Improvement of Calcium Cation-Chloride Anion Interaction Lennard-Jones Parameters for Molecular Dynamics Simulations

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吳瑞庭(WU, JUI-TING) 查詢紙本館藏

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化學學系

論文名稱

(Improvement of Calcium Cation-Chloride Anion Interaction Lennard-Jones Parameters for Molecular Dynamics Simulations)

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摘要(中)

在理論和模擬不同種的實驗方法下,水溶液中離子與離子對的水合結構、水合能、分子動態學是一個長期研究且具吸引力的主題，值得一提的是鈣離子與鎂離子在細胞膜生理功能上扮演極具影響的角色，另一方面在各組研究顯示鈣離子與水的配位的結果是不一致的。早前的古典力場分子模擬研究指出高濃度電解液中會觀察到過多離子簇生成，其原因來自於使用Lorentz-Berthelot combining rule的方法來估算陽離子與陰離子的蘭納-瓊斯作用力，此近似的方法使用在系統預設值來進行分子動態模擬產生陽、陰離子相互作用力是不當的。
此次的研究，我們採用Luo與 Roux所提出的方法來改善鈣離子與氯離子蘭納-瓊斯作用參數，有兩組力場參數需要進行優化，第一組為Roux的鈣離子與氯離子蘭納-瓊斯作用參數(CHARMM預設值，鈣與水形成五角雙錐體)第二組Lim的參數(鈣與水形成四角反稜柱)。基於使用Lim的鈣離子蘭納-瓊斯參數下，來修正鈣離子與氯離子蘭納-瓊斯作用力，我們模擬結果發現Lim參數可以重現在近乎飽和濃度下的滲透壓實驗值且鈣離子與氯離子蘭納-瓊斯作用參數還能重現大範圍濃度滲透壓的結果，但在Roux鈣離子蘭納-瓊斯參數下卻是辦不到的，再者使用我們優化Lim的鈣離子與氯離子蘭納-瓊斯作用力的結果還能支持近期鈣離子與水配位為八的結果，且改善方法容易操作在CHARMM與NAMD的軟體中。

摘要(英)

Abstract
Hydrated structure, molecular dynamics, and hydration energies of ions and ion-pairs in aqueous solution have long been an attractive topic under investigated in terms of various experimental, theoretical, and simulation methods. Particularly, calcium ion (Ca2+) and magnesium ion (Mg2+) play significant roles for biochemical functions of cells. Experimental and simulation results regarding the Ca2+H2O coordination number are pretty diverse. Previous studies have shown that the excess ion cluster formation in concentrated electrolyte solutions observed in classical molecular dynamics simulations (MD) is arisen from the improper cation-anion Lennard-Jones (LJ) interacting parameters, approximated by Lorentz-Berthelot combining rule, which are generally default used in MD simulations. In this study, we follow the same methodology proposed by Luo and Roux1 to determine the Ca2+Cl LJ interaction parameter. Two sets of Ca2+ LJ parameters are used for optimization: Roux’s (pentagonal bipyramidal hydrated structure; default used in CHARMM)(see Figure S2) and Lim’s parameters (square antiprism hydrated structure). Based on the Lim’s Ca2+ LJ parameters, the Ca2+Cl LJ interaction parameter is able to be optimized to experimentally-measured osmotic pressure at nearly saturated concentration, whereas Roux’s Ca2+ LJ parameters are not. Using the optimized Ca2+Cl LJ interaction parameter, the osmotic pressures at a wide range of CaCl2 concentration are well reproduced. Furthermore, it gives a concentration-independent Ca2+H2O coordination number of 8, which supports the recent new experimental results. Our results can be simply implemented in CHARMM and NAMD softwares for further biomolecule simulations.

關鍵字(中)

★ 離子交互作用力

關鍵字(英)

★ Interaction

論文目次

Contents

摘要 I
Abstract II
Contents III
List of Figures IV
List of Tables V
Chapter 1-Introduction 1
Chapter 2-Methods 8
2.1 Strategy for Optimizing the Ca2+-Cl- LJ Parameters 8
2.2 Simulation Methods 10
2.3 Calculations of Osmotic Pressure 12
Chapter 3-Results and Discussion 15
3.1 Performance of Ca2+ Force Field before Optimization 15
3.2 Optimization of Ca2+-Cl- LJ Interaction Parameter 21
3.3 Performance of Optimized Ca2+-Cl- LJ Interaction Parameter 26
Chapter 4-Conclusions and Summary 33
References 35

參考文獻

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指導教授

蔡惠旭

審核日期

2017-10-17

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