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This work investigated the use of large tetradentate mixed nitrogen and oxygen donor macrocycles as potential ligands for titanium(IV).These large ligands are capable of encapsulating the metal ion, thereby protecting it from reacting further. In addition, titanium complexes of this type had not been reported previously.Molecular modelling was utilised to evaluate and predict the coordinating potential of the macrocycles investigated.An alternative synthetic strategy was needed to achieve coordination complexes with titanium. This involved the use of a benzene based solvent system and rigorously dry reaction conditions.The final part of the work involved a detailed study of the kinetics of the hydrolysis of the titanium complexes investigated. / Doctor of Philosophy (PhD)

No / No Abstract

Dissolution of cellulose is an important but complicated step in biofuel production fromlignocellulosic materials. Steam and supercritical carbon dioxide (SC-CO2) explosion are two effective methods for dissolution of some lignocellulosic materials. Loading and explosion are the major processes of these methods. Studies of these processes were performed using grand canonical Monte Carlo and molecular dynamics simulations at different pressure/ temperature conditions on the crystalline structure of cellulose. The COMPASS force field was used for both methods.The validity of the COMPASS force field for these calculations was confirmed by comparingthe energies and structures obtained from this force field with first principles calculations.The structures that were studied are cellobiose (the repeat unit of cellulose), water–cellobiose, water-cellobiose pair and CO2-cellobiose pair systems. The first principles methods were preliminary based on B3LYP density functional theory with and without dispersion correction.A larger disruption of the cellulose crystal structure was seen during loading than that during the explosion process. This was seen by an increased separation of the cellulose chains from the centre of mass of the crystal during the initial stages of the loading, especially for chains in the outer shell of the crystalline structure. The ends of the cellulose crystal showed largerdisruption than the central core; this leads to increasing susceptibility to enzymatic attack in these end regions. There was also change from the syn to the anti torsion angle conformations during steam explosion, especially for chains in the outer cellulose shell. Increasing the temperature increased the disruption of the crystalline structure during loading and explosion. / Akademisk avhandling som för avläggande av teknologie doktorsexamen vid Chalmers tekniska högskola försvaras vid offentlig disputation den 10 oktober 2014,klockan 13.00 i KS101-salen, Kemigården 4, Göteborg.

Interactions between single and double stranded oligonucleotides with SiO2 surfaces and the interactions between oligonucleotides and immobilized oligomers have been studied computationally. The oligonucleotide is the 18-base-pair sequence for the survival motor neuron gene SMN1. The oligomer consisted of a 50 unit 2-hydroxyethyl methacrylate (PHEMA) molecule. A linker used to tether the oligonucleotide was either a 10 Å or a 30 Å long succinimdyl 4-[N-maleimidomethyl]cyclohexane-1-caroxylate (sulfo-SMCC-Cn). The surface consisted of a SiO2 crystal that was 50 Å long and 50 Å wide, one unit thick and covered with modified-(3-aminopropyl)trimethoxysilane (m-APTMS) molecules. It was determined that explicit water, sodium counterions and excess salt were necessary to produce computationally stable oligonucleotide structures on surfaces. Artificial partial charges were introduced to the surface, and linkers, oligomers and oligonucleotides were immobilized and studied. The linkers collapsed onto a positive but not onto a negative surface. Oligomers moved closer to the SiO2 surface regardless of the surface charge. Immobilized oligonucleotides tilted significantly from an initial upright position but did not collapse completely onto the surfaces. The interactions between immobilized oligonucleotides and oligomers were examined. The number of oligomers surrounding the oligonucleotide was varied between two and four. Single stranded oligonucleotides were prevented from interacting with the surface as they were inhibited by the presence of oligomers. Double stranded oligonucleotides collapsed onto the surface when only two oligomers were present but remained upright when four oligomers were present. This was due to the four oligomers interacting with one another and effectively shielding the surface. The oligomers interacted with the bases in the single stranded oligonucleotides, making them energetically accessible. Presence of a high density of oligomers prevented the dsDNA from collapsing onto the surface. These results suggest design criteria for preparation of mixed oligonucleotide and oligomer films for use in biosensors.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / O gÃs natural, cuja maior parte à constituÃda de metano, à um combustÃvel que vem se expandindo no mercado energÃtico global por possuir uma queima mais limpa que outros derivados petrolÃferos e por ser mais eficiente energeticamente. No entanto, ele possui como grande desvantagem frente a outros combustÃveis a dificuldade em ser armazenado devido a sua baixa densidade. Materiais microporosos vÃm sendo utilizados para aumentar tal densidade por meio da adsorÃÃo. No entanto, um dos problemas encontrados na utilizaÃÃo desses materiais se trata da diminuiÃÃo da capacidade adsortiva apÃs ciclos de carga e descarga de tanques de armazenamento. O estudo desse problema, porÃm, demanda um grande nÃmero de experimentos e uma aparelhagem relativamente sofisticada. Este trabalho propÃs a simulaÃÃo molecular como uma metodologia vÃlida a ser utilizada para o estudo da retenÃÃo de alcanos em carbono ativado e em oito estruturas metalorgÃnicas: IRMOF-1, ZIF-8, CuBTC, PCN-11, PCN-14, UiO-66, MIL-100 e MIL-101. Considerou-se o gÃs natural como uma mistura de metano (C1), etano (C2), propano (C3) e butano (C4) nas proporÃÃes de, respectivamente, 84,7:10:0,9:0,1. Para a validaÃÃo dos modelos utilizados nassimulaÃÃes, as isotermas simuladas de C1, C2, C3 e C4 foram ajustadas Ãs experimentais obtidas da literatura para cada um dos materiais. Foram entÃo realizadas isotermas multicomponentes e estudo de sÃtios de adsorÃÃo para o estudo da retenÃÃo de hidrocarbonetos e da influÃncia de fatores composicionais e estruturais nesse fenÃmeno. Observou-se que as MOFs MIL-100 e ZIF-8 sÃo as mais recomendadas para uso em tanques de GNA por critÃrios de capacidade, eficiÃncia adsortiva e estabilidade. Verificou-se ainda que MOFs que apresentam sÃtios de adsorÃÃo pouco dispersos apresentam uma maior tendÃncia à acumulaÃÃo de hidrocarbonetos. / Natural gas, which consists mostly of methane, is a fuel that has been expanding in the global energy market by having a cleaner burning than other petroleum derivatives and are more energy efficient. However, it has a great disadvantage compared to other fuels: it is difficult to be stored due to its low energy density. Microporous materials have been used to increase the energy density by adsorption. However, one of the problems encountered in using these materials it comes to the decrease in adsorption capacity after charge and discharge cycles of the storage tanks. The study of this problem, however, requires a large number of experiments and a relatively sophisticated equipment. This paper proposes themolecular simulation as a valid methodology to study the retention of alkanes in activated carbon, and eight metalorganic structures: IRMOF - 1, ZIF - 8, CuBTC, PCN- 11, PCN -14, UiO -66, MIL -100 and MIL- 101. We considered the natural gas as a mixture of methane (C1), ethane (C2), propane (C3) and butane (C4) in the proportions respectively 84,7:10:0,9:0,1. For the validation of the models used in the simulations, the simulated isotherms of C1, C2, C3 and C4 were adjusted to fit the experimental ones, obtained from the literature data for every material. Multicomponent isotherms were then performed, the retention of hydrocarbons were studied as well as the influence of compositional and structural factors to this phenomenon. We noticed that the MOFs MIL-100 and ZIF-8 are the most recommended to use in GNA tanks according to the criteria of capacity, adsorption efficiency and stability. We verified as well that MOFs that have adsorption sites too localized present a larger tendency to the accumulation of hydrocarbons.

En aquesta tesi s'ha desenvolupat i utilitzat una potent estrategia computacional per a l'estudi, tant estructural, dinàmic i energètic, de nous [2]rotaxanes que van ser sintetizats i caracteritzats experimentalment pel grup de recerca col·laborador del Prof. Donald Fitzmaurice de la University College Dublin, a Irlanda. Com a etapa preliminar, es van estudiar uns pseudorotaxans formats per les mateixes estacions que presentaven els nous [2]rotaxans. Es va modelitzar el comportament dels pseudorotaxans en diferents dissolvents (CH3CN i CH3OH) i amb la presència de dos tipus de contraions (PF6- i Br-). Es va voler aprofundir en el coneixement de les interaccions entre el macrocicle i les estacions. En aquesta direcció, es van determinar les energies de complexació dels complexes estació-macrocicle i també la variació energètica davant la posició del macrocicle respecte l'eix del pseudorotaxà. Els results obtinguts computacionalment van ser comparats amb els resultats obtinguts en estudis experimentals en dissolució (RMN, espectroscòpia d'absorció òptica, voltametria cíclica). Posteriorment, es va examinar el moviment traslacional del macrocicle degut a la reducció de les estacions del [2]rotaxà realitzant simulations de Perturbació d'Energia Lliure. Existeix una important contribució metodològica present en el desenvolupament de les parametritzacions per a modelitzar amb AMBER els ions PF6- i Br- i les estacions utilitzades en aquesta tesi. També s'han detectat deficiències en el mòdul RESP durant la comprovació del seu funcionament.Els [2]rotaxans estudiats són interessants ja que presenten força aplicacions pràctiques en el futur. Un dels grups bloquejador del [2]rotaxà es pot quedar unit a la superfície d'un elèctrode o alguna nanopartícula semiconductora. Així doncs, com a resultat de la col·laboració de tots dos grups es pot concloure que s'ha generat informació útil que pot ajudar a realitzar un millor disseny de [2]rotaxans i supermolècules relacionades que tinguin la capacitat de funcionar com a interrupturs bi-estables i puguin ésser utilitzats en la contrucció de futurs sistemes electrònics, en particular, com a dispositius bi-estables d'emmagatzematge d'informació. / En esta tesis se ha desarrollado y utilizado una potente estrategia computacional para el estudio, tanto estructural, dinámico como energético, de nuevos [2]rotaxanos que fueron sintetizados y caracterizados experimentalmente por el grupo de investigación colaborador del profesor Donald Fitzmaurice de la University College Dublin, en Irlanda. Como etapa preliminar, se estudiaron unos pseudorotaxanos formados por las mismas estaciones que presentaban los nuevos [2]rotaxanos. Se modelizó el comportamiento de pseudorotaxanos en diferentes disolventes (CH3CN y CH3OH) y con la presencia de dos tipos de contraiones (PF6- y Br-). Se quería profundizar en el conocimiento de las interacciones entre el macrociclo y las estaciones. En esta dirección, se determinaron las energías de complejación de los complejos estación-macrociclo y también la variación energética según la posición del macrociclo respecto el eje del pseudorotaxano. Los resultados obtenidos computacionalmente fueron comparados con los resultados obtenidos en estudios experimentales en disolución (RMN, espectroscopía de absorción óptica, voltametría cíclica). Posteriormente, se examinó el movimiento traslacional del macrociclo debido a la reducción de las estaciones del [2]rotaxano realizando simulaciones de Perturbación de Energía Libre. Existe una importante contribución metodológica presente en el desarrollo de las parametrizaciones para modelizar en AMBER los iones PF6- y Br- y las estaciones utilizadas en esta tesis. También se han detectado deficiencias en el módulo RESP durante la comprobación de su funcionamento.Los [2]rotaxanos estudiados son interesantes ya que presentan numerosas aplicaciones prácticas en el futuro. Uno de los bloqueadores del [2]rotaxano se puede unir a la superficie de un electrodo o a alguna nanopartícula semiconductora. Por tanto, como resultado de la colaboración de ambos grupos se puede concluir que se ha generado información útil que puede ayudar a realizar un mejor diseño de [2]rotaxanos y supermoléculas relacionadas que tengan la capacidad de funcionar como interruptores bi-estables y puedan ser utilizados en la construcción de futuros sistemas electrónicos, en particular, como dispositivos bi-estables de almacenamiento de información. / Powerful computational strategy is outlined and tested for studying the structure, dynamics and the energetics of novel modified [2]rotaxanes which were synthesized and experimentally characterized by a collaborative group of Prof. Donald Fitzmaurice from the University College Dublin, Ireland. As a first necessary step, [2]pseudorotaxanes had been examined that contain in the axles the same bipyridinyl stations of the [2]rotaxanes. The behavior of the pseudorotaxanes in two different solvents, acetonitrile and methanol is modeled at the presence of two types of counterions, PF6- and Br-. In this way an insight is gained into the interactions between the crown ether ring and the stations. Complexation energies for the viologen-crown complexes were determined, as well as the energy profiles for the movement of the crown macroring along the axle of the pseudorotaxane. The computed data for the [2]rotaxanes are compared with results from solution studies (NMR, optical absorption spectroscopy, cyclic voltametry). In addition, the shuttling of the ring in the [2]rotaxane induced by stepwise reduction of the viologen stations is examined by FEP simulations. An important methodological contribution presents the development of parameterizations for the modeling with AMBER of the hexafluorophosphate and the bromine anions and the viologens. Some deficiencies of RESP have been also noticed when testing its performance. The [2]rotaxanes studied present an interesting case with probable future practical applications. Namely, one of the bulky stoppers of the [2]rotaxane can be used to attach the rotaxane to the surface of an electrode or semiconductor nanoparticle. Thus the joint efforts of the two groups could be expected to produce useful information that can help in the rational design of [2]rotaxanes and related supermolecules capable of functioning as bi-stable switches for use in the next generation electronics, in particular as bistable devices for information storage.

Molecular modelling has become widely used in chemistry and biology. The aim of this project is to use a range of molecular modelling techniques to study enzymic actions. This thesis consists of two parts. Part A of this thesis describes computational studies conducted for the calpain-calpastatin system. Calpain is a cysteine protease. Over-expression of calpain is associated with many diseases. Calpastatin is the naturally occurring specific regulator of calpain activity. In this part of the thesis, the dynamic conformational preferences of region B of the inhibitory domain in calpastatin were examined in detail by using molecular dynamics simulations and stochastic dynamic simulations with Monte Carlo sampling. Part B of the thesis explores the structure and function of the enzyme 3-dexoy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtuDAH7PS). MtuDAH7PS catalyses the first reaction of the shikimate pathway and is a target for the development of anti-tuberculosis drugs. MtuDAH7PS is found to be synergistically inhibited by combinations of aromatic amino acids (Trp+Phe or Trp+Tyr), but not by any single aromatic amino acids. In this part of the thesis, this unique mechanism of allosteric regulation in MtuDAH7PS was investigated by using a range molecular modelling techniques. Firstly protein crystal structure refinements were conducted and those crystal structures of MtuDAH7PS in complex with various ligand molecules are described in Chapter 4. Secondly, the reaction mechanism and roles of active site residues were investigated in Chapter 5, through docking calculations (both rigid docking and induced fit docking) of a series of designed active site inhibitors. Finally, Chapter 6 discusses the molecular basis of the communication mechanism of allosteric regulation in MtuDAH7PS.

Interactions between single and double stranded oligonucleotides with SiO2 surfaces and the interactions between oligonucleotides and immobilized oligomers have been studied computationally. The oligonucleotide is the 18-base-pair sequence for the survival motor neuron gene SMN1. The oligomer consisted of a 50 unit 2-hydroxyethyl methacrylate (PHEMA) molecule. A linker used to tether the oligonucleotide was either a 10 Å or a 30 Å long succinimdyl 4-[N-maleimidomethyl]cyclohexane-1-caroxylate (sulfo-SMCC-Cn). The surface consisted of a SiO2 crystal that was 50 Å long and 50 Å wide, one unit thick and covered with modified-(3-aminopropyl)trimethoxysilane (m-APTMS) molecules. It was determined that explicit water, sodium counterions and excess salt were necessary to produce computationally stable oligonucleotide structures on surfaces. Artificial partial charges were introduced to the surface, and linkers, oligomers and oligonucleotides were immobilized and studied. The linkers collapsed onto a positive but not onto a negative surface. Oligomers moved closer to the SiO2 surface regardless of the surface charge. Immobilized oligonucleotides tilted significantly from an initial upright position but did not collapse completely onto the surfaces. The interactions between immobilized oligonucleotides and oligomers were examined. The number of oligomers surrounding the oligonucleotide was varied between two and four. Single stranded oligonucleotides were prevented from interacting with the surface as they were inhibited by the presence of oligomers. Double stranded oligonucleotides collapsed onto the surface when only two oligomers were present but remained upright when four oligomers were present. This was due to the four oligomers interacting with one another and effectively shielding the surface. The oligomers interacted with the bases in the single stranded oligonucleotides, making them energetically accessible. Presence of a high density of oligomers prevented the dsDNA from collapsing onto the surface. These results suggest design criteria for preparation of mixed oligonucleotide and oligomer films for use in biosensors.

The present thesis proposes to explore the potential of Zeolitic Imidazolate Framework ZIFs for CO2 capture applications in the conditions required by the Pressure Swing Adsorption separations process. Molecular modelling methods, combining Monte Carlo, Density Functional Theory and ab-initio simulations, were employed to mimic pure and mixture gas adsorption in ZIF materials. A transferable Force Field specifically developed for ZIFs materials is used to characterize a large variety of frameworks. Theses studies enable us to better understand the phenomena acting during adsorption process. Thereby several innovative modifications are proposed to enhance the ZIFs properties for CO2 capture and a series of hypothetical ZIFs are designed, characterized and compared to existing materials. The results cumulated during this thesis were then summarized to propose a first correlative model able to predict ZIF properties from a set of solids descriptors. This study enables to guide the structure design to optimize the ZIF properties.