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力场原子分辨率中的电荷灵敏度分析。

Charge sensitivity analysis in force-field-atom resolution.

机构信息

K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland.

出版信息

J Mol Model. 2011 Sep;17(9):2217-26. doi: 10.1007/s00894-011-1006-7. Epub 2011 Mar 3.

DOI:10.1007/s00894-011-1006-7
PMID:21369935
Abstract

Charge sensitivity analysis (CSA) was extended to AMBER force-field resolution. The effective electronegativity and hardness data were found using evolutionary algorithms. Four model hardness matrices based on the classical electrostatic, Mataga-Nishimoto, Ohno, and Louwen-Vogt interpolation formulae were considered. Mulliken population analysis and electrostatically derived charges (CHELPG) were taken into account. It was demonstrated that the Ohno interpolation formula gives the best fit to Mulliken charges. For all molecules from the training set and all model hardness matrices, Mulliken charges were reproduced more accurately than CHELPG charges, indicating their good transferability from system to system. The effective electronegativities and hardnesses obtained were further verified by applying CSA to molecules from a validation set that was different from the training set. The correlation between CSA and Mulliken charges was of the same quality as that obtained for the training set.

摘要

电荷灵敏度分析 (CSA) 被扩展到 AMBER 力场解析。有效电负性和硬度数据是使用进化算法找到的。考虑了基于经典静电、Mataga-Nishimoto、Ohno 和 Louwen-Vogt 内插公式的四个模型硬度矩阵。Mulliken 布居分析和静电衍生电荷 (CHELPG) 被考虑在内。结果表明,Ohno 内插公式与 Mulliken 电荷拟合得最好。对于来自训练集的所有分子和所有模型硬度矩阵,Mulliken 电荷的重现性都比 CHELPG 电荷好,这表明它们在系统间具有良好的可转移性。通过将 CSA 应用于与训练集不同的验证集分子,进一步验证了所得到的有效电负性和硬度。CSA 与 Mulliken 电荷之间的相关性与训练集获得的质量相同。

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本文引用的文献

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2
Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.电负性均衡方法:使用默茨-科尔曼-辛格电荷分布方案对有机分子进行参数化和验证
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3
An Interpretation of Bond Lengths and a Classification of Bonds.
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4
Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM).
J Chem Inf Model. 2006 Jul-Aug;46(4):1657-65. doi: 10.1021/ci050505e.
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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.扩展蛋白质力场中主链能量学的处理方法:气相量子力学在分子动力学模拟中重现蛋白质构象分布方面的局限性。
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6
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