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用于预测复杂生物系统中弱相互作用能量的计算高效且定量准确的缩放MP2协议。

Computationally Efficient Yet Quantitatively Accurate Scaled MP2 Protocols for the Prediction of Weak Interaction Energies in Complex Biological Systems.

作者信息

Soriano-Agueda Luis, Flores Anaid, Zeron Paulino, Franco-Pérez Marco

机构信息

Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de Mexico, Mexico.

Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, 09340 Ciudad de México, Mexico.

出版信息

ACS Omega. 2025 Aug 20;10(34):39292-39308. doi: 10.1021/acsomega.5c07079. eCollection 2025 Sep 2.

DOI:10.1021/acsomega.5c07079
PMID:40918360
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12409536/
Abstract

In this study, we introduce a set of novel computational strategies based on second-order Mo̷ller-Plesset perturbation theory (MP2), enhanced through acceleration techniques, such as the resolution of the identity (RI). These approaches are further refined via spin-component scaling (SCS), following Grimme's methodology, and are specifically calibrated for the quantitatively accurate prediction of weak interaction energiesinteractions that play a critical role in biological systems. Among the developed methods, three variants exhibit outstanding performance, surpassing the accuracy of several state-of-the-art, nondynamical electronic structure techniques. Benchmarking against a comprehensive data set of 274 dimerization energies, computed at the CCSD-(T)/CBS level of theory, reveals that these models deliver quantitatively accurate interaction energies. In particular, the RIJCOSX-SCS-MP2 method, employing uniquely optimized scaling parameters, demonstrates exceptional accuracy (errors below 1 kcal/mol) while maintaining computational efficiency superior to widely used hybrid and meta-GGA density functional approximations (DFAs). This method reliably captures a range of biologically relevant interactions, including π-π stacking between nucleotide base pairs, halogen bonding, and dissociation energy profiles, showcasing its robustness and predictive power. Given its accuracy, efficiency, and versatility, RI-SCS-MP2, RIJK-SCS-MP2, and RIJCOSX-SCS-MP2 emerge as promising and reliable alternatives for modeling weak interactions in complex biological environments.

摘要

在本研究中,我们引入了一组基于二阶Møller-Plesset微扰理论(MP2)的新型计算策略,并通过诸如单位分解(RI)等加速技术进行了增强。这些方法通过遵循Grimme方法的自旋分量缩放(SCS)进一步优化,并专门针对生物系统中起关键作用的弱相互作用能量(相互作用)的定量准确预测进行了校准。在已开发的方法中,有三种变体表现出卓越的性能,超过了几种最先进的非动态电子结构技术的精度。以在CCSD-(T)/CBS理论水平计算的274个二聚化能量的综合数据集为基准,结果表明这些模型能够提供定量准确的相互作用能量。特别是,采用独特优化缩放参数的RIJCOSX-SCS-MP2方法,在保持计算效率优于广泛使用的混合和元广义梯度近似(DFA)的同时,展示了卓越的精度(误差低于1 kcal/mol)。该方法能够可靠地捕捉一系列与生物相关的相互作用,包括核苷酸碱基对之间的π-π堆积、卤键和离解能分布,展示了其稳健性和预测能力。鉴于其准确性、效率和通用性,RI-SCS-MP2、RIJK-SCS-MP2和RIJCOSX-SCS-MP2成为在复杂生物环境中模拟弱相互作用的有前景且可靠的替代方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/f890f8a76faa/ao5c07079_0009.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/98a8f14fb07e/ao5c07079_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/4c708666ec60/ao5c07079_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/2520e2decc36/ao5c07079_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/adce623730e2/ao5c07079_0007.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a6b/12409536/f890f8a76faa/ao5c07079_0009.jpg

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