The major goal of this M. Phil. research project is to systematically study the spectroscopic properties of various redox active forms of four aromatic amino acids (AAAs) and two quinone cofactors by means of a reliable computation on the basis of first principle and with a reasonable computational effort. By reliable we mean that, without application of the empirical scaling procedure, the computational results should be close enough to experimental values to allow a meaningful comparison. By reasonable eflort we mean that the computational method should be applicable to structure-spectra correlation for the larger molecular systems in reality. The attention has been focused on the identification of Raman and IR active normal modes that are unique to the chemistry of a particular amino...[ Read more ]

The major goal of this M. Phil. research project is to systematically study the spectroscopic properties of various redox active forms of four aromatic amino acids (AAAs) and two quinone cofactors by means of a reliable computation on the basis of first principle and with a reasonable computational effort. By reliable we mean that, without application of the empirical scaling procedure, the computational results should be close enough to experimental values to allow a meaningful comparison. By reasonable eflort we mean that the computational method should be applicable to structure-spectra correlation for the larger molecular systems in reality. The attention has been focused on the identification of Raman and IR active normal modes that are unique to the chemistry of a particular amino acid or quinone cofactor, although such properties as minimized energy, optimized geometry, charge distribution, spin density distribution are also calculated, and correlated to the experimental data whereever possible. The established vibrational markers are expected to serves as the identification of the oxidation state, the protonation state, and the environment of that amino acid in protein. A detailed comparative analysis has been carried out to assign the characteristic side chain vibrations of molecules mentioned based on isotope shifts.

Four AAAs are phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), and histidine (His), respectively. Two quinone cofactors are p-benzoquinone (pBQ) and 1,4-naphthoquinone (NQ). They have been generally known to play variety of roles in biological electron transfer. Their occurrences in selected biological systems are summarized in Chapter 1. The formulation and advantages of ab initio/DFT methods and a preliminary computational study of p-benzoquinone aimed at demonstrating the choice of the level are also included in this chapter. In the following chapters, a detailed vibrational analysis was implemented successively to exploit the structure-spectra correlations for these molecules as well as their important redox-active derivatives, pBQ (chapter 2), NQ (chapter 3), Phe (chapter 4), Tyr (chapter 5), Trp (chapter 6), His (chapter 7). Finally, a master-table containing the characteristic side chain vibrations is established in chapter 8 and this table will serve as the reference guide for the future study of bioprocesses involving AAA's and quinone cofactors by vibrational as well as magnetic spectroscopies.