Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada.
Center for Molecular Modeling, Ghent University, 903 Technologiepark, B-9050 Zwijnaarde, Belgium.
J Chem Theory Comput. 2012 Feb 14;8(2):554-62. doi: 10.1021/ct2007742. Epub 2012 Jan 23.
A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software "parafreq". The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.
本文提出了一种不依赖于内坐标冗余选择的力常数确定方法。该方法基于使用 Wilson B 矩阵分别求解每个键和角度项。该方法仅需要在最低能量结构下进行一次从头算频率计算，并且在软件“parafreq”中可用。该方法通过显示其可以比其他方法（例如在内部坐标中取 Hessian 的对角项或使用标准 AMBER 力场）更好地再现从头算频率，从而用一组小分子验证了其有效性。最后，通过参数化双二吡啶胺（BDPA）与磷酸酪氨酸结合的二锌支架来演示该方法的实用性，然后将其功能化为有前途的抗肿瘤药物蛋白模拟物。
