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用于生化应用的 ReaxFF 反应力场的系统评价。

Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications.

机构信息

Yusuf Hamied Department of Chemistry, University of Cambridge, Lens_eld Road, Cambridge CB2 1EW, U.K.

Division of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel.

出版信息

J Chem Theory Comput. 2021 Jan 12;17(1):497-514. doi: 10.1021/acs.jctc.0c01043. Epub 2020 Dec 18.

Abstract

Four established ReaxFF force fields, trained on biochemical systems, have been systematically benchmarked on 20 proteinogenic amino acids and 11 dipeptides. The force fields were compared with respect to geometries, energetics, and atomic charges of conformers for the amino acids. To assess the performance with respect to reactivity, the condensation reactions for the formation of dipeptides were investigated by calculating the reaction energetics and pathways. We found systematic errors in the torsion angles for the amino acids, with deviations over 100°, and a generally incorrect account of relative energies for amino acid conformers. In describing the reactivity, only one of the force fields could reproduce the reaction energies of amino acid condensations quantitatively. All four force fields predict unphysical mechanisms for these reactions, involving highly unstable intermediate structures, proton transfers involving aliphatic protons, and even five-coordinate carbon atoms. The corresponding energy landscapes exhibit fluctuations on small length scales and artificial minima.

摘要

四个已建立的 ReaxFF 力场,经过生化系统的训练,已针对 20 种蛋白质氨基酸和 11 种二肽进行了系统的基准测试。对氨基酸构象的几何形状、能量和原子电荷,对力场进行了比较。为了评估与反应性有关的性能,通过计算反应能和途径,研究了二肽形成的缩合反应。我们发现氨基酸的扭转角存在系统误差,偏差超过 100°,并且氨基酸构象的相对能量的描述通常是不正确的。在描述反应性时,只有一个力场可以定量地再现氨基酸缩合的反应能。所有四个力场都预测了这些反应的非物理机制,涉及高度不稳定的中间结构、涉及脂肪族质子的质子转移,甚至是五配位碳原子。相应的能量景观在小尺度上表现出波动和人为的最小值。

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