Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin
Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin
复制标题
基于群局域坐标的非简谐振动计算：在细菌视紫红质内部水分子中的应用
DOI：
10.1021/acs.jctc.1c00060
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发表时间：
2021
影响因子：
5.5
通讯作者：
Sugita Yuji
中科院分区：
文献类型：
--
作者：
Yagi Kiyoshi;Sugita Yuji
利用分子振动的局域性开发了一种有效的非简谐振动方法。定位于一组原子的振动坐标用于将系统的势能面（PES）分为组内和组间贡献。然后，基于 PES 求解振动薛定谔方程，其中群间耦合在谐波水平上被截断，同时考虑群内非谐性。该方法应用于由内部水分子和膜蛋白细菌视紫红质中的带电残基组成的五边形氢键网络（HBN）。 PES是通过B3LYP-D3/aug-cc-pVDZ级别的量子力学/分子力学（QM/MM）计算来计算的。红外 (IR) 光谱是通过二阶振动准简并微扰理论 (VQDPT2) 使用一组定位于每个水分子和氨基酸残基的坐标来计算的。基准计算表明，该方法产生的 N-D/O-D 拉伸频率误差为 7 cm-1，而成本降低了五倍以上。相比之下，谐波近似会产生 150 cm–1 的严重误差。此外，仔细评估 QM 区域的大小，发现 QM 区域不仅应包括五边形 HBN 本身，还应包括其 HB 伙伴。从分子动力学模拟获得的瞬态结构开始的 VQDPT2 计算表明，结构采样对计算的红外光谱有显着影响。非谐性、足够大的 QM 区域和结构采样的结合对于重现实验红外光谱至关重要。计算光谱为解码强 HBN 的红外信号铺平了道路，并有助于阐明它们在生物分子中的功能作用。
An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N–D/O–D stretching frequencies with an error of 7 cm–1at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm–1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.