Cardiff University | Prifysgol Caerdydd ORCA
Online Research @ Cardiff 
WelshClear Cookie - decide language by browser settings

Application of atomistic modelling to molecular solids containing hydrogen bonds

Maarof, Hasmerya 2009. Application of atomistic modelling to molecular solids containing hydrogen bonds. PhD Thesis, Cardiff University.

[thumbnail of U585311.pdf] PDF - Accepted Post-Print Version
Download (15MB)

Abstract

The work presented in this thesis is mainly concerned with crystal structures containing hydrogen bonds. Chapter 1 and 2 mainly discuss the background and basic concepts used in this study such as the importance of hydrogen bond in crystal engineering, co-crystals and polymorphism, and recent studies of urea co-crystals. Chapter 3 is a study about urea/oc,co-dihydroxyalkanes co-crystal structures. It begins with parameterising DMAREL to obtain lattice energy from a set of homologous co- crystals where DMA multipoles were generated from different method, GDMA and MOLPRO. The simulated lattice energy, structures and interaction energy were discussed and compared whether there is possibilities for the co-crystals to appear in different urea ribbon structures (parallel and anti-parallel) as these could not be crystallised experimentally. The energy data shows that urea/a,co-dihydroxyalkanes co-crystal of anti-parallel ribbon type structure are more thermodynamically favoured compared to the parallel structure. In latter part of this chapter, attempts to construct and simulate the anti-parallel urea ribbon co-crystal type structures from initial experimental structures were discussed. In Chapter 4, sulfur pair potential was modelled to fit for use in DMAREL for TTCA structure simulation. The original potentials were taken from Lennard Jones potential of a-S8 crystal structure. Initially, the potentials were modelled against a-Sg and thiourea crystal. Improved potentials were applied to a set of S-contained structure, specifically with similar environment to TTCA to validate the reliability of this potential against other molecules. Potentials works fairly well for 5 out of 10 molecules simulated, where TTCA shows poorest performance against the potential even though it has improved from the original sulfur potential. Contrasting crystal structure between TTCA and CA when substituted between each other is discussed. The final chapter, Chapter 5 is the continuation from work in Chapter 3. In urea co-crystal, it was found that urea structure was not exactly planar. We then continue on the search of different conformation of urea molecule in as and solid structure. First, the conformation of urea monomer were discussed and followed by calculation of larger planar urea clusters where one of the urea is substituted with either Cj or Cs conformers. Urea clusters were build systematically mimicking dense urea crystal structure. Planar structure was finally obtained by using 5 urea molecules involving four hydrogen bonds.

Item Type: Thesis (PhD)
Status: Unpublished
Schools: Chemistry
Subjects: Q Science > QD Chemistry
ISBN: 9781303217562
Date of First Compliant Deposit: 30 March 2016
Last Modified: 19 Mar 2016 23:31
URI: https://orca.cardiff.ac.uk/id/eprint/54922

Actions (repository staff only)

Edit Item Edit Item

Downloads

Downloads per month over past year

View more statistics