Subject: Re: CCL:ab initio bond minimizations

From: [email-masked] (Per-Ola Norrby)
Date: Wed, 16 Oct 1996 10:33:40 +0200

Dear Ray,

        Your problem is in no way unique, it happens to everybody who try
crystal structures in ab initio optimizations.  There are a couple of ways
you can do this.  First, the largest errors are for bonds to hydrogen, you
could simply set them manually at better positions before starting the
calculation (C-H ca 1.08Å, give C an idealized geometry like tetrahedron
for sp3, X-H generally shorter than C-H, there are lit. values for most
types).  This is easiest if you can generate a Z-matrix for your X-ray
structure.

        My favourite method is to bring the molecule into a molecular
mechanics program, restrain all heavy atoms and let the program optimize
the hydrogens.  Alternatively, you may want to allow also the heavy atoms
some movement, most MM programs can do some kind of "tethering" to allow
small relaxations.

        The most expensive option would be to restrict movement of the
heavy atoms in the ab initio program, and let it find optimum values for
the hydrogen, before starting the full optimization.

        An added complication: there is no guarantee that the crystal
geometry is a local minimum in vacuo, especially if you have systems with
strong charges, but it should definitely have a low energy if you allow
relaxation.

        Regards,

        Per-Ola Norrby

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 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
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