Conformation analysis of Val-Met dipeptide with molecular mechanical and quantum chemical methods

In this study Valine-Methionine dipeptide, which is a breakdown product of protein digestion or protein catabolism, has been investigated both theoretically and experimentally. Four different Val-Met conformations were formed by using the geometric parameters of Valin and Methionine amino acids taken from the literature. Optimized geometries and total energies of these four different conformations were calculated with the 6-31G (d, p), 6-31 ++ G (d, p) and 6-311 ++ G (d, p) basis sets using the DFT / B3LYP method. The vibration wave numbers of the two most stable conformation obtained were calculated by using the 6-311 ++ G (d, p). basis set. The potential energy distribution (PED for the molecules were obtained using the MOLVIB program and the modes corresponding to each vibrational wavenumber were determined. In addition, Using the Chem3d program, the Alingers'MM2 force field was applied and 113 conformations were obtained by Molecular Dynamic Simulation. The energy values of these conformations determined by Molecular Dynamic Simulation are calculated using the ab-initio calculations with the Density Function Theory (DFT) method using B3LYP method with the basis set of 6-311 ++ G (d, p). Two possible conformers are determined. In the experimental part of the study, spectra of molecules were recorded using Jasco 300E FT-IR spectrometer (at 2 cm-1 resolution) and NRS 3100 Dispersive Micro Raman spectrometer. The obtained calculation results and experimental results are given in tabular form in comparison with each other.