Stereochemical Analysis of Molecular Fragments
Program for the Stereochemical Analysis of Molecular Fragments by Means of Continous Shape Measures and Associated Tools
Shape calculates continuous shape measures (CShM’s) of a set of points (e.g. atomic positions) relative to the vertices of ideal reference polygons or polyhedra (referred in general as “polyhedra” from here on for simplicity), either centered or non centered. The non centered polyhedra are intended to represent structures of clusters without a central atom, whereas centered polyhedra typically represent the coordination sphere (vertices) of a central atom. Throughout this manual we will indistinctly refer to vertices and atoms as synonims. Shape also calculates deviations from minimal distortion paths and polyhedral interconversion generalized coordinates. This program is based on the algorithm described by Pinsky and Avnir for the calculation of continuous shape measures, and on the definitions of minimal distortion paths and generalized interconversion coordinates. For more information see the following references:
– Continuous shape measures algorithm: M. Pinsky, D. Avnir. Inorg. Chem., 37, 5575 (1998). – Minimal distortion paths: D. Casanova, J. Cirera, M. Llunell, P. Alemany, D. Avnir,
S. Alvarez. J. Am. Chem. Soc., 126, 1755-1763 (2004).
– Generalized interconversion coordinates: J. Cirera, E. Ruiz, S. Alvarez.
Chem. Eur. J., 12, 3162 (2006).
It must be noticed that the algorithm used by Shape does not distinguish the two enantiomers of a chiral shape. Therefore, whenever a chiral reference polyhedron is used, the resulting shape measures may not refer to that specific polyhedron but to its enantiomer.