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.

中文翻译：

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基于反应坐标的速率理论对化学反应进行建模的准确性：来自 Retinal 中热异构化的见解


现代势能表面已将注意力转移到化学反应的分子模拟上。虽然各种方法可以估计分子动力学模拟中构象转变的速率常数，但由于涉及高而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然不确定。本研究侧重于视网膜中的热顺反异构化，采用分子模拟并将基于一维速率理论的速率常数估计与基于采样转换和基于网格的低维集体变量空间模型的速率常数估计进行比较。尽管每种估计速率的单独方法都通过了其质量测试，但速率常数估计值表现出相当大的差异。事实证明，即使反应坐标经过优化，基于一维反应坐标的速率常数估计也很难收敛。然而，速率常数的一致估计是通过采样转换和基于多维网格的模型来实现的。