms, white sticks represent H atoms, and gray sticks represent C atoms.

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甘油对冰晶生长抑制作用的分子动力学模拟

Inhibitory Mechanism of Glycerol on the Growth of Ice Crystals by Molecular Dynamics^†

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甘油对冰晶生长抑制作用的分子动力学模拟

Inhibitory Mechanism of Glycerol on the Growth of Ice Crystals by Molecular Dynamics†

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Inhibitory Mechanism of Glycerol on the Growth of Ice Crystals by Molecular Dynamics^†