O objetivo deste trabalho é descrever a estrutura eletrônica da espécie diatôrnica BeMg, utilizando métodos ab initio multiconfiguracionais. A primeira descrição teórica da espécie BeMg foi feita por Chiles e Dykstra em 1982, empregando os métodos SCF, CCD e CEPA. Naquele trabalho, os autores propuseram que a estrutura eletrônica do BeMg seria intermediária entre a apresentada pelas espécies Be2 e Mg2. Em 1994, Boldyrev et al. empregaram o método QCISD e conjuntos de bases atômicas do tipo 6 - 311 + G* para calcular a distância de equilíbrio do BeMg. Até onde sabemos, não existe nenhum outro estudo téorico, nem experimental, sobre esta espécie. Apesar dos esforços anteriores, devido à natureza dos átomos envolvidos, para descrever com maiores detalhes e precisão não somente o estado fundamental, mas também diferentes estados eletrônicos excitados, é necessário empregar métodos ab initio multiconfiguracionais, fato explicitamente reconhecido por Boldyrev et al. Em 1994. No presente trabalho, as curvas de energia potencial para os estados eletrônicos energeticamente mais baixos, que correlacionam com os primeiros quatro canais de dissociação, da espécie BeMg foram descritas teoricamente empregando conjunto de bases atômicas do tipo cc-pVQZ e funções de onda do tipo CASSCF/MRCI. Todos os orbitais de valência, além de um conjunto adicional de funções de correlação do tipo s e p foram incluídos no espaço ativo. Diversas constantes espectroscópicas também foram calculadas para os estados eletrônicos selecionados. O estado fundamental foi caracterizado como de simetria 1Σ+ e fracamente ligado (De = 0,05 eV), possuindo consequentemente uma distância internuclear de equihbrio relativamente longa (3, 30 Å, ωe = 44, 2 cm-1). É interessante notar que nos trabalhos anteriores a distância internuclear de equilíbrio do estado fundamental foi calculada com sendo 4, 5 Å e 5,1 Å, por Chiles e Dykstra e Boldyrev et al., respectivamente. Os dois primeiros estados excitados são o a3II (Re = 2,416 Å, Te = 11029 cm-1) e o b3 Σ+ (Re = 2,578 Å, Te = 11058 cm-1), ambos com energia de dissociação igual a 1,28 eV. / The first theoretical description of BeMg (using the SCF, CCD, and CEPA methods) was done by Chiles and Dykstra in 1982, when it was proposed that its electronic structure would be intermediate to Be2 and Mg2. In 1994, Boldyrev et al., using the QCISD method and 6 - 311+G* basis sets, presented other results on this diatomic species. To the best of our knowledge, there are no other study about this diatomic species. However, due to the nature of the atoms involved, it is necessary to employ more sophisticated theoretical methods to describe BeMg accurately. In this study, potential energy curves for the lowest-lying electronic states correlating with the first four dissociation channels were determined using the cc-p VQZ basis sets and CASSCF /MRCI wave functions. All valence orbitals plus one set of s and p correlating functions were included in the active space. A whole set of spectroscopic constants completes the characterization of each state. In its ground state (X1Σ+) BeMg is weakly bond (De = 0.05 eV), and consequently has a long internuclear equilibrium distance (Re = 3.30 Å, we = 44.2cm-1). It is interesting to note that in previous theoretical works, the internuclear equilibrium distance was calculated to be around 4.5 Å and 5.1 Å. The first two excited states are an a3II (Re = 2.416 Å, Te= 11029 cm-1) and a b3Σ+ (Re = 2.578 Å, Te= 11058 cm-1), with the same dissociation energy, 1.28 eV.

In this thesis, we report on our studies of the transport properties, optical response and slow dynamical nature of novel room temperature ionic liquids. Using computer simulations we have demonstrated that the diffusive dynamics of these systems is in many ways analogous to that of other glassy or supercooled liquids. These solvents show non-Gaussian rotational and translational diffusion which have a temporal extent on the order of nanoseconds at room temperature. Our study of their response upon application of an external mechanical perturbation shows that even for systems with a box length as large as 0.03 microns the viscosities computed from perturbation wavenumbers compatible with this box size have not yet reached the hydrodynamic limit. We found these systems to behave in a non-Newtonian fashion and we also observe a clear break down of linear response theory on the nano- or sub-micrometer scale. Upon photoexcitation of an organic probe with lifetime shorter than the reorganization timescale in these ionic liquids, (which is quite long on the order of several nanoseconds at least), the emission spectrum is absorption wavelength dependent.Our computer simulations rationalized this observation in terms of local solvent environment around individual subensemble probe members. Excitation of different solute molecules in the liquid gives rise to site-specic optical responses. We revealed that the origin of this excitation wavelength dependence is the existence of persistent excited-state environments that do not get solvent averaged on a time scale relevant to fluorescence. The computed time resolved fluorescence spectra show that the full loss of correlation between absorption and emission frequencies for probes in room temperature ionic liquids occur on a time scale of nanoseconds. One of the most interesting features of ionic liquids is their uncommonly large range of dynamical time scales which in turn makes some of their properties to be quite different from that of most other conventional solvents. We hope that our understanding of these phenomena will be useful in the future in the development of tools to harness their potential to control the outcome of chemical and photo-chemical reactions.

Aminophosphonic and related compounds were almost unknown 50 years ago, but today the literature data have considerably increased. Their negligible mammalian toxicity and their similarity with aminoacids confer on these compounds a top place as potential candidates for drugs. The discovery of numerous natural aminophosphonic derivatives endowed with biological properties useful to both medicinal and agricultural fields enhanced the infatuation for synthetic analogs and homologs. Intensive work has been performed towards alpha-aminophosphonic compounds, the direct analogs of natural alpha-aminoacids, disclosing versatile strategies, compatible both with molecular diversity and asymmetric synthesis. Less synthetic effort was devoted to the synthesis of higher homologs. Recent developments of the Diels-Alder reaction offer an asymmetric and convergent entry to various six-membered highly functionalizable key intermediates, compatible with molecular variety. As it is, the Diels-Alder (D-A) reaction should provide an original and versatile entry to beta-, gamma- and delta-aminophosphonic compounds, a challenging research area. As a direct consequence of the strategy, one of the two D-A partners (diene or dienophile) will act as vehicle for the phosphonate moiety. By contrast to its common use for the stabilization of alpha-negative charges, its implication in D-A reactions remains scarce. Indeed, the phosphonate moiety is not an efficient substituent susceptible to activate the D-A reaction; its use requires compensation by the activation of the other partner or by specific activation. Both synthetic organic and computational chemistry will furnish information to propose a fine understanding of the key D-A steps, in view to optimize the achievement of the corresponding cycloadducts. These cycloadducts will be considered as synth-/chirons for the synthesis of aminophosphonic compounds.

Individual proteins, and small collections of proteins, have been extensively studied for at least two hundred years. Today, more than 350 genomes have been completely sequenced and the proteomes of these genomes have been at least partially mapped. The inventory of protein coding genes is the first step toward understanding the cellular machinery. Recent studies have generated a comprehensive data set for the physical interactions between the proteins of Saccharomyces cerevisiae, in addition to some less extensive proteome interaction maps of higher eukaryotes. Hence, it is now becoming feasible to investigate important questions regarding the evolution of protein-protein networks. For instance, what is the evolutionary relationship between proteins that interact, directly or indirectly? Do interacting proteins co-evolve? Are they often derived from each other? In order to perform such proteome-wide investigations, a top-down view is necessary. This is provided by network (or graph) theory. The proteins of the cell may be viewed as a community of individual molecules which together form a society of proteins (nodes), a network, where the proteins have various kinds of relationships (edges) to each other. There are several different types of protein networks, for instance the two networks studied here, namely metabolic networks and protein-protein interaction networks. The metabolic network is a representation of metabolism, which is defined as the sum of the reactions that take place inside the cell. These reactions often occur through the catalytic activity of enzymes, representing the nodes, connected to each other through substrate/product edges. The indirect interactions of metabolic enzymes are clearly different in nature from the direct physical interactions, which are fundamental to most biological processes, which constitute the edges in protein-protein interaction networks. This thesis describes three investigations into the evolution of metabolic and protein-protein interaction networks. We present a comparative study of the importance of retrograde evolution, the scenario that pathways assemble backward compared to the direction of the pathway, and patchwork evolution, where enzymes evolve from a broad to narrow substrate specificity. Shifting focus toward network topology, a suggested mechanism for the evolution of biological networks, preferential attachment, is investigated in the context of metabolism. Early in the investigation of biological networks it seemed clear that the networks often display a particular, 'scale-free', topology. This topology is characterized by many nodes with few interaction partners and a few nodes (hubs) with a large number of interaction partners. While the second paper describes the evidence for preferential attachment in metabolic networks, the final paper describes the characteristics of the hubs in the physical interaction network of S. cerevisiae.

In the present thesis, the reaction mechanisms of several di-zinc hydrolases have been explored using quantum chemical modeling of the enzyme active sites. The studied enzymes are phosphotriesterase (PTE), aminopeptidase from Aeromonas proteolytica (AAP), glyoxalase II (GlxII), and alkaline phosphatase (AP). All of them contain a binuclear divalent zinc core in the active site. The density functional theory (DFT) method B3LYP functional was employed in the investigations. The potential energy surfaces (PESs) for various reaction pathways have been mapped and the involved transition states and intermediates have been characterized. The hydrolyses of different types of substrates were examined, including phosphate esters (PTE and AP) and the substrates containing carbonyl group (AAP and GlxII). The roles of zinc ions and individual active-site residues were analyzed and general features of di-zinc enzymes have been characterized. The bridging hydroxide stabilized by two zinc ions has been confirmed to be capable of the nucleophile in the hydrolysis reactions. PTE, AAP, and GlxII all employ the bridging hydroxide as the direct nucleophile. Furthermore, it is shown that either one of or both zinc ions provide the main catalytic power by stabilizing the negative charge developing during the reaction and thereby lowering the barriers. In the cases of GlxII and AP, one of zinc ions also contributes to the catalysis by stabilizing the leaving group. These features perfectly satisfy the two requisites for the hydrolysis, i.e. sufficient nucleophilicity and stabilization of charge. A competing mechanism, in which the bridging hydroxide acts as a base, was shown to have significantly higher barrier in the case of PTE. For phosphate hydrolysis reactions, it is important to characterize the nature of the transition states involved in the reactions. Associative mechanisms were observed for both PTE and AP. The former uses a step-wise associative pathway via a penta-coordinated intermediate, while the latter proceeds through a concerted associative path via penta-coordinated transition states. Finally, with PTE as a test case, systematic evaluation of the computational performance of the quantum chemical modeling approach has been performed. This assessment, coupled with other results of this thesis, provide an effective demonstration of the usefulness and powerfulness of quantum chemical active-site modeling in the exploration of enzyme reaction mechanisms and in the characterization of the transition states involved. / QC 20100715 / Quantum Chemical Modeling of Binuclear Zinc Enzymes

The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature. In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results. / QC 20100727

This thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree-Fock calculations. Density matrix purification, which is a method used to construct the density matrix for a given Fock matrix, is also discussed. The methods described are not only applicable in the Hartree-Fock case, but also in Kohn-Sham Density Functional Theory calculations, where the Coulomb and exchange matrices are parts of the Kohn-Sham matrix. Screening techniques for reducing the computational complexity of both Coulomb and exchange computations are discussed, including the fast multipole method, used for efficient computation of the Coulomb matrix. The thesis also discusses how sparsity in the matrices occurring in Hartree-Fock and Kohn-Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them. / QC 20100817

This thesis presents a theoretical study on optical properties of molecular materials. Special emphasis has been put on the influence of solvent environment, nuclear vibrations, and aggregation effects on molecular properties like linear and nonlinear polarizabilities, one- and two-photon absorption probabilities. All calculations have been performed by means of time independent and dependent quantum chemical methods at the Hartree-Fock and density functional theory levels. Solvation models that include both long range and short range interactions have been employed for calculations of optical properties of molecules in solutions. Pure vibrational and zero-point vibrationally averaged contributions have been taken into account for linear and nonlinear polarizabilities. The linear coupling model is applied to simulate vibronic profiles of optical absorption spectra. The computational strategies described in this thesis are very useful for the design of efficient molecular photonic materials. More specifically, the nonmonotonic behavior of the solvatochromic shifts and the first hyperpolarizability of para-nitroaniline (pNA) with respect to the polarity of the solvents have been theoretically confirmed for the first time. The significant contributions of the hydrogen bonding on the electronic structures of pNA are revealed. Vibrational contributions to the linear and nonlinear polarizabilities of methanol, ethanol and propanol have been calculated both at the static limit and in dynamic optical processes. The importance of vibrational contributions to certain nonlinear optical processes have been demonstrated. A series of end-capped triply branched dendritic chromophores have been studied with the result that their second order nonlinear optical properties are found strongly dependent on the mutual orientations of the three chromophores, numbers of caps and the conjugation length of the chromophores. Several possible mechanisms for the origin of the Q-band splitting of aluminum phthalocyanine chloride have been examined. Calculated vibronic one-photon absorption profiles of two molecular systems are found to be in very good agreement with the corresponding experiments, allowing to provide proper assignments for different spectral features. Furthermore, effects of vibronic coupling in the nonradiative decay processes have been considered which helps to understand the aggregation enhanced luminescence of silole molecules. The study of molecular aggregation effects on two-photon absorption cross sections of octupolar molecules has highlighted the need to use a hybrid method that combines density functional response theory and molecular dynamics simulations for the design of molecular materials. / QC 20100820

The main theme of this thesis is to study effects of different environments on geometric and electronic structures, as well as optical responses, of molecules using time-(in)dependent density functional theory. Theoretical calculations have been carried out for properties that can be measured by conventional and advanced experimental techniques, including one-photon absorption (OPA), two-photon absorption (TPA), surface-enhanced Raman scattering (SERS) and second order nonlinear optical (NLO) response. The obtained good agreement between the theory and the experiment allows to further extract useful information about inter- and intra-molecular interactions that are not accessible experimentally. By comparing calculated one-photon absorption spectra of aluminum phthalocyanine chloride (AlPcCl) and AlPcCl -water complexes with the corresponding experiments, detailed information about the interaction between water molecules and AlPcCl, and geometric changes of AlPcCl molecule has been obtained. Effects of aggregation on two-photon absorption spectra of octupolar molecules have been examined. It is shown that the formation of clusters through inter-molecular hydrogen bonding can drastically change profiles of TPA spectra. It has also demonstrated that a well designed molecular aggregate/cluster, dendrimer, can enhance the second order nonlinear optical response of the molecules. In collaboration with experimentalists, a series of end-capped triply branched dendritic chromophores have been characterized, which can lead to large enhancement of the second order NLO property when the dipoles of the three branches in the dendrimers are highly parallelized. Surface-enhanced Raman scattering has made the detection of single molecules on metal surface become possible. Chemically bonded molecule-metal systems have been extensively studied. We have shown in a joint experimental and theoretical work that stable Raman spectra of a non-bonding molecule, perylene, physically adsorbed on Ag nano-particles can also be observed at low temperature. It is found that the local enhanced field has a tendency to drive molecule toward a gap of two closely lying nano-particles. The trapped molecule can thus provide a stable Raman spectrum with high resolution when its thermal motion is reduced at low temperature. For the ever growing size of molecular complexes, there is always the need to develop new computational methods. A conceptually simple but computationally efficient method, named as central insertion scheme (CIS), is proposed that allows to calculate electronic structure of quasi-periodic system containing more than 100,000 electrons at density functional theory levels. It enables to monitor the evolution of electronic structure with respect to the size of the system. / QC 20100823

This thesis presents theoretical studies of several x-ray spectroscopies - x-ray absorption, x-ray photoelectron emission, radiative and non-radiative resonant Raman scattering spectroscopy. The main focus point is investigating the influence of nuclear dynamics on these spectra for a variety of small molecules - naphthalene, biphenyl, ethylene, the water dimer, HCl, CO. The theoretical tools used consist of the basic equations of the relevant x-ray spectroscopy. Wave packet methods are also used. The molecular parameters needed for our simulations are obtained through suitable quantum chemical calculations, based on either wave function or density functional methods. Our simulations are compared to experimental data, where available. Simulations of x-ray absorption and x-ray photoionization spectra for naphthalene and biphenyl show that the spectral shapes are heavily influenced by the joint effect of two factors -- chemical shifts and excitations of vibrational progression. Comparison between the two molecules and also comparison to a reference case -- benzene, provides useful insight into the molecular behavior under core excitation. In a further step, we consider the O1s x-ray photoelectron spectrum of the water dimer. A substantial broadening of the two bands originating from the donor and the acceptor oxygen is found. It is caused by excitations of soft intermolecular vibrational modes, associated with the hydrogen bond. Another strong influence of the nuclear dynamics is clearly seen in the resonant x-ray Raman scattering of HCl. Vibrational collapse is observed experimentally and confirmed theoretically for distinctive situations. This effect allows to eliminate completely the vibrational broadening, and hence, considerably increase the spectral resolution. We considered also the vibrational dynamics in resonant soft x-ray Raman scattering from ethylene. The importance of vibronic coupling and symmetry effects is discussed and emphasized. We obtained excellent agreement with the experimental data. We predict an interference effect in the resonant Auger scattering from fixed-in-space molecules. By exciting a molecule to a dissociative state and measuring the angular distribution of the Auger electrons in coincidence with the molecular ion, one can observe this effect. The interference pattern can be used after Fourier transformation for extracting structural data about the studied system. We have found that two-center interference leads to an enhancement of the recoil effect. Finally, it is shown that core excitation to doubly-excited dissociative Pi state is accompanied by Doppler splitting of the atomic peak in resonant Auger scattering from carbon monoxide. / QC 20100910