Zhao Dongbo, Shen Xiaoling, Cheng Zheng, Li Wei, Dong Hao, Li Shuhua
School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China.
Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People's Republic of China.
J Chem Theory Comput. 2020 May 12;16(5):2995-3005. doi: 10.1021/acs.jctc.9b01298. Epub 2020 Apr 29.
We have implemented the calculations of NMR parameters within the generalized energy-based fragmentation (GEBF) method for condensed-phase systems with periodic boundary conditions (PBC). In this PBC-GEBF approach, NMR parameters of molecules in a unit cell are assembled as a linear combination of the corresponding quantities from a series of small embedded subsystems. To treat condensed-phase systems containing large molecules, we propose a novel "fragment-based" strategy for building subsystems, while our previously reported "molecule-based" strategy for construction of subsystems is appropriate for periodic systems with small molecules. The "fragment-based" strategy in PBC-GEBF is demonstrated to be much more efficient than its "molecule-based" counterpart to treat crystals of large molecules. With the "molecule-based" PBC-GEBF method, we obtained consistently good NMR parameters of liquid water with B3LYP on top of neural-network-potential-based molecular dynamics (AIMD) snapshots. With the "fragment-based" PBC-GEBF approach, we predicted the H chemical shifts of a large macrocycle in solution based on a series of classical MD snapshots. The calculated results are in good accord with the experimental chemical shifts. Therefore, the PBC-GEBF method is expected to be a reliable and efficient tool for predicting NMR parameters of large complex systems in solutions.
我们已经在具有周期性边界条件(PBC)的凝聚相系统的广义基于能量的碎片化(GEBF)方法中实现了核磁共振(NMR)参数的计算。在这种PBC-GEBF方法中,晶胞中分子的NMR参数被组装为一系列小的嵌入式子系统中相应量的线性组合。为了处理包含大分子的凝聚相系统,我们提出了一种新颖的构建子系统的“基于片段”策略,而我们之前报道的构建子系统的“基于分子”策略适用于小分子的周期性系统。结果表明,PBC-GEBF中的“基于片段”策略在处理大分子晶体时比其“基于分子”的对应策略效率高得多。使用“基于分子”的PBC-GEBF方法,我们在基于神经网络势的分子动力学(AIMD)快照之上,用B3LYP方法始终如一地获得了液态水良好的NMR参数。使用“基于片段”的PBC-GEBF方法,我们基于一系列经典MD快照预测了溶液中一个大的大环的H化学位移。计算结果与实验化学位移吻合良好。因此,PBC-GEBF方法有望成为预测溶液中大型复杂系统NMR参数的可靠且高效的工具。