The proposal concerns quantum chemical studies of the energies, structures, and reactivities of selected amino acids, peptides, carbohydrates, and their related model compounds. The GAUSSIAN program will be employed to carry out ab initio molecular orbital calculations using different basis sets with geometry optimizations. Electron correlation effects will be included at different levels for amino acids and model compounds. Conformational energy surfaces around the low energy minima of glycine, alanine, serine, cysteine, valine, and threonine will be calculated by geometry optimizations at the level of second-order Moller-Plesset perturbation theory with a split-valance plus polarization basis set. Conformations pertain to those arising from rotations about the single bonds of alpha- and beta-carbon atoms in NH2CHRCOOH. Results will be analyzed systematically for conformational trends that relate to the side chain R. The calculated energies and geometries and those from model compounds will be used to develop simple models for constructing conformational energy maps. Ab initio studies of the protonations of small peptides and carbohydrates initiated in this laboratory will be continued. The theoretical energies and structures of the neutral and protonated species will help identify the protonation sites used in sequencing biopolymers by mass spectrometry. Important intramolecular hydrogen bonding in these species will be identified, analyzed, and characterized. Findings will lead to a better understanding of the folding patterns in proteins. Theoretical structures obtained from the protonation studies will be used for exploratory investigations on proton transfer and hydration. In a protonated species the transition state and pathway for the proton transfer process will be located and the forward and reverse rates of this transfer will be estimated. The interaction between a zwitterion and water molecules will be examined with respect to energetic and structural changes in the hydrated species as the number of solvent molecules increases (zwitterion.nH2O for n = l - 6). These results will provide useful insights into the dynamics and mechanism of intramolecular and intermolecular hydrogen bonding.
| Chung-Phillips, Alice (2005) Polyglycine conformational analysis: calculated vs experimental gas-phase basicities and proton affinities. J Phys Chem A 109:5917-32 |
| Zhang, K; Chung-Phillips, A (1999) A computational study of intramolecular proton transfer in gaseous protonated glycine. J Chem Inf Comput Sci 39:382-95 |
