Alanine conformer relative energies

Initially, the conformational minima for each isolated monomer were calculated by rotating the

results obtained at the two computational levels considered here are almost identical. The [SL conformation is the most stable one for all cases except for glycine and alanine where it shows a relative energy of 0.4 and 3.6 kJ mol-1, respectively. The presence of fluorine atoms as XI or X2 substituents tends to destabilize the y and 8 conformations and favors the presence of and a ones that are absent in the rest of the cases. The intramolecular HB formed in each case is responsible for these tendencies. While the y and 8 conformations present an intramolecular HB that is disrupted by the presence of fluorine atoms at XI and X2, new HBs are formed in the and a conformation, stabilizing their relative energies. 

Alanine 18 is the smallest chiral common amino acid. It has been the subject of many computational studies but we focus here on three recent reports. Csaszar identified 13 conformations of alanine and optimized the structures at HF/6-31G, HF/6-31H-I-G, B3LYP/6-31H-I-G, and MP2/6-311++G. The relative energies for some of the low lying conformations, computed with the latter three methods, are reported in Table 3.14. The two lowest energy conformations correspond with the two conformations identified in an earlier microwave experiment. ... 

The experimentally determined (S)/(R)-ratio of 18/82 was compared with the relative stabilities of the two diastereomeric products ([Co((S),(S)-ppm)((R)-ala)] / [Co((S),(S)-ppm)((S)-ala)] ), calculated by strain-energy minimization. The reported strain energies, based on a single conformer for each of the two diastereomeric products (identical to the crystal structure of the complex with coordinated (R)-alanine [328]), are in good agreement with the experimentally determined data (23/77 versus 18/82). A full conformational analysis led to a ratio of 30/70 when only conformational flexibility is allowed, or 33/67 when other isomers were also included in the analysis [294]. The assumption in the original report was that the enantio-selectivity is based on the relative energies of the diastereomeric forms of the cobalt(III) products [327]. Fortunately, a qualitatively similar result is expected if the stereoselectivity is controlled by the deprotonated intermediates. However, a quantitatively accurate prediction of the product ratio is not expected in this case. 

The glycine and alanine dipeptide analogs (GDA and ADA) have recently garnered theoretical attention, because they are the two simplest models of a polypeptide. Molecular mechanical force fields designed to model proteins are often parameterized to reproduce, as well as possible, the geometries and relative energies of the various GDA and ADA conformers. Since few experimental data are available, one must rely on theoretical studies. To date, DFT calculations on peptides have been limited to GDA and ADA. ... 

As an example of the relative performance of explicit and implicit solvation models in calculations of conformational equilibria, Scarsi et al. [60] compared the calculated conformational properties obtained by the CHARMM force field of liquid 1,2-dichloroethane and of terminally blocked alanine dipeptide in aqueous solution. They employed (i) a systematic conformational search with solvation energies cal-... 

Fig. 1. Conformational energy map of N-acetyl L-alanine N-methyl amide Of =0°) in CCI4. Ftotai is given in kcal/mole relative to the global minimum indicated as X.

Table 5 HF, MP2 , and DFT > Relative Conformational Energies (kcal/mol) for the Glycine and Alanine Dipeptide Analogs (from Reference 12)...

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