Re: CCL:summary for program for superimposing (small) molecules and new question

Title: Re: CCL:summary for program for superimposing (small)
        Dear Daniel,

Before I present the summary, I was to ask the (neccessary)
follow-up question:  In your experience, when a comparison
of an experimental molecular structure (i.e. X-rays) and its
calculated (Gaussian) counterpart is done, which will be the
treshold RMSD value which can be considered acceptable ?

        The RMSD value is NOT a good measure of quality.  One reason is that soft modes (mainly torsions) are easily distorted by crystal packing, leading to huge discrepancies if you only look at RMSD.  A case in point is biphenyl, where the crystal adopts a planar structure becuase it packs better, whereas the gas phase global minimum has a torsion angle around 41 degrees.

        You can either use a comparison that is insensitive to these discrepancies, or do the calculation in the crystal (requiring QM with periodic boundaries, not in Gaussian).  I'd recommend comparison of lists of bond lengths and angles.  Alternatively, you can use the energy of the crystal structure calculated by Gaussian and compare it to the global minimum in Gaussian, but that requires constrained relaxation of the crystal structure to allow for differences in paradigm between X-ray and QM.

        Best regards,

        Per-Ola Norrby
--
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Department of Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon~at~kemi.dtu.dk  tel +45-45252123,  fax +45-45933968