School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic, Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, 210023, P. R. China.
Phys Chem Chem Phys. 2021 Sep 15;23(35):19394-19401. doi: 10.1039/d1cp02814f.
A generalized energy-based fragmentation (GEBF) approach has been combined with a universal solvation model based on solute electron density (SMD) to compute the solvation energies of general large systems (such as protein molecules) in solutions. In the GEBF-SMD method, the solvation energy of a target system could be combined by the corresponding solvation energies of various subsystems, each of which is embedded in the background point charges and surface charges on the surface of solute cavity at the positions of its atoms and neighbouring atoms outside of the subsystem. Our results show that the GEBF-SMD model could reproduce the conventional SMD solvation energies quite well for various proteins in solutions, and could significantly reduce the computational costs for the SMD calculations of large proteins. In addition, the GEBF-SMD approach is almost independent of the basis sets and the types of solvents (including protic, polar, and nonpolar ones). Also, the GEBF-SMD approach could reproduce the relative energies of various conformers of large systems in solutions. Therefore, the GEBF-SMD method is expected to be applicable for computing the solvation energies of a broad range of large systems.
一种广义基于能量的碎裂（GEBF）方法与基于溶质电子密度的通用溶剂化模型（SMD）相结合，用于计算溶液中一般大系统（如蛋白质分子）的溶剂化能。在 GEBF-SMD 方法中，目标系统的溶剂化能可以通过各个子系统的相应溶剂化能组合而成，每个子系统都嵌入在溶质腔表面的背景点电荷和表面电荷中，其位置为子系统中原子及其外部原子的位置。我们的结果表明，GEBF-SMD 模型可以很好地再现溶液中各种蛋白质的传统 SMD 溶剂化能，并可以显著降低大蛋白质 SMD 计算的计算成本。此外，GEBF-SMD 方法几乎与基组和溶剂类型（包括质子、极性和非极性溶剂）无关。此外，GEBF-SMD 方法可以再现溶液中大系统各种构象的相对能量。因此，GEBF-SMD 方法有望适用于计算广泛的大系统的溶剂化能。
