Subject: IR INTENSITIES BY MM, SUMMARY

From: elewars <[email-masked]>
Date: Mon, 28 May 2001 22:14:23 -0400

2001 May 28

Here is the summary of answers to my question whether molecular
mechanics can calculate IR intensities.
I thank all who showed an interest; they are acknowledged (#1- - #6)
below--I hope I haven't missed anyone.

Briefly, MM can. One such commercially-available program is a version of
MM3, developed by the Allinger group.

Dr J-H Lii of the University of Georgia (USA) was kind enough to
calculate some IRs for me.

E. Lewars
=====

The Question:

2001 May 22

Hello,

    Molecular mechanics programs can now calculate the positions
(cm**-1) of normal-mode vibrations. However, MM by itself cannot
calculate the _intensities_ of these vibrations, since this depends on
the change in dipole moment, which in turn depends on electron
distribution, a concept outside MM theory.

    It seems, however, that in principle MM could calculate intensities
using assigned bond moments or atom charges, which would provide a rapid

way of calculating IR spectra. Has this been implemented in any program?

Thanks

E. Lewars
========
The Answers:

#1

Hi,

 For periodic systems, try GULP (General Utility Lattice Program, by
Dr. Julian Gale <[email-masked]> )
 I've never done it, but this is from the help file:

-------------------------------------------------------------------------

 @@intensity
Topic   : intensity
Type    : Information
Info    : Infra-red phonon intensities are output when the eigenvectors
        : have been calculated using "eigen". Intensities are in nominal

        : units of charge**2. Raman intensities are also now output.
        : However, it should be noted that they are approximate and only

        : valid for systems with a single type of bond in (such as a
        : silicate).
-------------------------------------------------------------------------

Hope this helps.

Ricardo

Ricardo Grau-Crespo
[email-masked]
Centro de Investigaciones del Petroleo
CUBA
================

#2

Hi,

you can calculate the intensities from the dipole moment change as a
function of the Cartesian coordinates. In principle
the charges can be whatever, but the intensities will be extremely
dependent on them. A way to obtain good and cheap
charges is to use QCFF/PI (see, for example Warshel,
Computers&Chemistry, 1,195-202,1977), but if you are not so
worried about the charges quality even with regular CFF (see
Warshel-Levitt-Lifson, J. Mol. Spectr. 33,84-99(1970))
you can do the above job. Apart from QCFF/PI I don't know which other
programs have this implemented. Sorry about
that.

Jordi

Jordi Villa i Freixa
[email-masked]   http://laetro.usc.edu/wgroup/people/jorgevil
Department of Chemistry, University of Southern California
Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
================

#3

Greetings,

Allinger has published a paper on IR intensities...  I might guess in J
Comp
Chem..

Regards,

John McKelvey

    [email-masked]
===================

#4

You should check the book by K. Machida "Principles of molecular
mechanics". I believe that the RISE program by the same author is able
to calculate IR intensities.

Rehards

--
Dr. Rafael R. Pappalardo
Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla
(Spain)
e-mail: [email-masked]
===========

#5

could you summarize the answers you will get.
Thanks regards
Francois
 --
F.-Y. Dupradeau
http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm
==============

#6

Dear Lewars,

The MM3 program uses bond dipole moments and bond charge flux to
calculate
the IR intensity. Here is the reference you might want to look at....

Lii, J.-H. and Allinger, N.L. "Intensities of Infrared Bands in
Molecular
Mechanics (MM3)", J. Comput. Chemistry, 13, 1138-1141 (1992)

Best regards,

-Robert

 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Dr. Jenn-Huei Lii
   Computational Center for Molecular Structure and Design
   Department of Chemistry, University of Georgia, Athens, USA
   Tel: (706)542-2044                     Fax: (404)542-2673
   CCMSD Home Page:  http://europa.chem.uga.edu
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Dear Professor Lewars,

Let me answer your questions in turns...

(1) Yes, MM3 is available from Tripos, Inc. It also available from QCPE
for
academic users.

(2) MM3 uses bond moments instead. It converts bond moment to atomic
charge
then calculate IR intensity.

(3) We found Bond Charge Flux (even Angle Charge Flux) parameters play
important role in IR intensity calculation in MM. Therefore, I am not
sure
if the error were small in Benzene or not. It needs to be investigated.

-Robert

----- Original Message -----
From: "elewars" <[email-masked]>
To: "Jenn-Huei Lii" <[email-masked]>
Sent: Sunday, May 27, 2001 5:46 PM
Subject: Re: QUICK QUESTIONS

> Hello,
>
> May I ask just three short questions?
>
> (1) Is the version of MM3 you used to calculate intensities
commercially
> available, and if so who sells it?
> (2) Does MM3 use atom charges to calculate dipole moments and thus
intensities
> (e.g. C and  H for benzene)?
> (3) I think for benzene you mean that you are still working on
parameterizing
> charges (?); can I assume any error for that calculation was fairly
small?
> Thank you very much.
> E. Lewars
> ===========
==============