In this theoretical study, the role of the side chain moiety of C-terminal residue in influencing the structural and molecular properties of dipeptides is analyzed by considering a series of seven dipeptides. The C-terminal positions of the dipeptides are varied with seven different amino acid residues, namely. Val, Leu, Asp, Ser, Gln, His, and Pyl while their N-terminal positions are kept constant with Sec residues. Full geometry optimization and vibrational frequency calculations are carried out at B3LYP/6-311++G(d,p) level in gas and aqueous phase. The stereo-electronic effects of the side chain moieties of C-terminal residues are found to influence the values of and dihedrals, planarity of the peptide planes, and geometry around the C7？？ -carbon atoms of the dipeptides. The gas phase intramolecular H-bond combinations of the dipeptides are similar to those in aqueous phase. The theoretical vibrational spectra of the dipeptides reflect the nature of intramolecular H-bonds existing in the dipeptide structures. Solvation effects of aqueous environment are evident on the geometrical parameters related to the amide planes, dipole moments, HOMOLUMO energy gaps as well as thermodynamic stability of the dipeptides. 1. Introduction Generally, twenty canonical amino acid residues adequately build up the proteins and enzymes necessary to support most of the cellular functions in all the three domains of life on earth. Selenocysteine (Sec) and pyrrolysine (Pyl) are the two rarely occurring genetically encoded amino acids whose presence in the active sites of some enzymes enables them to sustain life in some extraordinarily unique ways [1–7]. The chemical structures of Sec and Pyl are portrayed in Figure 1. Although the distribution of Pyl is limited to methanogenic archea and certain bacteria, Sec is commonly found in eubacteria, archaea, and eukarya [5]. Sec and Pyl are cotranslationally inserted into proteins corresponding to UGA (opal codon) and UAG codons (canonical stop codon) respectively, which are generally responsible for terminating the process of protein biosynthesis. Figure 1: Chemical structures of selenocysteine (Sec) and pyrrolysine (Pyl). The dynamic properties and functional specificity of the proteins and polypeptides are known to depend primarily on the linear sequence of amino acid residues [8]. Therefore, over the last few decades, small amino acid sequences like di- or tripeptides have been used extensively as model systems in the experimental and theoretical studies concerning the structure of proteins and energetics of protein folding.
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