有机分子构象采样的张量序列优化。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2025-02-11 Epub Date: 2025-01-22 DOI:10.1021/acs.jctc.4c01275
Christopher Zurek, Ruslan A Mallaev, Alexander C Paul, Nils van Staalduinen, Philipp Pracht, Roman Ellerbrock, Christoph Bannwarth
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引用次数: 0

摘要

探索分子的构象空间仍然是量子化学的一个基本重要挑战:在环境条件下识别相关的构象可以预测模拟几乎任意的性质。在这里,我们提出了一种称为TTConf的新方法,以实现大型有机分子的构象采样,其中可能的构象的组合爆炸阻止了使用暴力系统构象搜索。我们采用张量训练作为一种高效的降维算法,有效地减少了从指数到多项式的缩放。在我们的方法中,构象搜索被表示为高维二面角网格中的全局能量最小化任务。降维是通过高维扭转空间的张量列表示实现的。该方法的性能在多种药物类分子上进行了评估,并与CREST中实现的最先进的基于元动力学的构象搜索进行了直接比较。比较显示了显著的加速度,高达一个数量级,同时保持相当的精度。更重要的是,所提出的方法可以处理比元动力学更大的分子。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Tensor Train Optimization for Conformational Sampling of Organic Molecules.

Exploring the conformational space of molecules remains a challenge of fundamental importance to quantum chemistry: identification of relevant conformers at ambient conditions enables predictive simulations of almost arbitrary properties. Here, we propose a novel approach, called TTConf, to enable conformational sampling of large organic molecules where the combinatorial explosion of possible conformers prevents the use of a brute-force systematic conformer search. We employ tensor trains as a highly efficient dimensionality reduction algorithm, effectively reducing the scaling from exponential to polynomial. In our approach, the conformational search is expressed as global energy minimization task in a high-dimensional grid of dihedral angles. Dimensionality reduction is achieved through a tensor train representation of the high-dimensional torsion space. The performance of the approach is assessed on a variety of drug-like molecules in direct comparison to the state-of-the-art metadynamics based conformer search as implemented in CREST. The comparison shows significant acceleration of up to an order of magnitude, while maintaining comparable accuracy. More importantly, the presented approach allows treatment of larger molecules than typically accessible with metadynamics.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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