A computational study of biological and optical materials

Abstract

This thesis reports computational studies about protein-ion binding in part I, and optical properties of organic materials in part II. It is very difficult to investigate a whole protein computationally. So here I proposed smaller models to probe protein-ion binding: a short triple helix (triple chain), a short peptide chain, and individual amino acids. The binding energies, and particularly the differences in binding energy between Na⁺ and K⁺ ions, do depend on the model and the constraints. I have applied these models to understand experimental observations about the distinct roles of Na⁺ and K⁺ in collagen aggregation and fibrillogenesis. I have calculated the binding energies for the Na⁺ and K⁺ with several key amino acids in collagen, selected by analysis of collagen sequence, using density functional theory (DFT). In part II, I have focused on first and second hyperpolarizabilities of anthraquinoidtype π-extended tetrathiafulvalene, referred to as TTFAQ, and its analogues. This project has employed a wide range of functional groups to exploit the electron donor capability of TTFAQ in order to explore the hyperpolarizabilities of its derivatives. I have assessed size and charge distribution metrics as predictors for NLO response of the TTFAQ derivatives.