Conformational analysis of For-L-Ser-L-Ala-NH2 protected dipeptide using quantum calculations: A DFT study

Subject Areas :

Behzad Chahkandi ¹ , Rezvan Mohammad Abadi ² , Mehdi Nekoei ³

1 -
2 - دانشگاه ازاد اسلامی واحد شاهرود
3 - دانشگاه ازاد اسلامی واحد شاهرود

Received: 2019-06-03 Accepted : 2019-10-11 Published : 2019-11-22

Keywords: For-Ser-Ala-NH2, DFT, sidechain, Keywords: Dipeptide model, Ramachandran plot,

Abstract :

IIn this study conformational analysis of HCO-Ser-Ala-NH2 dipeptide were performed using DFT method at the B3LYP/6-31G(d) level of theory. For this purpose 54 conformations of serine-alanine protected dipeptide that derived from varying the backbone and sidechain dihedral angles ( and ), were optimized. Then by using frequency calculations at the same level of calculations the stable conformers and thermodynamic values were obtained. Of the 54 considered conformations in this research, 35 conformations were found and 19 conformers were not found. Those that were not found have converged to a different geometry of lower energy and greater stability. Among 35 found conformers the and have the lowest and highest relative energy respectively, therefore are the most stable and unstable conformers respectively. The relative energy of is 14.64 kcalmol-1. The migration pattern show that of the 19 not found conformers with and general structures, migration to is more favorable. Keywords: Dipeptide model; For-Ser-Ala-NH2; Ramachandran plot; sidechain; DFT.