Optical Spectroscopic Studies of L-Alanyl-L-Alanine
J. Šebek1,2, B. Gyurcsik3, J. Kapitán2, J. Šebestík2 and P. Bouř2
1Institute of Chemical Technology, Technická 5, 166 28 Praha
2Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha
3University of Szeged, P.O.Box 440, H-6701 Szeged, Hungary
Many spectroscopic methods used in analyses of biomolecules make use of their chirality. For example, the electronic circular dichroism (ECD) spectroscopy and Raman optical activity (ROA) are often used for structural and dynamical studies of peptides and proteins. The interpretation of the spectra is based on ab initio computations, which cannot be applied directly for bigger molecules. Therefore, we study the role of geometry fluctuations and the polar solvent (water) in formation of the spectral shapes of usual peptide structures on a simple model dipeptide – L-Alanyl-L-Alanine (Ala-Ala). The solvent is modeled explicitly as well as by a polarizable continuum dielectric model (PCM).
Both ECD and ROA spectra of Ala-Ala dipeptide in all the three ionic forms were simulated using combined quantum mechanics and molecular mechanics (QM/MM) procedures. Cluster geometries were obtained from MD simulations (TINKER software, AMBER forcefield).
In the case of ECD, calculated spectral frequencies and intensities reasonably well correspond to the experiment, but only when the explicit solvent is used. Also the amide geometry dispersion has to be included for faithful modeling. Preliminary ROA simulations indicate that the Raman spectroscopy probes the peptide structure more locally, while the ECD spectra are more sensitive to the solvent.
 Kapitán, J.; Baumruk, V.; Kopecký, V.; Bouř, P., J. Phys. Chem. A 2006, 110, 4689-4696.