Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-10-08 DOI:10.1007/s00894-024-06155-0
Williams García-Argote, Lina Ruiz, Diego Inostroza, Carlos Cardenas, Osvaldo Yañez, William Tiznado
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Abstract

Context

Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima.

Methods

Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.

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介绍 KICK-MEP:探索具有显著非共价相互作用的系统中的势能面。
背景:探索势能面(PES)是计算化学的基础,因为它能让我们深入了解分子能量、几何形状和化学反应性之间的关系。我们介绍的 Kick-MEP 是一种混合方法,用于探索原子团簇和分子团簇的势能面,尤其是那些由非共价相互作用主导的原子团簇和分子团簇的势能面。Kick-MEP 计算两个相互作用片段在 0.001 a.u. 电子密度等值面上最大和最小静电势值之间的库仑积分。这种方法可以有效地估算相互作用能量,并以较低的计算成本选择低能配置。Kick-MEP 在硅锂团簇、水团簇和包裹在葫芦[7]脲中的百里酚上进行了评估,一致确定了最低能量结构,包括全局最小值和相关局部最小值:Kick-MEP 使用随机 Kick 算法生成初始分子结构群,该算法结合了两个分子片段(A 和 B)。每个片段在 0.001 a.u. 电子密度等值面上的分子静电势(MEP)值用于计算它们之间的库仑积分。通过基于梯度的优化和 PBE0-D3/Def2-TZVP 水平的 DFT 计算,选出库仑积分最低的结构并加以完善。使用 AutoDock Vina 对百里酚-葫芦[7]脲复合物进行了分子对接模拟,以进行基准测试。Kick-MEP 在不同的分子体系中都得到了验证,证明了其在识别最低能量结构(包括全局最小值和相关局部最小值)方面的有效性,同时保持了较低的计算成本。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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