Subject: Re: CCL:Re:REPLY TO HOW TO FIND BONDS

From: Mark Forster <[email-masked]>
Date: Tue, 29 Feb 2000 09:33:33 +0000

Dear CCL

On the subject of defining a bond:

The 'Atoms in Molecules' methodology of Richard Bader
provides an objective means to define atoms and bonds,
thereby linking chemical intuition with quantum mechanics.

Check out the site

    http://www.chemistry.mcmaster.ca/faculty/bader/aim/

it is very informative.

elewars wrote:

> Hello,
>
> So far as I know there is no "true definition" of a bond. At one level the concept is simple, at another level sophisticated. Given
> the cartesian coordinates of a molecule, the simplest way to get the "bonds" is to draw a line between all pairs of nuclei within a
> distance that experience or general agreement says is bonding; there are programs that will do this (e.g. Molwin, some versions of
> Spartan). This shows you what the molecule looks like, which is sometimes all you want.
> Of course bonds can be assigned from calculated bond order, determined by the coefficients of the basis functions in the occupied
> MOs (e.g. Lo:wdin B.O., Meyer B.O., Mulliken B. O), or from an analysis of the calculated electron density: AIM analysis--atoms in
> molecules (Bader analysis).
>
> EL
> =====
>
> li guo hui wrote:
>
> > Dear Netters:
> > i would like to know what is the true definition of bond, this question can also be given in the following:
> > given a file only including coordinates of atoms in molecule, there are not connectivities between atoms in molecule, just from
> > this file how can i find the bonds or connectivities? using Van der walls radius or covalance radius of atoms or some results of

> > population analysis from theoretical calcualtion?
> >
> > thank you
> >
> >
> > Li Guo Hui
> > State Key Laboratory of Molecular Reaction Dynamics
> > Dalian Institute of Chemical Physics
> > Liao Ning Province, P.R.China
> >
> > Mailing Address:
> > Room 715
> > Xing Hai Third Street, 59 #
> > Sha He Kou District
> > Dalian, Liaoning Province
> > P.R.China, 116023
> >
>
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--

  Dr Mark J Forster Ph.D.
  Principal Scientist
  Informatics Laboratory
  National Institute for Biological Standards and Control
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