TS-tools:根据文本反应 SMILES 输入快速自动定位过渡状态。

IF 3.4 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY Journal of Computational Chemistry Pub Date : 2024-06-08 DOI:10.1002/jcc.27374
Thijs Stuyver
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引用次数: 0

摘要

这里介绍的 TS-tools 是一个 Python 软件包,它可以根据文本反应 SMILES 输入自动定位过渡态 (TS)。过渡态搜索可以在 xTB 或 DFT 理论水平上进行,前者以微不足道的计算成本获得猜测结果,后者以更高的成本直接获得精确结构。在单分子和双分子反应的基准数据集上,TS-tools 在 xTB 理论水平上已经达到了 95% 的出色成功率。对于三分子和多分子反应途径--在开发新的自动 TS 搜索方法时通常不会对其进行基准测试,但对于各种类型的反应(如溶剂反应、自催化反应和酶反应),TS-tools 仍能识别 TS 几何结构,不过在许多情况下,DFT 处理变得必不可少。在介绍的整个应用过程中,特别强调了溶解引起的机理变化,这也是迄今为止自动 TS 搜索文献中关注有限的另一个问题。
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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TS-tools: Rapid and automated localization of transition states based on a textual reaction SMILES input

Here, TS-tools is presented, a Python package facilitating the automated localization of transition states (TS) based on a textual reaction SMILES input. TS searches can either be performed at xTB or DFT level of theory, with the former yielding guesses at marginal computational cost, and the latter directly yielding accurate structures at greater expense. On a benchmarking dataset of mono- and bimolecular reactions, TS-tools reaches an excellent success rate of 95% already at xTB level of theory. For tri- and multimolecular reaction pathways - which are typically not benchmarked when developing new automated TS search approaches, yet are relevant for various types of reactivity, cf. solvent- and autocatalysis and enzymatic reactivity - TS-tools retains its ability to identify TS geometries, though a DFT treatment becomes essential in many cases. Throughout the presented applications, a particular emphasis is placed on solvation-induced mechanistic changes, another issue that received limited attention in the automated TS search literature so far.

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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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Issue Information Issue Information DC24: A new density coherence functional for multiconfiguration density‐coherence functional theory Excited state relaxation mechanisms of paracetamol and acetanilide. Stable, aromatic, and electrophilic azepinium ions: Design using quantum chemical methods
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