研究生: |
許家偉 |
---|---|
論文名稱: |
水中疏水性分子之動力學模擬 Molecular Dynamics Simulations of Hydrophobic Solutes in Liquid Water |
指導教授: | 李哲倫 |
學位類別: |
碩士 Master |
系所名稱: |
化學系 Department of Chemistry |
論文出版年: | 2007 |
畢業學年度: | 95 |
語文別: | 英文 |
論文頁數: | 60 |
中文關鍵詞: | 疏水效應 |
英文關鍵詞: | hydrophobic effect |
論文種類: | 學術論文 |
相關次數: | 點閱:133 下載:0 |
分享至: |
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
本篇論文使用分子動力學模擬來研究小型非極性粒子在水中的疏水作用。兩個粒子之間的交互作用我們可以利用平均力位能來描述。一般而言兩個非極性分子在水中的平均力位能的圖形具有兩個極小值。一個是較穩定的接觸型態以及次穩定的溶液分隔型態。在此兩個型態之間具有一個位能障壁。有趣的是當我們與一個使用量子機構計算的平均力位能比較時,發現量子的結果中,位能的障壁變的很不明顯,而且接觸型態的穩定程度也相對的提高。我們猜想這可能是由於古典模擬中排斥力過於強大,影響了周圍氫鑑的網絡性,而水分子與溶質間的作用力成為了主要的因素。我們藉由在古典模擬中使用不同的排斥力大小來試著解釋上述的猜測。而且也對於在疏水性分子周邊水合層的水分子網絡結構進行了探討。我們的結果說明了平均力位能在古典以及量子中差異的原因。.
1
W. Kauzmann Advan. Protein Chem., vol. 14, pp. 1-63, 1959.
2
C. Czaplewski, S. Rodziewica-Motowidlo, A. Liwo, D. R. Ripoll, R. J. Wawak, and H. A. Scheraga Protein Science, vol. 9, pp. 1235-1245, 2000.
3
B. Guillot, Y. Guissani, and S. Bratos J. Chem. Phys., vol. 95, p. 3643, 1991.
4
D. E. Smith and A. D. J. Haymet, ``Free energy, entropy, and internal energy of hydrophobic interactions: Computer simulations,'' J. Chem. Phys., vol. 98, pp. 6445-6454, 1993.
5
W. S. Young and C. L. Brooks III J. Chem. Phys., vol. 106, pp. 9265-9269, 1997.
6
A. P. Lyubartsev, O. K. Førrisdahl, and A. Laaksonen J. Chem. Phys., vol. 108, p. 227, 1998.
7
S. Lüdemann, H. Schreiber, R. Abseher, and O. Steinhauser, ``The influence of temperature on pairwise hydrophobic interactions of methane-like particles: A molecular dynamics study of free energy,'' J. Chem. Phys., vol. 104, p. 286, 1996.
8
S. Shimizu and H. S. Chan, ``Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond,'' J. Chem. Phys., vol. 115, pp. 1414-1421, 2001.
9
S. Shimizu and H. S. Chan, ``Temperature dependence of hydrophobic interactions: A mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures,'' J. Chem. Phys., vol. 113, pp. 4683-4700, 2000.
10
M. S. Moghaddam, S. Shimizu, and H. S. Chan, ``Temperature dependence of three-body hydrophobic interactions: Potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity,'' J. Am. Chem. Soc., vol. 127, p. 303, 2005.
11
B. Gelin and M. Karplus, ``Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment,'' Biochemistry, 1979.
12
A. Vedani, ``Yeti: An interactive molecular mechanics program for small-molecular protein complexes,'' Journal of Computational Chemistry, vol. 9, p. 269, 1988.
13
P. J. Goodfprd, ``A computational procedure for determining energetically favorable binding sites on biologically important macromolecules,'' Journal of Medicinal Chemistry, vol. 28, pp. 849-857, 1985.
14
A. Rahman and F. H. Stillinger, ``Hydrogen-bond patterns in liquid water,'' J. Am. Chem. Soc., vol. 95, pp. 7943-7948, 1973.
15
T. Head-Gordon Proc. Natl. Acad. Sci. U.S.A., vol. 92, pp. 8308-8312, 1995.
16
B. Widom, P. Bhimalapuram, and K. Koga Phys. Chem. Chem. Phys., vol. 5, pp. 3085-3093, 2003.
17
A. E. M. Kovacs H and W. F. van Gunsteren, ``Solvent structure at a hydrophobic protein surface,'' Proteins: Structure Function and Genetics, vol. 27, pp. 395-404, 1997.
18
W. L. Jorgensen, R. W. I. J Chandrasekhar, J D Madura, and M. L. Klein, ``Comparison of simple potential functions for simulating liquid water,'' J. Chem. Phys., vol. 79, pp. 926-935, 1983.
19
W. F. v. G. Berendson H C, J P M Postma and J. Hermans, ``Interaction models for water in relation to protein hydration,'' Intermolecular Forces, pp. 331-342, 1981.
20
J. R. G. Berendson H C and T. P. Straastsma, ``The missing term in effective pair potentials,'' J. Phys. C, vol. 91, pp. 6269-6271, 1987.
21
J. D. Bernal and R. H. Fowler, ``A theory of water and ionic solution, with particular reference to hydrogen and hydroxy ions,'' J. Chem. Phys., vol. 1, pp. 515-548, 1933.
22
F. H. Stillinger and A. Rahman, ``Improved simulation of liquid water by molecule dynamics.,'' J. Chem. Phys., vol. 60, pp. 1545-1557, 1974.
23
D. M. Ferguson, ``Parameterisation and evaluation of a flexible water model,'' J. Chem. Phys., vol. 16, pp. 501-511, 1995.
24
F. London, ``Zur theori und systematik der molekulärkrafte,'' Zeitschrift fur Physik, 1930.
25
L. Verlet Phys. Rev., vol. 159, p. 98, 1967.
26
P. H. B. Swope W C, H C Anderson and K. R. Wilson, ``A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to samll water clusters,'' J. Chem. Phys., vol. 76, p. 637649, 1982.
27
A. R. Leach, Molecular modelling principles and application.
Pearson Education, 2 ed., 2001.
28
G. M. Torrie and J. P. Valleau, ``Nonphysical sampling distributions in monte carlo free-energy estimation: Umbrella sampling,'' J. Comp. Phys., vol. 23, pp. 187-199, 1977.
29
B. D. O. D. J. S. S. S. Bernard R. Brooks, Robert E. Bruccoleri and M. Karplus, ``Charmm: A program for macromolecular energy, minimization and dynamics calculations,'' Journal of Computational Chemistry, vol. 4, pp. 187-217, 1983.
30
C. T. Je-Luen Li, Roberto Car and N. S. Wingreen, ``Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water,'' Proceeding of the National Academy of Science of the United States of America, vol. 104, pp. 2626-2630, 2007.
31
P. T. Thompson, C. B. Davis, and R. H. Wood J. Phys. Chem, vol. 92, pp. 6386-6399, 1988.
32
J. C. Grossman, E. Schwegler, and G. Galli, ``Quantum and classical molecular dynamics simulations of hydrophobic hydration structure around small solutes,'' J. Phys. Chem. B, vol. 108, pp. 15865-15872, 2004.