<p>The realm of molecular physical chemistry ranges from the structure of matter and the fundamental atomic and molecular interactions to the macroscopic properties and processes arising from the average microscopic behaviour.</p><p>Herein, the conventional electrodic problem is recast into the simpler molecular problem of finding the electrochemical, real chemical, and chemical potentials of the species involved in redox half-reactions. This molecular approach is followed to define the three types of absolute chemical potentials of species in solution and to estimate their standard values. This is achieved by applying the scaling laws of statistical mechanics to the collective behaviour of atoms and molecules, whose motion, interactions, and properties are described by first principles quantum chemistry. For atomic and molecular species, calculation of these quantities is within the computational implementations of wave function, density functional, and self-consistent reaction field theories. Since electrons and nuclei are the elementary particles in the realm of chemistry, an internally consistent set of absolute standard values within chemical accuracy is supplied for all three chemical potentials of electrons and protons in aqueous solution. As a result, problems in referencing chemical data are circumvented, and a uniform thermochemical treatment of electron, proton, and proton-coupled electron transfer reactions in solution is enabled.</p><p>The formalism is applied to the primary and secondary radiation damage to DNA bases, e.g., absorption of UV light to yield electronically excited states, formation of radical ions, and transformation of nucleobases into mutagenic lesions as OH radical adducts and 8-oxoguanine. Based on serine phosphate as a model compound, some insight into the direct DNA strand break mechanism is given.</p><p>Psoralens, also called furocoumarins, are a family of sensitizers exhibiting cytostatic and photodynamic actions, and hence, they are used in photochemotherapy. Molecular design of more efficient photosensitizers can contribute to enhance the photophysical and photochemical properties of psoralens and to reduce the phototoxic reactions. The mechanisms of photosensitization of furocoumarins connected to their dark toxicity are examined quantum chemically.</p>

The realm of molecular physical chemistry ranges from the structure of matter and the fundamental atomic and molecular interactions to the macroscopic properties and processes arising from the average microscopic behaviour. Herein, the conventional electrodic problem is recast into the simpler molecular problem of finding the electrochemical, real chemical, and chemical potentials of the species involved in redox half-reactions. This molecular approach is followed to define the three types of absolute chemical potentials of species in solution and to estimate their standard values. This is achieved by applying the scaling laws of statistical mechanics to the collective behaviour of atoms and molecules, whose motion, interactions, and properties are described by first principles quantum chemistry. For atomic and molecular species, calculation of these quantities is within the computational implementations of wave function, density functional, and self-consistent reaction field theories. Since electrons and nuclei are the elementary particles in the realm of chemistry, an internally consistent set of absolute standard values within chemical accuracy is supplied for all three chemical potentials of electrons and protons in aqueous solution. As a result, problems in referencing chemical data are circumvented, and a uniform thermochemical treatment of electron, proton, and proton-coupled electron transfer reactions in solution is enabled. The formalism is applied to the primary and secondary radiation damage to DNA bases, e.g., absorption of UV light to yield electronically excited states, formation of radical ions, and transformation of nucleobases into mutagenic lesions as OH radical adducts and 8-oxoguanine. Based on serine phosphate as a model compound, some insight into the direct DNA strand break mechanism is given. Psoralens, also called furocoumarins, are a family of sensitizers exhibiting cytostatic and photodynamic actions, and hence, they are used in photochemotherapy. Molecular design of more efficient photosensitizers can contribute to enhance the photophysical and photochemical properties of psoralens and to reduce the phototoxic reactions. The mechanisms of photosensitization of furocoumarins connected to their dark toxicity are examined quantum chemically.

Els brassinoesteroides són fitohormones naturals que presenten un potencial molt prometedor per a ser aplicats a l’agricultura. L’elevat cost d’obtenció d’aquests compostos ha estimulat la recerca d’anàlegs que ofereixin una bona relació entre la seva activitat biològica i el seu cost. En aquest sentit, es creu interessant abordar la cerca de compostos d’estructura no esteroïdal amb activitat brassinosteroide mitjançant mètodes computacionals. Per assolir aquest objectiu s’han plantejat dos enfocaments: per una banda, buscar estructures totalment noves i, per l’altra, buscar estructures que puguin mimetitzar només l’esquelet esteroidal d’anàlegs brassinoesteroides androstànics actius per a, posteriorment, ancorar hi la cadena addient. Amb la primera aproximació s’han realitzat processos de virtual screening sobre bases de dades de screening compounds comercials mitjançant dues estratègies: un model de QSAR, desenvolupat amb descriptors independents de l’alineament amb el programa ALMOND, i l’aplicació de la metodologia FLAP. Després d’un procés de filtració, a partir dels dos mètodes s’han proposat una serie de candidats, l’activitat dels quals ha estat avaluada amb el test d’inclinació de la làmina d’arròs (RLIT). En total, s’han trobat 7 hits, 4 dels quals formen una sèrie en la que comparteixen l’estructura de N (2 hidroxietil)piperazina. Aquests compostos es plantegen com a nous referents per obtenir estructures no esteroidals amb activitat brassinoesteroide. Per altra banda, amb la segona aproximació, s’ha aplicat la metodologia de scaffold hopping amb el programa SHOP per trobar estructures que puguin mimetitzar esquelets androstànics brassinoesteroides. Aquesta metodologia s’ha aplicat sobre dues bases de dades: una de building blocks comercials i una disenyada ad hoc prenent com a referència estructures basades en coneixements previs. Després d’una etapa de selecció mitjançant alineaments flexibles efectuats amb el programa MOE, 11 estructures han estat proposades per a la síntesis d’anàlegs. S’ha intentat la síntesis de 3 compostos a partir d’estructures anàlogues de l’esquelet androstànic escollides preliminarment. Els grups protectors escollits i les condicions de reacció assajades no han rendit els compostos desitjats però han proporcionat informació per afrontar la síntesi de futurs anàlegs brassinoesteroides amb estructures no esteroïdals. / Los brasinoesteroides son fitohormonas naturales que presentan un potencial muy prometedor para ser aplicados en la agricultura. El elevado coste de obtención de estos compuestos ha estimulado la búsqueda de análogos que ofrezcan una buena relación entre su actividad y su coste. En este sentido, se cree interesante abordar la búsqueda de compuestos de estructura no esteroidal con actividad brasinoesteroide mediante técnicas computacionales. Para lograr este objetivo se han planteado dos enfoques: por un lado, buscar estructuras totalmente nuevas y, por el otro, buscar estructuras que puedan mimetizar solo el esqueleto esteroidal de análogos brasinoesteroides androstánicos activos para, posteriormente, anclar la cadena adecuada. Con la primera aproximación se han realizado procesos de virtual screening sobre bases de datos de screening compounds comerciales mediante dos estrategias: un modelo de QSAR, desarrollado con descriptores independientes del alineamiento con el programa ALMOND, y la aplicación de la metodología FLAP. Después de un proceso de filtrado, a partir de los dos métodos se han propuesto una serie de candidatos, la actividad de los cuales ha sido evaluada con el test de inclinación de la lámina de arroz (RLIT). En total, se han encontrado 7 hits, 4 de los cuales forman una serie que comparte la estructura de N (2 hidroxietil)piperazina. Estos compuestos se plantean como nuevos referentes para obtener estructuras no esteroidales con actividad brasinoesteroide. Por otro lado, con la segunda aproximación, se ha aplicado la metodología de scaffold hopping con el programa SHOP para encontrar estructuras que puedan mimetizar esqueletos androstánicos brasinoesteroides. Esta metodología se ha aplicado sobre dos bases de datos: una de building blocks comerciales y otra diseñada ad hoc tomando como referencia estructuras basadas en conocimientos previos. Después de una etapa de selección mediante alineamientos flexibles realizada con el programa MOE, 11 estructuras han sido propuestas para la síntesis de análogos. Se ha intentado la síntesis de 3 nuevos compuestos a partir de estructuras análogas del esqueleto androstánico escogidas preliminarmente. Los grupos protectores escogidos i las condiciones de reacción ensayadas no han rendido los compuestos deseados pero han proporcionado información para afrontar la síntesis de futuros análogos brasinoesteroides con estructuras no esteroidales. / Brassinosteroids are natural phytohormones that present a promising potential in agricultural applications. The high cost to obtain these compounds has promoted the research of analogues that offer a good relationship between their biological activity and their cost. Keeping this idea in mind, the search of compounds with non-steroidal structure with brassinosteroid activity using computational methods was considered an interesting goal. To achieve this objective two approaches has been proposed: on one side, to search completely new structures and, on the other, to search structures mimetic to the steroidal skeleton of active androstane brassinosteroid analogues, where the adequate side chain has to be anchored. With the first approach, virtual screening processes over commercial screening compound databases have been performed using two strategies: a QSAR model developed with alignment-free descriptors with the program ALMOND, and the application of FLAP methodology. After a filtering process, some structures have been proposed as candidates, whose biological activity in the Rice Lamina Inclination Test (RLIT) has been measured. Totally, 7 hits have been found, from which 4 form a series sharing the N (2 hidroxiethyl)piperazine. These compounds are proposed as new referents to find non steroidal structures with brassinosteroid activity. With the second approach, the scaffold hopping methodology has been applied with SHOP program to find structures mimetic to androstane brassinosteroid skeletons. This methodology has been applied over two databases: a commercial building blocks one and an ad hoc designed one, taking as reference structures based on previous knowledge. After a filtering step with flexible alignments performed with the program MOE, 11 structures have been proposed for the synthesis of new compounds. The synthesis of 3 new compounds has been tried starting from preliminary selected structures analogous to the androstane skeleton. The chosen protecting groups and the tested reaction conditions have not yielded the desired compounds but have given information to face the future synthesis of brassinosteroid analogues with non-steroidal structures.

Doped ZnO nanoparticles were synthesized by three different methods – electrochemical deposition under oxidizing conditions (EDOC) , combustion method and wet chemical synthesis – for investigating the oxygen gas sensing response. Ga-doped ZnO was mostly synthesized but also In-doped ZnO was made. The samples were analyzed by XRD, SEM, EDX and TEM. Gas response curves are given alongside with Langmuir fitted curves and data for pure ZnO and Ga-doped ZnO. DFT quantum chemical investigation of cluster models ZnO nanoparticles were performed to evaluate defect effects and oxygen and nitrogen dioxide reactions with the ZnO surface. Defects were investigated by DOS and HOMO-LUMO plots , and are oxygen vacancy, zinc vacancy, zinc interstitial and gallium doping by replacing zinc with gallium. Oxygen and nitrogen dioxide reactions were investigated by computing Mulliken charges, bond lengths, DOS spectra and HOMO-LUMO plots.

L’any 2002 tres grups de recerca, entre ells el nostre grup, van demostrar teòricament que la interacció entre anions i anells aromàtics electrodeficients, anomenada interacció anió–, era favorable. Des de llavors s’ha dut a terme un intens estudi de la seva naturalesa física fins la total comprensió. Aquesta tesi es basa amb l’estudi de la interacció anió– des de tres punts de vista. Primerament, la investigació es basa en el disseny teòric de motius estructurals per donar lloc a un receptor on la interacció anió– siga molt favorable, per posteriorment avaluar la força de la interacció experimentalment en dissolució. A continuació, es va analitzar la interrelació entre un gran nombre de combinacions d’interaccions no covalents. A partir d’aquest estudi es defineixen nous conceptes i es proposen diferents formules per calcular efectes de cooperativitat. Finalment, hem anat un pas més enllà en l’estudi de la interacció analitzant: 1) l’impacte de la interacció anió– a sistemes biològics; 2) la influència de modificacions a l’anió sobre la naturalesa física de la interacció. / In 2002 three research groups, among them our research group, theoretically demonstrated that the interaction between anions and electron-deficient aromatic rings, named anion– interaction, was favourable. Since then, an intense study of its physical nature has been performed to understand it completely. This thesis is based on the study of the anion– interaction from three points of view. Firstly, theoretical design of binding units to build a receptor and to obtain the most favourable binding based on anion– interactions. The binding properties of these receptors have been experimentally assessed in solution. Secondly, we have studied the interplay between a great combination of noncovalent interactions. From this study, new concepts and formula to calculate cooperativity effects have been described. Finally, we have study one step further the anion– interaction analysing: 1) the impact of anion– interaction in biological systems; 2) how the modifications in the anion influence the physical nature of the interaction.

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to

In this work, we theoretically study the properties of diatomic molecular systems, their dynamics, and the control thereof through the use of laser fields. We more specifically study three compounds:<p>1) HeH+, a species of great astrochemical importance which is thought to be the first molecular species to have formed in the universe;<p>2) CO2+, a metastable dication of particular interest in quantum control experiments due to its long-lived lowest vibrational level;<p>3) 41K87Rb, a polar molecule that can be formed at very low temperature and trapped, making it a good candidate for quantum computing schemes.<p>First, we use ab initio methods to compute accurate potential energy curves for the lowest singlet and triplet states of HeH+ as well as the potential energy curves, transition dipole moments and nonadiabatic radial couplings of the ground 3Π state of CO2+ and of its 11 lowest 3Σ- states.<p>In a second step, we use this ab initio data to compute the photodissociation and radiative association cross sections for the a and b 3Σ+ states of HeH+, as well as the values of the corresponding rate constants for astrophysical environments. The photodissociation cross sections from the lowest vibrational level of CO2+ is also determined.<p>Going one step further, we optimize laser control fields that drive the photodissociation dynamics of HeH+ and CO2+ towards specific channels. We compare two field optimization methods: a Møller operator-based Local Control approach and Optimal Control Theory. In both cases, we add a constraint that minimizes the area of the optimized fields.<p>Finally, we focus on one of the potential applications of high-fidelity laser control: the use of small molecular systems as quantum computers. We more specifically study the potential implementation of both intra- and intermolecular logic gates on data encoded in hyperfine states of trapped ultracold polar 41K87Rb molecules, opening interesting perspectives in terms of extensibility.<p>/<p>Dans cette thèse, nous étudions théoriquement les propriétés de molécules diatomiques, leur dynamique de réaction ainsi que le contrôle de cette dynamique à l'aide de champs laser. Notre travail porte plus spécifiquement sur trois espèces :<p>1) HeH+, un composé-clé en astrochimie considéré comme la première espèce moléculaire qui s'est formée dans l'univers ;<p>2) CO2+, un dication métastable qui se prête bien à des expériences de contrôle quantique en raison du relativement long temps de vie de son état vibrationnel le plus bas ;<p>3) 41K87Rb, une molécule polaire qui présente la particularité de pouvoir être formée à très basse température et piégée, ce qui en fait un bon support physique potentiel pour la réalisation d'un ordinateur quantique moléculaire. <p>Nous utilisons tout d'abord des méthodes de calcul ab initio afin d'obtenir les courbes d'énergie potentielle des premiers états singulets et triplets de HeH+ avec un haut de degré de précision, ainsi que les courbes d'énergie potentielle, les moments dipolaires de transition et les couplages non-adiabatiques radiaux de l'état fondamental 3Π de CO2+ et de ses 11 premiers états 3Σ-.<p>Ensuite, nous utilisons ces données ab initio pour calculer les sections efficaces de photodissociation et d'association radiative des états a et b 3Σ+ de HeH+, ainsi que les constantes cinétiques associées à ces processus dans les conditions rencontrées dans des environnements astrophysiques. Les sections efficaces de photodissociation du niveau vibrationnel le plus bas de CO2+ sont également calculées. <p>Nous allons ensuite un cran plus loin en optimisant des champs laser qui guident la dynamique de photodissociation de HeH+ et CO2+ vers des canaux de dissociation spécifiques. Nous comparons deux méthodes d'optimisation de ces champs: une approche de contrôle local basée sur les opérateurs de Møller et la théorie du contrôle optimal. Dans le deux cas, nous incluons une contrainte qui minimise l'aire des champs. <p>Enfin, nous nous concentrons sur l'une des applications possibles du contrôle laser à haute fidélité :l'utilisation de petits systèmes moléculaires comme ordinateurs quantiques. Nous étudions plus spécifiquement l'implémentation possible d'opérations logiques intra- et intermoléculaires sur des données encodées dans des états hyperfins de molécules de 41K87Rb piégées, ce qui ouvre des perspectives intéressantes en terme d'extensibilité. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished