Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO-MST Continuum Solvation Model

IF 3.4 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Journal of Computational Chemistry Pub Date : 2025-01-11 DOI:10.1002/jcc.70027
R. D. Cunha, S. Romero-Téllez, F. Lipparini, F. J. Luque, C. Curutchet
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Abstract

Continuum solvation models such as the polarizable continuum model and the conductor-like screening model are widely used in quantum chemistry, but their application to large biosystems is hampered by their computational cost. Here, we report the parametrization of the Miertus–Scrocco–Tomasi (MST) model for the prediction of hydration free energies of neutral and ionic molecules based on the domain decomposition formulation of COSMO (ddCOSMO), which allows a drastic reduction of the computational cost by several orders of magnitude. We also introduce several novelties in MST, like a new definition of atom types based on hybridization and an automatic setup of the cavity for charged regions. The model is parametrized at the B3LYP/6-31+G(d) and PM6 levels of theory and compared to the performance of IEFPCM/MST. Then, we demonstrate the robustness of the parametrization on the SAMPL2, SAMPL4, and C10 datasets. The ddCOSMO/MST models provide errors of ~0.8 and ~3.2 kcal/mol for neutrals and ions, respectively, showing a remarkable balanced and accurate description of cations and anions.

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将MST模型扩展到大型生物分子系统:ddCOSMO - MST连续溶剂化模型的参数化
连续介质溶剂化模型如极化连续介质模型和类导体筛选模型在量子化学中被广泛应用,但它们在大型生物系统中的应用受到其计算成本的限制。在这里,我们报告了miertus - scocco - tomasi (MST)模型的参数化,该模型用于预测中性和离子分子的水化自由能,该模型基于COSMO (ddCOSMO)的域分解公式,可以将计算成本大幅降低几个数量级。我们还介绍了MST中的一些新颖之处,如基于杂化的原子类型的新定义和带电区腔的自动设置。该模型在理论的B3LYP/6‐31+G(d)和PM6水平上进行参数化,并与IEFPCM/MST的性能进行比较。然后,我们在SAMPL2、SAMPL4和C10数据集上证明了参数化的鲁棒性。ddCOSMO/MST模型对中性和离子的误差分别为~0.8和~3.2 kcal/mol,对阳离子和阴离子的描述非常平衡和准确。
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来源期刊
CiteScore
6.60
自引率
3.30%
发文量
247
审稿时长
1.7 months
期刊介绍: This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
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