基于键偶极模型的多肽-水体系多体极化作用强度高效计算新方法  

A Novel Efficient Method Based on the Bond Dipole Model for Computing Many-body Polarization Strength in Peptide-Water Systems

作　　者：祝佳怡 姜笑楠[1] 郑笑函 郝强 王长生[1] ZHU Jiayi;JIANG Xiaonan;ZHENG Xiaohan;HAO Qiang;WANG Changsheng(School of Chemistry and Chemical Engineering,Liaoning Normal University,Dalian 116029,China)

机构地区：[1]辽宁师范大学化学化工学院,大连110629

出　　处：《高等学校化学学报》2025年第4期60-69,共10页Chemical Journal of Chinese Universities

基　　金：国家自然科学基金(批准号:21773102);辽宁省教育厅基础研究项目(批准号:LJKMZ20221411)资助。

摘　　要：为解决传统非极化力场无法准确描述三体及更高阶多体作用的问题,并精确模拟液态水环境下蛋白质的结构和功能,提出了一种可以快速准确计算多肽-水体系中的多体极化作用强度的新方法.该方法将多肽分子中的N—H和C=O极性化学键及水分子的O—H键视为键偶极,周围环境对化学键的极化作用使得该化学键上产生了诱导键偶极,使用键偶极之间的相互作用来描述体系中的多体极化作用.通过拟合模型体系中三体作用能随分子间距离变化的势能曲线确定所需参数.将该方法应用于多肽-水体系中的三体作用强度计算,并与高精度的MP2方法和AMOEBABIO18可极化力场方法进行了系统比较.结果表明,本文方法计算的6个多肽水团簇(共包含92290个三体作用)的总三体作用强度与MP2方法的计算结果具有极高的线性相关性(线性相关系数为0.9965,均方根误差为7.29 kJ/mol),准确度略优于AMOEBABIO18可极化力场方法(其与MP2方法的线性相关系数为0.9950,均方根误差为10.74 kJ/mol).此外,本文方法的计算效率与AMOEBABIO18可极化力场方法相比也有显著提高,在涉及超过20000次三体相互作用的模拟中,计算时间缩短了约50%.本文提出的高效方法为大规模蛋白质-水体系的多体作用模拟提供了新思路,在相关领域中具有重要应用潜力.To address the limitations of traditional non-polarizable force fields in describing three-body and higherorder many-body interactions,and to accurately simulate protein structure and function in liquid water environments,we present a novel method for the efficient and accurate calculation of many-body polarization strengths in peptidewater systems.The N—H and C=O polar bonds in peptide molecules and the O—H bonds in water were treated as bond dipoles.The polarization effect of the environment on the chemical bond causes an induced bond dipole,and interactions of bond dipoles were employed to describe the many-body polarization interaction.The required parameters were determined by fitting the three-body interaction energy curves of the model molecules with different interaction distance.The method and parameters were applied to calculate the three-body polarization strength in peptide-water systems and the results were compared with those of high-precision MP2 method and the AMOEBABIO 18 polarizable force field method.It is showed that the results of our method have a high linear correlation with those of MP 2 method(correlation coefficient=0.9965,RMSE=7.29 kJ/mol)in the calculation of three-body interaction strengths in six peptide-water clusters(with a total of 92290 three-body interactions),which is superior to AMOEBABIO 18 polarizable force field method(correlation coefficient=0.9950,RMSE=10.74 kJ/mol with the MP 2 method).Moreover,the computational efficiency is significantly improved,with calculation time reduced by approximately 50%compared to AMOEBABIO 18 polarizable force field method in simulations involving clusters with over 20000 three-body interactions.This efficient method offers a new approach for large-scale simulations of many-body interactions in protein-water systems,demonstrating significant potential for applications in related fields.

关 键 词：多体极化作用 化学键偶极 诱导键偶极 多肽-水体系 三体作用能 

分 类 号：O641.3[理学—物理化学]