Ce travail, effectué dans le cadre d’une collaboration entre l’IPN d’Orsay et EDF, contribue aux études destinées à améliorer la compréhension du comportement des radioéléments en production (centrale en fonctionnement) et à l’aval du cycle électronucléaire (stockage géologique profond des déchets). Le comportement et l’évolution des radioéléments sont fortement dépendants des interactions aux interfaces eau / surface minérale, phénomènes complexes et souvent difficiles à caractériser in situ (en particulier, dans le cas du circuit primaire des centrales REP). La dynamique moléculaire basée sur la théorie de la fonctionnelle de la densité apporte des éléments de compréhension sur l’évolution des structures d’équilibre en prenant en compte explicitement la solvatation et les effets de la température sur les mécanismes d’interaction. Dans un premier temps, le comportement de l’ion uranyle en solution et à l’interface d’un système modèle eau / TiO2 à température ambiante a été simulé et validé par la confrontation avec des résultats expérimentaux et des calculs de DFT statiques. Dans un deuxième temps, cette approche a été employée sur ce même système, à des fins prédictives, pour étudier l’effet d’une élévation de la température. La rétention de l’ion augmente avec la température en accord avec les données expérimentales obtenues sur d’autres systèmes, et conduit également à une modification du complexe de surface. Dans un troisième temps, une étude similaire a été effectuée à l’interface eau / NiO, produit de corrosion présent dans le circuit primaire des centrales nucléaires, pour lequel peu de données expérimentales sont disponible actuellement. / This study, performed within the framework of an EDF and IPN of Orsay partnership, contributes to the studies intended to improve the understanding of the radioelement behaviour in service (nuclear power plant) and at the end of the uranium fuel cycle (deep geologic repository). The behaviour and the evolution of radioelement depend mainly on the interactions at the water / mineral interfaces, which are complex and often difficult to characterize in situ (in particular, in the PWR primary circuit). Molecular dynamic simulations based on the Density Functional Theory provide some insight to understand the evolution of the structures against the solvation and the effects of the temperature on the interaction mechanisms. At first, the behaviour of the uranyl ion at room temperature in solution and at the water / TiO2 interface, as a system model, has been studied and validated by the systematic comparisons with the experimental and static DFT calculations data. Secondly, this approach was used on the same system, in predictive purposes, to study the effect of a temperature rise. The retention of the ion increases with the temperature in agreement with the experimental data obtained on other systems, and led also to a modification of the surface complex. Finally, a similar study has been performed at the water / NiO interface, which corresponds to a corrosion product present in the primary circuit of nuclear power plants, but for which few experimental data are currently available.

One of the most important advances in modern theoretical surface science and catalysis research has been the advent of Ab-Initio Density Functional Theory (DFT). Based on the electronic structure formulation of Pierre Hohenberg, Walter Kohn and Lu Jeu Sham, DFT has revolutionized theoretical research in heterogeneous catalysis, electrocatalysis, batteries, as well as homogeneous catalysis using first-principles electronic structure simulations. Combined with statistical mechanics, kinetic theory, and experimental inputs, DFT provides a powerful technique for investigating surface structure, reaction mechanisms, understanding underlying reactivity trends, and using them for rational and predictive design of materials for various catalytic chemistries, including those that can propel us towards a clean energy future – for example water gas shift (WGS), methanol synthesis, oxidation reactions, CO2 electroreduction, among many others. Fueled by advances in supercomputing facilities, numerous early and current DFT studies have been primarily focused on idealized simulations aimed at obtaining qualitative insights into experimental observations. However, as the immense potential of DFT has been unfolding, the demand for closer representation of realistic catalytic situations have rapidly emerged, and with it, the recognition of the need to reduce the disparity between theoretical DFT structures and real catalytic environments. Bridging this ‘materials gap’ necessitates using more rigorous catalyst structures in DFT calculations that can capture realistic experimental geometries, while at the same time, are creatively simplified to be computationally tractable. This thesis is a compilation of several projects on metals and metal/oxide systems that have been undertaken using DFT, in collaboration with experimental colleagues, with the goal of addressing some of the challenges in heterogeneous catalysis, while decreasing the ‘materials gap’ between theory and experiments.<div><br></div><div>The first several chapters of this thesis focus on bifunctional, metal/oxide systems. These systems are quintessential in numerous heterogeneous catalysis applications and have been the subject of extensive study. More interestingly, they sometimes exhibit synergistic enhancement in rates that is greater than the sum of the individual rates on the metal (on an inert support) or on the oxide in isolation. Such bifunctionality often stems from the modified properties at the nanoscale interface between the metal and the oxide and is an active field of research. In particular, while a large body of literature exists that investigates the activity of metals, the role of the support in bifunctional systems is often uncertain and is the subject of investigation of the first few chapters of this thesis. We chose to study WGS on Au as support effects are particularly prominent on this system. The second chapter examines WGS on Au/ZnO, where realistic catalytic environment at the interface is reproduced by analyzing the thermodynamics of surface hydroxylation of the oxide under reaction conditions, and its effect on WGS kinetics is quantified through a microkinetic analysis. This study highlights the importance of considering spectator species which can drastically influence the energetics and kinetics of a reaction at a metal/oxide interface. In addition, fundamental aspects of the effect of surface hydroxyls on the electronic structure at the interface is also discussed.<br></div><div><br></div><div>The third chapter of the thesis builds on this theme and analyzes the effect of systematic perturbation of electronic structure at the interface through substitutional doping of the oxide. Chapters 3 and 4 focus on Au/MgO, a system which has been previously studied in extensive detail in our group and benchmarked through experiments. The effects of a series of dopants of varying electronic valences have been analyzed on a number of properties at the interface – vacancy formation energies, adsorption energies of intermediates, scaling properties, activation energy barriers and so on. Exciting new scaling relationships are identified at this interface, having properties different from that observed on extended surfaces, and are interpreted using an electrostatic model. In the subsequent chapter, we identified Bronsted-Evans-Polanyi relationships for the different steps in the WGS pathway for a series of dopants. Coupled with the scaling relations, these trends were then used in conjunction with a dual-site microkinetic model to perform a volcano analysis for interfacial rates. Our analysis thus builds, for the first time, a rational design paradigm for electronic structure perturbation of the support at a bifunctional interface. The next chapter further investigates support effects, both geometric and electronic, in greater detail for Au supported on a series of oxide supports and discusses accelerated identification of an activity descriptor through a close fusion between computations and experiments.<br></div><div><br></div><div>In addition to interfacial effects of the support, this thesis also briefly examines a more apparent role of the oxide, wherein it influences the geometry of the supported metal. Two different Au-based systems are investigated using surface science approaches in Chapter 6 - the segregation properties of a bimetallic Au/Ir alloy on anatase and wetting behavior of Au-FexOy heterodimers – both of which are representative of the structural evolution of a supported catalyst under reaction conditions. Through our analysis, we show that the oxide directly influences these behaviors of the supported metal.<br></div><div><br></div><div>The next few chapters explore catalysis using metallic systems, focusing on transition metals, an important class of materials in heterogeneous catalysis and constitutes the major body of DFT literature for trend based catalytic analyses. A crucial factor that contributed to the success of such high-throughput screening studies was identification of linear scaling relationships on transition metals, whereby the adsorption energy of complex molecular fragments was linearly related to that of simple atomic adsorbates. However, while these relationships are valid for low adsorbate coverages, at higher, catalytically relevant coverages, deviations from linearity are common, thus presenting a materials gap in volcano analyses. The incorporation of coverage effects, therefore, in scaling relations has been a pressing challenge. This thesis describes a simple means of systematically capturing changes in reaction energies due to coverage effects through a pairwise interaction model, where the changes in adsorption energies are shown to be a direct function of the number of neighbors and interaction parameters determined through DFT. In addition, we also draw a mathematical correspondence between scaling relations at high coverage and that at low coverage and discuss its implications on the existence of linear scaling relations.<br></div><div><br></div><div>In Chapter 8, we discuss collaborative work on Pt based catalysts, an active catalyst for many chemical and electrochemical systems. We explore trends in WGS on bimetallic Pt-M systems and identify an activity descriptor by correlating experimental rates with the binding strength of OH* on model surfaces of bimetallic alloys. In addition, we also investigate the interaction between Na promoter and Pt under reaction conditions, using an inverse oxide model, to obtain insights into the nature of promotion of alkali metals on WGS on Pt catalysts.<br></div>

In modern technology exciting developments are related to the ability to understand and control interfaces. Particularly, magnetic interfaces revealing spindependent electron transport are of great interest for modern spintronic devices, such as random access memories and logic devices. From the technological point of view, spintronic devices based on magnetic interfaces enable manipulation of the magnetism via an electric field. Such ability is a result of the different quantum effects arising from the magnetic interfaces (for example, spin transfer torque or spin-orbit torque) and it can reduce the energy consumption as compared to the traditional semiconductor electronic devices. Despite many appealing characteristics of these materials, fundamental understanding of their microscopic properties and related phenomena needs to be established by thorough investigation. In this work we implement first principles calculations in order to study the structural, electric, and magnetic properties as well as related phenomena of two types of interfaces with large potential in spintronic applications: 1) interfaces between antiferromagnetic 3d-metal-oxides and ferromagnetic 3d-metals and 2) interfaces between non-magnetic 5d(4d)- and ferromagnetic 3d-metals. A major difficulty in studying such interfaces theoretically is the typically large lattice mismatch. By employing supercells with Moir e patterns, we eliminate the artificial strain that leads to doubtful results and are able to describe the dependence of the atomic density at the interfaces on the component materials and their thicknesses. After establishing understanding about the interface structures, we investigate the electronic and magnetic properties. A Moir e supercell with transition layer is found to reproduce the main experimental findings and thus turns out to be the appropriate model for simulating magnetic misfit interfaces. In addition, we systematically study the magnetic anisotropy and Rashba band splitting at non-magnetic 5d(4d) and ferromagnetic 3d-metal interfaces and their dependences on aspects such as interdiffusion, surface oxidation, thin film thickness and lattice mismatch. We find that changes of structural details strongly alter the electronic states, which in turn influences the magnetic properties and phenomena related to spin-orbit coupling. Since the interfaces studied in this work have complex electronic structures, a computational approach has been developed in order to estimate the strength of the Rashba band splitting below and at the Fermi level. We apply this approach to the interfaces between a Co monolayer and 4d (Tc, Ru, Rh, Pd, and Ag) or 5d (Re, Os, Ir, Pt, and Au) transition metals and find a clear correlation between the overall size of the band splitting and the charge transfer between the d-orbitals at the interface. Furthermore, we show that the spin splitting at the Fermi surface scales with the induced orbital moment weighted by the strength of the spin-orbit coupling.

Nanoscale materials are not new in either nature or physics. However, the recent technological improvements have given scientists new tools to understand and quantify phenomena that occur naturally due to quantum confinement effects. In general, these phenomena induce remarkable optical, magnetic, and electronic properties in nanoscale materials in contrast to their bulk counterpart. In addition, scientists have recently developed the necessary tools to control and exploit these properties in electronic devices, in particular field effect transistors, magnetic memories, and gas sensors. In the present thesis we implement theoretical and computational tools for analyzing the ground state and electronic transport properties of nanoscale materials and their performance in electronic devices. The ground state properties are studied within density functional theory using the SIESTA code, whereas the transport properties are investigated using the non-equilibrium Green's functions formalism implemented in the SMEAGOL code. First we study Si-based systems, as Si nanowires are believed to be important building blocks of the next generation of electronic devices. We derive the electron transport properties of Si nanowires connected to Au electrodes and their dependence on the nanowire growth direction, diameter, and length. At equilibrium Au-nanowire distance we find strong electronic coupling between electrodes and nanowire, resulting in low contact resistance. For the tunneling regime, the decay of the conductance with the nanowire length is rationalized using the complex band structure. The nanowires grown along the (110) direction show the smallest decay and the largest conductance and current. Due to the high spin coherence in Si, Si nanowires represent an interesting platform for spin devices. Therefore, we built a magnetic tunneling junction by connecting a (110) Si nanowire to ferromagnetic Fe electrodes. We have find a substantial low bias magnetoresistance of ~ 200%, which halves for an applied voltage of about 0.35 V and persist up to 1 V. In order to account for shallow impurities coming from bulk Si, the nanowire is doped with either P or B atoms (n or p type). Doping in general decreases the magnetoresistance as soon as the conductance is no longer dominated by tunneling. On the other hand, we study the electron transport properties of Si nanotubes connected to Au electrodes. The general properties turn out to be largely independent of the nanotube chirality, diameter, and length. However, the tunneling conductance of Si nanotubes is found to be significantly larger than in Si nanowires, while having a comparable band gap. For this reason we simulate a Si nanotube field effect transistor by applying an uniform potential gate. Our results demonstrate very high values of the transconductance, outperforming the best commercial Si field effect transistors, combined with low values of the subthreshold swing. Phosphorene (monolayer black P) is the only elemental two-dimensional material besides graphene that can be mechanically exfoliated and also can support electronics. Specific dislocations of the atoms in the phosphorene lattice generate another stable two-dimensional allotrope with buckled honeycomb lattice, blue P. We demonstrate structural stability of monolayer zigzag and armchair blue P nanotubes by means of molecular dynamics simulations. The vibrational spectrum and electronic band structure are determined and analyzed as functions of the tube diameter and axial strain. The nanotubes are found to be semiconductors with a sensitive indirect band gap that allows flexible tuning. We study the adsorption of CO, CO2, NH3, NO, and NO2 molecules on blue P nanotubes. They are found to surpass the gas sensing performance of other nanoscale materials. Investigations of the gas adsorption and induced charge transfer indicate that blue P nanotubes are highly sensitive to N-based molecules, in particular NO2, due to covalent bonding. The current-voltage characteristics of nanotubes connected to Au electrodes is used to evaluate the change in resistivity upon adsorption. The observed selectivity and sensitivity properties make blue P nanotubes superior gas sensors for a wide range of applications. Using black P and blue P nanoribbons, we configure field effect transistors with atomically perfect junctions by using armchair nanoribbons as semiconducting channel and zigzag nanoribbons as metallic leads. We characterize the devices and observe a performance superior to Si-based devices, with on/off ratio of ~ 103, low subthreshold swing of ~ 60 mV/decade, and high transconductance of ~ 104 S/m.

Wurtzite III-nitride semiconductor materials have many technically important applications in optical and electronic devices. As GaN-based visible light-emitting diodes (LEDs) and lasers starts to mature, interest in developing UV devices starts to rise. The search for materials with larger bandgaps and high refractive index contrast in the UV range has inspired multiple studies of BN-based materials and their alloys with traditional III-nitrides. Additionally, alloying III-nitrides with boron can reduce their lattice parameters giving a new option for strain engineering and lattice matching. In this work I investigate the refractive indices of BAlN and BGaN over the entire compositional range using hybrid density functional theory (DFT). An interesting non-linear trend of the refractive index curves appears as boron content is increased in the BAlN and BGaN alloys. The results of this calculation were interpolated and plotted in three dimensions for better visualization. This interpolation gives a 3D dataset that can be used in designing a myriad of devices at all binary and ternary alloy compositions in the BAlGaN system. The interpolated surface was used to find an optimum design for a strain-free, high reflection coefficient and high bandwidth DBR. The performance of this DBR was quantitatively evaluated using finite element simulations. I found that the maximum DBR reflectivity with widest bandwidth for our materials occurs at a lattice parameter of 3.113 Å using the generated 3D dataset. I use the corresponding material pair to simulate a DBR at the wavelength 375 nm in the UVA range. A design with 25 pairs was found to have a peak reflectivity of 99.8%. This design has a predicted bandwidth of 26 nm measured at 90% peak performance. The high reflectivity and wide bandwidth of this lattice-matched design are optimal for UVA VCSEL applications. I have assisted in exploring different metalorganic chemical vapor deposition (MOCVD) techniques, continuous growth and pulsed-flow modulation, to grow and characterize BAlN alloys. Samples grown using continuous flow show better optical quality and are characterized using spectroscopic ellipsometry. The refractive index of samples obtained experimentally is significantly below the predicted value using DFT.

No description available.

Identification of polysaccharides is not a straightforward task due to the high degree of stereochemistry present in their isobaric monomers. Their isobaric nature causes traditional mass spectrometry to fall short when trying to differentiate not only the conformation of the monomers but the position of the glycosidic bonds that bind them. This structural information is important for biochemists as they study the role of different glycans in biological processes. Tandem mass spectrometry (MS/MS) allows the study of the fragment ions formed during collision induced dissociation (CID), the fragments formed depend on the structure and stability of the precursor molecule and can be used to identify the compounds. These fragmentation pathways will be as complex as the species that form them. To date, typical saccharide fragments are separated into three groups that represent the major fragments: Cross-ring cleavages (A/X), and those resulting from cleaving different sides of the glycosidic bond (B/Y) and (C/Z). Ion mobility separation (IMS) has shown to have some success at discerning polysaccharide conformers and those of other biopolymers such as proteins and polynucleotides. Ion mobility separates gas-phase ions by colliding them with non-reactive gases and relating respective increase in flight time to their collision cross-section (CCS). In this study, the relative energetics of the first steps of the cross-ring cleavage and both glycosidic bond cleavage channels for isomaltotriose [glc(α1-6)glc(α1-6)glc] as well as a minor water loss channel were explored using density functional theory (DFT) calculations at the B3LYP/6-31+g(d) level of theory. It was demonstrated that charge-remote mechanisms are a viable alternative to charge-directed mechanisms when under the high energy short time scale conditions present during an ESI-MS/MS experiment. To verify the efficiency of ion mobility for isomeric separation, the relative experimental CCS of isomaltotriose [glc(α1-6)glc(α1-6)glc], maltotriose [glc(α1-4)glc(α1-4)glc], panose [glc(α1-6)glc(α1-4)glc] and raffinose [gal(α1-6)glc(α1-2)fru] were determined by comparison with literature CCS values for dextran, a variable-length oligomer of α1-6 linked glucose was used as an external calibrant. The experimental CCS of the precursor ions were compared to literature values when available as well as the calculated effective values of the optimized DFT geometries using the trajectory method of the MOBCAL computational suite. As phosphate is often used as an adducting agent to increase the intensity of the precursor ion when running an IMS experiment, the effect of its presence on the fragmentation of isomaltotriose and large isomaltooligosaccharides was studied. It was seen that depending on the location of the phosphate ion, it will preferentially dissociate leaving behind a neutral glycan. This explains the low abundance of fragment ions observed when selecting a phosphate-adducted precursor ion during an MS/MS experiment. IMS and MS-MS are complementary methods that can be used to identify monomers within a polysaccharide and how they are bound.

The main goal of the presented thesis is a theoretical study of heat of formation for high-nitrogen energetic materials. A modification of the classical approach to the isodesmic reactions is realized with the intent that molecules on both sides of the corresponding equation have not only the same number of atoms but also approximately the same size and skeletal similarity. This approach is designated as a method "Alternative Isodesmic Reaction (AIR method)". At its base, using the DFT B3LYP / cc-pVTZ and B3PW91 / cc-pVTZ, for the high nitrogen heterocycles, which are selected from the group of triazoles, triazines, tetrazines, the enthalpy of formation values the gaseous phase f H°(298,g), were obtained whose values are close to the published f H°(298,g). Their application in the calculation of the relevant characteristics of these heterocycles detonation gave real values.

In this work I briefly described the basic ideas of density functional theory (DFT) for calculations of an electronic structure of molecules, solids and surfaces. I also summarized the fundamentals of DFT based Fireball code that was used for calculations of the atomic and electronic structures of several models. Fur- ther I described theory of scanning tunnelling microscopy (STM) and mentioned some approaches of simulating STM maps by means of results of DFT calcula- tions. The studied models were reconstructions of a Si (111) surface, namely the 7×7, 2×1 Pandey chain and reconstructions with periodicity √ 3 × √ 3, where finding proper atomic structure, fitting to a new experimental observations, was required. I compared energetic favourableness of the reconstructions. I also stud- ied an adsorption of benzene on 7×7. I have analysed the atomic and electronic structure of all the models and made STM simulations using STM code. I com- pared the results with experimental STM maps in literature and with results of the STM experiments made by RNDr. Pavel Kocán, Ph.D. (reconstruction v √ 3 × √ 3) and by Prof. Alastair McLean (benzene on 7×7). Probable model of observed metastable reconstruction √ 3 × √ 3 was found. The proof that benzene chamisorbate in so called di-σ-bridge position was also made. 1

Nanoscale materials have many potential advantages because of their quantum confinement, cost and producibility by low-temperature chemical methods. Advancement of theoretical methods as well as the availability of modern high-performance supercomputers allow us to control and exploit their microscopic properties at the atomic scale, hence making it possible to design novel nanoscale molecular devices with interesting features (e.g switches, rectifiers, negative differential conductance, and high magnetoresistance). In this thesis, state-of-the-art theoretical calculations have been performed for the quantum transport properties of nano-structured materials within the framework of Density Functional Theory (DFT) and the Nonequilibrium Green's Function (NEGF) formalism. The switching behavior of a dithiolated phenylene-vinylene oligomer sandwiched between Au(111) electrodes is investigated. The molecule presents a configurational bistability, which can be exploited in constructing molecular memories, switches, and sensors. We find that protonation of the terminating thiol groups is at the origin of the change in conductance. H bonding at the thiol group weakens the S-Au bond, and thus lowers the conductance. Our results allow us to re-interpret the experimental data originally attributing the conductance reduction to H dissociation. Also examined is current-induced migration of atoms in nanoscale devices that plays an important role for device operation and breakdown. We studied the migration of adatoms and defects in graphene and carbon nanotubes under finite bias. We demonstrate that current-induced forces within DFT are non-conservative, which so far has only been shown for model systems, and can lower migration barrier heights. Further, we investigated the quantum transport behavior of an experimentally observed diblock molecule by varying the amounts of phenyl (donor) and pyrimidinyl (acceptor) rings under finite bias. We show that a tandem configuration of two dipyrimidinyl-diphenyl molecules improves the rectification ratio, and tuning the asymmetry of the tandem set-up by rearranging the molecular blocks greatly enhances it. It has been recently demonstrated that the large band gap of boronitrene can be significantly reduced by carbon functionalization. We show that specific defect configurations can result in metallicity, raising interest in the material for electronic applications. In particular, we demonstrate negative differential conductance with high peak-to-valley ratios, depending on the details of the material, and identify the finite bias effects that are responsible for this behavior. Also, we studied the spin polarized transport through Mn-decorated topological line defects in graphene. Strong preferential bonding is found, which overcomes the high mobility of transition metal atoms on graphene and results in stable structures. Despite a large distance between the magnetic centers, we find a high magnetoresistance and attribute this unexpected property to very strong induced π magnetism. Finally, the results obtained herein advance the field of quantum electronic transport and provide significant insight on switches, rectification, negative differential conductance, magnetoresistance, and current-induced forces of novel nanoscale materials.