Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
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DOI：
10.1002/jcc.1065
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发表时间：
2001-07-30
影响因子：
3
通讯作者：
Kollman, P
中科院分区：
文献类型：
--
作者：
Cieplak, P;Caldwell, J;Kollman, P
我们已经开发了一种方法来推导RESP电荷的分子力学模型，包括“孤对”的孤对施主网站和原子中心的极化率。这种方法使用非常高水平的从头计算cc-pVTZ基组，（1）其中分子的多极矩尽可能准确。部分电荷自洽地导出，使模型，其静电势来自部分电荷和诱导偶极子，再现量子力学静电势。然后，我们研究了这种模型的能力，以重现甲醇和N-甲基乙酰胺（NMA）的水溶剂化自由能，Hobza等人分析的26个碱基对的碱基对氢键，和5个N-甲基取代的核酸碱基的氯仿/水分配系数。在修正N-H键的货车德瓦耳斯参数以给出合理的碱基对氢键距离后，用原子中心加性模型描述了碱基对氢键能。甲醇和NMA的实验溶剂化自由能（气体->水）得到了很好的描述，水/CHCl 3分配系数在添加剂模型上得到了改进，而没有任何参数变化。(C)John Wiley & Sons，Inc. J Comput Chem 22：1048-1057，2001.
We have developed a methodology to derive RESP charges for molecular mechanical models that include "lone pairs" on lone-pair donor sites and atom-centered polarizabilities. This approach uses a very high level ab initio cc-pVTZ basis set,(1) where the multipole moments of the molecules are as accurate as possible. The partial charges are derived self-consistently so that the model, whose electrostatic potential comes from both partial charges and induced dipoles, reproduces the quantum mechanical electrostatic potential. We then study the ability of such models to reproduce the aqueous solvation free energy of methanol and N-methyl acetamide (NMA), the base pair hydrogen bonding of the 26 base pairs analyzed by Hobza et al, and the chloroform/water partition coefficients of the five N-methyl substituted nucleic acid bases. The base pair H-bond energies are described as well as the atom centered additive model, after modifying the van der Waals parameter on the N-H to give reasonable base pair H-bond distances. The experimental solvation free energies (gas --> water) of methanol and NMA are well described, and the water/CHCl3 partition coefficients are improved over the additive model, without any parameter changes. (C) 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1048-1057, 2001.