Li Junjie, Iyengar Srinivasan S
Department of Chemistry and Department of Physics, Indiana University , 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States.
J Chem Theory Comput. 2015 Sep 8;11(9):3978-91. doi: 10.1021/acs.jctc.5b00433. Epub 2015 Aug 20.
Here, we demonstrate the application of fragment-based electronic structure calculations in (a) ab initio molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H₉O₄⁺, H₁₃O₆⁺ and H(H₂O)₂₁⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD(T) calculations over 693 different geometries for the H₉O₄⁺ system. For the larger H(H₂O)₂₁⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. Ab initio dynamics calculations were performed for H₉O₄⁺ and H₁₃O₆⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their Fourier transforms computed from the fragment-based AIMD approaches were found to be in excellent agreement with those computed using the respective higher level of theory from the chosen hybrid calculation.
在此，我们展示了基于片段的电子结构计算在（a）从头算分子动力学（AIMD）和（b）降维势计算中的应用，用于中等大小和大尺寸的质子化水团簇。这里使用的特定片段化算法源自ONIOM，但包括多个重叠的“模型”系统。各种重叠模型系统之间的相互作用是：（a）通过在选定的更高理论水平上调用包含 - 排斥原理来近似，以及（b）在选定的较低理论水平上进行的实际计算中。片段化算法本身是使用位操作算术编写的，这将被证明是有利的，因为此类方法中的片段数量有随系统大小呈指数增长的趋势。对三种不同的质子化水团簇进行了基准计算：H₉O₄⁺、H₁₃O₆⁺和H(H₂O)₂₁⁺。对于势能面基准，我们对正规坐标进行采样，并将我们的表面能与完整的MP2和CCSD(T)计算结果进行比较。对于H₉O₄⁺系统的693种不同几何结构，基于片段的算法与MP2计算相比，平均绝对误差<0.05 kcal/mol，与CCSD(T)计算相比，平均绝对误差<0.07 kcal/mol。对于更大的H(H₂O)₂₁⁺水团簇，与84种不同几何结构的完整MP2计算相比，平均绝对误差约为0.1 kcal/mol，而计算成本仅为其一小部分。对H₉O₄⁺和H₁₃O₆⁺进行了从头算动力学计算，发现对于短轨迹（皮秒量级），能量守恒约为0.01 kcal/mol。轨迹保持较短是因为我们的算法目前不包括动态片段化，这将在未来的出版物中考虑。然而，从基于片段的AIMD方法计算得到的速度自相关函数及其傅里叶变换与使用所选混合计算中各自更高理论水平计算得到的结果非常吻合。
