Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR , Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1 , I-56124 Pisa , Italy.
Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.
J Chem Theory Comput. 2019 May 14;15(5):3170-3184. doi: 10.1021/acs.jctc.9b00120. Epub 2019 Apr 17.
Computational simulation of UV/vis spectra in condensed phases can be performed starting from converged molecular dynamics (MD) simulations and then performing quantum mechanical/molecular mechanical (QM/MM) computations for a statistically significant number of snapshots. However, the need of variational solutions (e.g., ONIOM/EE) for a huge number of snapshots makes unpractical the use of state-of-the-art QM Hamiltonians. On the other hand, the effectivity of perturbative approaches (e.g., perturbed matrix method, PMM) comes at the price of poor convergence for configurations strongly different from the reference one. In this paper we introduce an integrated strategy based on a cluster analysis of the MD snapshots. Next, a representative configuration for each cluster is treated at the ONIOM/EE level, whereas local fluctuations within each cluster are described at the PMM level. Some representative systems (uracil in dimethylformamide and in water and tyrosine zwitterion in water) are analyzed to show the effectivity and flexibility of the proposed strategy.
可以从收敛的分子动力学(MD)模拟开始,对凝聚相的 UV/vis 光谱进行计算模拟,然后对大量的快照进行量子力学/分子力学(QM/MM)计算。然而,对于大量的快照,需要变分解(例如,ONIOM/EE),这使得使用最先进的量子哈密顿量变得不切实际。另一方面,微扰方法(例如,微扰矩阵方法,PMM)的有效性是以参考构型相差较大的构型的收敛性差为代价的。在本文中,我们引入了一种基于 MD 快照聚类分析的集成策略。接下来,对每个簇的代表性构型进行 ONIOM/EE 处理,而对每个簇内的局部波动则采用 PMM 处理。分析了一些代表性体系(二甲基甲酰胺和水中的尿嘧啶以及水中的酪氨酸两性离子),以显示所提出策略的有效性和灵活性。