Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
Phys Chem Chem Phys. 2020 Apr 14;22(14):7169-7192. doi: 10.1039/c9cp06869d. Epub 2020 Feb 19.
We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.
我们提出并讨论了一种通过半经验紧束缚方法结合元动力学驱动搜索算法对分子化学空间部分进行计算机采样的有效方案。这项工作的重点是在量子化学水平上为构象生成适当的热力学系综,但也讨论了质子化态、互变异构和非共价络合几何形状的类似程序。通常,由所有明显占据的最低能量结构组成的构象系综构成了进一步的、主要是 DFT 计算工作的基础,例如光谱或宏观性质的计算。通过使用基本的量子化学方法,可以考虑电子效应或可能的键断裂/形成,并获得候选结构的非常合理的初始能量排序。由于快速低成本量子化学方法带来的巨大计算加速,即使对于具有数百个原子(通常是药物大小的分子)的系统,也可以实现总体较短的计算时间。此外,还讨论了专门的应用,例如带有隐式溶剂化模型的采样或用于过渡态的约束构象采样、金属、表面或非共价结合的络合物,为现代计算化学和药物发现开辟了许多可能的应用。这些过程已在一个名为 CREST 的免费计算机代码中实现,该代码利用了快速可靠的 GFNn-xTB 方法。