Hnizdo Vladimir, Fedorowicz Adam, Singh Harshinder, Demchuk Eugene
National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505-2888, USA.
J Comput Chem. 2003 Jul 30;24(10):1172-83. doi: 10.1002/jcc.10289.
A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical-mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical-mechanical properties corresponding to a given internal rotational degree of freedom are reduced. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed.
一种统计估计方法被应用于平均力阻碍势中一维内旋转的问题。该阻碍势可能具有完全一般的形状，通过傅里叶级数展开，其系数通过将适当的统计力学分布拟合到内旋转角的随机变量来估计。内旋转折合转动惯量的函数在随机模拟中获得的分子原子构型的热力学系综上进行平均。当量子效应不重要时，可以准确估计具有单个可旋转键的分子的绝对内旋转熵。当存在多个可旋转键时，对应于给定内旋转自由度的“边际”统计力学性质会降低。使用两种与公共卫生相关的卤代烃分子（每个分子具有单个内旋转自由度）的蒙特卡罗模拟以及一种免疫相关多肽的分子动力学模拟（其中分析了几个二面角）来说明该方法。
