Theoretical calculations, including ab initio Car-Parrinello Molecular Dynamics
(CPMD), geometry optimisation on the principal grid-based conformers, Infra-red vibrational frequencies, and charge density analysis (Atoms In Molecules, AIM), were performed on three important chemical systems (glycine, 3-
isocyanatopropyltriethoxysilane (ICS), 3-styrylethyltrimethoxysilane (STYRX))
under a variety of different pH conditions and solvents (H₂0, CCl₄, ethanol and
mixed solvents, both using implicit Polarisable Continuum solvation models and
explicitly solvated). CPMD studies were carried out at 300.15 K, with 10,000-step
trajectories covering the timescale of ≈1 picosecond. Molecular dynamics, AIM and grid-based approaches were compared and combined to give accurate descriptions of molecular behaviour and preferred geometrical conformations of the aforementioned systems. The aim in characterising these systems is to build a better understanding of protein structure and functioning, as well as to analyse two examples of what we believe are very promising silicon-based coupling agents.
Theoretical calculations were validated by experimental results. A computer
application was developed to help in conformer-specific analysis and presentation of Infra-red Spectroscopy data.
A molecular geometry and van der Waals radii-based explicit solvation method was developed, and another more advanced charge distribution based solvation method proposed. Both methods near-optimally solvate molecules using a minimal but sufficient amount of any solvent, under various conditions.
A set of computer applications was developed to aid in creating, executing and doing preliminary analyses of theoretical physical chemistry calculations.
As a result, a complete characterisation of the glycine amino acid behaviour and
preferred conformations for gas phase non-protonated and singly-protonated states was accomplished. The successful synergy between experiment and theory for the STYRX and ICS silane coupling agents allowed for a theoretical conformational analysis of these systems in various solvent conditions and quantitative assignment of molecular vibrations to the major peaks present in the Fourier Transform Infrared Spectroscopy (FTIR) results.