Mechanical Interpretation of Coarse-grained Stiffness Matrix Based on Elastic-body Modeling of Molecular Assemblies

We have been developing a method for coarse-graining the low-frequency vibration modes of molecular assemblies, which affords a numerical representation of the down-sized stiffness matrix. In this study, we present an analytical representation of the stiffness matrix based on the elastic-body modeling of molecular assemblies. Comparison between the numerical and analytical data allows the 13 parameters regarding the dimension and mechanical properties of the putative elastic body. The results for 57 molecular dimers with various hydrogen-bond multiplicity demonstrate that the obtained parameters were physically reasonable and well-reproduced the wavenumbers of normal-mode vibrations.