A computational study of biological and optical materials

Fatima, Shaheen (2014) A computational study of biological and optical materials. Doctoral (PhD) thesis, Memorial University of Newfoundland.

[English] PDF (Migrated (PDF/A Conversion) from original format: (application/pdf)) - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. Download (6MB) [English] PDF - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. (Original Version)

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.

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