Quantum chemical studies of the energies, structures, and basicities of selected amino acids, peptides, carbohydrates, and model compounds will be carried out using the ab initio molecular orbital approach. Molecular geometries will be optimized using the Hartree-Fock, density functional, or second-order Moller-Plesset perturbation theory with an appropriate basis set. Electron correlation effect will be examined for model systems at a higher level of theory. Conformational potential energy surfaces around the low energy minima of glycine, alanine, serine, valine, and threonine will be calculated for internal rotations about the single bonds of alpha- and beta-carbon atoms in NH2CHRCOOH. Results will be analyzed systematically for trends that relate to the side chain R. The calculated energies, geometries, and atomic charges will be used to develop simple models for estimating conformational energies. Ab initio studies of the protonations of biomolecules initiated in this laboratory will be continued for serine, tetraglycine, and sucrose. The theoretical energies and geometries 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 and analyzed. Intramolecular proton transfers among the nitrogen and oxygen sites in the termini and backbone of protonated peptide will be studied using diglycine and its analogue. The theoretical minimum-energy paths will elucidate the kinetic mechanism without the interference of solvent. The calculated thermodynamic and kinetic properties for protonation and proton transfer (Gibbs free energy, equilibrium constant, and the forward and reverse rate constants) are fundamental to a quantitative understanding of biological processes.
| 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 |
