期刊
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
卷 94, 期 2, 页码 655-665出版社
CHEMICAL SOC JAPAN
DOI: 10.1246/bcsj.20200258
关键词
Optimal superimposition for minimum RMSD; Data chemistry; Non-valence bond and transition state structures
GRMSD is an optimization method for calculating the minimal RMSD value of two atomic structures, applicable to various types of chemical structures and allowing for successful classification and mapping of molecular structures.
We present the Generalized Root Mean Square Deviation (GRMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. G-RMSD is not restricted to systems with an equal number of atoms to compare or a unique atom mapping between two molecules. The method can handle any type of chemical structure, including transition states and structures which cannot be explained only with valence bond (VB) theory (non-VB structures). It requires only Cartesian coordinates for the structures. Further information, i.e. atom- and bond types can also be included. Applications of G-RMSD to the classification of a-D-glucose conformers and 3D partial structure search using a dataset containing equilibrium (EQ), dissociation channel (DC), and transition state (TS) structures are demonstrated. We find that G-RMSD allows for a successful classification and mapping for a wide variety of molecular structures.
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