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    Theoretical study of weakly interacting systems : noble gas compounds : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Albany, New Zealand
    (Massey University, 2023) Florez Hincapie, Edison Ferney
    The dispersion bonds − also known as London or Van der Waals interactions − are usually considered the weakest and the least important of the several types of chemical bonding models known. However, dispersion interactions play a crucial role in chemistry; particularly, in defining functions and structural stability of proteins and Watson-Crick pairs in biochemical systems, to name just a few. Through the Periodic Table, noble gas aggregates are one of the prime examples of systems strongly influenced by dispersion interactions. In addition, from helium − the smallest and most unreactive − to radon, periodic trends emerge; the atomic mass/radius and the dispersion interactions increase, resulting in increasing melting points, boiling points, enthalpies of vaporization, etc. However, Oganesson (Og, Z=118) − the heaviest noble gas and element synthesized at the limit of nuclear mass and charge − may behave differently from what would be predicted by simple extrapolations in the Periodic Table. This is due to relativistic effects. Those effects are more pronounced in heavier elements (high nuclear charge Z) and significantly influence both chemical and physical properties. The research presented here is divided into three parts. First, we explore the behavior of neon clusters under high magnetic fields in the range of 0 to 7.5x10⁵ Tesla. Under these extreme conditions, atoms and molecules reveal exotic chemical characteristics such as squeezed and twisted structures as dispersion interactions are affected by the so-called perpendicular paramagnetic bonding giving rise to molecules and materials that do not exist on Earth (but in environments of white dwarfs and magnetic stars). Our results show that, regarding the field-free case, there is an energetic stabilization for the neon interaction in a magnetic field, leading to enhanced melting temperatures of more than 70% and reducing the entropy of the system, squeezing the structures perpendicular to the applied magnetic field. Second, we analyzed the chemical nature of Flerovium clusters and their noble gas-like behavior upon melting. Here, we studied closed-shell flerovium in detail to predict solid-state properties including the melting point from a decomposition of the total energy into many-body forces derived from relativistic coupled-cluster and density functional theory. Our results show that the noble gas behavior of flerovium enhances resistance to bond formation. Flerovium atoms are only weakly bound, less compared to mercury, but more than in xenon. This makes the accurate prediction of phase transitions very difficult. Nevertheless, we made the first prediction by Monte-Carlo simulation estimates the melting point at 284 K (std. 50 K). Finally, we studied the structure, stability, and chemical bonding of fluorides noble gas compounds, NgFₙ (n=2, 4, 6), where Ng comes from Argon, Krypton, Xenon, Radon, and Oganesson. The heaviest element, Oganesson, unlike all other noble gas compounds, is enhancing the tendency to adopt a tetrahedral local environment. These results indicate that there may be a partial role reversal of the elements Fl and Og important in the future of atom-at-a-time chemistry. Oganesson di- and tetra-fluorides are stable with and without relativistic effects, whereas hexafluoride is unstable. This creates such a radical departure from periodic group trends that the rules of the periodic table appear to be broken by relativity, suggesting an end to periodicity.
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    Molecular dynamics simulation of inter-molecular interactions : a thesis submitted to Massey University in Albany, Auckland in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry
    (Massey University, 2019) Shadfar, Shamim Zahra
    Many aspects of the operation of chemical and biological systems are based on intermolecular interactions. In this work, binding modes and interactions between molecules at a range of scales have been studied, using molecular dynamics (MD) simulations. The first chapter provides an introduction of each of the different chemical and biological systems that are studied in this work. It also introduces MD and its role in the context of this research. The second chapter corresponds to the study of host-guest interactions for cyclodextrin- bullvalene complexes. Bullvalene is a shapeshifter molecule, which interconverts between different isomers at room temperature. The goal of this chapter is to capture one favourable isomer of bullvalene (guest molecule) by binding it to cyclodextrin as a host molecule. This chapter consists of two smaller chapters (2i and 2ii). The former details the development and validation of a “host-guest binding potential energy profiling” (HGBPEP) method, which is a rotational interaction energy screening method designed for prediction of the most favourable orientation and position of bullvalene isomers with respect to cyclodextrin. The latter investigates the interaction of bullvalene isomers and cyclodextrin molecules, and finally binding free energy values of the complexes are calculated. The third chapter describes KstR, a transcriptional repressor in Mycobacteria. KstR is required for Mycobacterium tuberculosis (Mtb) pathogenesis as well as regulating the initial steps in cholesterol degradation by controlling the expression of the enzymes that carry out the early stages of cholesterol catabolism. Therefore, this protein is of great interest for development of new tuberculosis treatments. In this chapter, the stability and conformational changes of KstR in its different states – apo, DNA-bound and ligand-bound –have been studied. The main goal is to investigate the binding mechanism of KstR to DNA, as well as the effect of DNA and ligand binding on the structure and dynamics of KstR more generally, using MD simulations. In the fourth chapter, KstR2, another Mtb transcriptional repressor, is studied. KstR2 represses a 14-gene regulon involved in the later steps of cholesterol degradation. It is structurally similar to KstR, but has been proposed to act through a novel scissor-like mechanism. This chapter investigates two key questions regarding the mechanism of action of KstR2: first, the effect of mutating the key switch residue ARG170 to ALA, and second, the effect of ligand binding on its structure and motion. The focus of the fifth and final chapter is phosphatidylinositide 3-kinases (PI3Ks), which are proteins that take part in signalling pathways regulating factors like cell growth, survival and proliferation, which in turn are involved in cancer. The interaction between PI3Kα and another protein, RAS, is very important in the formation, growth and maintenance of RAS- driven tumours. A model of PI3Kα (class IA PI3K) has therefore been built, as well as of RAS associated with a model cell membrane, and MD simulations used to investigate the process by which the two proteins interact with one another and with the lipid bilayer. Altogether, this thesis uses MD simulations to provide insight into intermolecular interactions at a range of scales, with a particular focus on proteins involved in tuberculosis and in cancer.