Os calcogenetos têm atraído atenção devido à variedade de propriedades físicas e químicas que exibem, apontando para sua utilização em muitas aplicações tecnológicas, incluindo a possibilidade de se obter novos materiais bidimensionais. Os calcogenetos quaternários A2MIIMIV3Q8, onde A = K, Cs; MII = Mg, Zn, Cd, Hg; MIV = Ge, Sn; Q = S, Se, Te, possuem uma grande variabilidade de band gaps e portanto eles podem ser estudados para engenharia de band gap através de mudanças na composição química. Além disso, dois tipos de estruturas cristalinas são observados nessa família, um formado por empilhamento de camadas, e outro definido por uma rede tridimensional fechada. Assim, é importante entender os fatores que afetam a estabilidade de estruturas em camadas desses compostos complexos. Nesse trabalho, os materiais A2MIIMIV3Q8 são estudados com cálculos de teoria do funcional da densidade, usando funcionais de troca e correlação semi-local e híbrido, e correções de van der Waals. Os parâmetros de rede variam com a composição conforme o esperado com base no raio atômico. A redução do número atômico de um dos componentes, principalmente Q, aumenta a energia de coesão, devido à intensificação das interações iônicas. Os resultados de energia de ligação entre camadas demonstram a importância das interações de van der Waals, e os valores são similares aos reportados na literatura para vários materiais. Seguindo a tendência de funcionais semi-locais, os band gaps são subestimados, mas cálculos com o funcional híbrido fornecem valores mais apropriados. Os resultados mostram a diversidade de band gaps e uma correlação aproximadamente linear entre band gap e volume da célula unitária. O band gap é principalmente afetado pela mudança do calcogênio, em que o aumento do número atômico diminui o band gap, devido ao aumento da energia dos estados p de Q. As análises dos coeficientes de absorção óptica e elementos de matriz de transição mostram que não existe diferença significativa entre band gap fundamental e óptico nesses materiais. O estudo de estabilidade relativa das estruturas em 9 compostos, com diferentes A e Q, mostra que os raios atômicos têm um importante papel. A estrutura sem formação de camadas é favorecida comparada com as estruturas em camadas apenas na região de raios intermediários, o que é explicado com base na diminuição das tensões na estrutura e em interações coulombianas entre íons da rede. / Chalcogenides have attracted attention due to the variety of physical and chemical properties which they display, pointing to their use in many technological applications, including the possibility to obtain new bidimensional materials. The quaternary chalcogenides A2MIIMIV3Q8, where A = K, Cs; MII = Mg, Zn, Cd, Hg; MIV = Ge, Sn; Q = S, Se, Te, have a large variability of band gaps and therefore they can be studied for band gap engineering through changes in the chemical composition. Futhermore, two types of crystal structure are observed in this family, one formed by the stacking of layers, and the other defined by a closed three dimensional framework. Thus, it is important to understand the factors that affect the stability of layered structures of these complex compounds. Here, the materials A2MIIMIV3Q8 are studied with density functional theory calculations, using semi-local and hybrid exchange-correlation functionals, and van der Waals corrections. Lattice parameters vary with composition according to expected based on the atomic radius. The reduction of the atomic number of one of the components, mainly Q, increases the cohesive energy, due to the intensification of the ionic interactions. The results of interlayer binding energies demonstrate the importance of van der Waals interactions, and the values are simillar to those reported in the literature for several materials. Following the trend of semi-local functionals, band gaps are underestimated, but hybrid functional calculations provide more accurate values. The results show the diversity of band gaps and an approximate linear correlation between band gap and unit cell volume. The band gap is mainly affected by changing the chalcogen, in which the increase of the atomic number decreases the band gap, due to the increase in the energy of Q p states. The analysis of optical absorption coefficients and transition matrix elements show that there is no significative difference between fundamental and optical band gap in these materials. The study of relative stability of the structures in 9 compounds, with different A and Q, shows that the atomic radii have an important role. The structure without layer formation is favored compared with the layered structures only in the region of intermediate radii, which is explained based on the reduction of strain in the structure and coulomb interactions between ions in the framework.

Clusters sub-nanométricos de metais de transição (TM) têm atraído grande atenção devido às suas propriedades físicas e químicas singulares, muito diferentes dos homólogos na fase bulk. Estas propriedades incomuns podem variar de acordo com o tamanho, a composição e o estado de carga para clusters em fase gasosa. Uma compreensão aprofundada da evolução das propriedades em função de tais parâmetros é um pré-requisito necessário para potencializar diversas aplicações, desde catálise até armazenamento magnético, bem como para responder questões fundamentais relacionadas com a estabilidade intrínseca desses sistemas. Porém, esse entendimento ainda não é satisfatório. Neste projeto, usando cálculos de primeiros princípios baseados na teoria do funcional da densidade dentro da aproximação de gradiente generalizado na formulação proposta por Perdew-Burke-Ernzerhoff, investigamos as estruturas atômicas, as propriedades eletrônicas e a estabilidade de todos os TM (30 elementos) clusters unários em função do tamanho (2 – 15 átomos). Para estudar a influência da carga, consideramos clusters de Cun e Ptn (n = 2 – 14) nos estados catiônico, neutro e aniônico, enquanto os efeitos de composição foram considerados para clusters bimetálicos de PtnCum com m = 2,3, · · · ,14 e n = 0,1, · · &middot ;,m. Nossos resultados sugerem que: (i) Os mecanismos de estabilização para os TM clusters unários baseiam-se na natureza das ligações químicas, em que a ocupação dos orbitais d ligantes ou antiligantes e a hibridização s – d afetam fortemente as propriedades. Por exemplo, a maioria dos TM clusters mágicos são acompanhados por picos de hibridização s – d e momentos de dipolo elétrico nulos.(ii) Diferentes parâmetros afetam as estruturas de TM clusters nesse regime de tamanho, tais como, propriedades do átomo livre, interações magnéticas de troca e efeitos relativísticos. (iii) As propriedades são muito susceptíveis ao estado de carga; em particular, as estruturas tendem a diminuir a coordenação atômica quando um elétron é adicionado ao sistema, o que afeta fortemente a transição 2D-3D. (iv) Energia de excesso negativa foi obtida para a maioria dos Pt–Cu clusters, o que fornece uma forte evidência para a formação de clusters bimetálicos. Além disso, nossas análises sugerem que a formação de estruturas tipo caroço(Cu)-casca(Pt) começa neste regime de tamanho, afim de liberar energia de tensão. (v) O centro de gravidade dos estados d ocupados da liga Pt–Cu varia com a composição, e se aproxima do orbital mais alto ocupado para composições em torno de 50%-50%. Em particular, nossos cálculos sugerem um aumento na energia de adsorção de CO e NO sobre Pt7Cu6 em comparação com os clusters unários de Pt13 e Cu13. Consequentemente, estes resultados constituem uma base para compreender a formação de partículas maiores bem como para investigar sistemas mais complexos e realistas, como reações químicas de sistemas moleculares adsorvidos sobre TM clusters estabilizados por ligantes ou suportados. / Sub-nanometre sized transition metal (TM) clusters have attracted great attention due to their unique physical and chemical properties, very different from the bulk counterparts. These unusual properties can vary with size, composition and state of charge for gas-phase clusters. An in-depth understanding of the properties evolution in function of such parameters is a necessary prerequisite to leverage diverse applications, from catalysis to magnetic storage, as well as to answer fundamental questions related with the intrinsic stability of these systems. However, this understanding is not yet satisfactory. In this project, using first-principles calculations based on density functional theory within the generalized gradient approximation in the formulation proposed by Perdew-Burke-Ernzerhoff, we investigate the atomic structures, electronic properties and stability of all TM (30 elements) unary clusters in function of size (2 – 15 atoms). To study the influence of the charge we considered Cun and Ptn (n = 2 – 14) clusters in the cationic, neutral and anionic states, while compositional effects were considered for bimetallic PtnCum–n clusters with m = 2,3, · · · ,14 and n = 0,1, · · · ,m. Our results suggest that: (i) The stabilization mechanisms for unary clusters are based on the nature of chemical bondings, on which the occupation of the bonding or antibonding d orbitals and the s – d hybridization strongly affect the properties. For example, most magic TM clusters are accompanied by peaks in s – d hybridization and null electric dipole moments.(ii) Different parameters affect TM cluster structures in that size regime, such as, free-atom properties, magnetic exchange interactions and relativistic effects. (iii) The properties are very susceptible to the charge state; in particular, the structures tend to decrease the atomic coordination when one electron is added to the system, which strongly affects the 2D-3D transition. (iv) Negative excess energy was obtained for the most PtCu clusters, which provides a strong evidence for the formation of these bimetallic clusters. Moreover, our analyzes suggest that the formation of core(Cu)-shell(Pt) like structures starts at this size regime, in order to release strain energy. (v) The center of gravity of the occupied d states of the Pt–Cu alloy vary with composition and approaches to the highest occupied molecular orbital for compositions around 50%-50%. In particular, our calculations suggest an increase in the adsorption energy of CO and NO on Pt7Cu6 in comparison with Pt13 and Cu13 unary clusters. Thus, these results form a basis to understand the formation of greater particles as well as to investigate more complex and realistic systems, such as chemical reactions of molecular systems adsorbed on ligand stabilized or supported TM clusters.

Dirhodium complexes such as carboxylates and carboxylamidates are very efficient metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. Recent experimental work has indicated that there are significant differences in the isomeric ratios obtained among the possible products when synthesizing these complexes. The relative stabilities of the Rh2(NPhCOCH3)4 tolunitrile complexes, Rh2(NPhCOCH3)4(NCC6H4CH3)2, were determined at the HF/LANL2DZ ECP, 6-31G and DFT/B3LYP/LANL2DZ ECP, 6-31G levels of theory using NWChem 6.3. The LANL2DZ ECP (effective core potential) basis set was used for the rhodium atoms and 6-31G basis set was used for all other atoms. Specifically, the o-tolunitrile, m-tolunitrile, and p-tolunitrile complexes of the 2,2-trans and the 4,0- isomers of Rh2(NPhCOCH3)4 were compared.

Heteroaryl nitrone spin traps have been suggested to act as free radical scavengers. The geometry optimizations and the single-point energies of the spin trapping reactions of the heteroaryl nitrones, 5,5-dimethylpyrroline-N-oxide (DMPO) and α-phenyl-N-t-butylnitrone (PBN) have been computationally studied using ab initio (Hartree-Fock (HF) and second-order Møller-Plesset (MP2)) methods and Density Functional Theory (DFT) methods. The effects of new heteroaryl substituents on a parent nitrone spin trap have been examined at the HF and MP2 levels with the 6-31G*, and cc-pVnZ (n=D, T, Q) basis sets. The thermodynamics of the spin trapping at the C-site and O-site with •H, •CH3 and •OH radicals were studied at the HF/6-31G* and DFT/m06/6-31G* levels. The addition reactions favor at the C-sites and the double adducts are thermodynamically more stable than the mono adducts. The spin trapping of DMPO, PBN and α(Z)-(3-methylfuroxan-4-yl)-N-tert-butylnitrone (FxBN) with •OH have also been studied.

The steady march of new technology depends crucially on our ability to discover and design new, advanced materials. Partially due to increases in computing power, computational methods are now having an increased role in this discovery process. Advances in this area speed the discovery and development of advanced materials by guiding experimental work down fruitful paths. Density functional theory (DFT)has proven to be a highly accurate tool for computing material properties. However, due to its computational cost and complexity, DFT is unsuited to performing exhaustive searches over many candidate materials or for extracting thermodynamic information. To perform these types of searches requires that we construct a fast, yet accurate model. One model commonly used in materials science is the cluster expansion, which can compute the energy, or another relevant physical property, of millions of derivative superstructures quickly and accurately. This model has been used in materials research for many years with great success. Currently the construction of a cluster expansion model presents several noteworthy challenges. While these challenges have obviously not prevented the method from being useful, addressing them will result in a big payoff in speed and accuracy. Two of the most glaring challenges encountered when constructing a cluster expansion model include:(i) determining which of the infinite number of clusters to include in the expansion, and (ii) deciding which atomic configurations to use for training data. Compressive sensing, a recently-developed technique in the signal processing community, is uniquely suited to address both of these challenges. Compressive sensing (CS) allows essentially all possible basis (cluster) functions to be included in the analysis and offers a specific recipe for choosing atomic configurations to be used for training data. We show that cluster expansion models constructed using CS predict more accurately than current state-of-the art methods, require little user intervention during the construction process, and are orders-of-magnitude faster than current methods. A Bayesian implementation of CS is found to be even faster than the typical constrained optimization approach, is free of any user-optimized parameters, and naturally produces error bars on the predictions made. The speed and hands-off nature of Bayesian compressive sensing (BCS) makes it a valuable tool for automatically constructing models for many different materials. Combining BCS with high-throughput data sets of binary alloy data, we automatically construct CE models for all binary alloy systems. This work represents a major stride in materials science and advanced materials development.

In the most recent two decades, the development of impurity controls with ultra-high precision in semiconductors motivates people to put more and more attentions on the solotronic devices, whose properties depend on one or a few dopants. One of the most promising applications of solotronic device is the qubit in quantum computing. In the procedure of exploring qubit candidates, the most straightforward challenges we need face include that the qubit must be highly isolated and can be initialized/manipulated efficiently with high fidelities. It has been proved that qubits based on single defects have excellent performances as quits. For instance, the NV center in diamond forms a ground spin triplet which can be manipulated at room temperature with electromagnetic fields. This work focuses on searching for new single defects as qubit candidates with density functional theory. Lanthanides element possesses excellent optical characteristics and extremely long nuclear coherence time. Therefore, combining it into the diamond platform can be possible design for integrated quantum information processing devices in the future. To investigate the stability of lanthanides dopants in the diamond matrix, the formation energies of charge states of complexes are calculated. The broadening of Eu(III) peak in the photoluminescence spectrum can be verified according to the existence of more than stable configuration and steady 4f electron occupation. In the case of transition-metal dopant in the silicon carbide, it is found that both silicon and carbon substituted nickels in 3C-SiC shows a magnetic-antimagnetic transition under applied strains. The virtual hopping rate of electrons strongly depends on the distance between the spin pair residing in the nickel and dangling bonds. Therefore, the Heisenberg exchange coupling between them can be adjusted subtly by controlling the external strain. According to the the spin Hamiltonian of the defect, the spin state can be manipulated universally with strain and electromagnetic fields. In contrast, the nickel dopant in 4H-SiC exhibits a very stable magnetic property. Other than that, the electronic structure of Cr in 4H-SiC implies that optical manipulations of spin states might be realized in the excited state.

Density functional theory (DFT) has become the most widely used first-principles computational method to simulate different atomic, molecular, and solid phase systems based on electron density assumptions. The complexity of describing a many-body system has been significantly reduced in DFT. However, it also brings in potential error when dealing with a system that involves the interactions between metallic and non-metallic species. DFT tends to overly-delocalize the electrons in metallic species and sometimes results in the overestimation of reaction energy, metallic properties in insulators, and predicts relative surface stabilities incorrectly in some instances. There are two approaches to overcoming the failure of DFT using standard exchange-correlation functionals: One can either use a higher level of theory (and thus incur a greater computational cost) or one can apply an efficient correction scheme. However, inaccurate corrections and improper calculation models can also lead to more errors. In the beginning of this dissertation, we introduce the correction methods we developed to accurately model the structure and electron density in material surfaces; then we apply the new methods in surface reactivity studies under experimental conditions to rationalize and solve real life problems. We first investigate the post-DFT correction method in predicting the chemisorption energy (Echem) of a NO molecule on transition metal surfaces. We show that DFT systematically enhances back-donation in NO/metal chemistorption from the metal d-band to NO 2π* orbital, and relate the back-donation charge transfer to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ-←X2Π excitation. We establish linear relationships between Echem and ΔEG←X and formulate an Echem correction scheme to the (111) surfaces of Pt, Pd, Rh and Ir. As a precursor to further optimization of DFT corrections on transition metal oxide surfaces, we systematically compare the alumina (α-Al2O3) and hematite (α-Fe2O3) (0001) surfaces to study how the atomic positions treatment during geometry optimizations would affect the electronic structure and modeled reactivity, since they are often reported to have a minimal effect. Our results suggest that both can vary significantly in quantitative and qualitative ways between partially constrained or fully relaxed slab models. We continue to use the α-Fe2O3 (0001) surfaces to optimize the Hubbard U method implemented in DFT that determines the Coulomb repulsion correction (Ud) to localize Fe d-electrons. It successfully restores the insulating properties of bulk hematite, but underestimates the stability of the oxygen-terminated surface. It is mainly due to the fact that all the chemically distinct surface Fe atoms were treated the same way. Here we develop a linear response technique to derive specific Ud values for all Fe atoms in several slab geometries. We also find that in a strongly correlated system, the O p-orbitals also need the Hubbard correction (Up) to accurately predict the structural and electronic properties of bulk hematite. Our results show that the site-specific Ud, combined with Up as Ud+p, is crucial in obtaining theoretical results for surface stability that are congruent with the experimental literature results of α-Fe2O3 (0001) surface structure. Besides methodology development, we continue to apply our specific Ud+p method in the engineered application of the Chemical Looping Combustion (CLC) process in which transition metal oxides play the role of oxidizing fuel molecules for full CO2 capture. Current molecular dynamic studies use partially constrained surface models to simulate the CH4 reaction on hematite surfaces without the detailed comparison of the early stage adsorption products. Here we use hematite (α-Fe2O3) and magnetite (Fe3O4) surfaces as analogous to systematically study the early adsorption products of CH4. Our results show that the reaction favors the homolytic pathway on O-terminated surface, and that as a reduced form of hematite, the magnetite surface also shows excellent reactivity on CH4 dissociation. Knowing how to simulate DFT surface model properly we continue to enrich our theoretical methods for more complicated systems under aqueous conditions. We focus on various structures of the lithium-ion battery material, LiCoO2 (LCO) (001) surface, involving hydroxyl groups. We assess the relative stabilities of different surface configurations using a thermodynamic framework, and a second approach using a surface-solvent ion exchange model. We find that for both models the –CoO–H1/2 surface is the most stable structure near the O-rich limit, which corresponds to ambient conditions. We also found that this surface has nonequivalent surface geometry with the stoichiometric –CoO–Li1/2 surface, leading to distinct band structures and surface charge distributions. We go on to probe how those differences affect the surface reactivity in phosphate anion adsorption. All of the work presented in this dissertation reveals the importance of accurately modeled material structures in theoretical studies to achieve correct physical properties and surface reactivity predictions. We hope our DFT correction schemes can continue to contribute to future surface studies and experimental measurements, and to enlighten new ideas in future DFT methodology improvements.

First-principles density functional theory calculations were performed on a number of important energetic molecular crystals, pentaerythritol tetranitrate (PETN), cyclotetramethylene tetranitramine (HMX), cyclotrimethylene trinitramine (RDX), and nitromethane. Simulations of hydrostatic and uniaxial compressions, as well as predictions of ground-state structures at ambient conditions, were performed using the DFT codes CASTEP and VASP. The first calculations done with CASTEP using GGA-PW yielded reasonable agreement with experiment for the calculated isothermal EOS for PETN-I from hydrostatic compression data, yet the EOS for β -HMX shows substantial deviation from experiment. Interesting anisotropic behavior of the shear-stress maxima were exhibited by both crystals upon uniaxial compression. It was predicted that the <100> direction, the least sensitive direction of PETN, has significantly different values for shear stress maxima τyx and τzx, in contrast to the more sensitive directions, <110> and <001>. In addition, non-monotonic dependence of one of the shear stresses as a function of strain was observed upon compression of PETN in the <100> direction. VASP calculations were later performed, and the results yielded good qualitative agreement with available experimental data for the calculated isothermal EOS and equilibrium structures for PETN-I, β-HMX, α-RDX, and nitromethane. Using VASP, uniaxial compression simulations were performed in the <100>, <010>, <001>, <110>, <101>, <011>, and <111> directions for all crystals up to the compression ratio V/V0 = 0.70. The VASP calculations of PETN reproduced the CASTEP results of significantly different values of τyx and τzx for the insensitive <100> compression, and relatively high and equal values of τyx and τzx for the sensitive <110> and <001> compressions. A correlation between this behavior of shear stress upon uniaxial compression and sensitivity was suggested, and predictions of anisotropic sensitivity of HMX, RDX, and nitromethane were made. Further analysis of the VASP results for PETN do not indicate a correlation between sensitivity and shear stress maxima as a function of longitudinal stress, where longitudinal stress is an appropriate experimental independent variable for comparison. The validity of a correlation between shear stress maxima and sensitivity requires further investigation. Further characterization of the anisotropic constitutive relationships in PETN was performed.

We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.

<p>Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.</p><p>The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.</p><p>Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.</p>