Alanine, optimized geometries

Fig.3 The dependences on the dihedral angles(< >,i /), of the isotropic chemical shielding constant for the L-alanine residue Cp- (a)and Ca-(b) carbons in peptides. Chemical shielding calculations were carried out using the GIAO-CHF method with 4-31G ab initio MO basis set. The 4-31G optimized geometries for the model molecules, N-acetyl-N -methyl-L-alanineamide, were employed.

Figure 5.2 Optimized geometries of the three local minima of alanine. The carboxyl group lies in the xy-plane with the y-axis pointing upward and the x-axis to the right.

Fig. 1.1 Optimized geometries of glycine and S-alanine left, neutral forms right, Zwitterionic forms...

Then, the basis set has to be selected. Let s take as an example the amino acid alanine. It is a small enough system so that a fairly large basis set could be used, such as 6-31G. Suppose one is interested in the optimum geometry of the molecule, as obtained at Hartree-Fock level and at the energy corresponding to this geometry. Then, geometry optimization has to be performed so the card will read ... 

Ewbank, J. D., V. J. Klimkowski, K. Siam, and L. Schafer. 1987. Conformational Analysis of the Methyl Ester of Alanine by Gas Election Diffraction and Ab Initio Geometry Optimization. J. Mol. Struct. 160, 275-285. 

Van Alsenoy, C., M. Cao, S. Q. Newton, B. Teppen, A. Perczel, I. G. Csizmadia, F. A. Momany, and L. Schafer. 1993. Conformational Analysis and Structural Study by Ab Initio Gradient Geometry Optimizations of the Model Tripeptide N-formyl L-alanyl L-alanine Amide. J. Mol. Struct. (Theochem) 286,149-163. 

Figure 5.4 Geometries of glycine, alanine, and proUne optimized at a B3LYP/6-311G level. The solid lines show intramolecular dihydrogen bonds. (Reproduced with permission from ref. 6.)...

Fig. 6, Dependence of the chemical shielding on the dihedral angles (, for C" carbons of L-alanine in peptides. The chemical shieldings are calculated with the Gl AO-CHE method using a 4-3IG basis set. The geometry of TV-acetyl-TV -methyl L-alanine amide was optimized on the 4-31G HE level. The different panels show (a) the isotropic value, as well as the tensor components, (b) cth, (c) 022, and (d) 0 33 (adapted from Asakawa et al. with permission of the authors).

Figure 1 The helical alanine 12-mer, a recent landmark for full ab initio geometry optimizations of biomolecules. See Ref. 36. (See color plate at end of chapter.)...

Finally we have computed the GPA for glycine and alanine amino-acids. The results are collected in Table 10 together with the available experimental data. Single point calculations on the optimized MP2/6-31G geometry have been performed at MP2 and MP4 levels with different basis sets (see Table 10). 

Possible tautomeric equilibria were studied for P-alanine and GABA in chloroform and DCM [13, 48]. For P-alanine, the lEF-PCM geometry optimization started from the zwitterionic geometry that was obtained through structure optimization in continuum water solvent [13]. The extra proton on the -NHj" group jumped over to the carboxylate site, and the structure was stabilized by an intramolecular hydrogen bond in the form of H2N- -H0C=0 in chloroform, where the carboxylic group adopted the otherwise less stable anti conformation. 

---