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.