A COMBINED QUANTUM CHEMICAL-MOLECULAR DYNAMICS INVESTIGATION ON SOME MODEL DIPEPTIDES

Abstract

The goal of the thesis is the study of two dipeptide systems, Ac-Ala-NHMe and Ac-Gly-NHMe with two different theoretical calculation methods.The former method includes quantum mechanical calculations: Density Functional Theory (DFT) calculations using functionals, such as B3LYP, B97-D, B3PW91, LC-WPBE, MP2/6-31+G(d,p), ωB97X-D, M06-2X, CAM-B3LYP both in vacuum and in water with Polarizable Continuum Model (PCM) and ab initio methods such as MP2; the latter is referred to Molecular Dynamics (MD) simulations, using three force fields: Amber99, Amber99sb, and Amber99sb-ildn, and the model water in explicit solvent described withTIP3P. MD simulations and quantum mechanical calculations are performed to both calculate the different conformation energies of the two systems and identify the most stable geometries.Correlation-consistent basis sets , such as aug-cc-pVDZ, aug-cc-pVTZ and cc-pVTZ,were added to the functionals and MP2 method.The results were compared with the conformers studied in literature, calculating the Mean Absolute Deviation and the Absolute Maximum Deviation.The last step was the comparison of MD and quantum mechanical results in order to elucidate the different features of these methods and the conformational results obtained.