López-Sosa L, Calaminici P, Köster A M
Departamento de Química, CINVESTAV, Mexico, Mexico.
J Comput Chem. 2023 Nov 15;44(30):2358-2368. doi: 10.1002/jcc.27202. Epub 2023 Aug 28.
With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.
随着量子力学/分子力学（QM/MM）方法的兴起，对分子聚集体计算的兴趣大幅增加。此类聚集体的结构和动力学通常在很大程度上受分子间相互作用支配。因此，相应的势能面拓扑结构丰富且具有许多浅的极小值。所以，QM/MM分子聚集体的局部结构优化可能具有挑战性，特别是在施加优化约束时。为克服这一问题，提倡在正规坐标空间中进行结构优化。为此，通过笛卡尔坐标空间中的投影矩阵将分子的外部自由度与内部自由度分离。在此，我们将此方法扩展至笛卡尔约束。为此，我们设计了一种算法，该算法将笛卡尔约束直接添加到投影矩阵中，从而在分子进行优化的约化坐标空间中消除这些约束。为分析正规坐标空间中约束优化算法的性能和稳定性，我们采用QM/MM约束优化方法，给出了气相以及水中小分子体系和氨基酸的约束极小化结果。所有计算均在程序deMon2k中实现的辅助密度泛函理论框架下进行。
