University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
J Mol Model. 2020 May 24;26(6):152. doi: 10.1007/s00894-020-04399-0.
Polarizable force fields are emerging as a more accurate alternative to additive force fields in terms of modeling and simulations of a variety of chemicals including biomolecules. Explicit treatment of induced polarization in charged species such as phosphates and sulfates offers the potential for achieving an improved atomistic understanding of the physical forces driving their interactions with their environments. To help achieve this, in this study we present balanced Drude polarizable force field parameters for molecular ions including phosphates, sulfates, sulfamates, and oxides. Better balance was primarily achieved in the relative values of minimum interaction energies and distances of the anionic model compounds with water at the Drude and quantum mechanical (QM) model chemistries. Parametrization involved reoptimizing available parameters as well as extending the force field to new molecules with the goal of achieving self-consistency with respect to the Lennard-Jones and electrostatic parameters targeting QM and experimental hydration free energies. The resulting force field parameters achieve consistent treatment across the studied anions, facilitating more balanced simulations of biomolecules and small organic molecules in the context of the classical Drude polarizable force field. Graphical abstract.
极化力场作为一种更精确的替代方法,在对各种化学物质(包括生物分子)进行建模和模拟方面,优于加和力场。在带电荷的物种(如磷酸盐和硫酸盐)中显式处理感应极化,为实现对驱动其与环境相互作用的物理力的原子级理解提供了潜力。为了帮助实现这一目标,本研究提出了用于包括磷酸盐、硫酸盐、磺胺酸盐和氧化物在内的分子离子的平衡 Drude 极化力场参数。在 Drude 和量子力学(QM)模型化学中,阴离子模型化合物与水的最小相互作用能和距离的相对值的更好平衡主要通过重新优化可用参数以及将力场扩展到新分子来实现,目的是实现与针对 QM 和实验水合自由能的 Lennard-Jones 和静电参数的自洽性。所得力场参数在研究的阴离子中实现了一致的处理,促进了在经典 Drude 极化力场背景下对生物分子和小分子的更平衡模拟。