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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping
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Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping

机译：通过使用非绝热FDFT映射来量化溶液和蛋白质中质子转移反应的自由能分布

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摘要

Reliable studies of proton transfer (PT) reactions in solution and in enzymes by combined quantum. mechanical/ molecular mechanics (QM/MM) approaches with an ab initio description of the quantum region present a major challenge to computational chemists. The main problem is the need for extensive computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. The present work presents a new effective way for performing such calculations by using the frozen density functional (FDFT) approach, to generate diabatic surfaces that are used to generate a mapping potential that takes the system from the reactant to the product state. The resulting umbrella sampling/free energy perturbation (US/FEP) mapping is done in full analogy with the approach used in the empirical valence bond (EVB) treatment, moving from the diabatic mapping potential to the adiabatic ground state surface, while an ab initio Hamiltonian is used for the QM part. The present approach provides a particularly effective way for evaluating the free energy associated with both the substrate and the solvent motions. This allows us to obtain a free energy barrier that properly reflects the solute entropy. This advance allows one to obtain ab initio QM/MM (QM(ai)/MM) free energy surfaces for very challenging cases such as the autodissociation of water in water, proton transfer between methanol and water in water, and the effect of Mg2+ ion. on such a reaction. We also consider as a benchmark the initial PT reaction in the catalytic cycle of triose phosphate isomerase and obtain excellent results without any adjustable parameters. Our results point out that. the present implementation of the FDFT approach provides a very promising approach for evaluating QM(ai)/MM free energy surfaces.
机译：通过组合量子对溶液和酶中质子转移（PT）反应的可靠研究。从头开始描述量子区域的机械/分子力学（QM / MM）方法对计算化学家提出了重大挑战。主要问题是需要大量的计算机时间来评估QM能量，这反过来又使执行正确的配置采样变得极具挑战性。本工作提出了一种新的有效方法，该方法通过使用冻结密度泛函（FDFT）方法来执行此类计算，以生成非绝热表面，该绝热表面用于生成将系统从反应物转移到产物状态的映射电位。产生的伞状采样/自由能扰动（US / FEP）映射完全类似于经验价键（EVB）处理中使用的方法，从绝热映射势移至绝热基态表面，而从头算哈密​​顿量用于QM部分。本方法提供了一种特别有效的方式来评估与底物和溶剂运动相关的自由能。这使我们能够获得能正确反映溶质熵的自由能垒。这一进步使人们能够从头开始获得QM / MM（QM（ai）/ MM）自由能表面，用于极富挑战性的情况，例如水中的水自离解，甲醇与水中的水之间的质子转移以及Mg2 +离子的作用。在这样的反应上。我们还将磷酸三糖异构酶催化循环中的初始PT反应作为基准，并获得了无需任何可调整参数的优异结果。我们的结果指出了这一点。 FDFT方法的当前实现为评估QM（ai）/ MM自由能表面提供了非常有前途的方法。

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