Nakata Hiroya, Fedorov Dmitri G, Zahariev Federico, Schmidt Michael W, Kitaura Kazuo, Gordon Mark S, Nakamura Shinichiro
Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
J Chem Phys. 2015 Mar 28;142(12):124101. doi: 10.1063/1.4915068.
Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
基于片段分子轨道方法（FMO），已针对自旋受限密度泛函理论（DFT）开发了能量相对于核坐标的解析二阶导数。这些推导是针对三体展开（FMO3）进行的，通过忽略三体校正可得到二体表达式。此外，通过忽略与密度泛函相关的项，可以得到FMO3的受限Hartree-Fock（RHF）海森矩阵。在FMO-RHF和FMO-DFT海森矩阵中，为了计算效率，某些量级较小的项被忽略。针对一组多肽和水簇评估了FMO-DFT海森矩阵在吉布斯自由能方面的准确性，发现其与相应的完整（非片段化）从头算计算结果相差在1 kcal/mol以内。FMO-DFT方法还应用于SN2反应的过渡态以及小Trp笼蛋白（PDB：1L2Y）的红外和拉曼光谱计算。还给出了一些计算时间分析。
