Modeling of THE
VIBRATIONAL CIRCULAR DICHROISM OF SolvatED peptides
David Michalík,1
Marie Urbanová,1 Petr Bouř1,2
1 Department of Analytical Chemistry and Department of Physics and
Measurement, Institute of Chemical Technology, Technická 5, 166 28, Prague 6,
Czech Republic
2 Institute of Organic Chemistry and Biochemistry, Academy of Sciences of
the Czech Republic, 166 10, Prague 6,
Czech Republic
Vibrational circular
dichroism (VCD) spectra of newly synthesized short proline-containing peptides
Tyr-Asp-Pro-Ala-(Pro)N have been measured, in order to elucidate
there solution geometries. We are developing a theoretical model for spectra
simulations, based on complex molecular dynamics and ab initio DFT
calculations. Structures of the peptide and the water layer are obtained by
molecular dynamic, with the Amber force field. Then the peptide and closest
water molecules are partially optimized, using the restricted normal technique,
with the ONIOM method implemented in Gaussian 03, at the PM3/BPW91/6-31G** level.
This new method should provide more realistic models that the continuum solvent
models used previously [1]. The calculated infrared absorption and VCD spectra
profiles are sensitive to the hydration and conformation of the peptide and
reasonably well reproduce the experimental intensities.
[1] Bour, P.; Kubelka, J.; Keiderling, T. A. Biopolymers, 65, (2002), 45-69.