Subject: [Summary] CD spectrum simulation

From: Edgar Luttmann <edgar/at/upb.de>
Date: Mon, 30 Jun 2003 09:16:16 +0200

Here the Summary of the replies regarding my initial question:
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I would like to know if there is any method to simulate (at least a
rough) CD spectrum of a small peptide. I do have a PDB file (so I have
3D coordinates) and it would be great to predict a spectrum from this.

Any hints are welcome and I will give a summary.
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Here the different replies:
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If you mean circular dichroism spectrum, you may contact SCM
(http://www.scm.com),
because there will be a new implementation available (later this year, I
think)
within the ADF program.
You might look for papers by Jochen Autschbach
(Jochen.Autschbach/at/chemie.uni-erlangen.de).
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Hello,

For ab initio calc of CD spectra see

1) P. J. Stephens et al, J Phys Chem, 1994, 98, 11623.

2) F. J. Devlin et al, J Phys Chem A, 1997, 101, 6322.

E. Lewars
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Hi Edgar,

  > I would like to know if there is any method to simulate (at least a
  > rough) CD spectrum of a small peptide. I do have a PDB file (so I have
  > 3D coordinates) and it would be great to predict a spectrum from this.

If you have enough computer power you can calculate the spectrum
ab initio // (TD)DFT. (Dalton, Gaussian'03). But currently it would need
to be a very small peptide, and you'd need a good idea of conformational
distribution in solution at your experimental conditions.

Maybe someone has made or should make a semi-empirical extention
of e.g. ZINDO that can do the required electric and magnetic transition
dipole moments etc.

Otherwise, there's empirical correlations.

hope this helps,

Jeremy
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Jeremy Greenwood                                  jeremy/at/greenwood.net
Department of Medicinal Chemistry                      bh +45 35306117
The Danish University of Pharmaceutical Sciences       fx +45 35306040
Universitetsparken 2, DK-2100 Copenhagen, Denmark      ah +45 32598030
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Hi Edgar,
Simulation of CD spectra can be done by ab initio methods which are
available in QC codes like Turbomole and Gaussian03. See f.x. J. Am.
Chem. Soc., 122 (8), 1717-1724, 2000.

You might also consider contacting Professor Fleischhauer at the RWTH in
Aachen. He has developed software code for prediction of protein CD
spectra using a semi-empirical approach. See:
http://134.130.101.5/akflei/index.html

However, I guess you are interested in simulating the solution CD
spectrum. This is not so easy for a small peptide, since they often have
no single well-defined structure in solution. The CD spectrum in
solution will thus represent a weighted average of the spectra of a
large number of conformers of the peptide. Obviously, this will require
some effort to model.

Good luck,
Peter

-- Peter W. Thulstrup Chemistry Department / Royal Veterinary and
Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C /
Denmark Phone (Chemistry Dep't): +45 35282400 / Fax: +45 35282398 Phone
(Office - direct): +45 35282464 / E-mail: pwt/at/kvl.dk
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See
C. Diedrich S. Grimme, Systematic investigation of Modern Quantum Chemical
Methods to Predict Electronic Circular Dichroism Spectra, J. Phys. Chem. A,
107, (2003), 2524-2539.
for a recent investigation.
Stefan
_________________________________________________________
Prof. Dr. Stefan Grimme
Organisch-Chemisches Institut (Abt. Theoretische Chemie)
Westfaelische Wilhelms-Universitaet, Corrensstrasse 40
D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax)
Email:grimmes/at/uni-muenster.de
http://www.uni-muenster.de/Chemie/OC/research/grimme/
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CD spectra for any closed-shell molecule with up to 50 to 100
atoms can be efficiently and accurately calculated with the
Amsterdam Density Functional (ADF) program. For larger systems,
the rest of the system ("environment") will need to be modeled
in a more approximate way.

Please have a look at the recent papers by Dr. Jochen Autschbach
(currently in Erlangen) and Prof. Tom Ziegler in J. Chem. Phys.
and other journals on CD spectra simulations with ADF.

If you would like to obtain further information, let me know.

Best regards,
Stan van Gisbergen
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Thanks again for all your help.