Ghysbrecht Simon, Donati Luca, Keller Bettina G
Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
J Comput Chem. 2025 Jan 5;46(1):e27529. doi: 10.1002/jcc.27529.
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit considerable disparities. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models.
现代势能面已将注意力转向化学反应的分子模拟。虽然各种方法可以在分子动力学模拟中估计构象转变的速率常数，但由于涉及高且尖锐的能垒和复杂的反应坐标，它们在研究化学反应中的适用性仍不确定。本研究聚焦于视黄醛中的热顺反异构化，采用分子模拟，并将基于一维速率理论的速率常数估计值与基于低维集体变量空间的采样跃迁和基于网格的模型的估计值进行比较。尽管每种估计速率的单独方法都通过了质量测试，但速率常数估计值仍存在相当大的差异。基于一维反应坐标的速率常数估计值即使在反应坐标优化后也难以收敛。然而，通过采样跃迁和多维基于网格的模型可以实现速率常数的一致估计。
