Abstract：
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers\' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
摘要：
为了详细了解自然界和工业中的化学过程，我们需要复杂环境中化学反应的精确模型。虽然Eyring过渡态理论通常用于模拟化学反应，对于气相中的小分子是最准确的。存在广泛的替代速率理论，可以更好地捕获涉及复杂分子和环境影响的反应。然而,它们要求通过分子动力学模拟对化学反应进行采样。这是一个艰巨的挑战，因为可访问的模拟时间尺度比化学反应的典型时间尺度小许多数量级。为了克服这些限制,使用涉及增强分子动力学采样的罕见事件方法。在这项工作中,使用紧密结合密度泛函理论研究了视网膜的热异构化。将过渡态理论的结果与从增强采样获得的结果进行比较。使用不频繁的元动力学模拟从动态重新加权获得的速率与过渡态理论获得的速率非常一致。同时,发现将Kramers\'速率方程应用于沿扭转二面角反应坐标的采样自由能曲线所获得的速率高达三个数量级。这种差异引起了人们对将速率方法应用于化学反应中的一维反应坐标的担忧。
