Density functional theory is the most commonly used computational tool to study properties of solids and molecules. Self-interaction error, that arises due to improper cancellation of the self-Hartree and the self exchange correlation energy, has long been identified as a major limitation of practical density functional approximations. We develop and test the performance of different self-interaction corrected functionals in accurately predicting a wide range of properties. This work focuses on use of the Fermi-L\"{o}wdin orbital self-interaction correction (FLOSIC) method to study neutral water complexes and interaction of ions with water clusters. The strongly constrained and appropriately normed (SCAN) density functional approximation (DFA) has been found to give the correct energy ordering of low-lying isomers of water hexamers, resolves the density anomaly between water and ice, and improves the relative lattice energy of ice polymorphs and the infrared spectra of liquid water. However, SCAN is not without its drawbacks. The binding energies of water clusters and lattice energies of ice phases are overestimated by SCAN. We find that by explicitly removing the self-interaction error, the hydrogen-bond binding energy of water clusters can be significantly improved. In particular, self-interaction correction to the SCAN functional (FLOSIC-SCAN) improves binding energies without altering the correct energetic ordering of the low-lying water hexamers. So, orbital-by-orbital removal of self-interaction error applied on top of a proper DFA can lead to an improved description of water complexes. To gain further insight into the performance of different functionals on the relative stability of water clusters, we decompose the total interaction energy into many-body components. We see that the major portion of error in SCAN comes from the two-body interaction, and the FLOSIC-SCAN improves two-body interactions over SCAN and predicts higher-order many-body interactions with about the same accuracy as SCAN. The SCAN functional gives good account of monomer deformation energy (one-body energy), PBE estimated it too low and self-interaction corrected methods FLOSIC-PBE and FLOSIC-SCAN estimated too high monomer deformation energies. Improvement in the total interaction energy by FLOSIC-PBE and FLOSIC-SCAN is happening because of error cancellation by one-body interaction energy. Aqueous solutions of ions are of particular interest due to their profound applications in environmental chemistry, solvation mechanics, the desalination process, etc. This motivated us to study ion-water systems, which include hydronium ion-water clusters, hydroxyl ion-water clusters, halide ion-water clusters, and alkali ion-water clusters. The erroneous delocalization of the extra-electron in anions obtained with DFAs is basis-set dependent. DFAs like LSDA, PBE, or SCAN can bind only a fraction of the excess electron in the complete basis set limit, implying that a moderate-sized localized basis would be a good choice for them. But, accurate description of hydrogen bonds often requires a large basis with some extra diffuse functions. So, in negatively charged hydrogen-bonded systems like deprotonated water clusters, the suitable choice of basis-set is both difficult and ambiguous. We explore this issue systematically in this work. Further, we have found that the better performance by application of FLOSIC is seen in all systems that are connected at least with one hydrogen bond and the error in the binding energy decreases with increase in the size of an ion or equivalently decreases with the length of the hydrogen bond. Moreover, within the same ion-water system, error in the binding energy decreases with increase in the size of the cluster. Non-hydrogen-bonded water-alkali clusters are not affected by the self-interaction errors. / Physics

No description available.

Resilin is a disordered elastomeric protein and can be found in specialized regions of insect cuticles. Its protein sequence, functions and dynamic mechanical properties vary substantially across the species. Resilin can operate across the frequency range from 5 Hz for locomotion to 13 kHz for sound production. To understand the functions of different exons of resilin, we synthesize recombinant resilin-like hydrogels from different exons, and investigate the water content and dynamic mechanical properties, along with estimating surface energies relevant for adhesion. The recombinant resilin-like hydrogel has 80wt% water and does not show any sign of tack even though it satisfies the Dahlquist criterion. Finally, doubly shifted dynamic moduli master curves are developed by applying the time-temperature concentration superposition principle (TTCSP), and compared to results obtained with natural resilin from locusts, dragonflies and cockroaches. The resulting master curves show that the synthetic resilin undergoes a prominent transition, though the responsible mechanism is unclear. Possible explanations for the significant increase in modulus include the formation of intramolecular hydrogen bonds, altered structural organization, or passing through a glass transition, all of which have been reported in the literature for polymeric materials. Results show that in nature, resilin operates at a much lower frequency than this glass transition frequency at room temperature. Moreover, recombinant resilins from different clones have comparable resilience with natural resilin, though the modulus is around 1.5 decades lower. Results from the clones with and without chitin binding domains (ChBD) indicate that the transition for the clone without ChBD occurs at lower frequencies than for those with the ChBD, perhaps due to the disordered nature of the clone without ChBD. Atomistic molecular modeling is applied on the repetitive motifs of resilin and different elastomeric proteins to better understand the relationship between elastomeric behavior and amino acid sequences. Results show that the motifs form a favorable bent conformation, likely enabled by glycine's lack of steric hindrance and held in place through intramolecular hydrogen bonds. During Steered Molecular Dynamic (SMD) pulling of these motifs, the hydrogen bonds break and they reform again when the peptides are released to move freely, returning to similar bent conformations. The transition seen in the master curves of recombinant resilins might be due to either these intramolecular hydrogen bonds or to glass transition behavior, though evidence indicates that the transition probably due to the glass transition. What we learned from the synthesized recombinant resilin and simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide deeper understanding of their unique properties. / Ph. D.

Ce travail a pour objectif d’augmenter la diversité des foldamères par le développement d’une nouvelle classe d’architectures abiotiques mimant le repliement des feuillets β protéiques. La stratégie employée repose sur des processus de structuration qui diffèrent de ceux observés au sein du vivant. Les deux éléments essentiels des systèmes naturels, à savoir la boucle courte et flexible d’acides aminés et les brins β liés entre eux par des liaisons hydrogènes, sont ici substitués respectivement par un coude rigide formé de noyaux aromatiques et par des oligoarylamides plans interagissant par empilement aromatique.Ces objets ont été conçus pour adopter des structures repliées caractérisables en solution par spectroscopie RMN et à l’état solide par diffraction des rayons X. Dans une première partie, l’optimisation du pseudo-coude β et de la séquence des brins, ainsi que l’exploration des premières architectures en feuillet seront étudiées à travers la conception, la synthèse et les études structurales de ces oligoamides et oligoamines aromatiques. Dans une seconde partie, le concept mis en oeuvre sera étendu à la synthèse de foldamères plus élaborés à brins courbés, ouvrant ainsi des perspectives intéressantes vers l’obtention d’architectures toujours plus complexes. / The purpose of this work is to expand foldamer diversity by developing a novel class of abiotic β-sheet-like architectures. Our strategy uses inter-strand π-π aromatic stacking between sequences of aromatic oligoamides and oligoamines to mimic the natural stabilization of β-strands, which occurs through a network of regularly spaced hydrogen bonds. These oligamide and oligoamine sequences are connected by a rigid U-shaped moiety that creates a turn and initiates strand formation.These molecules have been designed to adopt compact folded structures that can be studied in solution by NMR spectroscopy and in the solid state by X-ray crystallography. In the first part of this dissertation, we report our stepwise approach in the development of β-sheet-like aromatic amide-based foldamers: from the optimization of the design elements and the use of macrocycles, to the synthesis of multi-turn structures. In the second part, the concept will be extented to the synthesis of more elaborate curving strand β-sheet-like foldamers, opening up new perspectives for more complex architectures.

As ligações de hidrogênio (LH), fundamentais na determinação da estrutura da água, proteínas, etc., são muito importantes no reconhecimento molecular e nos mecanismos de reações enzimáticas. A determinação da energia das LHs intramoleculares em proteínas e intermoleculares entre uma proteína e o solvente água, porque fornece informações sobre a estrutura secundária, terciária e quaternária das proteínas. Um método para quantificar e qualificar as LHs foi desenvolvido utilizando critérios de distância, geométricos e energéticos a partir das trajetórias obtidas por simulações de dinâmica molecular. O método foi testado com o monômero de uma fosfolipase A2 homodimérica, sem atividade catalítica, isolada do veneno da Bothrops asper(BaspMT-II). No dímero, a análise das LHs mostrou que elas são também essenciais na manutenção da estrutura quaternária. Essa análise permitiu identificar movimentos do tipo dobradiça acompanhados da formação transitória, na interface dimérica, de LHs controladas pelo triptofano na posição 77. Esses movimentos podem estar associados à ação danosa às membranas, uma vez que podem promover a inserção da região C-terminal na membrana. Estudos prévios mostraram que o peptídeo sintético (3Y codificado pelos aminoácidos 115-129 da BaspMT-II) apresenta atividade bactericida e citolítica. Um outro peptídeo (3W), mutante de 3Y, no qual três resíduos tirosina são substituidos por triptofano, apresenta um aumento do dano às membranas e do efeito miotóxico. Os mecanismos de ação desses peptídeos e as suas estruturas foram estudados por dinâmica molecular, dicroísmo circular (DC), microscopia de fluorescência e monocamadas de Langmuir (Mlang). As adsorções dos peptídeos em monocamadas de ácido dimiristoil fosfatídico (DMPA) e dimiristoilfosfatidilcolina (DMPC) se processam por mecanismos diferentes ocasionados pelas diferentes naturezas físico-químicas dos resíduos tirosina e triptofano. A microscopia de fluorescência acoplada a Mlang de DMPA com 3W adsorvido mostra um aumento da fluidez da monocamada, enquanto que o 3Y modifica os domínios do DMPA para pequenas estruturas circulares. Foram realizadas simulações dos peptídeos 3Y e 3W em meio aquoso e nas regiões interfaciais água/n-hexano e água/bicamadas de DMPC. Os resultados confirmam os obtidos por Mlang, demonstrando que os peptídeos interagem diferentemente com as membranas por adotar conformações alternativas definidas previamente. Essas conformações, diferentes das observadas em meio aquoso, dependem da natureza da interface. As estruturas encontradas no final das simulaçoes corroboram o mecanismo proposto por Mlang, assim como as estruturas sugeridas por DC. Isso sugere que a atividade biológica reduzida do peptídeo 3Y ocorre porque os seus dois resíduos Leu se adsorvem na interface sem penetrá-la. Ao contrário de 3W, os resíduos carregados do peptídeo 3Y não estão localizados corretamente para promover uma interação suficientemente atrativa para permitir a sua inserção na membrana celular. / Hydrogen bonds (HB) are highly important in the determination of the structure of the water and proteins. They also play a important role in molecular recognition and in enzyme reaction mechanisms. The determination of protein/water intermolecular and protein intramolecular HB energies provide information with respect to the formation and stabilization of secondary, tertiary and quaternary protein structure. A method that quantifies and qualifies the properties of HB was developed using distance, geometric and energy criteria as applied to data obtained from the atomic trajectories generated by molecular dynamics simulations. The method was tested with a monomer of a catalytically inactive homodimeric phospholipase A2 from Bothrops asper(BaspMT-II) venom. HBs at dimmer interface are essential for maintaining the quaternary structure, and are highly conserved during hinge-like movements of the dimmer. HB formed by tryptophan residue at position 77 controls this movement. These motions can be associated to the membrane damaging action since they facilitate the insertion of the C-terminus into the cellular membrane. Previous studies have shown that synthetic peptide (3Y, coding the amino acids 115-129 of BaspMT-II ) presents bactericidal and cytolitic activities. A peptide variant ( 3W ), in which tyrosine residues were substituted by tryptophan residues, presents an enhanced membrane damaging activity increased miotoxic effect. The mechanism of action of the peptides and their structures were studied by molecular dynamics simulations, circular dichroism (CD), fluorescence microscopy and Langmuir monolayers (Mlang). The adsorption of the peptides on a monolayer composed of dimiristoyl phosphatidic acid (DMPA) and dimiristoylphosphatidyl choline (DMPC) occurs through different processes due to the differences in the physic-chemical nature of the tyrosine and tryptophan residues. Fluorescence microscopy together with Mlang of DMPA with adsorbed 3W indicates an increase of the membrane fluidity while small circular domains are formed with DMPA. Simulations were conducted with the 3Y and 3W peptides in aqueous media, is a water/n-hexane and water/DMPC bilayers. The results confirm the Mlang results, showing that the peptides interact differently with the membranes by adopting alternative previously defined conformations. These two conformations, both of which are different to those observed in water, are dependent of the nature of the interfaces. The final simulated configurations confirm the mechanism proposed by Mlang and the structures proposed by CD. It is suggest that the reduced biological activity of the 3Y peptide is due to the two Leu residues that only adsorb to the cellular membrane without penetrating the bilayer. In contrast to the 3W peptide, no charged residue is correctly located to promote the interaction and insertion of the 3Y peptide into the membrane.

A natureza das ligações de hidrogênio e a influência destas interações na estrutura eletrônica de complexos neutros, catiônicos, aniônicos e radicalares foi estudada utilizando-se análises geométricas, energéticas, eletrônicas e topológicas. Inicialmente, verificaram-se alterações na aromaticidade do cátion pirílio após a complexação com uma a três moléculas de água. Tais complexos foram ainda estudados em meio reacional com constante dielétrica igual a da água com o emprego do modelo PCM (Polarizable Continuum Model). Adicionalmente, os efeitos da hidroxilação na estrutura eletrônica dos cátions benzopirílio e flavílio foram considerados. Posteriormente, analisaram-se os efeitos das fortes ligações de hidrogênio na ressonância do grupo carboxila em complexos formados entre o radical hidroperoxil e os ácidos fórmico, acético e trifluoroacético. Como extensão desse trabalho, estudos envolvendo complexos obtidos com e sem restrições na otimização de geometria possibilitaram obter informações a respeito da ressonância dos grupos carboxila e carboxilato quando o fluoreto de hidrogênio interage linear ou perpendicularmente com todos os átomos do ácido fórmico e do ânion formiato. O desenvolvimento das atividades supracitadas compreendeu a análise da função de onda pelos métodos NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory) e AIM (Atoms in Molecules). As alterações em parâmetros geométricos e nas cargas atômicas foram consideradas. Uma análise energética foi realizada com o emprego do método de decomposição de energia proposto por Xantheas. As freqüências vibracionais e a intensidade das bandas do estiramento do grupo X-H, doador da ligação de hidrogênio, foram analisadas. As densidades de spin para os complexos radicalares também foram obtidas. A influência das ligações de hidrogênio e o efeito do substituinte na aromaticidade dos cátions foram verificados com o emprego dos métodos e índices NICS (Nucleus Independent Chemical Shifts), HOMA (Harmonic Oscillator Model of Aromaticity), HOSE (Harmonic Oscillator Stabilization Energy) e PDI (para-Delocalization Index). Os cálculos foram efetuados com os modelos B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd) e UB3LYP/6-311++G(3df,3pd). Ocasionalmente, outras funções de base (EPR-III e cc-pVDZ), assim como o método MP2, foram utilizados para testar a confiabilidade dos resultados obtidos. As interações intermoleculares pouco alteraram a estrutura eletrônica e a aromaticidade do cátion pirílio. Analogamente, a substituição de um átomo de hidrogênio por um grupo hidroxila em diversas posições dos cátions benzopirílio e flavílio também não provocou modificações muito significativas na estrutura eletrônica desses cátions, embora tenha se verificado uma dependência da aromaticidade com a posição da hidroxila. Por outro lado, a distorção geométrica associada às ligações de hidrogênio foram responsáveis pelo incremento ou diminuição da ressonância do grupo carboxila nos ácidos fórmico, acético, trifluoroacético e do grupo carboxilato no ânion formiato. Os efeitos dos grupos doador e sacador de elétrons na estabilização dos complexos radicalares foram evidenciados. Adicionalmente, pode-se atribuir um caráter covalente parcial em algumas ligações de hidrogênio. / The nature of hydrogen bonds and their influence on electronic structure of neutral, cationic, anionic, and radical complexes was studied by using geometric, energetic, electronic, and topological analysis. The changes in aromaticity of the pyrylium cation upon complexation with one up to three water molecules were investigated. The PCM (Polarizable Continuum Model) model was employed to study the pyrylium-water complexes in a water reaction medium. In addition, the effects of hydroxylation on electronic structure of the benzopyrylium and flavilium cations were also considered. In addition, the effects of strong hydrogen bonds on carboxyl group resonance in the complexes formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were analyzed. In extension of this work, studies including complexes, obtained with and without geometric restrictions, provided information about the resonance of the carboxyl and carboxylate groups when the hydrogen fluoride interacts, linear or perpendicularly, with all atoms of formic acid and formate anion. The analysis of the wavefunction by using NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory), and AIM (Atoms in Molecules) methods was necessary to the development of the above mentioned activities. The changes in geometric parameters and atomic charges were also considered. An energetic analysis of complexes was done with the energy decomposition method proposed by Xantheas. The vibrational frequencies and the intensity of the X-H (hydrogen bond donor group) stretching bands were studied. The spin densities for the radical complexes were also obtained. The Nucleus Independent Chemical Shifts (NICS), Harmonic Oscillator Model of Aromaticity (HOMA), HOSE (Harmonic Oscillator Stabilization Energy), and PDI (para-Delocalization Index) aromaticity criteria were employed to verify the hydrogen bond influence and the effect of hydroxylation in the aromaticity of the cations. The calculations were carried out by using B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd), and UB3LYP/6-311++G(3df,3pd) models. Occasionally, other basis set (EPR-III and cc-pVDZ), as well as the MP2 method, were applied to test the accuracy of the results. The intermolecular interactions lead to small alterations in the electronic structure and aromaticity of pyrylium cation. Similarly, the substitution at different positions of the benzopyrylium and flavilium cations by a hydroxyl group does not cause significant changes in the electronic structure of these cations. However, a dependence of the hydroxyl group position on aromaticity was observed. On the other hand, for formic, acetic, trifluoroacetic acids, as well as for the formate anion, the resonance of the carboxyl and carboxylate groups is affected not only by the geometric distortions but also by the hydrogen bonds. The effects of the electron-donating and electron-withdrawing groups in the stabilization of radical complexes were characterized. Furthermore, a partial covalent character can be attributed to some hydrogen bonds.

Die Struktur von DNS Molekülen und ihre Wechselwirkung mit Wasser werden seit langer Zeit heiß diskutiert. In der vorliegenden Arbeit wird nichtlineare Spektroskopie zur Untersuchung dieser Systeme angewendet. Oligomere, die aus 23 alternierenden Adenin-Thymin-Basenpaaren bestehen und eine Doppelhelix bilden, wurden mit Hilfe von 2D IR Spektroskopie für verschiedene Hydratisierungsgrade untersucht. Für DNS-Filme bei 0% relativer Feuchte (r.F.) erlauben die transienten Spektren eine Unterscheidung der NH Streckschwingung von Thymin ((NH)), der symmetrischen und asymmetrischen NH2 Streckschwingung von Adenin (s(NH2) and a(NH2)) sowie die Bestimmung der jeweiligen Linienprofile. Die Spektren zeigen eine homogene Verbreiterung für die (NHT) wohingegen die s(NH2) and a(NH2) eine ausgeprägte und zeitunabhängige inhomogene Verbreiterung zeigen, welche auf Unordnungen in der DNS-Struktur hinweisen. Außerdem kann Energietransfer von der a(NH2) zur (NH) beobachtet werden. Bei Erhöhung der r.F. hat die erhöhte Anzahl von Wassermolekülen nur einen geringen Einfluss auf die Positionen und Linienprofile der NH Streckschwingungen. Dadurch wird nahegelegt, dass die spektrale Dynamik vom DNS Molekül selbst und nicht vom umgebenen Wasser bestimmt ist. Im Gegensatz dazu zeigt die OH Streckmode der Wasserhülle um die DNS spektrale Diffusion auf einer 500 fs Zeitskala. Guanosin-Cytidin(GC)-Basenpaare wurden in Chloroformlösung untersucht, um die Wechselwirkung zwischen Basenpaaren zu verstehen. Dabei wurden die NH Schwingungen in einer local mode Darstellung betrachtet, die zwei freie NH Gruppen von G und C und drei wasserstoffverbrückte NH Gruppen beeinhaltet. Die Kopplungen und Relaxationsdynamik der NH Streckanregungen wurden mit Femtosekunden-Pump-Probe und 2D IR Experimenten studiert. Die Ergebnisse zeigen eine Verringerung der Lebensdauer mit der Bildung von Wasserstoffbrücken sowie Energietransfer zwischen zwei wasserstoffverbrückten NH Streckschwingungen. / The structure of DNA molecule and the interactions with its surrounding water is a hot topic for long time. In this thesis, we employ the nonlinear spectroscopy, including femtosecond pump-probe and two-dimensional infrared (2D IR) experiment, to study the vibrational dynamics of the systems. Double-stranded DNA short oligomers containing 23 alternating adenine-thymine base pairs were studied at different hydration levels by femtosecond 2D IR spectroscopy. For a DNA film at 0% relative humidity, the transient spectra enable a separation of the NH stretching mode of thymine from the symmetric and asymmetric NH2 stretching modes of adenine and determine the individual line shapes. For the NH stretch of thymine, the spectra demonstrate an essential homogeneous broadening, whereas for the symmetric and asymmetric NH2 stretches a pronounced and time-independent inhomogeneous broadening suggests a disorder in DNA structure. An energy transfer from the asymmetric NH2 stretch of adenine to the NH stretch of thymine is also observed. When the relative humidity increases, the increased water molecules have limited influence on the positions and line shapes of NH stretching frequencies, suggesting the spectral dynamics governed by DNA rather than water fluctuations. In contrast, the OH stretching mode of water shell around hydrated DNA undergoes a spectral diffusion on a 500 fs time scale, which is slower than the neat water. The guanosine-cytidine (GC) base pairs in chloroform solution were investigated to understand the interactions within base pairs. A local mode representationof NH stretching mode is adopted, consisting two free NH groups of G and C and three hydrogen bonded NH groups. The coupling and relaxation dynamics of the NH stretching excitations are studied by femtosecond pump-probe and 2D IR experiments. The results demonstrate a lifetime shortening upon the formation of hydrogen bonds, and an energy transfer between two hydrogen-bonded NH stretches.

Neste trabalho filmes finos de silício amorfo hidrogenado (a-Si:H) foram depositados no reator magnetron sputtering do laboratório de sistemas integráveis (LSI), a temperaturas menores que 100 °C, pela introdução do gás hidrogênio junto com o de argônio para pulverização de um alvo de silício policristalino. As condições de deposição investigadas estão compreendidas em pressões totais de 5 e 10 mTorr para as quais a potência de RF variou de 150 a 300 W, para a menor pressão, e de 200 a 300 W, para a maior pressão, sendo que para cada condição de potência a concentração de hidrogênio nos gases de descarga variou de pelo menos 0 % a no máximo 60 %. Como os substratos utilizados foram carbono vítreo, lâminas oxidadas de silício e placas de vidro para microscópio óptico os filmes depositados sobre o carbono foram caracterizados por RBS, os depositados sobre as lâminas oxidadas de silício por FTIR e medidas IV e os depositados sobre o vidro por espectroscopia de absorção óptica na região do ultravioleta-visível. A caracterização RBS forneceu informações tanto sobre o tipo e quantidade de impurezas eventualmente incorporadas durante a deposição como sobre a densidade superficial do silício que permitiu a obtenção da densidade volumétrica pela utilização dos parâmetros de espessura obtidos pela técnica de perfilometria. Através da análise dos espectros FTIR o hidrogênio incorporado pode ser quantificado na forma de mono e polihidretos de silício. As medidas IV foram realizadas através de contatos de alumínio, evaporados sobre os filmes, para a obtenção tanto da condutividade de escuro como da fotocondutividade e a análise dos espectros de absorção óptica dos filmes permitiu a obtenção tanto dos valores de energia do gap óptico, pelo método Tauc, como do parâmetro B que é inversamente proporcional à largura da cauda das bandas de valência e de condução que por sua vez aumentam com o aumento da densidade de defeitos dos filmes. Desta forma os filmes que apresentaram as maiores fotosensibilidades (razão entre a fotocondutividade e a condutividade de escuro), consideradas para a escolha dos melhores resultados, foram os depositados a 10 mTorr uma vez que eles apresentam uma maior concentração tanto de ligações SiH 2 como de SiH 3 e menores concentrações totais de hidrogênio incorporado ao filme que os filmes depositados a 5 mTorr o que acabou contribuindo para a diminuição da densidades de estados localizados da banda de mobilidade, provavelmente devido a nucleação de cristais, o que ocorre tipicamente para filmes depositados por sistemas magnetron sputtering a grandes pressões totais e grandes pressões parciais de hidrogênio, estando, desta forma, tanto as ligações SiH 2 como SiH 3 situadas nos contornos de grão. Assim os filmes depositados a 10 mTorr apresentam concentrações quase nula de ligações SiH, mas as maiores fotosensibilidades. / In this work thin films of hydrogenated amorphous silicon (a-Si:H) were deposited in the magnetron sputtering reactor of the Laboratório de Sistemas Integráveis (LSI), at temperatures lower than 100 °C, by the introduction of hydrogen and argon gasses for the sputtering of a policrystalline silicon target. The deposition conditions investigated are total pressures of 5 and 10 mTorr for which the RF power varied from 150 to 300 W, for the lowest pressure, and from 200 to 300 W, for the highest pressure. For each power condition the hydrogen concentration in the discharge gases ranged from 0 % to maximum 60 %. The substrates used were glassy carbon, for RBS characterization, oxidized silicon wafers for FTIR and IV measurements and glass plate for optical microscope and visible-ultraviolet spectroscopy absorption. The RBS characterization provided information about both the type and quantity of impurity incorporated during the deposition and the amorphous silicon superficial density that allowed obtaining the volumetric density by the utilization of the thickness parameter obtained by the profilometry technique. Through the analyses of the FTIR spectra the hydrogen incorporated could be quantified in the form of mono and poli silicon hydrides. The IV measurements were performed, through aluminum contacts evaporated on the films, to obtain the dark and photoconductivity and the films ultraviolet-visible absorption spectra. Through ultraviolet-visible analysis was possible to obtain both the optical energy gap values, by the Tauc method, and the B parameter, which is inversely proportional to the valence and conduction tail width. The B parameter increases with the defect density of the films. Thus, the films that showed the biggest photosensitivity (relation between the photoconductivity and dark conductivity) were deposited at 10 mTorr. These films showed a higher concentration of both SiH 2 and SiH 3 bonds but a lower concentration of total hydrogen incorporated, which contributed to the decrease of the density of states in the mobility band, probably due to the nucleation of crystals typical of films deposited by the magnetron sputtering system at high pressure and high hydrogen concentration. In this way the SiH 2 and SiH 3 would be in the grain boundary. So the films deposited at 10 mTorr showed almost null concentration of SiH bonds, but the highest photosensitivities.

Neste trabalho filmes finos de silício amorfo hidrogenado (a-Si:H) foram depositados no reator magnetron sputtering do laboratório de sistemas integráveis (LSI), a temperaturas menores que 100 °C, pela introdução do gás hidrogênio junto com o de argônio para pulverização de um alvo de silício policristalino. As condições de deposição investigadas estão compreendidas em pressões totais de 5 e 10 mTorr para as quais a potência de RF variou de 150 a 300 W, para a menor pressão, e de 200 a 300 W, para a maior pressão, sendo que para cada condição de potência a concentração de hidrogênio nos gases de descarga variou de pelo menos 0 % a no máximo 60 %. Como os substratos utilizados foram carbono vítreo, lâminas oxidadas de silício e placas de vidro para microscópio óptico os filmes depositados sobre o carbono foram caracterizados por RBS, os depositados sobre as lâminas oxidadas de silício por FTIR e medidas IV e os depositados sobre o vidro por espectroscopia de absorção óptica na região do ultravioleta-visível. A caracterização RBS forneceu informações tanto sobre o tipo e quantidade de impurezas eventualmente incorporadas durante a deposição como sobre a densidade superficial do silício que permitiu a obtenção da densidade volumétrica pela utilização dos parâmetros de espessura obtidos pela técnica de perfilometria. Através da análise dos espectros FTIR o hidrogênio incorporado pode ser quantificado na forma de mono e polihidretos de silício. As medidas IV foram realizadas através de contatos de alumínio, evaporados sobre os filmes, para a obtenção tanto da condutividade de escuro como da fotocondutividade e a análise dos espectros de absorção óptica dos filmes permitiu a obtenção tanto dos valores de energia do gap óptico, pelo método Tauc, como do parâmetro B que é inversamente proporcional à largura da cauda das bandas de valência e de condução que por sua vez aumentam com o aumento da densidade de defeitos dos filmes. Desta forma os filmes que apresentaram as maiores fotosensibilidades (razão entre a fotocondutividade e a condutividade de escuro), consideradas para a escolha dos melhores resultados, foram os depositados a 10 mTorr uma vez que eles apresentam uma maior concentração tanto de ligações SiH 2 como de SiH 3 e menores concentrações totais de hidrogênio incorporado ao filme que os filmes depositados a 5 mTorr o que acabou contribuindo para a diminuição da densidades de estados localizados da banda de mobilidade, provavelmente devido a nucleação de cristais, o que ocorre tipicamente para filmes depositados por sistemas magnetron sputtering a grandes pressões totais e grandes pressões parciais de hidrogênio, estando, desta forma, tanto as ligações SiH 2 como SiH 3 situadas nos contornos de grão. Assim os filmes depositados a 10 mTorr apresentam concentrações quase nula de ligações SiH, mas as maiores fotosensibilidades. / In this work thin films of hydrogenated amorphous silicon (a-Si:H) were deposited in the magnetron sputtering reactor of the Laboratório de Sistemas Integráveis (LSI), at temperatures lower than 100 °C, by the introduction of hydrogen and argon gasses for the sputtering of a policrystalline silicon target. The deposition conditions investigated are total pressures of 5 and 10 mTorr for which the RF power varied from 150 to 300 W, for the lowest pressure, and from 200 to 300 W, for the highest pressure. For each power condition the hydrogen concentration in the discharge gases ranged from 0 % to maximum 60 %. The substrates used were glassy carbon, for RBS characterization, oxidized silicon wafers for FTIR and IV measurements and glass plate for optical microscope and visible-ultraviolet spectroscopy absorption. The RBS characterization provided information about both the type and quantity of impurity incorporated during the deposition and the amorphous silicon superficial density that allowed obtaining the volumetric density by the utilization of the thickness parameter obtained by the profilometry technique. Through the analyses of the FTIR spectra the hydrogen incorporated could be quantified in the form of mono and poli silicon hydrides. The IV measurements were performed, through aluminum contacts evaporated on the films, to obtain the dark and photoconductivity and the films ultraviolet-visible absorption spectra. Through ultraviolet-visible analysis was possible to obtain both the optical energy gap values, by the Tauc method, and the B parameter, which is inversely proportional to the valence and conduction tail width. The B parameter increases with the defect density of the films. Thus, the films that showed the biggest photosensitivity (relation between the photoconductivity and dark conductivity) were deposited at 10 mTorr. These films showed a higher concentration of both SiH 2 and SiH 3 bonds but a lower concentration of total hydrogen incorporated, which contributed to the decrease of the density of states in the mobility band, probably due to the nucleation of crystals typical of films deposited by the magnetron sputtering system at high pressure and high hydrogen concentration. In this way the SiH 2 and SiH 3 would be in the grain boundary. So the films deposited at 10 mTorr showed almost null concentration of SiH bonds, but the highest photosensitivities.

Biological processes are so complicated that to understand the mechanisms underlying the functioning of biomolecules it is inevitable to study them from various perspectives and with a wide range of tools. Understanding the function at the molecular level obviously requires the knowledge of the three dimensional structure of the biomolecules. Experimentally this can be obtained by techniques such as X‐ray crystallography and NMR studies. Computational biology has also played an important role in elucidating the structure function relationship in biomolecules. Computationally one can obtain the temporal as well as ensemble behavior of biomolecules at atomic level under conditions that are experimentally not accessible. Molecular dynamics(MD) study is a technique that can be used to obtain information of the dynamic behavior of the biomolecules. Dynamics of large systems like proteins can be investigated by classical force fields. However, the changes at the level of covalent bond involve the reorganization of electron density distribution which can be addressed only at Quantum mechanical level. In the present thesis, some of the biological systems have been characterized both at the classical and quantum mechanical level. The systems investigated by MD simulations and the insights brought from these studies are presented in Chapters 3 and 4. The unusual bonds such as pyrophosphate linkage in ATP and short strong hydrogen bonds in proteins, investigated through high level quantum chemical methods, are presented in Chapters 5, 6 and 7. Part of this thesis is aimed to address some important issues related to the dynamics of Tryptophanyl tRNA synthetase (TrpRS) which belongs to classic of aminoacyl‐tRNA synthetases (aaRS). aaRSs are extremely important class of enzymes involved in the translation of genetic code. These enzymes catalyze the aminoacylation of tRNAs to relate the cognate amino acids to the anticodon trinucleotide sequences. aaRSs are modular enzymes with distinct domains on which extensive kinetic and mutational experiments as well as structural analyses have been carried out, highlighting the role of inter‐domain communication (Alexander and Schimmel, 2001). The overall architecture of tRNA synthetases consists of primarily two domains. The active site domain is responsible for the activation of an amino acid with ATP in synthesizing an enzyme‐bound aminoacyl‐adenylate, and transfer of the aminoacyl‐adenylate intermediate to the 3’end of tRNA. The second domain is responsible for selection and binding of the cognate tRNA. aaRSs are allosteric proteins in which the binding of tRNA at the anticodon domain influences the activity at the catalytic region. These two binding sites are separated by a large distance. One of the aims of this thesis is to characterize such long distance communication (allosteric communication) at atomic level in Tryptophanyl tRNA synthetase. This is achieved by generating ensembles of conformations by MD simulations and analyzing the trajectories by novel graph theoretic approach. Graph and network based approaches are well established in the field of protein structure analysis for analyzing protein structure, stability and function (Kannan and Vishveshwara, 1999; Brinda and Vishveshwara, 2005). The parameters such as clusters, hubs and shortest paths provide valuable information on the structure and dynamics of the proteins. In this thesis, network parameters are used for the analysis of molecular dynamics MD) simulation data, to represent the global dynamic behavior of protein in a more elegant way. MD simulations are performed on some available (and modeled) structures of TrpRS bound to a variety of ligands, and the protein structure networks( PSN) of non‐covalent interactions are characterized in dynamical equilibrium. The ligand induced conformational changes are investigated through structure networks. These networks are used to understand the mode of communication between the anticodon domain and the active site. The interface dynamics is crucial for the function of TrpRS (since it is a functional dimer) and it is investigated through interface clusters. The matter embodied in the thesis is presented as 9 chapters. Chapter 1 lays the suitable background and foundation for the study, surveying relevant literature from different fields .Chapter 2 describes in detail the various materials, methods and techniques employed in the different analyses and studies presented in this thesis. A brief description of well‐known methods of molecular dynamics simulations, essential dynamics calculations, cross correlation maps, conformational clustering etc.is presented. The methods for constructing protein structure graphs and networks, developed in our lab, are described in detail. The use of network parameters for the analysis of MD simulation data to address the problem of communication between the two distal sites is also presented. Some descriptions of the ab initio quantum mechanical methods, which are used to investigate the unusual bonds in biomolecules, are also presented in this chapter. Chapter 3 is devoted in discussing the results from several normal as well as high temperature MD simulations of ligand‐free and ligand bound Bacillus stearothermophilus Tryptophanyl‐tRNA synthetase (bsTrpRS). The essential modes of the protein in the presence of different ligands are captured by essential dynamics calculations. Different conformations of the protein associated with the catalysis process of TrpRS, as captured through experiments, are discussed in the context of conformational sampling. High temperature simulations are carried out to explore the larger conformational space. Chapter 4 is focused on the results obtained from the MD simulation of human Tryptophanyl‐tRNA synthetase (hTrpRS). The structure of human TrpRS bound to the activated ligand (TrpAMP) and the cognate tRNA(tRNATRP) is modeled since no structure in the presence of both TrpAMP and tRNATRP is available. MD simulations on these modeled as well as other complexes of hTrpRS are performed to capture the dynamical process of ligand induced conformational changes (Hansiaetal., communicated). Both the local and the global changes in the protein conformation from the protein structure network (PSN) of MD snapshots are analyzed. Several important information such as the ligand induced correlation between different residues of the protein, asymmetric binding of the ligands to the two subunits of the protein, and the path of communication between the anticodon region and the aminoacylation site are obtained. Also, the role of the dimmer interface, from a dynamic perspective, is obtained for the first time. The interface dynamics which stabilize different quaternary structures of lectins (with high sequence and structure similarity) were investigated in a collaborative work (Hansiaetal.,2007). The lectin peanut agglutinin (PNA) is a tetramer with three different types of interfaces. The interface dynamics of this protein in the presence and in the absence of metal ions was investigated and the paper reporting the results from this study is included as appendix in this thesis. Chapter 5 deals with high level ab initio quantum chemical calculations on tri‐ and diphosphate fragments of adenosine triphosphate (ATP). Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of calculations (Hansiaetal., 2006a). The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the‘‘highenergy’’character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results aid in the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. Hydrogen bonding is fundamental in understanding the structure and properties of molecules of biological interest including proteins. A recent analysis carried out in our lab showed that a significant number of short hydrogen bonds (SHB) are present in proteins (Rajagopal and Vishveshwara, 2005). Chapters 6 and 7 elucidate the results obtained from ab initio quantum chemical calculations on some of these SHBs to get aquantitative estimation of their geometry and strength. In chapter 6, asystematic analysis of the geometries and the energetics of possible SHB systems, which are frequently encountered in proteins, are presented at different levels of theory (HF,DFTandMP2). It is found that the SHBs involving both charged residues in the proteins are intrinsic in nature. However, two neutral residues form a SHB in the protein crystal structures either due to geometric constraints or due to the environment of these residues. This analysis enables one to distinguish SHBs which are formed because of geometric constraints from those which are formed because of the inherent property of the chemical groups involved in the hydrogen bonding. These results are useful in refining protein structures determined by crystallographic or NMR methods. In addition, sulfur atom of methionine and cysteinein proteins also participate in SHBs, which are not so well characterized. Chapter 7 presents the similar analysis carried out on short hydrogen bonds in proteins involving sulfur atom. A detailed analysis of SHBs of sulfur containing groups in a data set of proteins has been carried out. Some of the residue pairs from this analysis were considered for ab initio calculations. However, the optimization of these examples resulted in breaking of the hydrogen bonds involving sulfur atoms and formation of new hydrogen bonds with oxygen and/or nitrogen atoms. Hence model systems, which mimic the real examples, were designed to carry out ab initio studies and to investigate the short hydrogen bonds involving sulfur atoms. Another study on the protein‐water interaction, which does not fall under the realm of the main objective of the thesis, is discussed in Chapter 8. Protein–water interaction is crucial for accomplishing many biological functions of proteins. In the recent past, natural probe tryptophan, located at the protein surfaces, has been extensively investigated using femtosecond spectroscopy experiments to understand salvation dynamics (Peonetal.,2002). In this chapter a method is described to follow up the molecular events of the protein–water interactions in detail. Tryptophan–water interaction in the protein Monellin is investigated in order to get the atomic level insights into the hydration dynamics, by carrying out MD simulations on Monellin (Hansiaetal.,2006b). The results are compared with those obtained from femtosecond resolved fluorescence spectroscopy. The time constants of the survival correlation function match well with the reported experimental values.This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general. The last chapter (Chapter9) summarizes the results obtained from various studies and discusses the future directions. First part of this thesis aims to present the analysis by carrying out MD simulations on monomeric and dimeric TrpRS protein in order to understand the two steps of the aminoacylation reaction: activation of the aminoacid Trp in the first step and the transfer of the activated amino acid in the next step. In the second part, quantitative estimation of the geometry and the strength of pyrophosphate bond and short hydrogen bonds in proteins are reported in detail by subjecting the systems to high levels of quantum mechanical calculations(QM). The use of ab initio QM/MM calculations by combining the quantum mechanics(QM) with the molecular mechanics(MM) in order to study the enzymatic reactions is discussed as the future