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基于单一路径采样模拟的催化循环最优动力学。

Optimal kinetics for catalytic cycles from a single path-sampling simulation.

作者信息

Bolhuis Peter G

机构信息

van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1090 GD, The Netherlands.

出版信息

Proc Natl Acad Sci U S A. 2025 Jul 29;122(30):e2500934122. doi: 10.1073/pnas.2500934122. Epub 2025 Jul 24.

Abstract

A catalyst's efficiency for accelerating a reaction rate is determined by its molecular structure and interactions with the substrate. While one can predict kinetics for a particular molecular model, tuning the (potentially many) model parameters to reach a desired or optimal kinetics for a catalytic cycle is usually considered computationally prohibitively expensive, especially in solvated systems. Here, we show for a simple model representing a minimal catalytic cycle that such optimization is possible using only one single (path-sampling) simulation, by applying a maximum caliber based path reweighting method. We compute the path ensemble for a single parameter setting of the molecular interactions and then expand the kinetic landscape around these parameters. We find that optimal catalytic turnover or efficiency is orders of magnitude improved and is achieved by relevant parameters that induce strain in the system. Thus, path-reweighting based optimization is not only capable of finding important ingredients that lead to desired kinetic rates but can also identify the mechanistic origins of the rate optimization at a fraction of the costs of a direct evaluation. We demonstrate the versatility of the methodology on a minimal model for kinase signaling. The approach promises efficient computational design of (complex) catalysts using realistic models.

摘要

催化剂加速反应速率的效率取决于其分子结构以及与底物的相互作用。虽然可以预测特定分子模型的动力学,但调整(可能有很多)模型参数以实现催化循环所需的或最佳的动力学通常被认为在计算上成本过高,尤其是在溶剂化体系中。在此,我们针对一个代表最小催化循环的简单模型表明,通过应用基于最大口径的路径重加权方法,仅使用一次(路径采样)模拟就可以实现这种优化。我们计算分子相互作用的单个参数设置下的路径系综,然后围绕这些参数扩展动力学景观。我们发现,最佳的催化周转或效率提高了几个数量级,并且是通过在系统中引入应变的相关参数实现的。因此,基于路径重加权的优化不仅能够找到导致所需动力学速率的重要因素,还能够以直接评估成本的一小部分识别速率优化的机制起源。我们在激酶信号传导的最小模型上展示了该方法的通用性。该方法有望使用现实模型对(复杂)催化剂进行高效的计算设计。

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