The genetic algorithm based on the Multi-Niche Crowding (MNC) method is used with the semi-empirical methods AM1 and PM3 in order to scan the potential energy surface (PES) of neutral and protonated glycine. The algorithm is implemented as a package of programs interfaced with MOPAC and piloted by scripts. Both methods AM1 and PM3 located six minima on the PES of neutral glycine and seven on the protonated glycine one, of which three are those of the N -protonated form and four of the O -protonated one.

We performed here a systematic ab initio calculations on neutral gas-phase L-proline. A total of 8 local minima were located by geometry optimization of the trial structures using density functional theory (DFT) with B3LYP three parameter hybrid potential coupled with the 6-31G)d( basis set. The absolute minimum obtained will be subject to a rigid potential energy surface (PES) scan by rotating its carboxylic group using the same method with more accurate basis set B3LYP/6-311++G(d,p), to get a deeper idea about its conformational stability. The main aim of the present work was the study of the rigidity of the L-proline structure and the puckering of its pyrrolidine ring.

This work reports a detailed conformational study on N-formyl-L-tyrosinamide diamide system through genetic algorithm based on multiniche crowding technique. We tried to evaluate the effect of the OH hydroxyl substitution of the benzene ring on the adopted folds by comparing them with those found previously for the N-formyl-L-phenylalaninamide. Among the 26 and 28 conformations detected for both systems N-formyl-Ltyrosinamide and N-formyl-L-phenylalaninamide successively, 19 conformations have similar geometrical structures (identical backbones and side-chain orientations). The comparison of 19 common conformation geometries of both systems revealed nearly perfect linear adjustments with R 2 values of 0.9997, 0.9996, 0.9998, and 0.9996 for the dihedral angles 4, j, c 1 , and c 2 successively. This work also includes a comparison between theoretical calculations and experimental results of X-ray crystallography and nuclear magnetic resonance spectroscopy extracted from protein data bank.

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