Development and applications of quantum chemistry to open shell systems

This thesis investigates the applicability of a range of computational techniques across a range of open shell chemical systems from the geometrically simple but electronically complex to the geometrically complex but electronically simple. Initially an investigation into a range of geometrically simple but electronically complicated systems is presented. The Monte Carlo Configuration Interaction method (MCCI) is applied to challenging transition metals dimers such as ScNi in order to establish the ground state potential energy surface, from equilibrium bond lengths through to dissociation using highly compact wavefunctions compared to Full Configuration Interaction (FCI). It shall be demonstrated that the ScNi dimer represents the current limit of this technique. Software development of MCCI is then undertaken in order to perform calculations of spin-orbit coupling interactions. Results on B, C, O, F, Si, S, F, Cl, OH, NO, CN and C2 species are shown to be comparable with other techniques using the one-electron Breit-Pauli Hamiltonian. The application of quantum chemistry to geometrically complex but electronically simple systems is then considered. Density Functional Theory (DFT) is used to investigate the mechanism and energetic barriers leading to ring inversion of the biscalix[4]arene supra-molecule. A minimum barrier height of 19.31 kcalmol−1 to inversion is elucidated along with details of the complete mechanistic pathway to inversion. The focus then moves to polymetallic clusters of calix[4]arene. A DFT study is made of the preferential binding of calix[4]arene towards first row transition metals of various oxidation and spin states. Results indicate that Cu3+ (singlet) species will preferentially bind to the lower rim over other metals in the study. The final DFT-related work presented is a study of the preferential binding at the upper rim of polymetallic calix[4]arene clusters towards a range of important small gas molecules. It was found that gases such as NH3 and SO2 bind most strongly to the upper rim with the inclusion of a transition metal at the lower rim providing strengthening of the host-guest binding

Monte Carlo study of trans- and cis-azobenzene bulk phases with coarse-grained two-site Gay-Berne model

Abstract. Azobenzene is a broadly studied molecule that forms liquid crystal phases under certain circumstances. It has two distinctive geometries, a flat trans and a bent cis isomer. Through a reversible photoisomerisation process, the molecule can be forced to transform from one isomer to another. Because only the trans isomer forms a nematic liquid crystal phase at room temperature, this process additionally triggers a phase transition. Unique qualities of azobenzene and its derivatives are a key to multiple practical applications, such as using polymeric azobenzene films as image storage. The primary goal of the study was to identify liquid crystal (LC) phases of trans- and cis-azobenzene by building phase diagrams from the simulation results. A bulk of 2000 azobenzene molecules was studied with Monte-Carlo simulations at constant pressure and temperature. The molecules were modelled with a coarse-grained two-site Gay-Berne (GB) potential, which was created by fitting the model into quantum-chemical azobenzene dimer interaction energies. Separate cis and trans parametrisations were acquired; this made mixed cis-trans simulations arduous to implement, so the carried out simulations only contained either isomer. The phase structure of the two isomers was presented along with thermodynamic quantities and structural parameters. As a result, a crystal-nematic-isotropic phase structure was identified in the trans isomer with well-defined transition temperatures, and a more vague crystal-isotropic structure in the cis isomer. There are two reasons for the lack of interesting LC phases in the cis simulations. Firstly, the molecule itself is relatively short and has a sharper bending angle than many LC-forming bent-core molecules. Secondly, the least squares fit resulted in an almost-spherical parametrisation, a form that is very unlikely to form LC phases. Trans simulation results were anticipated to some extent, based on previous one-site GB studies with a similar parametrisation. A significant divergence here is the absence of the smectic phase, though, indicated by a comparatively small translational order parameter value. In previous related studies, smectic-A and smectic-B phases have been identified by using a similar single-site GB parametrisation and even by using a rodlike two-site GB model

Electronic Structure Methods for Large Molecular Systems and Materials in Strong Magnetic Fields

The high-rank polynomial scaling of modern electronic structure methods can present significant limitations on the size of molecular systems that can be accurately studied. This issue is further exasperated when using non-perturbative approaches for studying systems within arbitrary strength magnetic fields due to the requirements for complex algebra and reduced permutational symmetry. One such attempt at overcoming this issue is the concept of fragmentation, which has shown promise in recent years for accurately determining the electronic structure of systems that can be sensibly fragmented into smaller subunits. The main aim in this work is to combine the concepts of one such method, the embedding fragment method (EFM), with recent advances in non-perturbative treatment of external fields, enabling the study of increasingly large or complex systems. The implementation of this approach is presented for systems in strong magnetic fields. The method is applied to determine energetic, structural and magnetic response properties of systems beyond the scope of more conventional methods. The EFM is shown to provide an accurate electronic structure approximation when studying systems within extremely strong magnetic fields, with errors generally 70000 Tesla. Its application to large water clusters is presented showing how external magnetic fields strengthen intermolecular interactions, as has previously been demonstrated through experiment, but that the origin of this strengthening is not as straightforward as the altering of the hydrogen bonding present at zero field, a rational often considered alongside experimental results. Also demonstrated is how this approach can be used to accurately model solvation effects when calculating magnetic properties of solute molecules. In this work the calculation of nuclear magnetic resonance chemical shifts is considered, using the EFM and comparing to both gas phase calculations and calculations including solvent effects using the polarisable continuum method. To aid in the interpretation of results, two additional tool sets have been development. The first is a suite of tools to analyse the complex current vector field induced by exposing a molecule to an external field. The second is a new molecular viewer software package, improving the ability to analyse the effects of external magnetic fields on molecular systems

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.Comment: 23 pages, 17 figure

Electronic Structure Methods for Large Molecular Systems and Materials in Strong Magnetic Fields

The high-rank polynomial scaling of modern electronic structure methods can present significant limitations on the size of molecular systems that can be accurately studied. This issue is further exasperated when using non-perturbative approaches for studying systems within arbitrary strength magnetic fields due to the requirements for complex algebra and reduced permutational symmetry. One such attempt at overcoming this issue is the concept of fragmentation, which has shown promise in recent years for accurately determining the electronic structure of systems that can be sensibly fragmented into smaller subunits. The main aim in this work is to combine the concepts of one such method, the embedding fragment method (EFM), with recent advances in non-perturbative treatment of external fields, enabling the study of increasingly large or complex systems. The implementation of this approach is presented for systems in strong magnetic fields. The method is applied to determine energetic, structural and magnetic response properties of systems beyond the scope of more conventional methods. The EFM is shown to provide an accurate electronic structure approximation when studying systems within extremely strong magnetic fields, with errors generally 70000 Tesla. Its application to large water clusters is presented showing how external magnetic fields strengthen intermolecular interactions, as has previously been demonstrated through experiment, but that the origin of this strengthening is not as straightforward as the altering of the hydrogen bonding present at zero field, a rational often considered alongside experimental results. Also demonstrated is how this approach can be used to accurately model solvation effects when calculating magnetic properties of solute molecules. In this work the calculation of nuclear magnetic resonance chemical shifts is considered, using the EFM and comparing to both gas phase calculations and calculations including solvent effects using the polarisable continuum method. To aid in the interpretation of results, two additional tool sets have been development. The first is a suite of tools to analyse the complex current vector field induced by exposing a molecule to an external field. The second is a new molecular viewer software package, improving the ability to analyse the effects of external magnetic fields on molecular systems

Understanding electronic properties of water: a theoretical approach to the calculation of the adiabatic band gap of liquid water

Tese de doutoramento em Química (Química-Física), apresentada à Universidade de Lisboa através da Faculdade de Ciências, 2008Electronic properties of condensed phase water are not very well understood. They are, however, of fundamental importance for a molecular level understanding of the properties of water as well as the role of water, both as participant and medium where chemical reactions occur. It is generally accepted that bulk water can be described as a lone pair amorphous insulator or a large gap lone-pair amorphous semiconductor and the condensed phase ionization potential de_ned as a vertical quantity. A usually accepted value is 8.7 _ 0.5 eV. However, a de_nition of condensed phase properties such as the condensed phase ionization potential is not straightforward and ultimately dependent our understanding of the elementary mechanisms for ionization/excitation in condensed phase water. A longstanding issue is the concearns the fact that hydrated electrons are produced by photoabsorption at _6.5 eV. It has recently been pointed out that the ability of water to reorganize about charged (and neutral) molecules, as well as the reactive nature of electronically excited water molecules, should be taken into account in explaining observed aqueous anion thermochemical and photochemical properties. Moreover, it has been shown that an adiabatic route for accessing the conduction band of liquid water can be de_ned and that the bottom of the conduction band is characterized by the reorganization of the water molecules around the H3O+ cation and OH radical as well as by the presence of a delocalized or quasi-free electron. A _6.9 eV value was proposed by J.V. Coe [Int. Rev. Phys. Chem. 20, 33, 2001], based on known aqueous anion thermochemical and photochemical properties,The present work presents a theoretical estimate for two key reference quantities required for the quantitative estimate of the adiabatic band gap of pure liquidwater as de_ned by J.V. Coe: the hydration energy of the hydroxyl radical andthe electron a_nity of liquid water. The hydration of the hydroxyl radical wasinvestigated by microsolvation modeling and statistical mechanics Monte Carlosimulation. The electron electronic density of states and a_nity of liquid water wasinvestigated trough a sequential Quantum Mechanical / Monte Carlo methodology.Finally, as the adiabatic approach for a de_nition of a band gap for pure liquidwater is based on macroscopic quantities, a molecular level veri_cation of the adiabatic picture was also undertaken

A theoretical study of TPA-like tumour promotors and inositol polyphosphates

In this thesis, the structures and selected properties of TPA-like tumour promoters and of Myo-inositol polyphosphates are calculated and compared with their promoting and calcium releasing activities respectively. Three different levels of theory are used in the calculations, namely ab initio, semi empirical and molecular mechanics, though the majority of the calculations are performed using the MNDO derived semi-empirical methods implemented in MOPAC. A detailed description of the phorbol ester / DAG binding site is obtained from the structure / activity relationships derived for the tumour promoters and molecular dynamics simulations of the phorbol ester, TPA, in a lipid bilayer is carried out to investigate the position of the binding groups in relation to the surface of the bilayer. In order to carry out this simulation, a method (HYDRO) has been developed to produce close packed heterogeneous bilayers in which the headgroups of the components lie in random orientations. Thus the simulations are more realistic than calculations in which the lipids are placed in a regular array and interstitial spaces due to the difference in surface area of the bilayer components are kept to a minimum. The effects of the number and position of phosphate groups on the ring conformations of myo -inositol phosphates and the connection between this and calcium releasing activity are studied in chapter 5. As the molecules are particularly flexible with a large number of potential local minima, phosphate groups have been added sequentially to keep the required number of starting points as low as possible and rotation of phosphate hydroxyls has been ignored. The heats of formation, calculated with the different semi-empirical parametrisations, differ considerably, so the final calculations chapter compares energies and selected properties calculated for model organics phosphates using different methods and theory. The results using the new parametrisation, PM3, are compared with those of the earlier AMI for both the phorbol systems and the inositol phosphates to test its suitability

High quality electron densities as a tool in Kohn-Sham theory

In this thesis high quality electron densities are used to provide insight into density functional theory (DFT) and to improve the quality of DFT calculations. Chapter 1 provides an introduction to ab initio molecular wavefunction calculations with particular emphasis on the Hartree-Fock method. Chapter 2 outlines important concepts in density functional theory (DFT). This includes a discussion of the Zhao, Morrison and Parr (ZMP) method, which is the key to calculating DFT quantities from high quality densities. In Chapter 3, high quality densities are used to gain an understanding of dispersion interactions in the helium dimer. The investigation seeks to understand the correlation potentials associated with a density distortion that gives rise to the correct dispersion forces. Chapter 4 presents a study of response properties using orbitals and eigenvalues determined from high quality densities. Both magnetic and electric properties are considered and comparisons are made with conventional DFT functionals and wavefunction methods. Chapter 5 makes a comparison between Kohn-Sham eigenvalues and related properties, generated both by conventional functionals and from densities. The influence on NMR shielding constants is considered and two approaches to correcting LUMO eigenvalues are presented. In chapter 6, a DFT exchange-correlation functional determined from a lit to high quality densities is applied to study the gauche effect in 2-fluoroethylamine, 2-fluoroethanol and their protonated analogues. Conclusions are presented in Chapter 7

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations