Subject: Re: CCL:partial charges for large molecules

From: "C.F. Matta" <[email-masked]>
Date: Sun, 12 Jul 1998 01:44:32 -0400 (EDT)

Dear Dr. Kroemer,

   The only theoretically sound partitioning of ANY molecular property
(including atomic populations) into a sum of atomic contributions is the
Bader (or virial) partitioning [2].  Bader and his coworkers generalized
quantum mechanics to "subsystem" quantum mechanics in which parts of a
system are treated on the same footing as the total system. However, the 
total system cannot be arbitrarily partitioned.  It can be
rigorously proved that the total molecular system can ONLY be partitioned
at the so called zero-flux surfaces which satisfy the quantum boundary
condition [2]: 
 
     grad rho (r) .  n(r) = 0        for all r belonging to the surface.

   These surfaces always enclose regions of the molecular space with only
one nucleus and fall between neighboring atom, which justify their
identification as "inter-atomic surfaces".

   An atomic population is computed by integrating the  electron density
bounded by all the interatomic surfaces of the atom and an exterior
envelope in the electron density.  The resulting population can then be
easily translated to an atomic charge.[2]

   The atomic charges computed in this way retain a remarkable stability
and transferability among different molecules.  These charges are
independent of basis functions centered on neighboring atoms and retain
the characteristic signature of the "atoms of wet chemistry" even when
bonded to dissimilar neighboring atoms.

  With this transferability in mind, we have just completed a study (to
be submitted to publication soon) of the atomic properties of the
genetically-coded amino acids, which will become our electron density
building blocks (exactly what nature does!).[1]  All the atomic properties
(including the populations) retain a remarkable stability on going from
amino acids to dipeptides to tripeptides etc. which justifies the approach
of building a polypeptide density by sticking amino acid fragments
together at their common inter-atomic surface.[1]

  I suggest you have a look at:

     [1] C. Chang and R. F. W. Bader "Theoretical Construction of a
	 Polypeptide", J. Phys. Chem. Vol. 96, No.4 (1992), p.1654.

     [2] R. F. W. Bader "Atoms in Molecules: A Quantum Theory",
	 Clarendon Press, (Oxford, 1990).

  Or visit the web site (where you can also download all the software
  related to the theory):
               
         http://www.chemistry.mcmaster.ca/faculty/bader/aim/

Sincerely,

Cherif Matta
Graduate student
Department of Chemistry
McMaster University
Hamilton, Ontario
Canada L8S 4M1

On Thu, 9 Jul 1998, Romano Kroemer wrote:

> 
> Dear all,
> 
> could somebody point me to references for the following problem/method:
> 
> I have a large molecule and want to calculate partial charges with a fairly
>   sophisticated method. As the molecule is too large, I divide it into
>   moderately sized _overlapping_ pieces, calculate the partial charges for
>   each of these chunks, and derive then the charges for the whole molecule.
>   The "overlapping pieces" procedure is necessary in order to avoid
>   "boundary problems".
> 
> Comments on the advantages and drawbacks of such an approach (such as the
>   perturbations of the charges on one end of the molecule by the charges
>   on the other end when the molecule is not linear) are of course
>   welcome. 
> 
> Thank you very much in advance for your input. I will post a summary to the
>   list.
> 
> Yours sincerely,
> Romano Kroemer
> 
> -- 
> ===============================================================================
> Dr. Romano T. Kroemer
> Phys. & Theoret. Chem. Lab.
> University of Oxford
> South Parks Rd.                       | Tel:     ++44-1865-275475 
> Oxford OX1 3QZ                        | Fax:     ++44-1865-275410
> England, U.K.                         | Email:   [email-masked]
> ===============================================================================
> 
> 
> ---
> Administrivia: This message is automatically appended by the mail exploder:
> [email-masked]: Everybody | [email-masked]: Coordinator
> [email-masked]: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
> Anon. ftp: www.ccl.net   | [email-masked] -- archive search
>              Web: http://www.ccl.net/chemistry.html 
> ---
> 
>