Conformational analysis and vibrational spectroscopic investigation of L-alanyl-L-glutamine dipeptide
Issue title: From Molecule to Tissue: XIII European Conference on the Spectroscopy of Biological Molecules, Palermo, Italy, August 28–September 2, 2009, Part 2 of 2
Affiliations: Faculty of Sciences, Department of Physics, Istanbul University, Istanbul, Turkey | Faculty of Science and Letters, Department of Physics, Istanbul Kultur University, Atakoy Campus, Istanbul, Turkey | Engineering Faculty, Department of Electrical-Electronics Engineering, Istanbul University, Avcilar, Istanbul, Turkey
Note: [] Corresponding author: S. Kecel, Faculty of Sciences, Department of Physics, Istanbul University, Vezneciler 34134, Istanbul, Turkey. E-mail: [email protected].
Abstract: In this study conformational behavior of anticancer chemotherapy dipeptide Ala-Gln and its dimers have been investigated by molecular mechanic and ab-initio calculations. The calculations on Ala-Gln dipeptide as a function of side chain torsion angles, enable us to determine their energetically preferred conformations. The relative positions of the side chain residues of the stable conformations of dipeptide were obtained, depending on the obtained conformational analysis results. The lowest energy conformation of the dipeptide has been determined by using the Ramachandran maps (Biopolymers 6 (1963), 1494; J. Mol. Biol. 7 (1963), 95) and compared with the quantum chemical ab-initio results. The geometry optimization, vibrational wavenumbers and intensity calculations of Ala-Gln dipeptide were carried out with the Gaussian03 program by using DFT with B3LYP functional and 6-31++G(d,p) basis set. The IR (4000–400 cm−1) and Raman spectra of the Ala-Gln dipeptide have been reported in solid phase, and compared with the theoretical vibrational data.
Keywords: Conformational analysis, IR and Raman spectra, DFT calculations, L-alanyl-L-glutamine dipeptide
DOI: 10.3233/SPE-2010-0433
Journal: Spectroscopy, vol. 24, no. 3-4, pp. 219-232, 2010
