Molecular Properties

Analysis > Molecular Properties... gives access to pDynamo tools that describe one structure: the frame shown in the 3D view. The atoms are the Active system or the Selected molecule(s) (a pruned copy). The window has three tabs.

• Symmetry: Find Point Group determines the point group of the structure, its rotational symmetry number, the symmetry operations and the groups of symmetry-equivalent atoms (pDynamo's point group finder). The Distance tolerance (default 0.1 Å) and Angle tolerance can be raised for slightly distorted structures (Figure 1).

• Stereochemistry (CIP): Find R/S and E/Z assigns the Cahn–Ingold–Prelog labels of stereocenters and double bonds; Show as Labels displays them in the 3D view. It needs all hydrogens and the bond orders (connectivity) of the system.

• Ion mobility (CCS): Calculate gives projection-approximation and hard-sphere collision cross sections and mobilities in helium (Shvartsburg and Jarrold, 1996), for charge +1 (multiply the mobility by |z| for other charges). pDynamo's hard-sphere radii cover H, C, N, O, Na, Si, P and Fe only.

The symmetry number found here is the same one suggested in the Thermochemistry (RRHO) window (see Normal modes and IR spectra).