Tuttle Tell, Thiel Walter
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK G1 1XL.
Phys Chem Chem Phys. 2008 Apr 28;10(16):2159-66. doi: 10.1039/b718795e. Epub 2008 Feb 25.
The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3).
已知OMx家族的半经验方法（正交化模型OM1、OM2和OM3）比诸如AM1等标准半经验方法能更准确地描述生化系统。我们研究了在不修改标准OMx参数的情况下，用从近期密度泛函工作中获取的经验色散项（OMx-D）增强这些方法的益处。对于非共价相互作用取得了显著改进，在JSCH - 2005数据库中，复合物结合能的平均绝对误差在OM2-D方法下为1.41千卡/摩尔，在OM3-D方法下为1.31千卡/摩尔。这支持了这些增强方法在生物分子的量子力学/分子力学（QM/MM）研究中的应用，例如在系统制备和平衡过程中。作为一个示例应用，我们展示了关于抗体34E4与半抗原之间结合的QM和QM/MM计算，其中OM3-D比没有色散项的方法（AM1、OM3）表现更好。
