Xie Wangshen, Gao Jiali
Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455.
J Chem Theory Comput. 2007 Nov;3(6):1890-1900. doi: 10.1021/ct700167b.
An electronic structure-based polarization method, called the X-POL potential, has been described for the purpose of constructing an empirical force field for modeling polypeptides. In the X-POL potential, the internal, bonded interactions are fully represented by an electronic structure theory augmented with some empirical torsional terms. Non-bonded interactions are modeled by an iterative, combined quantum mechanical and molecular mechanical method, in which the molecular mechanical partial charges are derived from the molecular wave functions of the individual fragments. In this paper, the feasibility of such an electronic structure force field is illustrated by small model compounds. A method has been developed for separating a polypeptide chain into peptide units and its parameterization procedure in the X-POL potential is documented and tested on glycine dipeptide. We envision that the next generation of force fields for biomolecular polymer simulations will be developed based on electronic structure theory, which can adequately define and treat many-body polarization and charge delocalization effects.
为构建用于多肽建模的经验力场，已描述了一种基于电子结构的极化方法，即X-POL势。在X-POL势中，内部的成键相互作用由电子结构理论充分描述，并辅以一些经验扭转项。非键相互作用通过一种迭代的、量子力学与分子力学相结合的方法进行建模，其中分子力学部分电荷源自各个片段的分子波函数。本文通过小分子模型化合物说明了这种电子结构力场的可行性。已开发出一种将多肽链分离为肽单元的方法，并记录了其在X-POL势中的参数化过程，并在甘氨酸二肽上进行了测试。我们设想，下一代用于生物分子聚合物模拟的力场将基于电子结构理论开发，该理论能够充分定义和处理多体极化和电荷离域效应。
