Computational approaches to the calculation of spectroscopic, structural and mechanical properties of polysaccharide chains : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Massey University

Abstract

In this thesis atomistic, statistical mechanical and coarse grained simulation techniques are used to study the properties of biopolymers and in particular the plant polysaccharide pectin. Spectroscopic aspects, structural and conformational behavior, and mechanical properties of the molecule in di erent physical states are addressed. After an introduction to the area and the theoretical techniques utilised herein (chapter 1), chapter 2 deals with the spectroscopic characterisation of pectin. Spectra were obtained theoretically by undertaking complete energy minimisation and Hessien calculations using DFT techniques implemented in Gamess (PC & US) packages. The calculated IR absorptions of di erent pectinic species and oligomers coupled on di erent surfaces were compared with experimental results. Herein, it is con rmed that experimental FTIR studies coupled with DFT calculations can be used as an e ective tool for the characterisation of pectin, and studying chemical coupling of the biopolymer to surfaces. In chapter 3, the properties of single chain polymer systems in controlled solvent conditions were studied using Brownian dynamics simulations, motivated by the formation of secondary structure architectures in biopolymer systems. We focus on the conformational properties of the chain in the presence of an additional torsional potential. New, interesting, and biologically relevant structures were found at the single molecule scale when a torsional potential was considered in the calculations. In chapter 4, results from DFT calculations carried out on single pectin sugar molecules (lengths and the free energies) are incorporated into a statistical mechanical model of polymer stretching, in order to obtain the force-extension behaviour of a single molecule pectin. This captures a good deal of the phenomenology of the single molecule stretching behavior of pectin. Chapter 5 summarises the conclusions of the work and nally chapter 6 suggests direction for further work.