Teses / dissertações sobre o tema "Physics chemistry"

We use non-adiabatic ab initio molecular dynamics to study the influence of substituent side groups on the photoactive unit (Z)-hexa-1,3,5-triene (HT). The Time-Dependent Density Functional Theory Surface Hopping method (TDDFT-SH) is used to investigate the influence of substituted isopropyl and methyl groups on the excited state dynamics. The 1,4 and 2,5-substituted molecules are simulated: 2,5-dimethylhexa-1,3,5-triene (DMHT), 2-isopropyl-5-methyl-1,3,5-hexatriene (2,5-IMHT), 3,7-dimethylocta-1,3,5-triene (1,4-IMHT), and 2,5-diisopropyl-1,3,5-hexatriene (DIHT). We find that HT and 1,4-IMHT have the lowest ring-closing branching ratios of 5.3% and 1.0%, respectively. For the 2,5-substituted derivatives, the branching ratio increases with increasing size of the substituents, exhibiting yields of 9.78%, 19%, and 24% for DMHT, 2,5-IMHT, and DIHT, respectively. The reaction channels are shown to prefer certain conformation configurations at excitation, where the ring-closing reaction tends to originate from the gauche-Z-gauche (gZg) rotamer almost exclusively. In addition, there is a conformational dependency on absorption, gZg conformers have on average lower S₁ ← S₀ excitation energies that the other rotamers. Furthermore, we develop a method to calculate a predicted quantum yield that is in agreement with the wavelength-dependence observed in experiment for DMHT. In addition, the quantum yield method also predicts DIHT to have the highest CHD yield of 0.176 at 254 nm and 0.390 at 290 nm.

Additionally, we study the vitamin D derivative Tachysterol (Tachy) which exhibits similar photochemical properties as HT and its derivatives. We find the reaction channels of Tachy also have a conformation dependency, where the reactive products toxisterol-D1 (2.3%), previtamin D (1.4%) and cyclobutene toxisterol (0.7%) prefer cEc, cEt, and tEc configurations at excitation, leaving the tEt completely non-reactive. The rotamers similarly have a dependence on absorption as well, where the cEc configuration has the lowest energy S ₁ ← S₀ excitation of the rotamers. The wavelength dependence of the rotamers should lead to selective properties of these molecules at excitation. An excitation to the red-shifted side of the maximum absorption peak will on average lead to excitations of the gZg rotamers more exclusively.

Energy generation via organic photovoltaic (OPV) cells provide many advantages over alternative processes including flexibility and price. However, more efficient OPVs are required in order to be competitive for applications. One way to enhance efficiency is through manipulation of exciton mechanisms within the OPV, for example by inserting a thin film of bathocuproine (BCP) and gold nanoparticles between the C₆₀/Al and ZnPc/ITO interfaces, respectively. We find that BCP increases efficiencies by 330% due to gains of open circuit voltage (V_oc) by 160% and short circuit current (J_sc) by 130%. However, these gains are complicated by the anomalous photovoltaic effect and an internal chemical potential. Exploration in the tuning of metallic nanoparticle deposition on ITO was done through four techniques. Drop casting Ag nanoparticle solution showed arduous control on deposited morphology. Spin-coating deposited very low densities of nanoparticles. Drop casting and spin-coating methods showed arduous control on Ag nanoparticle morphology due to clustering and low deposition density, respectively. Sputtered gold on glass was initially created to aid the adherence of Ag nanoparticles but instead showed a quick way to deposit aggregated gold nanoparticles. Electrodeposition of gold nanoparticles (AuNP) proved a quick method to tune nanoparticle morphology on ITO substrates. Control of deposition parameters affected AuNP size and distribution. AFM images of electrodeposited AuNPs showed sizes ranging from 39 to 58 nm. UV-Vis spectroscopy showed the presence of localized plasmon resonance through absorption peaks ranging from 503 to 614 nm. A linear correlation between electrodeposited AuNP size and peak absorbance was seen with a slope of 3.26 wavelength(nm)/diameter(nm).

Rhodopsin is a visual pigment found within the rod photoreceptor cells of the retina. It is a visual protein found within human beings and commonly shared amongst other vertebrate species. The major pigment protein is responsible for converting photons into chemical signals, which stimulates biological processes in the nervous system, and this allows the ability to then sense light.

The process of how rhodopsin is activated is believed to be understood with the introduction of a time ordered sequence of intermediate states. However, there are still major gaps and inconsistencies regarding the large-scale conformational changes that follow photoactivation.

The purpose of our experimental research is to use small angle neutron and x-ray scattering techniques to illuminate the structural changes and dynamics of rhodopsin that lead to the activation of the photoreceptor, and thus triggering of the amplified visual response.

The generation of attosecond-duration (1 as = 10^–18 s) coherent light through the process of high-order harmonic generation has opened the perspective for probing fundamental processes, such as photoionization, on the natural timescale of electron dynamics in matter. One probing technique is the attosecond streaking method, in which the momentum of the photoelectron is measured as a function of the time delay between the ionizing, attosecond extreme ultraviolet (XUV) pulse, and a weak, femtosecond near-infrared (NIR) pulse which streaks the momentum of the photoelectron, known as a streaking trace. The observed trace contains time information about the photoionization process in the form of a time offset to the vector potential of the streaking field, known as the streaking time delay. Theoretical simulations show that for one-photon ionization this time delay is accumulated by the photoelectron in the continuum when propagating away from the parent ion, whereas for resonant two-photon ionization there exists an additional absorption delay which depends on the properties of the XUV pulse. In this thesis, we use both analytical techniques and numerical simulations to study the contributions of the total time delay observed in streaking, and further explore applications of the streaking time delay to gain insights into the electron dynamics. We first derive an analytical formula for the streaking time delay in one-photon ionization. The predictions based on the model formula, which can be performed within seconds of computation time, are in good agreement with those of computationally extensive numerical simulations.

We demonstrate that the analytical formula not only allows deeper insight into the nature of the time delay, but also offers the opportunity to effectively analyze other theoretical interpretations and potential effects, such as the effect of a chirp in the ionizing attosecond pulse on the time delay measurement. We then apply time-dependent perturbation theory to derive an analytical formula for the absorption delay in resonant two-photon ionization. We use the analytical formula to demonstrate how the absorption delay can be controlled further by the attosecond pulse duration and central frequency in case of an isolated resonance. Furthermore, we show how multiple resonances within the bandwidth of the ionizing pulses as well as the streaking field influence the absorption delay in model systems as well as simple atoms and molecules. We conclude by exploring the option to apply isolated elliptically polarized attosecond pulses to obtain sub-attosecond temporal information via the observation of photoelectron angular distributions as a function of the ellipticity of the pulse.

A physical model for redox flow batteries is developed to estimate performance for any chemistry using parameters such as electrolyte conductivity and kinetic rate constants. The model returns the performance as a function of flow rate, current density, and state of charge. Two different models are developed to estimate the current density distribution throughout the electrode in order to evaluate physical performance of the battery. This is done using electrochemical parameters such as conductivity and kinetic rate constant. The models are analytical in order to produce a computationally cheap algorithm that can be used in optimization routines. This allows for evaluating the economic performance of redox flow batteries, and optimization of cost. The models are validated vs data and found to accurately predict performance in a V-V system for a wide variety of operating conditions.

Quantum Monte Carlo techniques stochastically evaluate integrals to solve the many-body Schrödinger equation. QMC algorithms scale favorably in the number of particles simulated and enjoy applicability to a wide range of quantum systems. Advances in the core algorithms of the method and their implementations paired with the steady development of computational assets have carried the applicability of QMC beyond analytically treatable systems, such as the Homogeneous Electron Gas, and have extended QMC’s domain to treat atoms, molecules, and solids containing as many as several hundred electrons.

FN-DMC projects out the ground state of a wave function subject to constraints imposed by our ansatz to the problem. The constraints imposed by the fixed-node Approximation are poorly understood. One key step in developing any scientific theory or method is to qualify where the theory is inaccurate and to quantify how erroneous it is under these circumstances.

I investigate the fixed-node errors as they evolve over changing charge density, system size, and effective core potentials. I begin by studying a simple system for which the nodes of the trial wave function can be solved almost exactly. By comparing two trial wave functions, a single determinant wave function flawed in a known way and a nearly exact wave function, I show that the fixed-node error increases when the charge density is increased. Next, I investigate a sequence of Lithium systems increasing in size from a single atom, to small molecules, up to the bulk metal form. Over these systems, FN-DMC calculations consistently recover 95% or more of the correlation energy of the system. Given this accuracy, I make a prediction for the binding energy of Li₄ molecule. Last, I turn to analyzing the fixed-node error in first and second row atoms and their molecules. With the appropriate pseudo-potentials, these systems are iso-electronic, show similar geometries and states. One would expect with identical number of particles involved in the calculation, errors in the respective total energies of the two iso-electronic species would be quite similar. I observe, instead, that the first row atoms and their molecules have errors larger by twice or more in size. I identify a cause for this difference in iso-electronic species. The fixed-node errors in all of these cases are calculated by careful comparison to experimental results, showing that FN-DMC to be a robust tool for understanding quantum systems and also a method for new investigations into the nature of many-body effects.

The Baranger model is used to compute collisional broadening and shift of the D1 and D2 spectral lines of M + Ng, where M = K, Rb, Cs and Ng = He, Ne, Ar, using scattering phase shift differences which are calculated from scattering matrix elements. Scattering matrix elements are calculated using the Channel Packet Method where the collisions are treated non-adiabatically and include spin-orbit and Coriolis couplings. Non-adiabatic wavepacket dynamics are determined using the split-operator method together with a unitary transformation between adiabatic and diabatic representations. Scattering phase shift differences are thermally weighted and integrated over energies ranging from E = 0 Hartree up to E = 0.0075 Hartree and averaged over values of total angular momentum that range from J = 0.5 up to J = 400.5. Phase shifts are extrapolated linearly to provide an approximate extension of the energy regime up to E = 0.012 Hartree. Broadening and shift coefficients are obtained for temperatures ranging from T = 100 K up to T = 800 K and compared with experiment. Predictions from this research find application in laser physics and specifically with improvement of total power output of Optically Pumped Alkali Laser systems.

This dissertation examines the influence which a geophysical process (giant impacts) has on a geochemical marker (composition) during terrestrial planet formation. Simultaneously studying all planets maximizes the available constraints and permits examination of controls on the overall composition of the Earth. I also examine the Galilean satellite system to determine the universality of the terrestrial conclusions.

The late stages of planetary accretion involve stochastic, large collisions. Impact-related erosion and fragmentation can have profound consequences for the rate and style of accretion and the bulk chemistries of terrestrial planets. However, the previous predominate assumption in computer models of accretion was that all collisions resulted in perfect merging despite the likelihood of these collisions producing a range of outcomes (e.g., hit-and-run, removal of material from target, or production of several post-collision bodies). In this work, I investigate the effects of late-stage accretion with multiple collision types and the consequences on the bulk (mantle/core) and isotopic (Hf–W) composition.

My model is composed of two parts: (1) N-body accretion code tracks orbital and collisional evolution of the bodies and (2) geochemical post-processing evolves composition in light of impact-related mixing, partial equilibration and radioactive decay. For terrestrial planets, Part (1) is Chambers (2013, Icarus) and incorporates multiple collisional outcomes. For Galilean satellites, Part (1) is Ogihara & Ida (2012, Icarus) and assumes perfect merging for all collisions thus the model is not self-consistent (it likely overestimates compositional changes).

For the terrestrial planets, the results are consistent with observed mantle/core ratios and tungsten isotopic anomalies. A moderate (approx. 0.4) core equilibration factor is preferred due to protracted accretion time. It is important to include multi-modal collisions when modeling planet formation if composition, timescales, or spatial distribution of mass are being investigated.

I could not reproduce the observed ice fraction gradient of the Galilean satellites, even with an initial compositional gradient and vaporization of water ice. Some other physical process(es) are needed, perhaps tidally-driven volatile loss at Io and Europa. Extensive inward radial migration smooths out initial compositional gradients.

The objective in this thesis is to study the structure of peptides using molecular spectroscopy. Molecular spectroscopy, both vibrational and electronic, can be used as a sensitive tool to study molecular structure. Since it is an inherently low resolution method, theoretical calculations are essential for a complete understanding of vibrational and electronic spectra. The first part of this thesis contains quantum chemical calculations of the molecular spectra of several small peptide systems with different secondary structures. Optical trapping is a method that allows for the manipulation of sub-micron scale objects using tightly focused laser light. Raman spectroscopy, which is sensitive to molecular vibrations also requires intense laser light. Combined with optical tweezing, Raman spectroscopy can prove to be a very powerful tool to study small sample volumes and probe single living cells. In the second part of this thesis, I detail the construction an such an instrument, an optical trapping Raman spectrometer (OTRS). Our OTRS can measure Raman spectra from sub micron systems while at the same time quantifying the mechanical forces that are acting upon them. Thus the OTRS can give insight into the relationship between mechanical forces acting upon cells and their molecular structure.

Equilibrium sampling is at the core of computational thermodynamics, aiding our understanding of various phenomena in the natural sciences including phase coexistence, molecular solvation, and protein folding. Despite the widespread development of novel sampling strategies over the years, efficient simulation of large complex systems remains a challenge. While the majority of current methods such as simulated tempering, replica exchange, and Monte Carlo methods rely solely on the use of equilibrium techniques, recent results in statistical physics have uncovered the possibility to sample equilibrium states through nonequilibrium simulations.

In our first study we present a new replica exchange sampling strategy, "Replica Exchange with Nonequilibrium Switches," which uses nonequilibrium simulations to enhance equilibrium sampling. In our method, trial swap configurations between replicas are generated through nonequilibrium switching simulations which act to drive the replicas towards each other in phase space. By means of these switching simulations we can increase an effective overlap between replicas, enhancing the probability that these moves are accepted and ultimately leading to more effective sampling of the underlying energy landscape. Simulations on model systems reveal that our method can be beneficial in the case of low replica overlap, able to match the efficiency of traditional replica exchange while using fewer processors. We also demonstrate how our method can be applied for the calculation of solvation free energies.

In a second, separate study, we investigate the dynamics leading to the dissociation of Na⁺Cl^– in water. Here we employ tools of rare event sampling to deduce the role of the surrounding water molecules in promoting the dissociation of the ion pair. We first study the thermodynamic forces leading to dissociation, finding it to be driven energetically and opposed entropically. In further analysis of the system dynamics, we deduce a) the spatial extent over which solvent fluctuations influence dissociation, b) the role of sterics and electrostatics, and c) the importance of inertia in enhancing the reaction probability.

Nuclear spin induced optical rotation (NSOR) is a novel technique for the detection of nuclear magnetic resonance (NMR) via optical rotation instead of conventional pick-up coil. Originating from hyperfine interactions between nuclei and orbital electrons, NSOR provides a new method to reveal nuclear chemical environments in different molecules. Previous experiments of NSOR detection have poor signal-to-noise ratio (SNR), which limits the application of NSOR in chemistry. In this work, based on a continuous-wave NMR scheme at a low magnetic field (5 G), we employ a multi-pass cavity and a 405 nm laser to improve the sensitivity of NSOR. By performing precision measurements of NSOR detection in a range of pure liquid organic chemicals, we demonstrate the capability of NSOR to distinguish 1H signals in different chemicals, in agreement with the first-principles quantum mechanical calculations. The NSOR of 19F is also measured at low fields with high SNR, showing that heavy nuclei have higher optical rotation signals than light nuclei.

In addition, in order to obtain NSOR at different chemical sites in the same molecule via chemical shift, we make efforts to develop a novel scheme based on liquid-core hollow fiber for the detection of NSOR under high magnetic fields. By coiling a long liquid-core fiber densely for many loops around a small rod combined with RF coils, it is possible to measure optical rotation signals inside a narrow-bore superconducting magnet. Manufactured by filling liquids into capillary tubings, those liquid-core fibers perform like multimode step-index fibers, and thereby exhibit linear birefringence and depolarization, significantly reducing the light polarization for the measurement of optical rotation. According to our attempts, it is possible to suppress the linear birefringence by filling chiral liquids in hollow fibers, and approach near single-mode operation by means of launching light beam into the fiber core under the mode match condition. Although some issues of hollow fibers obstruct the final measurement of high-frequency NSOR, our work on the liquid-core fiber provides the basis for future fiber-based NSOR experiments under high magnetic fields.

An approach has been developed for extracting approximate quantum state-to-state information from classical trajectory simulations which "quantizes" symmetrically both the initial and final classical actions associated with the degrees of freedom of interest using quantum number bins (or "window functions") which are significantly narrower than unit-width. This approach thus imposes a more stringent quantization condition on classical trajectory simulations than has been traditionally employed, while doing so in a manner that is time-symmetric and microscopically reversible.

To demonstrate this "symmetric quasi-classical" (SQC) approach for a simple real system, collinear H + H₂ reactive scattering calculations were performed [S.J. Cotton and W.H. Miller, J. Phys. Chem. A 117, 7190 (2013)] with SQC-quantization applied to the H ₂ vibrational degree of freedom (DOF). It was seen that the use of window functions of approximately 1/2-unit width led to calculated reaction probabilities in very good agreement with quantum mechanical results over the threshold energy region, representing a significant improvement over what is obtained using the traditional quasi-classical procedure.

The SQC approach was then applied [S.J. Cotton and W.H. Miller, J. Chem. Phys. 139, 234112 (2013)] to the much more interesting and challenging problem of incorporating non-adiabatic effects into what would otherwise be standard classical trajectory simulations. To do this, the classical Meyer-Miller (MM) Hamiltonian was used to model the electronic DOFs, with SQC-quantization applied to the classical "electronic" actions of the MM model—representing the occupations of the electronic states—in order to extract the electronic state population dynamics. It was demonstrated that if one ties the zero-point energy (ZPE) of the electronic DOFs to the SQC windowing function's width parameter this very simple SQC/MM approach is capable of quantitatively reproducing quantum mechanical results for a range of standard benchmark models of electronically non-adiabatic processes, including applications where "quantum" coherence effects are significant. Notably, among these benchmarks was the well-studied "spin-boson" model of condensed phase non-adiabatic dynamics, in both its symmetric and asymmetric forms—the latter of which many classical approaches fail to treat successfully.

The SQC/MM approach to the treatment of non-adiabatic dynamics was next applied [S.J. Cotton, K. Igumenshchev, and W.H. Miller, J. Chem. Phys., 141, 084104 (2014)] to several recently proposed models of condensed phase electron transfer (ET) processes. For these problems, a flux-side correlation function framework modified for consistency with the SQC approach was developed for the calculation of thermal ET rate constants, and excellent accuracy was seen over wide ranges of non-adiabatic coupling strength and energetic bias/exothermicity. Significantly, the "inverted regime" in thermal rate constants (with increasing bias) known from Marcus Theory was reproduced quantitatively for these models—representing the successful treatment of another regime that classical approaches generally have difficulty in correctly describing. Relatedly, a model of photoinduced proton coupled electron transfer (PCET) was also addressed, and it was shown that the SQC/MM approach could reasonably model the explicit population dynamics of the photoexcited electron donor and acceptor states over the four parameter regimes considered.

The potential utility of the SQC/MM technique lies in its stunning simplicity and the ease by which it may readily be incorporated into "ordinary" molecular dynamics (MD) simulations. In short, a typical MD simulation may be augmented to take non-adiabatic effects into account simply by introducing an auxiliary pair of classical "electronic" action-angle variables for each energetically viable Born-Oppenheimer surface, and time-evolving these auxiliary variables via Hamilton's equations (using the MM electronic Hamiltonian) in the same manner that the other classical variables—i.e., the coordinates of all the nuclei—are evolved forward in time. In a complex molecular system involving many hundreds or thousands of nuclear DOFs, the propagation of these extra "electronic" variables represents a modest increase in computational effort, and yet, the examples presented herein suggest that in many instances the SQC/MM approach will describe the true non-adiabatic quantum dynamics to a reasonable and useful degree of quantitative accuracy.

This dissertation describes the theoretial exploration of electron transfer (ET) processes at the interface between bulk and molecular or nanoscale materials. Analysis of simple model Hamiltonians, those for the two- and three-level electronic systems as well as for a single electronic level coupled to a continuum, inform an understanding of electron transfer in nontrivial systems. A new treatment of the three-level system at an undergraduate level encapsulates the hopping and superexchange mechanisms of electron transfer. The elegance of the behavior of ET from a single-level/continuum system precedes a treatment of the reverse process—quasicontinuum-to-discrete level ET. This reverse process, relevant to ET from a bulk material to a semiconductor quantum dot (QD) offers a handle for the coherent control of ET at an interface: the shape of an electronic wavepacket within the quasicontinuum. An extension of the single-level-to-continuum ET process is the injection of an electron from a QD to a wide-bandgap semiconductor nanoparticle (NP). We construct a minimal model to explain trends in ET rates at the QD/NP interface as a function of QD size. Finally, we propose a scheme to gate ET through a molecular junction via the coherent control of the torsional mode(s) of a linking molecule within the junction.

A large focus of this thesis was developing the experimental procedures involved in imaging VO₂ during the heating process. In order to study light interactions between an induced dipole and a sample surface to collect various data on its topography, amplitude and phase. Data is collected using a near-eld microscope (s-SNOM) and analyzed using various software that, normalize, lter and display the data in false color image. Specically, research behind this thesis, focuses on the phase transition of Vanadium Dioxide (VO₂) as it goes from an insulating to fully metallic phase. Using a wavelength of λ = 10:7μm to image the resonant behavior of the sample, the nucleation of VO₂ was imaged as the temperature increased.

Low interfacial electron-hole recombination rates are essential for low-noise electronic devices and high-efficiency solar energy converters. This recombination rate is dependent on both the surface electrical trap state density, NT,s, and the surface concentrations of electrons, ns, and holes, ps. A reduction in NT,s is often accomplished through surface chemistry, and lower recombination rates, through lower NT,s values, have been demonstrated in this work for surfaces chemically treated to produce methoxylated, Si-O-CH3, overlayers. The H-Si(111) surfaces can react with methanol quickly in the presence of an oxidant or slowly in neat anhydrous methanol. Mechanisms have been proposed for both reactions.

Low recombination rates can also be achieved through control of the surface physics; a large ns or ps can lower recombination rates. To date, low recombination rates have often been attributed only to a reduction in NT,s, without a direct measurement of ns and ps, partly because the importance of ns and ps has not been fully recognized and partly because an accurate evaluation of ns and ps can be very difficult. Surface recombination rates of silicon immersed in liquids containing various redox species (e.g., Fc+/0, I2, Me10Fc+/0, or CoCp2+/0) were studied using an rf photoconductivity decay apparatus and compared with ns and ps values obtained from Mott-Schottky and other analysis techniques. The results demonstrate that the observed recombination rates can only be correlated with NT,s values when ns [approx.] ps. In all other cases, the recombination rate was low due to a large ns or ps even for surfaces with large NT,s values.

The full impact of this work was further realized through a study of the recombination rates of H-Si immersed in solutions of 48% HF, 40% NH4F, and buffered HF (BHF), because such measurements are often performed for in situ monitoring of the surface quality during wafer processing steps. Our results demonstrate that only HF contacts can be used for in situ monitoring because ns [approx.] ps. For NH4F or BHF contacts, low recombination rates were observed only because ns » ps, and NT,s cannot be inferred from these measurements.