The spectroscopic analysis of cellulose is experimentally challenging while computationally accessible with recent developments in NMR code. However, prior to using density functional theory to calculate the NMR chemical shifts of cellulose, smaller, sugar-like molecule systems need to be benchmarked against experimental values. The quantum mechanical / molecular mechanical (QM/MM) calculations presented herein utilize six test systems: ethanol, pyridine, pyrrolidine, pyrrole, myo-inositol and scyllo-inositol in conjunction with the reference tetramethylsilane used to scale the calculated isotropic shielding tensors to relative chemical shifts. The effect of solvent on calculated NMR chemical shifts has also been investigated with regard to quantity of solvent surrounding the molecule of interest. Lastly, a mixed basis approach with two quantum regions has additionally been employed to investigate the effects of the number of basis functions on the relative cost of QM/MM NMR calculations.

Iron containing metalloenzymes are an extremely important class of biocatalysts conserved throughout evolution because of their vital role in the biochemistry of life. Here we discuss a specific class of these enzymes that use molecular oxygen binding to enable there activity. We also attempt to describe synthetic analogues whose chemistry is based on that seen in those natural systems. This dissertation will highlight how computational research can illuminate specific aspects of the reaction mechanisms that these systems catalyse, which in many cases are unable to be understood purely experimentally. We report on two combined QM/MM and density functional theory (DFT) projects, which describe the AlkB demethylation enzyme and the SyrB2 halogenase; both highlight the strengths and weaknesses of each method. Our DFT work on an i-propyl-bis(imino)pyridine, an equatorial tridentate ligand, developed by one of the papers’ co-authors (Badiei, Siegler et al. 2011) exampifies superoxo chemistry based on the dioxygenases. Our other projects focus on monooxygenase catalysed chemistry one based on the biomimic [FeIV(O)(TPA)Cl]+ reports on a halogenase mimic that shows exciting chemoselectivity in halogenation vs. hydroxylation. I also report on publications examining two other biomimetic ligands. A imido-bridged diiron-oxo phtalocyanine complex capable of hydroxylating methane and a nonheme iron system which gives us a good deal of insight into the effects of secondary coordination sphere chemistry [FeII(N4Py2Ph)(NCCH3)](BF4)2. My computational studies have given insight into the chemical properties of metal-oxo oxidants and their reactivity patterns with substrate and have been utilized to explain experimentally observed data.

Cytochrome P450 (P450) enzymes are found in all kingdoms of life, catalysing a wide range of biosynthetic and metabolic processes. They are, in fact, of particular interest in a variety of applications such as the design of agents for the inhibition of a particular P450 to combat pathogens or the engineering of enzymes to produce a particular activity. Bacterial P450BM3 is of particular interest as it is a self-sufficient multi-domain protein with high reaction rates and a primary structure and function similar to mammalian isoforms. It is an attractive enzyme to study due to its potential for engineering catalysts with fast reaction rates which selectively produce molecules of high value.In order to study this enzyme in detail and characterise intermediate species and reactions, the first step was to design a general hybrid quantum mechanical /molecular mechanics (QM/MM) computational method for their investigation. Two QM/MM approaches were developed and tested against existing experimental and theoretical data and were then applied to subsequent investigations.The dissociation of water from the water-bound resting state was scrutinised to determine the nature of the spin conversion that occurs during this transformation. A displacement of merely 0.5 Å from the starting state was found to trigger spin crossing, with no requirement for the presence of a substrate or large conformational changes in the enzyme.A detailed investigation of the sulfoxidation reaction was undertaken to establish the nature of the oxidant species. Both reactions involving Compound 0 (Cpd0) and Compound I (CpdI) confirmed a concerted pathway proceeding via a single-state reactivity mechanism. As the reaction involving Cpd0 was found to be unrealistically high, the reaction proceeds preferentially via the quartet state of CpdI. This QM/MM study revealed that the preferred spin-state and the transition state structure for sulfoxidation are influenced by the protein environment. P450cam and P450BM3 were found to have CpdI species with different Fe-S distances and spin density distributions, and the latter having a larger reaction barrier for sulfoxidation.A novel P450 species, the doubly-reduced pentacoordinated system, was characterised using gas-phase and QM/MM methods. It was discovered to have a heme radical coupled to two unpaired electrons on the iron centre, making it the only P450 species to have similar characteristics to CpdI. Calculated spectroscopic parameters may assist experimentalists in the identification of the elusive CpdI.

No description available.

Les molécules se trouvent très rarement isolées, ceci implique qu'une modélisation de leur environnement doit être faite lors du calcul de propriétés physiques ou chimiques. Il est possible de considérer l'environnement par plusieurs méthodes de chimie théorique. Le modèle du continuum polarisable est un exemple dont les premières applications ont maintenant plus de 30 ans. Ce modèle permet de reproduire l'influence d'un solvant mais n'est pas capable de représenter des milieux fortement anisotropes tels que les macro-molécules. Afin de représenter de tels environnements, des méthodes couplant la mécanique quantique, pour le traitement de la partie d'intérêt chimique ou physique, et la mécanique moléculaire pour la représentation de l'environnement, ont été développées. Cette thèse est consacrée à l'étude de complexes de ruthénium en interaction avec l'ADN. Leurs spectres d'émission présentent des particularités trés intéressantes dues à cette interaction. Nous montrons que les propriétés photophysiques calculées doivent prendre en compte l'environnement. En particulier, nous avons utilisé une méthode permettant de modéliser la réponse électronique de l'environnement lors de transitions électroniques verticales. Les états triplets de ces complexes intercalés entre deux paires de bases de l'ADN sont également étudiés. En effet, les propriétés d'émission sont liées à la nature de ces derniers et il est important de modéliser de façon correcte le double-brin pour comprendre les mécanismes mis en jeu. Nous avons ainsi donné une interprétation physique à l'effet light-switch / Molecules are rarely isolated and a modelisation of their environment must be carried out when computing their physical or chimical properties. Quantum chemistry offers various ways to take into account this environment. For instance, polarizable continuum model is available for more than 30 years. This model is able to reproduce the influence of a solvent upon a solute but while the environment is becoming less isotropic, serious limitations are found for the model. In order to represent such environments, methods coupling quantum mechanics, for the treatment of the physically or chemically interesting part, and molecular mechanics for the environment have been developped. This thesis is dedicated to the study of ruthenium complexes in interaction with DNA. Moreover, their emission spectra are strongly modified by this interaction. We show that the photophysical properties calculated must take into account the environment. Eventually, we used a methodology able to include effects linked to the electronic response of the surroundings when computing vertical transitions. Triplets of these complexes intercalated between 2 DNA base pairs are also studied. Indeed, emission properties are linked to the nature of these and it is necessary to modelize correctly the double-strand to better understand mecanisms involved. The light-switch effect is then elucidated

Neste trabalho estudamos as propriedades estruturais e eletrônicas do CO2 supercrítico, iniciando com a avaliação de campos de força balizados por aplicações anteriores de simulação quântica do tipo Dinâmica Molecular de Born-Oppenheimer (BOMD). A aplicação principal é a descrição do espectro de absorção da paranitroanilina (pNA) em CO2 supercrítico. O CO2 supercrítico pode ser considerado como uma ``alternativa verde para os solventes orgânicos convencionais e a busca por solventes mais seguros, juntamente com a crescente consciência sobre a questão ambiental, tem levado a uma ``química verde com o intuito de se buscar soluções sustentáveis. A princípio estudamos três campos de força tradicionais para o CO2, aplicados na região supercrítica. Estes campos de força podem ser validados por meio de simulação de primeiros principios. Iniciamos considerando a condição supercrítica para o CO2 como T = 315 K, = 0.81 g/cm³ e o campo de força clássico de Zhang e Duan. Depois fizemos uma análise consistindo de uma alteração de cargas e também da geometria do CO2, que seria um caso não linear no qual foi considerado um ângulo (O-C-O) = 176° . O estudo do solvatocromismo da pNA em CO2 supercrítico foi feito considerando todas estas situações descritas para o campo de força, avaliando os resultados experimentais e teóricos já existentes. A simulação gera estruturas usando Monte Carlo e são usadas em cálculos de Mecânica Quântica do tipo DFT (CAM-B3LYP). Por fim, para verificar a importância da geometria do sistema, ou seja, a propriedade estrutural, consideramos uma outra geometria para a pNA, diferente da geometria que utilizamos a princípio nas simulações com o CO2 supercrítico. Essa ``geometria modificada\" da pNA foi obtida de uma simulação existente de Born-Oppenheimer e a utilizamos numa simulação Monte Carlo com o caso não linear para o CO2 supercrítico. Os resultados de todas essas simulações nos indicaram que a alteração das cargas e por consequência a alteração da polarização do solvente, não possui muita importância na mudança do espectro de absorção da pNA. Ao se considerar o CO2 não linear, obtivemos resultados um pouco melhor, mas não muito, comparados com a previsão teórica. Mas os resultados mais significativos são os obtidos para a situação em que utilizamos a geometria modificada da pNA. Uma parte do deslocamento do máximo da banda de absorção no espectro da pNA vem com a contribuição eletrostática da interação soluto-solvente e a outra parte vem da mudança estrutural. / In this work we study the structural and electronic properties of CO2 supercritical starting with the evaluation of force fields based on previous ab initio Born-Oppenheimer molecular dynamics (BOMD). The main application is the description of the absorption spectrum of paranitroanilina (pNA) in supercritical CO2. The supercritical CO2 is considered a ``green alternative\" to conventional organic solvents and the search for safer solvents, along with the increasing awareness of environmental issues has led to the interest in ``green chemistry\", seeking sustainable solutions. At first we studied three traditional force fields for CO2, applied in the supercritical region. These force fields can be validated by first principles simulation. We considered the supercritical condition for CO2 as T=315K, =0.81g/cm³ and the classical force field of Zhang and Duan. We also did an analysis consisting of a change of the atomic point charges and the geometry of CO2, including a non-linear case in which an angle (O-C-O)=176° was considered. The study of the solvatochromism of pNA in supercritical CO2 was made considering all these situations, evaluating the theoretical outcome and the experimental results. The simulation generates structures using Monte Carlo and are used in quantum mechanics calculations of DFT (CAM-B3LYP). To verify the importance of geometry in the system, that is, the structural property, we considered another geometry for the pNA geometry different from that we used initially in the simulations with supercritical CO2. This ``modified geometry\" of pNA was obtained from a previous Born-Oppenheimer simulation and was used in a Monte Carlo simulation with the non-linear case for supercritical CO2. The results of all these simulations indicated that the alterations of charge and thus the change in the polarization of the solvent, has no great importance in the change of the absorption spectrum of the pNA. When considering the nonlinear CO2, we obtained slightly better results. But the most significant results are obtained for the situation in which we use the modified geometry of pNA. Part of the shift in the absorption spectrum of the pNA comes with the electrostatic contribution of solute-solvent interaction and the other part comes from the structural change.

El Premio Nobel de Química de 2013 ha sido otorgado a A. Warshel, M. Levitt y M. Karplus debido al desarrollo de métodos híbridos de cálculo para química computacional. En este artículo se presentará una breve introducción del uso de los métodos de química computacional. Se describirá cómo se desarrollaron, y por qué, los métodos híbridos de cálculo, conocidos como QM/MM (Quantum Mechanics/Molecular Mechanics) para el estudio de sistemas macromoleculares, sobre todo para el caso de su aplicación en enzimas y bioquímica. Finalmente, se comentarán los alcances y expectativas futuras para estos métodos, desarrollados en los años 70. / The 2013 Nobel Prize in chemistry was awarded to A.Warshel, M.Levitt and M.Karplus for their contribution to the development of hybrid methods for computational chemistry. In this article a brief introduction about computational chemistry methods is presented. This paper will show the order in which the QM/MM (Quantum Mechanics/Molecular Mechanics) methods were developed for the study of macromolecular systems and specially their application in enzymes and biochemistry. Finally, the reach and future prospects of these methods originally developed by A. Warshel, M.Levitt and M. Karplus in the seventies will be discussed.

Neste trabalho estudamos as propriedades estruturais e eletrônicas do CO2 supercrítico, iniciando com a avaliação de campos de força balizados por aplicações anteriores de simulação quântica do tipo Dinâmica Molecular de Born-Oppenheimer (BOMD). A aplicação principal é a descrição do espectro de absorção da paranitroanilina (pNA) em CO2 supercrítico. O CO2 supercrítico pode ser considerado como uma ``alternativa verde para os solventes orgânicos convencionais e a busca por solventes mais seguros, juntamente com a crescente consciência sobre a questão ambiental, tem levado a uma ``química verde com o intuito de se buscar soluções sustentáveis. A princípio estudamos três campos de força tradicionais para o CO2, aplicados na região supercrítica. Estes campos de força podem ser validados por meio de simulação de primeiros principios. Iniciamos considerando a condição supercrítica para o CO2 como T = 315 K, = 0.81 g/cm³ e o campo de força clássico de Zhang e Duan. Depois fizemos uma análise consistindo de uma alteração de cargas e também da geometria do CO2, que seria um caso não linear no qual foi considerado um ângulo (O-C-O) = 176° . O estudo do solvatocromismo da pNA em CO2 supercrítico foi feito considerando todas estas situações descritas para o campo de força, avaliando os resultados experimentais e teóricos já existentes. A simulação gera estruturas usando Monte Carlo e são usadas em cálculos de Mecânica Quântica do tipo DFT (CAM-B3LYP). Por fim, para verificar a importância da geometria do sistema, ou seja, a propriedade estrutural, consideramos uma outra geometria para a pNA, diferente da geometria que utilizamos a princípio nas simulações com o CO2 supercrítico. Essa ``geometria modificada\" da pNA foi obtida de uma simulação existente de Born-Oppenheimer e a utilizamos numa simulação Monte Carlo com o caso não linear para o CO2 supercrítico. Os resultados de todas essas simulações nos indicaram que a alteração das cargas e por consequência a alteração da polarização do solvente, não possui muita importância na mudança do espectro de absorção da pNA. Ao se considerar o CO2 não linear, obtivemos resultados um pouco melhor, mas não muito, comparados com a previsão teórica. Mas os resultados mais significativos são os obtidos para a situação em que utilizamos a geometria modificada da pNA. Uma parte do deslocamento do máximo da banda de absorção no espectro da pNA vem com a contribuição eletrostática da interação soluto-solvente e a outra parte vem da mudança estrutural. / In this work we study the structural and electronic properties of CO2 supercritical starting with the evaluation of force fields based on previous ab initio Born-Oppenheimer molecular dynamics (BOMD). The main application is the description of the absorption spectrum of paranitroanilina (pNA) in supercritical CO2. The supercritical CO2 is considered a ``green alternative\" to conventional organic solvents and the search for safer solvents, along with the increasing awareness of environmental issues has led to the interest in ``green chemistry\", seeking sustainable solutions. At first we studied three traditional force fields for CO2, applied in the supercritical region. These force fields can be validated by first principles simulation. We considered the supercritical condition for CO2 as T=315K, =0.81g/cm³ and the classical force field of Zhang and Duan. We also did an analysis consisting of a change of the atomic point charges and the geometry of CO2, including a non-linear case in which an angle (O-C-O)=176° was considered. The study of the solvatochromism of pNA in supercritical CO2 was made considering all these situations, evaluating the theoretical outcome and the experimental results. The simulation generates structures using Monte Carlo and are used in quantum mechanics calculations of DFT (CAM-B3LYP). To verify the importance of geometry in the system, that is, the structural property, we considered another geometry for the pNA geometry different from that we used initially in the simulations with supercritical CO2. This ``modified geometry\" of pNA was obtained from a previous Born-Oppenheimer simulation and was used in a Monte Carlo simulation with the non-linear case for supercritical CO2. The results of all these simulations indicated that the alterations of charge and thus the change in the polarization of the solvent, has no great importance in the change of the absorption spectrum of the pNA. When considering the nonlinear CO2, we obtained slightly better results. But the most significant results are obtained for the situation in which we use the modified geometry of pNA. Part of the shift in the absorption spectrum of the pNA comes with the electrostatic contribution of solute-solvent interaction and the other part comes from the structural change.

No description available.

Halogenases are enzymes with the ability to regioselectively and stereoselectively form carbon-halogen bonds, transferring a halogen onto various carbon scaffolds forming organohalogens. These organohalogens have many biological properties, for example, antibacterial, antifungal, anti-inflammatory, anti-proliferative, anti-fouling, anti-feedant, cytotoxic, ichthyotoxic and insecticidal activity. Additionally, the halogen is highly important for biological activity and consequently pharmaceutical and agrochemical industries are interested in environmentally sustainable and economically viable methods to selectively halogenate various organic scaffolds used during organic synthesis. One such method is to use nonheme iron halogenases, which are structurally and biochemically similar to nonheme iron hydroxylases. Common to both groups is the reactive intermediate, the iron(IV)-oxo, which abstracts a hydrogen atom from a substrate. Post hydrogen atom abstraction the catalytic cycle bifurcates, producing either hydroxylated or halogenated products. Of current debate are the factors separating halogenation and hydroxylation and in this thesis we have investigated the mechanisms of the nonheme iron halogenase (HctB) and hydroxylase (P4H) using a combination of density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) to gain further insight into the bifurcation factors. The QM/MM and DFT studies on the hectochlorin biosynthesis enzyme HctB revealed that substrate binding and positioning are key for optimal substrate halogenation. Additionally, key residues (Glu223) were found to influence the charge density on the chloride ligand pushing the mechanism toward halogenation. Furthermore, the influence of substrate binding and positioning was explored further in a QM/MM and MD study on the nonheme iron hydroxylase, P4H, which hydroxylates proline residues to produce 4-hydroxyproline. The QM/MM and MD study identified that mutations to either Trp243 or Tyr140 disrupted both long and short-range interactions resulting in alterations to the enzymes regioselectivity and stereoselectivity. This study also revealed that Arg161 and Glu127 formed key interactions with the substrate, which became the focus of the next study on P4H. Together these two studies on P4H, highlighted the importance of substrate positioning and selective hydrogen bonding between the protein and substrate for correct product outcome. Additionally, we were able to explore several mutations to Trp243, Tyr140, Arg161 and Glu127, identifying mutations which resulted in changes to the enzyme’s regioselectivity and stereoselectivity. Finally, in this thesis we also investigated the ability of a nonheme iron halogenase to transfer groups other than a halogen, such as nitrate and azide, using the biomimetic system , [FeIV(O)(TPA)X]+, TPA = tris(2-pyridylmethy1)amine whereby X = Cl, NO2, N3. The reaction of TPA with ethyl benzene revealed that the product distributions vary with the nature of the equatorial ligand at the metal centre. The results of this study also predict the effect of other substituents potentially opening up the application of halogenases to transferring groups other than halogens. Altogether, the studies in this thesis have looked at the different factors influencing substrate halogenation from various perspectives and have revealed the fascinating biochemistry of these enzyme’s and models to perform regioselective and stereoselective reactions with potential future industrial application.