Theoretical and Computational Chemistry

G-RMSD: Root Mean Square Deviation Based Method for Three-dimensional Molecular Similarity Determination

Hiroko Satoh University of Zurich


We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. The method is not restricted to systems with an equal number of atoms or a unique atom matching and can handle any type of chemical structure, including transition states and non-valence bond structures. It requires only Cartesian coordinates for the structures, but can also include further information, i.e. atom and bond types. Applications of G-RMSD to the classification of alpha-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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First submission


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Supplementary material

Thumbnail image of aDglucose-GRRM-RHF631G.txt
download asset aDglucose-GRRM-RHF631G.txt 1 MB [opens in a new tab]
Thumbnail image of CH2OH-anion-B3LYP631Gd.txt
download asset CH2OH-anion-B3LYP631Gd.txt 0.00 MB [opens in a new tab]
Thumbnail image of CH2OH-cation-B3LYP631Gd.txt
download asset CH2OH-cation-B3LYP631Gd.txt 0.00 MB [opens in a new tab]
Thumbnail image of CH3-anion-B3LYP631Gd.txt
download asset CH3-anion-B3LYP631Gd.txt 0.00 MB [opens in a new tab]
Thumbnail image of CH3-cation-B3LYP631Gd.txt
download asset CH3-cation-B3LYP631Gd.txt 0.00 MB [opens in a new tab]
Thumbnail image of H4C2O2-GRRM-B3LYP631Gd.txt
download asset H4C2O2-GRRM-B3LYP631Gd.txt 0.53 MB [opens in a new tab]

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