Conformational preferences of praline analogues with different ring size

Article Abstract:

The conformation study on L-azetidine-2-carboxylic acid and (S)-piperidine-2-carboxylic acid is carried out using ab initio HF and density functional methods to explore the differences in conformational preferences and cis-trans isomerization for praline residue and its analogues with different ring size in the gas phase and in solution. The change of ring size by deleting a C[H.sub.2] group from or adding a C[H.sub.2] group to the prolyl ring has resulted in remarkable changes in backbone and ring structures compared with those of the Pro dipeptide.

Density functionals, Density functional theory, Carboxylic acids

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Which functional form is appropriate for hydrogen bond of amides?

Article Abstract:

Four types of the functional form, which are the Morse, Lennard-Jones 10-12, 6-12, and 6-9 types of the potential function used to describe hydrogen bonds, are tested against ab initio MP2/6-31G** calculations for their ability to describe dimerization energies. The Morse function results in the best fit to the scaled MP2/6-31G** energies of three amides both at short and long distances, whereas other functions are satisfactory only at long distances.

Methods, Hydrogen bonding

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Conformational and enantioselectivity in host-guest chemistry: The selective binding of cis amides examined by free energy calculations

Article Abstract:

Relative binding free energies of amino acid derivatives to the host macrobicycle 12 in chloroform were calculated in order to determine the effect of stereochemistry and amide bond conformation. Monte Carlo simulations were used to perform simulations for three different amino acid derivatives, free energy perturbations, and the generalized born/surface area solvation model.

Amino acids, Monte Carlo method, Monte Carlo methods

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