水モデル
出典: フリー百科事典『ウィキペディア（Wikipedia）』 (2021/01/26 10:06 UTC 版)
計算化学において、古典的水モデル（みずモデル）は、水クラスターや液体の水、露な溶媒を用いた水溶液のシミュレーションのために用いられる。水モデルは量子力学や分子力学、実験結果、これらの組み合わせによって決定される。分子の特定の性質を模倣するため、多くの種類のモデルが開発されている。一般的に、これらは (i) 「サイト」と呼ばれる相互作用点の数、(ii) モデルが剛直なのか柔軟なのか、(iii) モデルが分極効果を含んでいるか、という3つの点によって分類することができる。
- ^ Skyner, R.; McDonagh, J. L., Groom, C. R., van Mourik, T., Mitchell, J. B. O. (2015). “A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution”. Phys Chem Chem Phys (RSC, PCCP) 17: 6174–91. doi:10.1039/C5CP00288E. PMID 25660403.
- ^ Allen and Tildesley. (1989). Computer Simulation of Liquids
- ^ Kirby BJ.. Micro- and Nanoscale Fluid Mechanics: Transport in Microfluidic Devices
- ^ Dyer, KM; Perkyns, JS; Stell, G; Pettitt (2009). “An angle dependent site-renormalized theory for the conformations of n-butane in a simple fluid”. Mol. Phys. 107: 423–431. PMC: 2909681. PMID 20664717.
- ^ Jorgensen, W. L. Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Am. Chem. Soc. 1981, 103, 335-340.
- ^ H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans, In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331.
- ^ a b Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein (1983). “Comparison of simple potential functions for simulating liquid water”. J. Chem. Phys 79: 926–935. doi:10.1063/1.445869.
- ^ Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P.; The; Pair Potentials, Effective (1987). “The missing term in effective pair potentials”. J. Phys. Chem 91: 6269–6271. doi:10.1021/j100308a038.
- ^ MacKerell, A. D.; Jr; Bashford, D.; Bellott, R. L.; Dunbrack, R. L.; Jr; Evanseck, J. D.; Field, M. J. et al. (1998). “All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †”. J. Phys. Chem. 102: 3586–3616. doi:10.1021/jp973084f.
- ^ Mao, Y.; Zhang, Y.; Conductivity, Thermal; Viscosity, Shear; Specific; Water Models, Rigid (2012). “Thermal conductivity, shear viscosity and specific heat of rigid water models”. Chemical Physics Letters 542: 37–41. doi:10.1016/j.cplett.2012.05.044.
- ^ K. Toukan and A. Rahman (1985). “Molecular-dynamics study of atomic motions in water”. Physical Review B 31: 2643–2648. Bibcode: 1985PhRvB..31.2643T. doi:10.1103/PhysRevB.31.2643.
- ^ H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma (1987). “The missing term in effective pair potentials”. Journal of Physical Chemistry 91: 6269–6271. doi:10.1021/j100308a038.
- ^ M. Praprotnik, D. Janezic and J. Mavri (2004). “Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study”. Journal of Physical Chemistry A 108: 11056–11062. doi:10.1021/jp046158d.
- ^ Mahadevan TS, Garofalini SH (2007). “Dissociative water potential for molecular dynamics simulations”. J. Phys. Chem. B 111 (30): 8919-8927. doi:10.1021/jp072530o. PMID 17604393.
- ^ Naoki Kumagai, Katsuyuki Kawamura & Toshio Yokokawa (1994). “An Interatomic Potential Model for H2O: Applications to Water and Ice Polymorphs”. Molecular Simulation 12 (3-6). doi:10.1080/08927029408023028.
- ^ Christian J. Burnham, Jichen Li, Sotiris S. Xantheas and Maurice Leslie (1999). “The parametrization of a Thole-type all-atom polarizable water model from first principles and its application to the study of water clusters (n=2–21) and the phonon spectrum of ice Ih”. J. Chem. Phys. 110: 4566. doi:10.1063/1.478797.
- ^ Bernal, J. D.; Fowler, R.H. (1933). “A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl Ions”. J. Chem. Phys. 1: 515. doi:10.1063/1.1749327.
- ^ Jorgensen (1982). “Revised TIPS for simulations of liquid water and aqueous solutions”. J. Chem. Phys 77: 4156–4163. doi:10.1063/1.444325.
- ^ Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. (2004). “Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.”. J. Chem. Phys. 120: 9665–9678. doi:10.1063/1.1683075.
- ^ Abascal, J. L. F.; Sanz, E.; Fernández, R. García; Vega, C. (2005). “A potential model for the study of ices and amorphous water: TIP4P/Ice”. J. Chem. Phys. 122: 234511. doi:10.1063/1.1931662.
- ^ Abascal, J. L. F.; Vega, C. (2005). “A general purpose model for the condensed phases of water: TIP4P/2005”. J. Chem. Phys. 123: 234505. doi:10.1063/1.2121687.
- ^ Izadi, S.; Anandakrishnan, R.; Onufriev, A. V. (2014). “Building Water Models: A Different Approach”. The Journal of Physical Chemistry Letters 5 (21): 3863–3871. doi:10.1021/jz501780a.
- ^ Piana, Stefano; Donchev, Alexander G.; Robustelli, Paul; Shaw, David E. (2015). “Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States”. The Journal of Physical Chemistry B 119: 150312133835006. doi:10.1021/jp508971m. ISSN 1520-6106.
- ^ a b Stillinger, F.H.; Rahman, A.; Improved (1974). “Improved simulation of liquid water by molecular dynamics”. J. Chem. Phys. 60: 1545–1557. doi:10.1063/1.1681229.
- ^ Mahoney, M. W.; Jorgensen (2000). “A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions”. J. Chem. Phys. 112: 8910–8922. doi:10.1063/1.481505.
- ^ Rick, S. W. (2004). “A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums”. J. Chem. Phys. 120: 6085–6093. doi:10.1063/1.1652434.
- ^ Nada, H. (2003). “An intermolecular potential model for the simulation of ice and water near the melting point: A six-site model of H[sub 2]O”. J. Chem. Phys. 118: 7401. doi:10.1063/1.1562610.
- ^ José L. F. Abascal, Ramón García Fernández, Carlos Vega1 and Marcelo A. Carignano (2006). “The melting temperature of the six site potential model of water”. J. Chem. Phys. 125: 166101. doi:10.1063/1.2360276.
- ^ Florova, P.; Sklenovsky, P.; Banas, P.; Otyepka, M. (2010). “Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact”. J. Chem. Theory Comput 6: 3569–3579. doi:10.1021/ct1003687.
- ^ Silverstein, K. A. T.; Haymet, A. D. J.; Dill, K. A.; Effect, Hydrophobic (1998). “A Simple Model of Water and the Hydrophobic Effect”. J. Am. Chem. Soc. 120: 3166–3175. doi:10.1021/ja973029k.
- ^ Izvekov, S.; Voth, G. A.; Multiscale. “J. Chem. Phys. '”. 2005' 123: 134105. doi:10.1063/1.2038787.
- ^ Medders, G.R.; Paesani, F. (2015). “Infrared and Raman Spectroscopy of Liquid Water through "First Principles" Many-Body Molecular Dynamics”. J. Chem. Theory Comput 11: 1145–1154. doi:10.1021/ct501131j.
[続きの解説]
このページでは「ウィキペディア」から水モデルを検索した結果を表示しています。
Weblioに収録されているすべての辞書から水モデルを検索する場合は、下記のリンクをクリックしてください。
全ての辞書から水モデル を検索
Weblioに収録されているすべての辞書から水モデルを検索する場合は、下記のリンクをクリックしてください。
全ての辞書から水モデル を検索 - 水モデルのページへのリンク
