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针对小分子溶质的通用琥珀色力场的更新,重点在于水合自由能。

Update to the general amber force field for small solutes with an emphasis on free energies of hydration.

作者信息

Jämbeck Joakim P M, Lyubartsev Alexander P

机构信息

Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University , Stockholm SE-10691, Sweden.

出版信息

J Phys Chem B. 2014 Apr 10;118(14):3793-804. doi: 10.1021/jp4111234. Epub 2014 Mar 31.

Abstract

An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.

摘要

本文提出了一种对用于小分子有机溶质和类药物化合物的通用AMBER力场(GAFF)进行直接重新参数化的方法。该参数化基于溶剂与溶质之间的特定对相互作用,即调整溶质的构成原子与水的氧之间的相互作用,以重现小分子模型化合物的实验水合自由能。参数化的关键在于摒弃范德华相互作用的洛伦兹 - 贝特洛组合规则。然后将这些参数用于更大的溶质,以验证新推导的对相互作用。总共计算了近600个水合自由能,范围从简单烷烃到多功能药物化合物,并与实验数据进行比较。结果表明,所提出的参数在描述溶质与溶剂之间的相互作用方面表现良好,并且在绝对值上的一致性良好。这种GAFF的修改版本是大规模计算和预测水合自由能的良好候选者,这一直是计算化学家长期追求的目标,并且可用于合理药物设计。

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