Ferro-Costas David, Fernández-Ramos Antonio
Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
Front Chem. 2020 Jan 28;8:16. doi: 10.3389/fchem.2020.00016. eCollection 2020.
We propose an algorithm that is a combination of systematic variation of the torsions and Monte Carlo (or stochastic) search. It starts with a trial geometry in internal coordinates and with a set of preconditioned torsional angles, i.e., torsional angles at which minima are expected according to the chemical knowledge. Firstly, the optimization of those preconditioned geometries is carried out at a low electronic structure level, generating an initial set of conformers. Secondly, random points in the torsional space are generated outside the "area of influence" of the previously optimized minima (i.e., outside a hypercube about each minima). These random points are used to build the trial structure, which is optimized by an electronic structure software. The optimized structure may correspond to a new conformer (which would be stored) or to an already existing one. Initial torsional angles (and also final ones if a new conformer is found) are stored to prevent visiting the same region of the torsional space twice. The stochastic search can be repeated as many times as desired. Finally, the low-level geometries are recovered and used as the starting point for the high-level optimizations. The algorithm has been employed in the calculation of multi-structural quasi harmonic and multi-structural torsional anharmonic partition functions for a series of alcohols ranging from n-propanol to n-heptanol. It was also tested for the amino acid L-serine.
我们提出了一种算法，它是扭转角的系统变化与蒙特卡罗（或随机）搜索的结合。该算法从内部坐标中的一个试验几何结构和一组预处理扭转角开始，即根据化学知识预期出现最小值的扭转角。首先，在低电子结构水平上对这些预处理几何结构进行优化，生成一组初始构象异构体。其次，在先前优化的最小值的“影响区域”之外（即围绕每个最小值的超立方体之外）生成扭转空间中的随机点。这些随机点用于构建试验结构，该结构通过电子结构软件进行优化。优化后的结构可能对应于一个新的构象异构体（将被存储）或一个已有的构象异构体。存储初始扭转角（如果发现新的构象异构体，也存储最终扭转角），以防止两次访问扭转空间的同一区域。随机搜索可以根据需要重复多次。最后，恢复低水平几何结构并将其用作高水平优化的起点。该算法已用于计算从正丙醇到正庚醇的一系列醇类的多结构准谐波和多结构扭转非谐波配分函数。它也对氨基酸L-丝氨酸进行了测试。
