Re: QSAR - Cation-Pi interactions

Dear Dr. Jones,

If you are using Molecular mechanics with MM (molecular mechanics)
force fields, there are no electrons involved and you can not
learn anything about orbital energies. Those can only be studied
by Quantum mechanics approaches. The issue of using semiempirical
vs. ab initio (and there are many options in each of them)
should primarily be determined by the "resolution" of the
experiments that you wish to compare to. I suspect that if
you wish to compare to biological results, try first some
semiempirical QM method such as those that may be found
in the MOPAC packages (AM1, PM3 etc..). You could
later try a QM/MM approach if you need to look at larger systems.

Good luck,

Amiram Goldblum
At 03:28 02/08/2004, you wrote:

>NB: Unless you reset the To: line, your reply goes to the entire list
>---
>
>Please help a novice. I am a neurologist who is trying to
>learn to use computational chemistry for certain
>applications in understanding drug action. I have been
>experimenting with molecular dynamics to study the effects
>of cations on the orbital energies of aromatic systems in
>small molecules. Is this a valid approach? Is there a
>superior approach? Are semi-empirical or ab initio, or DFT
>methods capable/better for handling such "non-bonded"
>interactions?
>
>Sincerely,
>
>GLJones, MD
>_______________________________________________
>qsar_society mailing list
>qsar_society*accelrys.com
>http://ftp2.accelrys.com/mailman/listinfo/qsar_society

*************************************************************************
Amiram Goldblum, Ph.D. Cell: 972-54-653292
Professor of Medicinal Chemistry Tel: 972-2-6758701
Molecular Modeling and Drug Design Fax: 972-2-6758925
Department of Medicinal Chemistry and Natural Products
School of Pharmacy, Hebrew University of Jerusalem
ISRAEL 91120 email: amiram__vms.huji.ac.il
Internet: http://www.md.huji.ac.il/models/
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Received on 2004-08-02 - 17:52 GMT