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In this thesis, theoretical and computer simulation studies of vibrational phase relaxation in various molecular liquids are presented. That includes liquid nitrogen, both along the coexistence line and the critical isochore, binary liquid mixture and liquid water. The focus of the thesis is to understand the dependence of the vibrational relaxation on the density, temperature, composition and the role of different interactions among the molecules. The density fluctuation of the solute particles in a solvent is studied systematically, where the computer simulation results are compared with the mode coupling theory (MCT). The classical density functional theory (DFT) is used to study the vibrational relaxation dynamics in molecular liquids with an aim to understand the heterogeneous nature of the dynamics commonly observed in experiments. Chapter 1 contains a brief overview of the earlier relevant theories, their successes and shortcomings in the light of the problems discussed in this thesis. This chapter discusses mainly the basic features of the vibrational dynamics of molecular liquids and portrays some of the theoretical frameworks and formalisms which are widely recognized to have contributed to our present understanding. Vibrational dephasing of nitrogen molecules is known to show highly interesting anomalies near its gas–liquid critical point. In Chapter 2, we present the results of extensive computer simulation studies and theoretical analysis of the vibrational phase relaxation of nitrogen molecules both along the critical isochore and the gas–liquid coexistence line. The simulation includes the different contributions (density (ρ), vibration–rotation (VR), and resonant transfer (Rs)) and their cross–correlations. Following Everitt and Skinner, we have included the vibrational coordinate (q) dependence of the inter–atomic potential, which is found to have an important contribution. The simulated results are in good agreement with the experiments. The linewidth (directly proportional to the rate of the vibrational phase relaxation) is found to have a lambda shaped temperature dependence near the critical point. As observed in the experimental studies, the calculated lineshape becomes Gaussian–like as the critical temperature (Tc) is approached while being Lorentzian–like at the temperatures away from Tc. Both the present simulation and a mode coupling theory (MCT) analysis show that the slow decay of the enhanced density fluctuations near the critical point (CP), probed at the sub–picosecond timescales by the vibrational frequency modulation, and an enhanced vibration–rotation coupling, are the main causes of the observed anomalies. Dephasing time (тv) and the root mean square frequency fluctuation (Δ) in the supercritical region are calculated. The principal results are: 1. a crossover from a Lorentzian–like to a Gaussian–like lineshape is observed as the critical point is approached along the critical isochore, 2. the root mean square frequency fluctuation shows a non–monotonic dependence on the temperature along the critical isochore, 3. the temperature dependent linewidth shows a divergence–like (λ–shaped) behavior along the coexistence line and the critical isochore. It is found that the linewidth calculated from the time integral of the normal coordinate time correlation function (CQ(t)) is in good agreement with the known experimental results. The origin of the anomalous temperature dependence of linewidth can be traced to simultaneous effects of several factors, (i) the enhancement of the negative cross–correlations of ρ with VR and Rs and (ii) the large density fluctuations as the critical point (CP) is approached. Due to the negative cross–correlations of ρ with VR and Rs the total decay becomes faster (correlation times are in the femtosecond scale). The reason for the negative cross–correlation between ρ and VR is explored in detail. A mode coupling theory (MCT) analysis shows a slow decay of the enhanced density fluctuations near the critical point. The MCT analysis demonstrates that the large enhancement of VR–coupling near CP may arise from a non–Gaussian behavior of the equilibrium density fluctuations. This enters through a non–zero value of the triplet direct correlation function. Many of the complex systems found in nature and used routinely in industry are multi–component systems. In particular, binary mixtures are highly non–ideal and play an important role in the industry. The dynamic properties are strongly influenced by composition fluctuations which are absent in the one component liquids. In Chapter 3, isothermal–isobaric (NPT) ensemble molecular dynamics simulation studies of vibrational phase relaxation (VPR) in a model system are presented. The model considers strong attractive interaction between the dissimilar species to prevent phase separation. The model reproduces the experimentally observed non–monotonic, nearly symmetric, composition dependence of the dephasing rate. In addition, several other experimentally observed features, such as the maximum of the frequency modulation correlation time (т c) at a mole fraction near 0.5 and the maximum rate enhancement by a factor of about 3 above the pure component value, are also reproduced. The product of the mean square frequency modulation ((Δω2(0))) with тc indicates that the present model is in the intermediate regime of the inhomogeneous broadening. The non–monotonic composition (χ) dependence of тv is found to be primarily due to the non–monotonic χ dependence of тc, rather than due to a similar dependence in the amplitude of (Δω2(0)). The probability distribution of Δω shows a markedly non–Gaussian behavior at intermediate composition (χ - 0.5). We have also calculated the composition dependence of the viscosity (η∗) in order to explore the correlation between the viscosity with that of тv and тc. It is found that both the correlation times essentially follow the nature of the composition dependence of the viscosity. A mode coupling theory (MCT) analysis is presented to include the effects of the composition fluctuations in binary mixture. Water is an interesting and attractive object for research, not only because of its great importance in life processes but also due to its unusual and intriguing properties. Most of the anomalous properties of water are related to the presence of a three–dimensional network of hydrogen bonds, which is constantly changing at ultrafast, sub–picosecond timescales. Vibrational spectroscopy provides the means to study the dynamics of processes involving only certain chemical bonds. The dynamics of hydrogen bonding can be probed via its reflection on molecular vibrations, e.g., the stretching vibrational mode of the O–H bond. Recently developed femtosecond infrared vibrational spectroscopy has proved to be valuable to study water dynamics because of its unique temporal resolution. Recent studies have shown that the vibrational relaxation of the O–H stretch of HDO occurs at an extremely fast timescale with time constant being less than 100 femtosecond. Here, in Chapter 4, we investigate the origin of this ultrafast vibrational dephasing using computer simulation and appropriate theoretical analysis. In addition to the usual fast vibrational dynamics due to the hydrogen bonding excitations, we find two additional reasons: (a) the large amplitude of angular jumps of the water molecules (with 30–40 fs time intervals) provide large contribution to the mean square vibrational frequency and (b) the projected force along the O–H bond due to the solvent molecules, on the oxygen (FO(t)) and hydrogen (FH (t)) atoms of the O–H bond exhibit a large negative cross–correlation (NCC) between FO(t) and FH (t). This NCC is shown to be partly responsible for a weak, non–Arrhenius temperature dependence of the relaxation rate. In the concluding note, Chapter 5 starts with a brief summary of the outcome of this thesis and ends up with suggestions of a few relevant problems that may prove worthwhile to be addressed in the future.

Over the last century, despite enormous advancements in biomedical research and the development of sophisticated analytical instruments many diseases continue to be a burden on humankind particularly on the aged. This is because of a lack of complete understanding of the pathogenesis and specific therapies. Due to the complexity involved, we need to explore all facets of diagnosis and therapies. Therefore, there is a requirement for different strategies to combat these diseases. A quick diagnosis is the primary step towards improving treatment and increasing the chance of survival. To realize this goal we entail to monitor multiple biomarkers which will also help us to understand the progression of disease. Mid-Infrared (MIR) and Raman spectroscopic techniques are well established analytical methods to understand the molecular structure and chemical composition of heterogeneous systems. These techniques are rapid, non-destructive and offer multiple component analysis (global/multiplex) in a single measurement without any labels. Importantly, biological materials like proteins, carbohydrates, lipids, nucleic acids etc. have unique structures and therefore we can obtain unique spectral fingerprints of these molecules in different physiological and pathological conditions. This will provide a potential route to obtain diagnostic markers for diseases. Also, to improve the ability to diagnose and treat human diseases much more efficiently, understanding the mechanisms involved in the progression of disease is necessary. It would be time consuming and often unethical to perform these studies directly on humans. Therefore, there is a need for model organisms to explore the complexity of various diseases. A model organism is an animal, plant or microbe that is being studied to understand a range of biological phenomena. They should meet certain criteria such as short life cycles, easy to breed and maintain in large numbers under laboratory conditions, and the data generated through use of the model should be applicable to other higher organisms like humans. The microbial system, mouse, rat, Drosophila (fruitfly), C Elegans (nematode worm) and zebrafish are being used extensively for this purpose. The most adaptable organisms to study diseases in humans are the mice as they share almost 99% of their genes with humans. Mice are similar to humans in most physiological and pathological features such as nervous, cardiovascular, immune, liver etc. In addition to mice, Drosophila melanogaster (fruitfly) has been used for years as an attractive model organism to understand the mechanisms of underlying human diseases. This is because 75% of human disease genes have counterparts in Drosophila and it meets the above mentioned criteria to be a model organism. It also plays an important role for studying genetics and development biology. The average life span of Drosophila is 60-80 days; therefore it is a suitable model to study age related diseases. In the present thesis, the ability to probe low-micrometer domains using Raman and Fourier Transform Infrared (FTIR) microspectroscopy was utilized to monitor the chemical changes during various biomedical conditions using model systems. Chapter 1 of the thesis discusses about the origin of Raman and FTIR microspectroscopy along with instrumentation and applications. Various data analysis methods (both univariate & multivariate) and the validation criterion are described in chapter 2. Depending on the objective of the study and based on the technique (Raman or FTIR) used, one (or more) of these methods can be applied for effective interpretation of the data. Further, the thesis includes four different investigations; a) the FTIR spectroscopic study of hepatotoxicity due to acetaminophen using mice as model, b) the Raman spectroscopic studies of muscle-related disorders using Drosophila as a model, c) Vibrational spectroscopic study of septic shock using mice as model, d) Surface Enhanced Raman Spectroscopy (SERS) study of serum components using Lab-on-a-chip (LOC). The first part comprises mainly the FTIR microspectroscopy study of hepatotoxicity in mice post oral dosing of acetaminophen (paracetamol), which is extensively used worldwide as an analgesic and antipyretic drug (chapter 3). The infrared spectra of acetaminophen treated livers in BALB/c mice show a decrease in glycogen and an increase in amounts of cholesteryl esters and DNA. Importantly, analysis of sera identified the lowering of glycogen and increase in DNA and chlolesteryl esters earlier than the increase in alanine aminotransferase, which is routinely used to diagnose liver damage. Similar changes are also observed in C57BL/6 and Nos2−/− mice. Revert experiments using an antidote (L-methionine) demonstrate that depletion in glycogen and increase in DNA are abrogated with pre-treatment, but not post-treatment, with L-methionine. In the second study Raman spectroscopy is applied to discriminate between various muscle defects in Drosophila, since it can provide a unique molecular fingerprint of tissues on the basis of their biochemical composition (chapter 4). Raman spectra were collected from Indirect Flight Muscles (IFM) of mutants upheld1 (up1), heldup2 (hdp2), Myosin heavy chain7 (Mhc7), Actin88FKM88 (Act88FKM88), upheld101 (up101) and Canton-S (CS) for both 2 and 12-days old flies. The difference spectra (mutant minus CS) of all mutants have shown an increase in nucleic acids (DNA/RNA) content along with an increase in β-sheet and/or random coil content at the expense of α-helix. Interestingly, 12th day sample of up1 & Act88FKM88 exhibit significantly higher levels of glycogen and carotenoids than CS. A Principal Components based Linear Discriminant Analysis (PC-LDA) classification model was developed, which classifies the mutants according to their pathophysiology and yielded overall accuracy (OA) of 97% and 93% for 2 and 12-days old flies respectively. up1 & Act88FKM88 (nemaline myopathy phenotypes) form a group which is clearly separated in a Linear Discriminant (LD) Plane from up101 & hdp2 (cardiomyopathy phenotypes). In the third part we investigated septic shock, a life threatening condition associated with multiple organ dysfunctions, in mice (chapter 5). Salmonella typhimurium were given to BALB/c and 129/SvJ mice via the intraperitoneal route to induce infection. Liver, spleen and sera samples were studied using FTIR microspectroscopy. The infrared spectra of liver, spleen and serum samples in BALB/c (Nramp1-deficient) mice show significant spectral changes as early as 1 hour post infection but spleen shows changes only after 6 hour. Interestingly, 129/SvJ (Nramp1-sufficient) mice were resistant to sepsis and show significant spectral changes only at 12 hour post infection. This study demonstrates that suppression of Nramp-1, a renowned gene known to control susceptibility to infections by intracellular bacteria can be an effective cure for sepsis. The final study presented in this thesis demonstrates the use and benefits of lab-on-a-chip (LOC) devices in surface enhanced Raman spectroscopy (SERS) which is used to enhance the weak Raman signals (chapter 6). Most of the diseases have related proteins or analytes present in serum although in early stages their concentration in blood are low. The idea is to detect at low concentration using SERS the serum components which are related to progression of disease. Here, we have compared the effect of different aggregating agents on silver colloids and the resulting enhancement in Raman signals for tryptophan and Bovine Serum Albumin (BSA). Reproducibility issues, the key concern of static phase SERS, can be overcome by performing SERS spectroscopic measurements in automated flow cells. Further, pyridine and tryptophan were used to demonstrate SERS in a segmented flow system. The spectra from different drops were compared and demonstrate the high reproducibility in comparision to static SERS. Lastly, chapter 7 summarizes the entire work of the present thesis with future prospects of Raman and FTIR microspectroscopy to study the progression mechanism of various diseases like neurodegenerative diseases which is easy to follow in drosophila due to their short life span. Also, technological developments in the field of nanotechnology and micro-fluidics will enable the detection of early biochemical changes in bodily fluids such as urine, cerebral spinal fluid, tears etc. Building on the results demonstrated in this thesis, hopefully label-free vibrational (Raman and FTIR) microspectroscopic studies using model organisms would help in understanding the underlying mechanisms of progression of various other diseases which in turn would facilitate the development of effective therapies.

O trabalho anteriormente realizado pelo nosso grupo, onde foram simulados defeitos de nitrogênio em nanotubos de carbono, apresentou resultados interessantes relativos às energias e propriedades eletrônicas. A interpretacão dos resultados teóricos obtidos levou à proposta da Divacância rodeada por 4 Nitrogênios como estrutura mais estável para o nitrogênio tipo piridina, em constraste com aquela proposta pelos experimentais, uma Monovacância rodeada por 3 Nitrogênios. Os cálculos das propriedades eletrônicas da Divacância reproduziram as medidas experimentais na investigação de sensores de amônia. Dessa forma, como informação adicional na determinaçã da estrutura mais estável, o presente trabalho investigou as propriedades vibracionais daqueles sistemas que apresentaram menor energias de formação. Foram calculadas as freqüências vibracionais dos seguintes três defeitos: Nitrogênio Substitucional (1N), Monovacância rodeada por 3 Nitrogênios (3NV) e Divacância rodeada por 4 Nitrogênios (4ND) e comparadas com os resultados para os tubos puros. Utilizou-se a aproximação de supercélula, com 140 átomos para um tubo metálico (5,5) e 160 para um tubo semicondutor (8,0). Como o objetivo é identificar as características de cada sistema, focalizou-se na comparação dos valores das freqüências Raman ativas mais intensas. Os cálculos foram realizados com o código SIESTA, utilizando DFT com o formalismo dos pseudopotenciais e a aproximação GGA-PBE. As freqüências foram obtidas pelo Método Direto pelo mesmo programa. Os resultados mostraram diferenças quanto à quebra de degenerescências, que ocorre devido à quebra da simetria do sistema puro e quanto à mudança dos valores das freqüências dos modos. Como característica geral, os defeitos fazem com que as freqüências da banda mais baixa de energia do espectro Raman sofram shifts negativos, ou seja, afastam os picos para energias mais baixas. O modo de freqüência intermediária sofre um shift positivo e os modos da banda G voltam a apresentar valores negativos. Os splittings, bem como os valores numéricos dos shifts variam conforme o tipo de defeito e o tipo de sistema dopado (armchair ou zig-zag). Apesar de não apresentar diferenças consideravelmente grandes para os valores de shifts e splittings entre os defeitos, o comportamento qualitativo distinto para os modos RBMs é uma boa ferramenta para a diferenciação desses defeitos através de espectroscopia vibracional. / A previous work developed in our own group on which nitrogen defects on carbon nanotubes were simulated presented very interesting results regarding the energetics and the electronic properties. The interpretation of the theoretical outcomes led us to propose the Divacancy surrounded by 4 nitrogen atoms as the most stable structure for a pyridine-like nitrogen, in contrast to the one proposed by the experimentalists, namely the Monovacancy surrounded by 3 nitrogen atoms. Calculations of the electronic properties of the Divacancy have reproduced the experimental data. In this way as additional information for determining the actual most stable structure the present work investigated the vibrational properties of those systems that showed the lowest formation energies. We performed the calculations of the vibrational frequencies for the following three defects: Substitutional nitrogen atom (1N), Monovacancy surrounded by 3 nitrogen atoms (3NV) and Divacancy surrounded by 4 nitrogen atoms (4ND). Then the frequencies were compared to those ones from the pure tubes. We used the supercell approximation with 140 atoms for a (5,5) metallic tube and 160 for a (8,0) semiconducting tube. Since the present work aims to identify the main features of each system we focused on the comparison of the values of the strongest Raman active modes. All the calculations were carried out by the SIESTA code, using DFT with the pseudopotential formalism and GGA approximation. Then the frequencies were evaluated using the Direct Method. The results showed differences on the degeneracy splittings, which are caused by the symmetry-breaking due to the introduction of defects, and also differences on the shifts of the numerical values of the frequencies. As general feature, the defects caused the low band frequencies modes of Raman spectrum to have a negative shift, i.e. they push the peaks further to lower energies. The intermediate mode shifts positively and the G band modes show negative shifts again. The splittings as well as those shifts change depending on the type of the defect and the type of the doped system (armchair or zig-zag). Although not showing significant differences for shifts and splittings between the defects, the qualitatively distinct behavior for RBMs modes is a good tool to tell them apart using vibrational spectroscopy.

ABSTRACT A theoretical and experimental study of the vibrational and chemical relaxation rates of diatomic gases, in flows behind shock waves and along nozzles,is made here. ¶ The validity of the conventional relaxation rate models, which are generally used to analyse experiments, is tested by developing a detailed microscopic description of the diatomic relaxation processes. Assuming the diatomic molecules to be represented by the anharmonic Morse Oscillator, the vibrational Master equation, which describes the time variation of each vibrational energy level population, is constructed by allowing one-quantum vibration to translation (V-T) energy exchanges and vibration to vibration (V-V) energy exchanges between the molecules. Dissociation and recombination are allowed to occur from, and to, the uppermost vibrational level. Solving the Master equation, it is found that a number of effects are explained by the inclusion of V-V transitions. In particular it is found that V-V energy exchanges cause the induction time for H2 dissociation to be increased; suggest that the linear rate law, for H2 and Ar mixtures, fails for a H2 mole fraction above 20%; give an acceleration of vibrational excitation as equilibrium is approached for H2 and N2; cause the vibrational temperature to be lower than the value found without V-V transitions for vibrational de-excitation in nozzle flows of H2 and N2, and conversely for recombination of H2 in nozzle flows. The most important result is the demonstration that conventional nozzle flow calculations, with shock-tube-determined dis-sociation and vibrational excitation rates, appear to be valid for the recombining and vibrationally de-excitating flows considered. ¶ The dissociation rates of undiluted nitrogen are measured in the free-piston shock tube DDT, using time-resolved optical interferometry, over a temperature range of 6000-14000K and confirm the strong temperature dependence of the pre-exponential factor observed by Hanson and Baganoff (1972). ¶ The vibrational de-excitation and excitation rates are determined in the small free-piston shock tunnel T2 over temperature ranges of 2000-4000K and 7000-10300K, respectively, by measuring the shock angles and curvatures, from optical interferograms, of flow over an inclined flat plate in the nonequilibrium nozzle flow. The de-excitation rate is found to be within a factor of ten of the excitation rate, while the excitation rate of N2 by collision with N is found to be less than about 50 times the excitation rate of N2 by N2. The dissociation rates of nitrogen, in the flow behind a shock attached to a wedge, are investigated in the large free-piston shock tunnel, using the shock curvature technique. The discrepancy, reported by Kewley and Hornung (1974b), between theory and experiment at the highest enthalpy is found to be resolved by including the measured helium contamination (Crane 1975) in the free-stream. Reasonable agreement is obtained between experimental shock curvatures and calculations using accepted dissociation rates.

O trabalho anteriormente realizado pelo nosso grupo, onde foram simulados defeitos de nitrogênio em nanotubos de carbono, apresentou resultados interessantes relativos às energias e propriedades eletrônicas. A interpretacão dos resultados teóricos obtidos levou à proposta da Divacância rodeada por 4 Nitrogênios como estrutura mais estável para o nitrogênio tipo piridina, em constraste com aquela proposta pelos experimentais, uma Monovacância rodeada por 3 Nitrogênios. Os cálculos das propriedades eletrônicas da Divacância reproduziram as medidas experimentais na investigação de sensores de amônia. Dessa forma, como informação adicional na determinaçã da estrutura mais estável, o presente trabalho investigou as propriedades vibracionais daqueles sistemas que apresentaram menor energias de formação. Foram calculadas as freqüências vibracionais dos seguintes três defeitos: Nitrogênio Substitucional (1N), Monovacância rodeada por 3 Nitrogênios (3NV) e Divacância rodeada por 4 Nitrogênios (4ND) e comparadas com os resultados para os tubos puros. Utilizou-se a aproximação de supercélula, com 140 átomos para um tubo metálico (5,5) e 160 para um tubo semicondutor (8,0). Como o objetivo é identificar as características de cada sistema, focalizou-se na comparação dos valores das freqüências Raman ativas mais intensas. Os cálculos foram realizados com o código SIESTA, utilizando DFT com o formalismo dos pseudopotenciais e a aproximação GGA-PBE. As freqüências foram obtidas pelo Método Direto pelo mesmo programa. Os resultados mostraram diferenças quanto à quebra de degenerescências, que ocorre devido à quebra da simetria do sistema puro e quanto à mudança dos valores das freqüências dos modos. Como característica geral, os defeitos fazem com que as freqüências da banda mais baixa de energia do espectro Raman sofram shifts negativos, ou seja, afastam os picos para energias mais baixas. O modo de freqüência intermediária sofre um shift positivo e os modos da banda G voltam a apresentar valores negativos. Os splittings, bem como os valores numéricos dos shifts variam conforme o tipo de defeito e o tipo de sistema dopado (armchair ou zig-zag). Apesar de não apresentar diferenças consideravelmente grandes para os valores de shifts e splittings entre os defeitos, o comportamento qualitativo distinto para os modos RBMs é uma boa ferramenta para a diferenciação desses defeitos através de espectroscopia vibracional. / A previous work developed in our own group on which nitrogen defects on carbon nanotubes were simulated presented very interesting results regarding the energetics and the electronic properties. The interpretation of the theoretical outcomes led us to propose the Divacancy surrounded by 4 nitrogen atoms as the most stable structure for a pyridine-like nitrogen, in contrast to the one proposed by the experimentalists, namely the Monovacancy surrounded by 3 nitrogen atoms. Calculations of the electronic properties of the Divacancy have reproduced the experimental data. In this way as additional information for determining the actual most stable structure the present work investigated the vibrational properties of those systems that showed the lowest formation energies. We performed the calculations of the vibrational frequencies for the following three defects: Substitutional nitrogen atom (1N), Monovacancy surrounded by 3 nitrogen atoms (3NV) and Divacancy surrounded by 4 nitrogen atoms (4ND). Then the frequencies were compared to those ones from the pure tubes. We used the supercell approximation with 140 atoms for a (5,5) metallic tube and 160 for a (8,0) semiconducting tube. Since the present work aims to identify the main features of each system we focused on the comparison of the values of the strongest Raman active modes. All the calculations were carried out by the SIESTA code, using DFT with the pseudopotential formalism and GGA approximation. Then the frequencies were evaluated using the Direct Method. The results showed differences on the degeneracy splittings, which are caused by the symmetry-breaking due to the introduction of defects, and also differences on the shifts of the numerical values of the frequencies. As general feature, the defects caused the low band frequencies modes of Raman spectrum to have a negative shift, i.e. they push the peaks further to lower energies. The intermediate mode shifts positively and the G band modes show negative shifts again. The splittings as well as those shifts change depending on the type of the defect and the type of the doped system (armchair or zig-zag). Although not showing significant differences for shifts and splittings between the defects, the qualitatively distinct behavior for RBMs modes is a good tool to tell them apart using vibrational spectroscopy.

L'objectif de ce travail consiste à étudier le mécanisme de photo-isomérisation d'une série de commutateurs moléculaires biomimétiques (IP) inspirés de la Rhodopsine (Rho), par spectroscopie d'absorption transitoire. Ce travail comprend également le développement puis l'utilisation d'une expérience d'absorption transitoire avec des impulsions sub-8 fs dédiée à la mesure des cohérences vibrationnelles concomitantes à la photoréactivité des IPs. [...] La description détaillée des deux montages de type pompe-sonde mis en œuvre pour ce travail, ainsi que le détail des analyses et corrections de données expérimentales effectuée ont été décrits. Les deux montages utilisés ont été alimenté par une même source, un laser Ti: saphir amplifié délivrant des impulsions à 800nm d'une durée de 40 fs. le premier est un montage d'absorption transitoire conventionnel permettant l'acquisition des spectres transitoires sur une large gamme de spectrale à l'aide d'un continuum de lumière blanche, avec une résolution de 70fs. Le second montage pompe-sonde dédié à la mesure de cohérence vibrationnelle a été développé au cours de la thèse. Dans ce dernier les impulsions pompes à 800nm sont comprimés d'une durée de 8fs, à l'aide d'un compresseur composé de fibre creuse contenant du gaz (Néon). Une conversion de fréquence permet de générer une impulsion centrée à 400 nm de largeur spectrale correspondant `a une durée de 8 fs. Un balayage rapide du délai entre la pompe et la sonde est mis en œuvre pour supprimer de manière efficace l’effet dominant du bruit à basse fréquence de l’intensité de la pompe sur les signaux d’absorption transitoire. [...] / The research presented durind this Phd work address one of the paradigms of atomic/molecular physics of modern era, namely the Born-Oppenheimer approximation. The chemical processes on the atomics level has been reliying on the ability to separate fast electron motion from that of heavy nuclei. We focus in the so called conical intersection (CI), whereby molecular isomerization proceed over timescale clearly violating this paradigmatic approximation. Arguably, the most spectacular example of such process is the primary photochemical event in vision. The key aspect of these ultrafast, and often remarkably efficient, transitions is the conversion of optical energy into mechanical energy through coherent channels, that is with negligible loss of energy due to the random dissipation. This work in many aspects expands on the scope and offers a very challenging, et attractive, endeavour into vibrational coherence of complex molecule in solution. Molecular complexity was primarely motivated by wide applicablity of research on synthetic molecules that mimic the photoreaction of Rhodopsin (Rho), to date the fastest and most efficient optomechanical photoswitch. To this end, we have developed and used a state-of-art ultrafast time domain vibrational coherence spectrometer (VCS), allowing sub-10 fs resolution, hence vibration windows up to 3000 cm-1. Such combinaison unlocks to new ways to control over chemical reactions, whereby mechanistic forces precede rather than outpley thermal fluctuations. This concept transcends chemistry, and as a matter pf example, it has only begun to be exploited in material science. [...]

No description available.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Molecular Dynamics (MD) simulations have played an important role in providing detailed atomic information for the study of biological systems. The quality of an MD simulation depends on both the degree of sampling and the accuracy of force field. Kirkwood-Buff (KB) theory provides a relationship between species distributions from simulation results and thermodynamic properties from experiments. Recently, it has been used to develop new, hopefully improved, force fields and to study preferential interactions. Here we combine KB theory and MD simulations to study a variety of intermolecular interactions in solution. Firstly, we present a force field for neutral amines and carboxylic acids. The parameters were developed to reproduce the composition dependent KB integrals obtained from an analysis of the experimental data, allowing for accurate descriptions of activities involved with uncharged N-terminus and lysine residues, as well as the protonated states for the C-terminus and both aspartic and glutamic acids. Secondly, the KB force fields and KB theory are used to investigate the urea cosolvent effect on peptide aggregation behavior by molecular dynamics simulation. Neo-pentane, benzene, glycine and methanol are selected to represent different characteristics of proteins. The chemical potential derivatives with respect to the cosolvent concentrations are calculated and analyzed, and the four solutes exhibit large differences. Finally, the contributions from the vibrational partition function to the total free energy and enthalpy changes are investigated for several systems and processes including: the enthalpy of evaporation, the free energy of solvation, the activity of a solute in solution, protein folding, and the enthalpy of mixing. The vibrational frequencies of N-methylacetamide, acetone and water are calculated using density functional theory and MD simulations. We argue that the contributions from the vibrational partition function are large and in classical force fields these contributions should be implicitly included by the use of effective intermolecular interactions.

Mechanistic aspects of phosphorylation, dephosphorylation, pyrophosphorylation and depyrophosphorylation reactions that mimic phosphorylases, dephosphorylases, pyrophosphorylases and depyrophosphorylases have been studied in the biologically important middle pH region. The different systems monitored are; (a) the reactions between [{CoN4(OH)(OH2)}]2+ and [HPO4]- for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [HPO4]2- ratios. (b) the reactions between [{CoN4PO4] and [O2NC6H4O]- (abbreviated as NP-) for 1:1, 2:1 and 3:1 [{CoN4PO4] to [O2NC6H4O]- ratios. (c) the reactions between [{CoN4(OH)(OH2)}]2+ and [O2NC6H4PO4]2- (abbreviated as NPP2-) for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [O2NC6H4PO4]2- ratios. (d) the reactions between [{CoN4(OH)(OH2)}]2+ and [H2P2O7]2- for 1:1, 2:1 and 3:1 [{CoN4(OH)(OH2)}]2+ to [H2P2O7]2- ratios. (e) the reactions between [{CoN4P2O7}]- and [O2NC6H4O]- for 1:1, 2:1 and 3:1 [{CoN4P2O7}]- to [O2NC6H4O]- ratios. Significant phosphorylation was noted for systems containing 1:1 molar ratio [{CoN4PO4] and [O2NC6H4O]-. Enhanced phosphorylation was depicted for system containing 1:1 molar ratio of [{CoN4(OH)}2PO4]+ and [O2NC6H4O]-. Pyrophosphorylation was noted for reactions of 1:1 molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. The rate of pyrophosphorylation was substantially reduced for systems that were 2:1 in molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. No appreciable pyrophosphorylation was noted for systems, which has a 3:1 molar ratio of [{CoN4P2O7}]- and [O2NC6H4O]-. Specific mechanistic features and the possible roles metal ions play in phosphorylase, dephosphorylase and pyrophosphorylase are highlighted from results of UV-Visible spectroscopy, 31P {1H} NMR spectroscopy and Surface Enhanced Raman Scattering (SERS) studies / Chemistry / D.Phil. (Chemistry)