Neste trabalho abordamos os processos de perdas colisionais por mudança de estrutura fina e por escape radiativo. Estes processos são importantes por serem os principais fatores limitantes da densidade e da permanência de átomos confinados em armadilhas magneto-ópticas. A utilização do formalismo de Wigner nos possibilitou tratar a dinâmica dos graus de liberdade internos do sistema de forma puramente quântica, enquanto tratamos os graus de liberdade translacionais de maneira semiclássica. Com este formalismo deduzimos equações inéditas para uma colisão unidimensional e desenvolvemos um algoritmo, também inédito, para a resolução numérica de tais equações. / In this work we study the collision loss processes caused by fine-structure change and radiative escape. These processes are important because they limit the density and the confinement time of atoms in magneto-optical traps. The use of the Wigner-function formalism allows us to treat the internal degrees of freedom purely quantum mechanically, while treating the dynamics of the external degrees of freedom quasi-classically. This dissertation employs this formalism to derive for the first time, quasi-classical equations describing one-dimensional cold collisions, including dissipation due to spontaneous emission, and an algorithm, also for the first time, to solve numerically the mentioned set of coupled equations.

<p dir="ltr">The objective of this research is to advance the development and application of laser diagnostics in gas phase medium, which ranges from atmospheric non-reacting flows to turbulent reacting flows in high-pressure, high-temperature environments. Laser diagnostic techniques are powerful tools for non-intrusive and in-situ measurements of important chemical parameters, such as temperature, pressure, and species mole fractions, in harsh environments. These measurements significantly advance the knowledge across various research disciplines, such as combustion dynamics, chemical kinetics, and molecular spectroscopy. In this thesis, detailed theoretical models and experimental analysis are presented for three different techniques: 1. Chirped-probe-pulse femtosecond coherent anti-Stokes Raman scattering (CPP fs CARS); 2. Two-color polarization spectroscopy (TCPS); 3. Ultrafast-laser-absorption-spectroscopy (ULAS). The first chapter provides a brief survey of laser diagnostics, including both linear and nonlinear methods. The motivations behind the three studies covered in this dissertation are also discussed. </p><p dir="ltr">In the second chapter, single-shot CPP fs CARS thermometry is developed for the hydrogen molecule at 5 kHz. The results are divided into two parts. The first part concentrates on the development of H₂ CPP fs CARS thermometry for high-pressure and high-temperature conditions. The second part demonstrates the application of H₂ CPP fs CARS in a model rocket combustor at pressures up to 70 bar. In the first part, H₂ fs CARS thermometry was performed in Hencken burner flames up to 2300 K, as well as in a heated gas-cell at temperatures up to 1000 K. It was observed that the H₂ fs CARS spectra are highly sensitive to the pump and Stokes chirp. Chirp typically originates from optical components such as windows and polarizers. As a result, the pump delay is modeled to provide a shift to the Raman excitation efficiency curve. With the updated theoretical model, excellent agreement was found between the simulated and experimental spectra. The averaged error and precision are 2.8% and 2.3%, respectively. In addition, the spectral phase and pump delay determined from the experimental spectra closely align with the theoretical predictions. It is also found that pressure does not have significant effects on the H₂ fs CARS spectra up to 50 bar at 1000 K. The collision model provides excellent agreement with the experiment. This allows the use of low-pressure laser parameters for high-pressure thermometry measurements. In the second part, spatially resolved H₂ temperature was measured in a rocket chamber at pressures up to 70 bar. This is the first demonstration of fs CARS thermometry inside a high-pressure rocket combustor. These results highlight the potential of using H₂ CPP fs CARS thermometry to provide quantitative data in high-pressure experiments for the study of combustion dynamics and model validation efforts at application relevant operating conditions.</p><p dir="ltr">The third chapter presents the development of a TCPS system for the study of the NO (<i>A</i>²Σ⁺-<i>X</i>²Π) state-to-state collision dynamics with He, Ar, and N₂. Two sets of TCPS spectra for 1% NO, diluted in different buffer gases at 295 K and 1 atm, were obtained with the pump beam tuned to the R₁₁(11.5) and ^OP₁₂(1.5) transitions. The probe was scanned while the pump beam was tuned to the line center. Collision induced transitions were observed in the spectra as the probe scanned over transitions that were not coupled with the pump frequency. The strength and structure of the collision induced transitions in the TCPS spectra were compared between the three colliding partners. Theoretical TCPS spectra, calculated by solving the density matrix formulation of the time-dependent Schrödinger wave equation, were compared with the experimental spectra. A collision model based on the modified exponential-gap law was used to model the rotational level-to-rotational level collision dynamics. An unique aspect of this work is that the collisional transfer from an initial to a final Zeeman state was modeled based on the difference in the cosine of the rotational quantum number <i>J</i> projection angle with the z-axis for the two Zeeman states. Rotational energy transfer rates and Zeeman state collisional dynamics were varied to obtain good agreement between theory and experiment for the two different TCPS pump transitions and for the three different buffer gases. One key finding, in agreement with quasi-classical trajectory calculations, is that the spin-rotation changing transition rate in the <i>A</i>²Σ⁺ level of NO is almost zero for rotational quantum numbers ≥ 8. It was necessary to set this rate to near zero to obtain agreement with the TCPS spectra. </p><p dir="ltr">The fourth chapter presents the development and application of a broadband ULAS technique operating in the mid-infrared for simultaneous measurements of temperature, methane (CH₄), and propane (C₃H₈) mole fractions. Single-shot measurements targeting the C-H stretch fundamental vibration bands of CH₄ and C₃H₈ near 3.3 μm were acquired in both a heated gas cell up to ~650 K and laminar diffusion flames at 5 kHz. The average temperature error is 0.6%. The average species mole fraction error are 5.4% for CH₄, and 9.9% for C₃H₈. This demonstrates that ULAS is capable of providing high-fidelity hydrocarbon-based thermometry and simultaneous measurements of both large and small hydrocarbons in combustion gases. </p>

<p dir="ltr">Laser absorption spectroscopy (LAS) is a widely used technique to acquire path-integrated measurements of gas properties such as temperature and mole fraction. Although extremely useful, the application of LAS to study heterogeneous combustion environments can be challenging. For example, beam steering can be one such challenge that arises during measurements in heterogeneous combustion environments such as metallized propellant flames or measurements at high-pressure conditions. The ability to only obtain path integrated measurements has been a major challenge of conventional LAS techniques, especially in characterizing combustion environments with a non-uniform thermo-chemical distribution along the line of sight (LOS). Additionally, simultaneous measurements of multiple species using LAS with narrow-bandwidth lasers often necessitates employing multiple light sources. Aerospace applications, such as characterizing hypersonic flows may require ultrashort time resolution to study fast-evolving chemistry. Similarly, atmospheric entry most often requires measurements of atoms and molecules that absorb at wavelengths ranging from ultraviolet to mid-infrared. The availability of appropriate light sources for such measurements has been limited. In the past, several researchers have come up with diagnostic techniques to overcome the above-mentioned challenges to a certain extent. Most often, these solutions have been need-based while compromising on other diagnostic capabilities. Therefore, LAS diagnostics capable of acquiring broadband measurements with ultrafast time resolution and the ability to acquire measurements at wavelengths in ultraviolet through mid-infrared is required to study advanced combustion systems and for the development of advanced aerospace systems for future space missions. Ultrafast laser absorption spectroscopy is one such technique that provides broadband measurements, enabling simultaneous multi-species and high-pressure measurements. The light source utilized for ULAS provides the ultrafast time resolution necessary for resolving fast-occurring chemistry and more importantly the ability to acquire measurements at a wide range of wavelengths ranging from ultraviolet to far-infrared. The development and application of ULAS for characterizing propellant flames and hypersonic flows under non-equilibrium conditions by overcoming the above-mentioned challenges is presented here. </p><p>This work describes the development of a single-shot ultrafast laser absorption spectroscopy (ULAS) diagnostic for simultaneous measurements of temperature and concentrations of CO, NO, and H₂O in flames and aluminized fireballs of HMX (C₄H₈N₈O₈). Ultrashort (55 fs) pulses from a Ti:Sapphire oscillator emitting near 800 nm were amplified and converted into the mid-infrared through optical parametric amplification (OPA) at a repetition rate of 5 kHz. Ultimately, pulses with a spectral bandwidth of ≈600 cm^-1 centered near 4.9 µm were utilized in combination with a mid-infrared spectrograph to measure absorbance spectra of CO, NO, and H₂O across a 30 nm bandwidth with a spectral resolution of 0.3 nm. The gas temperature and species concentrations were determined by least-squares fitting simulated absorbance spectra to measured absorbance spectra. Measurements of temperature, CO, NO, and H₂O were acquired in an HMX flame burning in air at atmospheric pressure and the measurements agree well with previously published results. Measurements were also acquired in fireballs of HMX with and without 16.7 wt% H-5 micro-aluminum. Time histories of temperature and column densities are reported with a 1-σ precision of 0.4% for temperature and 0.3% (CO), 0.6% (NO), and 0.5% (H₂O), and 95% confidence intervals (C.I.) of 2.5% for temperature and 2.5% (CO), 11% (NO), and 7% (H₂O), thereby demonstrating the ability of ULAS to provide high-fidelity, multi-parameter measurements in harsh combustion environments. The results indicate that the addition of the micron-aluminum increases the fireball peak temperature by ≈100 K and leads to larger concentrations of CO. The addition of aluminum also increases the duration fireballs remain at elevated temperatures above 2000 K.</p><p dir="ltr">Next, the application of ULAS for dual-zone temperature and multi-species (CO, NO, H₂O, CO₂, HCl, and HF) measurements in solid-propellant flames is presented. ULAS measurements were acquired at three different central wavelengths (5.121 µm, 4.18 µm, and 3.044 µm) for simultaneous measurements of temperature and: 1) CO, NO, and H₂O, 2) CO₂ and HCl, and 3) HF and H₂O. Absorption measurements with a spectral resolution of 0.35 nm and bandwidth of 7 cm^-1, 18 cm^-1, and 35 cm^-1, respectively were acquired. In some cases, a dual-zone absorption spectroscopy model was implemented to accurately determine the gas temperature in the hot flame core and cold flame boundary layer via broadband absorption measurements of CO₂, thereby overcoming the impact of line-of-sight non-uniformities. Results illustrate that the hot-zone temperature of CO₂ agrees well with the equilibrium flame temperature and single-zone thermometry of CO, the latter of which is insensitive to the cold boundary layer due to the corresponding oxidation of CO to CO₂.</p><p dir="ltr">The initial development and implementation of an ultraviolet and broadband ultrafast-laser-absorption-imaging (UV-ULAI) diagnostic for one dimensional (1D) imaging of temperature and CN via its <i>B</i>²Σ⁺←<i>X</i>²Σ⁺absorption bands near 385 nm. The diagnostic was demonstrated by acquiring single-shot measurements of 1D temperature and CN profiles in HMX flames at a repetition rate of 25 Hz. Ultrashort pulses (55 fs) at 800 nm were generated using a Ti:Sapphire oscillator and then amplification and wavelength conversion to the ultraviolet was carried out utilizing an optical parametric amplifier and frequency doubling crystals. The broadband pulses were spectrally resolved using a 1200 l/mm grating and imaged on an EMCCD camera to obtain CN absorbance spectra with a resolution of ≈0.065 nm and a bandwidth of ≈4 nm (i.e. 260 cm^-1). Simulated absorbance spectra of CN were fit to the measured absorbance spectra using non-linear curve fitting to determine the gas properties. The spatial evolution of gas temperature and CN concentration near the burning surface of an HMX flame was measured with a spatial resolution of ≈10 µm. 1D profiles of temperature and CN concentration were obtained with a 1-σ spatial precision of 49.3 K and 4 ppm. This work demonstrates the ability of UV-ULAI to acquire high-precision, spatially resolved absorption measurements with unprecedented temporal and spatial resolution. Further, this work lays the foundation for ultraviolet imaging of numerous atomic and molecular species with ultrafast time resolution.</p><p dir="ltr">Ultraviolet ULAS was applied to characterize the temporal evolution of non-Boltzmann CN (<i>X</i>²Σ⁺) formed behind strong shock waves in N₂-CH₄ mixtures at conditions relevant to entry into Titan's atmosphere. An ultrafast (femtosecond) light source was utilized to produce 55 fs pulses near 385 nm at a repetition rate of 5 kHz and a spectrometer with a 2400 lines/mm grating was utilized to spectrally resolve the pulses after passing through the Purdue High-Pressure Shock Tube. This enabled broadband single-shot absorption measurements of CN to be acquired with a spectral resolution and bandwidth of ≈0.02 nm and ≈6 nm (≈402 cm^-1 at these wavelengths), respectively. A line-by-line absorption spectroscopy model for the <i>B</i>²Σ⁺←<i>X</i>²Σ⁺ system of CN was developed and utilized to determine six internal temperatures (two vibrational temperatures, four rotational) of CN from the (0,0), (1,1), (2,2) and (3,3) absorption bands. Measurements were acquired behind reflected shock waves in 5.65% CH₄ and 94.35% N₂ with an initial pressure of 1.56 mbar and incident shock speed of ≈2.1 km/s. For this test condition, the chemically and vibrationally frozen temperature of the mixture behind the reflected shock was 5000 K and the pressure was 0.6 atm. The high repeatability of the shock-tube experiments (0.3% variation in shock speed across tests) enabled multi-shock time histories of CN mole fraction and six internal temperatures to be acquired with a single-shot time resolution of less than 1 ns. The measurements revealed that CN <i>X</i>²Σ⁺ is non-Boltzmann rotationally and vibrationally for greater than 200 µs, thereby strongly suggesting that chemical reactions are responsible for the non-Boltzmann population distributions. </p><p><br></p>

<p dir="ltr">Quantum-enhanced approaches enable high-resolution imaging and sensing with signal-to-noise ratios beyond classical limits. However, operating in the quantum regime is highly susceptible to environmental influences and experimental conditions. Implementing these techniques necessitates highly controlled environments or intricate preparation methods, which can restrict their practical applications. This thesis explores the practical applications of quantum sensing, focusing on thermal sensing with bright quantum sources in biological and electronic contexts. Additionally, I discuss the development of a multimode source for quantum imaging applications and an on-chip atomic interface for scalable light-atom interactions. I built all the experimental setups from the beginning; a microscope setup for nanodiamond-based thermal sensing inside living cells, a four-wave mixing setup using a Rb cell for thermal imaging of microelectronics and multimode source, and a vacuum chamber for on-chip atomic interface.</p><p dir="ltr">Quantum sensing can be realized using atomic spins or optical photons possessing quantum information. Among these, color centers inside diamonds stand out as robust quantum spin defects (effective atomic spins), maintaining their quantum properties even in ambient conditions. In this thesis, I studied the role of an ensemble of color centers inside nanodiamonds as a probe of temperature in a living cell. Our approach involves incubating nanodiamonds in endothelial culture cells to achieve sub-kelvin sensitivity in temperature measurement. The results reveal a temperature error of 0.38 K and a sensitivity of 3.46 K/sqrt(Hz)<i> </i>after 83 seconds of measurement. Furthermore, I discuss the constraints of nanodiamond temperature sensing in living cells, propose strategies to surmount these limitations, and explore potential applications arising from such measurements.</p><p dir="ltr">Another ubiquitous quantum probe is light with quantum properties. Photons, the particles of light, can carry quantum correlations and have minimal interactions with each other and, to some extent, the environment. This capability theoretically allows for quantum-enhanced imaging or sensing of sample’s properties. In this thesis, I report on the demonstration of quantum-enhanced temperature sensing in microelectronics using bright quantum optical signals. I discuss the first demonstration of quantum thermal imaging used to identify hot spots and analyze heat transport in electronic systems.</p><p dir="ltr">To achieve this, we employed lock-in detection of thermoreflectivity, enabling us to measure temperature changes in a micro-wire induced by an electric current with an accuracy better than 0.04 degrees, averaged over 0.1 seconds. Our results demonstrate a nearly 50 % improvement in accuracy compared to using classical light at the same power, marking the first demonstration of below-shot-noise thermoreflectivity sensing. We applied this imaging technique to both aluminum and niobium-based circuits, achieving a thermal resolution of 42 mK during imaging. We scanned a 48 × 48 μm<i> </i>area with 3-4 dB squeezing compared to classical measurements. Based on these results, we infer possibility of generating a 256×256 pixel image with a temperature sensitivity of 42 mK within 10 minutes. This quantum thermoreflective imaging technique offers a more accurate method for detecting electronic hot spots and assessing heat distribution, and it may provide insights into the fundamental properties of electronic materials and superconductors.</p><p dir="ltr">In transitioning from single-mode to multimode quantum imaging, I conducted further research on techniques aimed at generating multimode quantum light. This involved an in-depth analysis of the correlation characteristics essential for utilizing quantum light sources in imaging applications. To achieve the desired multimode correlation regime, I developed a system centered on warm Rubidium vapor with nonlinear gain and feedback processes. The dynamics of optical nonlinearity in the presence of gain and feedback can lead to complexity, even chaos, in certain scenarios. Instabilities in temporal, spectral, spatial, or polarization aspects of optical fields may arise from chaotic responses within an optical <i>x</i>(2) or <i>x</i>(3) nonlinear medium positioned between two cavity mirrors or preceding a single feedback mirror. However, the complex mode dynamics, high-order correlations, and transitions to instability in such systems remain insufficiently understood.</p><p dir="ltr">In this study, we focused on a <i>x</i>(3) medium featuring an amplified four-wave mixing process, investigating noise and correlations among multiple optical modes. While individual modes displayed intensity fluctuations, we observed a reduction in relative intensity noise approaching the standard quantum limit, constrained by the camera speed. Remarkably, we recorded a relative noise reduction exceeding 20 dB and detected fourth-order intensity correlations among four spatial modes. Moreover, this process demonstrated the capability to generate over 100 distinct correlated quadruple modes.</p><p dir="ltr">In addition to conducting multimode analysis to develop a scalable imaging system, I have explored methodologies aimed at miniaturizing light-atom interactions on a chip for the scalable generation of quantum correlations. While warm atomic vapors have been utilized for generating or storing quantum correlations, they are plagued by challenges such as inhomogeneous broadening and low coherence time. Enhancing control over the velocity, location, and density of atomic gases could significantly improve light-atom interaction. Although laser cooling is a common technique for cooling and trapping atoms in a vacuum, its implementation in large-scale systems poses substantial challenges. As an alternative, I focused on developing an on-chip system integrated with atomic vapor controlled by surface acoustic waves (SAWs).</p><p dir="ltr">Surface acoustic waves are induced by an RF signal along the surface of a piezoelectric material and have already been proven to be effective for manipulating particles within microfluidic channels. Expanding upon this concept, I investigated the feasibility of employing a similar approach to manipulate atoms near the surface of a photonic circuit. The interaction between SAWs and warm atomic vapor is expected as a mechanism for controlling atomic gases in proximity to photonic chips for quantum applications. Through theoretical analysis spanning molecular dynamics and fluid dynamics regimes, I identified the experimental conditions necessary to observe acoustic wave behavior in atomic vapor. To validate this theory, I constructed an experiment comprising a vacuum chamber housing Rb atoms and a lithium niobate chip featuring interdigital transducers for launching SAWs. However, preliminary experimental results yielded no significant signals from SAW-atom interactions. Subsequent analysis revealed that observing such interactions requires sensitivity and signal-to-noise ratio (SNR) beyond the capabilities of the current setup. Multiple modifications, including increasing buffer gas pressure and mitigating RF cross-talk, are essential for conclusively observing and controlling these interactions.</p>

<p>Bose-Einstein condensates (BECs) in light-induced synthetic gauge fields and spaces can provide a highly-tunable platform for quantum simulations. Chapter 1 presents a short introduction to the concepts of BECs and our BEC machine. Chapter 2 introduces some basic ideas of how to use light-matter interactions to create synthetic gauge fields and spaces for neutral atoms. Three main research topics of the thesis are summarized below.</p> <p>Chapter 3: Recently, using bosonic quasiparticles (including their condensates) as spin carriers in spintronics has become promising for coherent spin transport over macroscopic distances. However, understanding the effects of spin-orbit (SO) coupling and many-body interactions on such a spin transport is barely explored. We study the effects of synthetic SO coupling (which can be turned on and off, not allowed in usual materials) and atomic interactions on the spin transport in an atomic BEC.</p> <p>Chapter 4: Interplay between matter and fields in physical spaces with nontrivial geometries can lead to phenomena unattainable in planar spaces. However, realizing such spaces is often impeded by experimental challenges. We synthesize real and curved synthetic dimensions into a Hall cylinder for a BEC, which develops symmetry-protected topological states absent in the planar counterpart. Our work opens the door to engineering synthetic gauge fields in spaces with a wide range of geometries and observing novel phenomena inherent to such spaces.</p> <p>Chapter 5: Rotational properties of a BEC are important to study its superfluidity. Recent studies have found that SO coupling can change a BEC's rotational and superfluid properties, but this topic is barely explored experimentally. We study rotational dynamics of a SO-coupled BEC in an effective rotating frame induced by a synthetic magnetic field. Our work may allow for studying how SO coupling modify a BEC's rotational and superfluid properties.</p> <p>Chapter 6 presents some possible future directions.</p>

A Emodina (EMH) é uma das antraquinonas mais abundantes na natureza. Essa molécula vem sendo largamente usada como material de estudo científico por apresentar diversas atividades farmacológicas, tais como antiviral, antitumoral, antifungal, digestiva e outras. É conhecido que a Emodina em solução aquosa alcalina pode sofrer mais de um processo de desprotonação, apresentando-se na forma desprotonada, EM-, após a primeira desprotonação. Nesta tese de doutorado estudamos as propriedades estruturais e eletrônicas da molécula Emodina em meio solvente e em bicamadas lipídicas a fim de caracterizar as propriedades relacionadas à espectroscopia UV-Vis, à reatividade e à termodinâmica dessa molécula nesses ambientes. Realizamos cálculos quânticos com a Emodina em vácuo e em meio solvente, onde consideramos todos os possíveis sítios de desprotonação. Como resultados desses cálculos, identificamos os sítios da primeira, segunda e terceira desprotonação. Calculamos o pKa1 da Emodina em água e o pK*a1 em metanol através de simulações computacionais com o método Monte Carlo e cálculos quânticos, com o solvente descrito com o modelo contínuo polarizável. Nossos melhores valores para o pKa1 da Emodina determinados nesses solventes foram 8.4±0.5 e 10.3±1.5, que estão em boa concordância com os valores experimentais, (pKa1=8.0±0.2 e pK*a1=11.1±0.1) obtidos nesta tese para Emodina em água e metanol, respectivamente. Adicionalmente realizamos simulações com Dinâmica Molecular com as espécies EMH e EM- em bicamada lipídica de DMPC, para investigar a nível atômico as interações dessas espécies com a bicamada e determinar as posições preferenciais dessas espécies nesse ambiente anfifílico. Os resultados dessas simulações mostraram que as espécies EMH e EM- ficam inseridas na bicamada, na região polar dos lipídios, próximos aos gliceróis. Esses resultados corroboram as nossas medidas do espectro de absorção dessas espécies em bicamada lipídica, onde mostramos de forma qualitativa, que ambas as espécies ficam inseridas na bicamada, na região das cabeças polares dos lipídios. A análise das propriedades estruturais da bicamada na vizinhança das espécies da Emodina como área por lipídio e densidade eletrônica dos lipídios, mostrou que o efeito da EM- na estrutura da bicamada lipídica é maior do que o da EMH. Esses resultados corroboram as nossas medidas de DSC(Differential Scanning Calorimetry) das espécies da Emodina na bicamada. / Emodin (EMH) is one of the most abundant anthraquinone derivatives found in nature. This molecule has been used widely as research material, due to its biological and pharmacological activities such as antiviral, anticancer, antifungal, digestive and antibacterial activities. It is known that Emodin in alkaline aqueous solution can undergo more than one deprotonation, leading to the specie EM- in the first deprotonation process. In this PhD thesis, we studied the structural and electronic properties of this molecule in several solvents and lipid bilayers, in order to characterize the properties related to UV-Vis absorption spectroscopy, reactivity and thermodynamics of this molecule in these environments. Performing quantum mechanics (QM) calculations for all possible deprotonation sites and tautomeric isomers of Emodin in vacuum and in water, we identified the sites of the first, second and third deprotonations. We calculated the pKa1 of Emodin in water and pK*a1 in methanol with free energy perturbation method, implemented in the Monte Carlo simulation, and with QM calculations, where the solvent was treated as a polarizable continuum medium. Our best values for pKa1 of Emodin in these solvents were 8.4±0.5 and 10.3±1.5, which are in very good agreement with the experimental values obtained in this thesis pKa1=8.0±0.2 and pK*a1=11.1±0.1, for water and methanol, respectively. Additionally, we performed molecular dynamics simulations of both species in fully hydrated lipid bilayers of DMPC to investigate at atomic detail the molecular mechanism of the interaction of these species with lipid membrane and its preferred positions in this amphiphilic environment. As results of these simulations, we obtained that both species of Emodin have a strong tendency to insert into the lipid bilayer, remaining near the glycerol group of DMPC. These results corroborate our measured absorption spectra of these species in the bilayer, which qualitatively showed that both species are within the bilayer, inserted in the lipid headgroup region. Our results also show that the effect of EM- specie in the lipid bilayer structure is stronger than the EMH, which corroborate our DSC(Differential Scanning Calorimetry) measurements.

<p>Atoms, molecules and clusters all constitute building blocks of macroscopic matter. Therefore, understanding the electronic and geometrical properties of such systems is the key to understanding the properties of solid state objects.</p><p>In this thesis, some atomic, molecular and cluster systems (clusters of O₂, CH₃Br, Ar/O₂, Ar/Xe and Ar/Kr; dimers of Na; Na and K atoms) have been investigated using synchrotron radiation, and in the two last instances, laser light. We have performed x-ray photoelectron spectroscopy (XPS) on all of these systems. We have also applied ultraviolet photoelectron spectroscopy (UPS), resonant Auger spectroscopy (RAS) and near-edge x-ray absorption spectroscopy (NEXAFS) to study many of the systems. Calculations using <i>ab initio</i> methods, namely density functional theory (DFT) and Møller-Plesset perturbation theory (MP), were employed for electronic structure calculations. The geometrical structure was studied using a combination of <i>ab initio</i> and molecular dynamics (MD) methods.</p><p>Results on the dissociation behavior of CH₃Br and O₂ molecules in clusters are presented. The dissociation of the Na₂ molecule has been characterized and the molecular field splitting of the Na 2<i>p</i> level in the dimer has been measured. The molecular field splitting of the CH₃Br 3<i>d</i> level has been measured and the structure of CH₃Br clusters has been determined to be similar to the structure of the bulk solid. The diffusion behavior of O₂, Kr and Xe on large Ar clusters, as a function of doping rate, has been investigated. The shake-down process has been observed from excited states of Na and K. Laser excited Na atoms have been shown to be magnetically aligned. The shake-down process was used to characterize the origin of various final states that can be observed in the spectrum of ground-state K.</p>

Atoms, molecules and clusters all constitute building blocks of macroscopic matter. Therefore, understanding the electronic and geometrical properties of such systems is the key to understanding the properties of solid state objects. In this thesis, some atomic, molecular and cluster systems (clusters of O2, CH3Br, Ar/O2, Ar/Xe and Ar/Kr; dimers of Na; Na and K atoms) have been investigated using synchrotron radiation, and in the two last instances, laser light. We have performed x-ray photoelectron spectroscopy (XPS) on all of these systems. We have also applied ultraviolet photoelectron spectroscopy (UPS), resonant Auger spectroscopy (RAS) and near-edge x-ray absorption spectroscopy (NEXAFS) to study many of the systems. Calculations using ab initio methods, namely density functional theory (DFT) and Møller-Plesset perturbation theory (MP), were employed for electronic structure calculations. The geometrical structure was studied using a combination of ab initio and molecular dynamics (MD) methods. Results on the dissociation behavior of CH3Br and O2 molecules in clusters are presented. The dissociation of the Na2 molecule has been characterized and the molecular field splitting of the Na 2p level in the dimer has been measured. The molecular field splitting of the CH3Br 3d level has been measured and the structure of CH3Br clusters has been determined to be similar to the structure of the bulk solid. The diffusion behavior of O2, Kr and Xe on large Ar clusters, as a function of doping rate, has been investigated. The shake-down process has been observed from excited states of Na and K. Laser excited Na atoms have been shown to be magnetically aligned. The shake-down process was used to characterize the origin of various final states that can be observed in the spectrum of ground-state K.

The Phthalocyanines (Pc’s) are a group of macro-cyclic molecules, widely investigated due to the possibility to use them in a variety of applications. Electronic and geometrical structure investigations of molecular model systems of Pc’s adsorbed on surfaces are important for a deeper understanding of the functionality of different Pc-based devices. Here, Pc’s monolayers and films, deposited on different surfaces, were investigated by X-ray Photoelectron Spectroscopy (XPS), X-ray Absorption Spectroscopy (XAS) and Scanning Tunneling Microscopy (STM). In addition Density Functional Theory (DFT) simulations were performed. For molecular films of Metal-free (H2Pc) and Iron (FePc) Pc’s, on surfaces, it is found that the intermolecular interaction is weak and the molecules arrange with their molecular plane mainly perpendicular to the surface. Several monolayer systems were characterized, namely H2Pc and FePc adsorbed on Graphite, ZnPc on InSb(001)-c(8x2), H2Pc on Al(110) and on Au(111). For all the studied monolayers it was found that the molecules are oriented with their molecular plane parallel to the surface. The electronic structure of the molecules is differently influenced by interaction with the surfaces. For H2Pc adsorbed on Graphite the nearly negligible effect of the surface on the molecular electronic structure allowed STM characterization of different molecular orbitals. A strong interaction is instead found in the case of H2Pc on Al(110) resulting in molecules strongly adsorbed, and partly dissociated. Modifications of the electronic and geometrical structure induced by alkali doping of H2Pc films and monolayers were characterized. It is found both for the H2Pc film on Al(110) and monolayer adsorbed on Au(111), that the molecular arrangement is changed upon doping by Potassium and Rubidium, respectively. Potassium doping of the H2Pc films results in a filling of previously empty molecular orbitals by a charge transfer from the alkali to the molecule, with significant modification of the molecular electronic structure.

A Emodina (EMH) é uma das antraquinonas mais abundantes na natureza. Essa molécula vem sendo largamente usada como material de estudo científico por apresentar diversas atividades farmacológicas, tais como antiviral, antitumoral, antifungal, digestiva e outras. É conhecido que a Emodina em solução aquosa alcalina pode sofrer mais de um processo de desprotonação, apresentando-se na forma desprotonada, EM-, após a primeira desprotonação. Nesta tese de doutorado estudamos as propriedades estruturais e eletrônicas da molécula Emodina em meio solvente e em bicamadas lipídicas a fim de caracterizar as propriedades relacionadas à espectroscopia UV-Vis, à reatividade e à termodinâmica dessa molécula nesses ambientes. Realizamos cálculos quânticos com a Emodina em vácuo e em meio solvente, onde consideramos todos os possíveis sítios de desprotonação. Como resultados desses cálculos, identificamos os sítios da primeira, segunda e terceira desprotonação. Calculamos o pKa1 da Emodina em água e o pK*a1 em metanol através de simulações computacionais com o método Monte Carlo e cálculos quânticos, com o solvente descrito com o modelo contínuo polarizável. Nossos melhores valores para o pKa1 da Emodina determinados nesses solventes foram 8.4±0.5 e 10.3±1.5, que estão em boa concordância com os valores experimentais, (pKa1=8.0±0.2 e pK*a1=11.1±0.1) obtidos nesta tese para Emodina em água e metanol, respectivamente. Adicionalmente realizamos simulações com Dinâmica Molecular com as espécies EMH e EM- em bicamada lipídica de DMPC, para investigar a nível atômico as interações dessas espécies com a bicamada e determinar as posições preferenciais dessas espécies nesse ambiente anfifílico. Os resultados dessas simulações mostraram que as espécies EMH e EM- ficam inseridas na bicamada, na região polar dos lipídios, próximos aos gliceróis. Esses resultados corroboram as nossas medidas do espectro de absorção dessas espécies em bicamada lipídica, onde mostramos de forma qualitativa, que ambas as espécies ficam inseridas na bicamada, na região das cabeças polares dos lipídios. A análise das propriedades estruturais da bicamada na vizinhança das espécies da Emodina como área por lipídio e densidade eletrônica dos lipídios, mostrou que o efeito da EM- na estrutura da bicamada lipídica é maior do que o da EMH. Esses resultados corroboram as nossas medidas de DSC(Differential Scanning Calorimetry) das espécies da Emodina na bicamada. / Emodin (EMH) is one of the most abundant anthraquinone derivatives found in nature. This molecule has been used widely as research material, due to its biological and pharmacological activities such as antiviral, anticancer, antifungal, digestive and antibacterial activities. It is known that Emodin in alkaline aqueous solution can undergo more than one deprotonation, leading to the specie EM- in the first deprotonation process. In this PhD thesis, we studied the structural and electronic properties of this molecule in several solvents and lipid bilayers, in order to characterize the properties related to UV-Vis absorption spectroscopy, reactivity and thermodynamics of this molecule in these environments. Performing quantum mechanics (QM) calculations for all possible deprotonation sites and tautomeric isomers of Emodin in vacuum and in water, we identified the sites of the first, second and third deprotonations. We calculated the pKa1 of Emodin in water and pK*a1 in methanol with free energy perturbation method, implemented in the Monte Carlo simulation, and with QM calculations, where the solvent was treated as a polarizable continuum medium. Our best values for pKa1 of Emodin in these solvents were 8.4±0.5 and 10.3±1.5, which are in very good agreement with the experimental values obtained in this thesis pKa1=8.0±0.2 and pK*a1=11.1±0.1, for water and methanol, respectively. Additionally, we performed molecular dynamics simulations of both species in fully hydrated lipid bilayers of DMPC to investigate at atomic detail the molecular mechanism of the interaction of these species with lipid membrane and its preferred positions in this amphiphilic environment. As results of these simulations, we obtained that both species of Emodin have a strong tendency to insert into the lipid bilayer, remaining near the glycerol group of DMPC. These results corroborate our measured absorption spectra of these species in the bilayer, which qualitatively showed that both species are within the bilayer, inserted in the lipid headgroup region. Our results also show that the effect of EM- specie in the lipid bilayer structure is stronger than the EMH, which corroborate our DSC(Differential Scanning Calorimetry) measurements.