Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method.
Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method.
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DOI：
10.1063/1.4915068
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发表时间：
2015-03
期刊：
影响因子：
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通讯作者：
H. Nakata;D. Fedorov;F. Zahariev;Michael W. Schmidt;K. Kitaura;M. Gordon;Shinichiro Nakamura
中科院分区：
文献类型：
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作者：
H. Nakata;D. Fedorov;F. Zahariev;Michael W. Schmidt;K. Kitaura;M. Gordon;Shinichiro Nakamura
基于碎片分子轨道方法 (FMO)，已经为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。对三体展开式（FMO3）进行了推导，忽略三体修正即可得到二体表达式。此外，FMO3 的受限 Hartree-Fock (RHF) Hessian 矩阵可以通过忽略密度泛函相关项来获得。在 FMO-RHF 和 FMO-DFT Hessian 中，为了计算效率，某些小量级项被忽略。针对一组多肽和水簇评估了 FMO-DFT Hessian 的吉布斯自由能精度，结果发现其在相应完整（非碎片）从头计算的 1 kcal/mol 范围内。 FMO-DFT 方法还适用于 SN2 反应中的过渡态以及小 Trp 笼蛋白 (PDB: 1L2Y) 的红外和拉曼光谱的计算。还介绍了一些计算时序分析。
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.