<p> There is a dearth of experimental techniques that can probe the dynamic properties of non-equilibrium condensed phases, particularly in materials characterized by very slow kinetics, such as glasses. Although fundamental theories on the glass transition and the properties of glass forming liquids abound, none can be validated because there is insufficient experimental data on the molecular dynamics of these materials at temperatures near the glass transition. In this Dissertation, I demonstrate the utility of a novel technique, Fast Scanning Calorimetry (FSC), to interrogate the kinetic and thermodynamic parameters of non-equilibrium condensed phases. The custom-built, quasi-adiabatic, thin-wire calorimeter can quickly heat micrometer scale crystalline, liquid, or glassy samples, all rapidly prepared by vapor deposition, to obtain high resolution and accurate data for non-equilibrium structural relaxation. Essentially, fast temperature scanning vibrationally perturbs the material far from its initial or equilibrium state and the calorimeter can measure the structural response of the material to these thermal perturbations. </p><p> My FSC studies reveal that, in the limit of high heating rates on the order of 10⁶ K/s, the kinetics of any phase transition, e.g. glass devitrification, viscous liquid relaxation, or crystalline melting, simplify greatly to follow a zero-order rate law with an Arrhenius-like temperature dependence. The discovery of this unique kinetic regime, along with the analytical methodology developed in this Dissertation, have opened a new venue for gathering data on the molecular mobility of glassformers at low temperatures. Studies on the melting of superheated molecular crystals illustrate the capabilities of FSC and expose long-held misconceptions on the mechanism of heterogeneous melting. The observed high activation energy barriers to this diffusion-limited process demonstrate that, under conditions of rapid heating, the structure of the material at the crystalline-amorphous interface is surprisingly similar to that of a glass. </p><p> Furthermore, FSC studies that compare the devitrification of ordinary, melt-cooled glasses and vapor deposited amorphous phases confirm that both materials can undergo heterogeneous, surface-facilitated relaxation when heated with a sufficiently high rate. The high activation energies for these relaxation processes reflect the kinetic properties of the materials in their initial states at low temperatures, not at the temperatures at which transformation occurs. FSC studies that utilized a set of glass-forming liquid samples with well-defined initial states confirm the impact of initial sample temperature on the transformation rate and provide validation for a proposed model of front-propagated structural relaxation. In fact, the data measured by FSC can be used to calculate the thermodynamic driving force for front propagation and provide quantitative validation of the proposed relaxation mechanism. </p><p> Finally, the FSC relaxation rate data with the aforementioned sample set shows an astounding correlation with molecular self-diffusion at low temperatures, demonstrating that the technique can be used to measure diffusivity in condensed phases with very slow dynamics, even below the glass transition. The last study of this Dissertation is a preliminary exploration of the slow molecular kinetics in amorphous vapor-deposited materials with very stable initial structures. The results of these experiments implicate the existence of a crossover in equilibrium mobility parameters at temperatures below the glass transition, an unprecedented finding that may have a significant impact on developing an accurate theoretical framework for the formation and devitrification of glasses.</p><p>

<p> The acid-base chemistry that drives catalysis in pyridoxal-5'-phosphate (PLP)-dependent enzymes has been the subject of intense interest and investigation since the initial identification of its role as cofactor in this extensive class of enzymes. X-ray crystallography, optical spectroscopy, and physical-organic studies point to the importance of protonation/deprotonation at ionizable sites on the coenzyme, substrates, and sidechains to activate key steps in the catalytic process. Yet direct characterization remains elusive as these techniques cannot specifically identify proton locations or report unambiguously on local chemical environment. The chemical shift in nuclear magnetic resonance (NMR), however, is an extremely sensitive probe of chemical environment, but a large complex like a protein will give an enormous amount of data that can be inscrutable without guidelines for specific structure determination. The use of computational chemistry aids in the creation of models that rely on specific chemical-level details and predicts detailed information like chemical shift. We employ NMR crystallography &ndash; the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry - to define three-dimensional, chemically-detailed structures of the intermediates in the tryptophan synthase cycle under conditions of active catalysis. Together these methods can provide consistent and testable models for structure and function of enzyme active sites. Our results from studies on tryptophan synthase confirm some long-held mechanistic hypotheses, but also point to several novel structural hypotheses.</p><p>

<p> Quantum control theory (QCT) is concerned with the active manipulation of phys- ical and chemical processes on the atomic and molecular scale. For a specified con- trol objective, and with restrictions imposed by many possible constraints, the time- dependent field required to manipulate the system in a desired way can be designed using quantum control theory. This dissertation proposes several novel applications of QCT to actively manipulate the dynamics of both quantum and classical systems with and without interactions with an external environment, in both relativistic and non-relativistic regimes. In Chapter 2, the paradigm of spectral dynamic mimicry (SDM) in which laser fields are shaped to make any atomic and molecular systems look identical spectrally is put forward. SDM successfully avoids optimization rou- tines, and provides a powerful tool to find a laser pulse that induces a desired optical response from an arbitrary dynamical system. As illustrations, driving fields are com- puted to induce the same optical response from a variety of distinct systems (open and closed, quantum and classical). The formulation may also be applied to design materials with specified optical characteristics. These findings reveal unexplored flex- ibilities of nonlinear optics. Little is known about the control of relativistic quantum systems. Therefore, an extension of QCT to the Dirac equation is proposed. The main contributions are: (i) Chapters 3 and 4 reach an unprecedented level of control while providing exciting new insights on the complex quantum dynamics of relativis- tic electrons. The method developed provides a very powerful tool to generate new analytical solutions to the Dirac equation, (ii) Chapters 5 and 6 present an open system interaction formalism for the Dirac equation. The presented framework en- ables efficient numerical simulations of relativistic dynamics within the von Neumann density matrix and Wigner phase space descriptions, an essential requirement for the application of QCT, (iii) Chapter 7 proposes a Lindblad model of quantum elec- trodynamics (QED). The presented formalism enables a very efficient and practical numerical method to simulate QED effects, such as the Lamb shift and the anomalous magnetic moment of the electron, for a broad variety of systems.</p><p>

The field of analytical chemistry is very important to today's society as more and more regulations and legislations emerge regarding trace elements in food, consumer products, medicines, and the environment. Like many areas of science, the current goals of trace elemental measurements and speciation are to increase knowledge on the subject and to improve upon current techniques by enhancing the figures of merit, such as accuracy and reproducibility, meanwhile balancing with the cost and time of analysis. The topics covered in this work were investigated primarily through the use of inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma optical emission spectrometry (ICP-OES). The phenomenon of compound-dependent responses in plasma spectrometry is discussed, seeking possible causes of it and offering some advice on how to prevent it. A new method was developed for the speciation of selenium in dietary supplements using anion-exchange chromatography ICP-MS. A novel method for the determination of total mercury at trace concentrations in rice was developed for use with conventional ICP-MS. Inductively coupled plasma mass spectrometry was also used for fingerprinting the rare earth elements in Maya archaeological pottery for provenance studies.

Optical activity is the defining property of chiral materials that is essential for characterization in biology, chemistry, and physics. While a substantial body of research has provided a strong theoretical framework of the origin of optical activity, we still know very little by way of experiment about an individual molecule's contribution to the bulk optical activity. The chiroptical response of a single molecule can depend on molecular orientation and local molecular environment, information which is lost in ensemble averaging. This thesis focuses on establishing methods for a priori determination of chiral molecule orientations and refining measurements to probe the chiroptical response of a single molecule using a generalization of well-known defocused emission pattern imaging. Recent experiments probing the chiroptical response of single helicene dimer molecules offer new insight into the relationship between local molecular environment and coupling between chiral moieties. New experiments, such as probing the chiroptical response of an achiral, non-centrosymmetric molecular systems and polarization resolved spectral measurements which probe the Davydov splitting of coupled chromophore systems offer promising new avenues for understanding the connection between the polarization properties of single molecules and the ensemble.

We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behavior of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constantpressure molecular dynamics using the AMBER 94 force field, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as clusters, we gathered statistics on cluster sizes and percolating pathways as a function of temperature, for comparison with the same quantities extracted from neat imidazole liquid. We have found that, at a given temperature, the glass composed of imidazole 5-mers shows the same hydrogen bond mean cluster size as that from the 10-mer glass, and that this size is consistently larger than that in liquid imidazole. Hydrogen bond clusters were found to percolate across the simulation cell for all glassy and crystalline solids, but not for any imidazole liquid. The apparent activation energy associated with hydrogen bond lifetimes in these glasses (9.3 kJ/mol) is close to that for the liquid (8.7 kJ/mol), but is substantially less than that in the crystalline solid (13.3 kJ/mol). These results indicate that glassy oligomeric solids show a promising mixture of extended hydrogen bond clusters and liquid-like dynamics. This study prompted a continued look at smaller oligomers (monomers, dimers, trimers, and pentamers). Using many of the above statistics we found that decreased chain length decreased the tendency to form global hydrogen bonding networks (percolation pathways). We also developed an reorientational correlation for the imidazole ring which allowed us to extract a timescale for reorientation. Smaller chains produce faster reorientation timescales and thus there is a trade off between faster reorientation dynamics and long global hydrogen bonding networks. Moreover we showed that homogeneity of chain length has no effect on hydrogen bonding statistics. Initial development on a multi-state empirical valence bond model has been to study proton transfer in liquid imidazole. We have shown that GAFF produces very large proton transfer barriers created by a highly repulsive N˙ ˙ ˙H VDW interaction at the transition point. In order to produce an acceptable fit to the potential energy surface while still producing stable dynamics this interaction must be turned off. This is in contrary to what is reported in the literature [14]. Using our model we have produced simulations with acceptable drift in the total energy (3.2 kcal/mol per ns) and negligible drift in the temperature (.12 K/ns).

We have modeled proton transfer using quantum chemical methods in important catalytic material namely Zeolite and polymeric systems to design anhydrous proton exchange membranes for fuel cells (charge transporting materials). In the H-Y Zeolite proton transfer study, we computed the total mean rate coefficient for proton transfer in bare H-Y Zeolite, for comparison with NMR experiments and previous calculations. The proton transfer energies were calculated using two-layer ONIOM calculations on an 8T-53T cluster, where xT indicates x tetrahedral atoms. Rate coefficients were computed using truncated harmonic semi-classical transition state theory. The zero-point energy (ZPE) corrected proton site energies in H-Y (FAU structure) were found to be O3 (0 kJ mole -1), O1 (2.1 kJ mole-1), O2 (16.1 kJ mole-1 ) and O4 (17.5 kJ mole-1), in quantitative agreement with previous calculations and in qualitative agreement with neutron diffraction occupancies. The ZPE corrected activation energies range from 35 to 123 kJ mole-1. Total mean rate coefficients were found to exhibit a strong non-Arrhenius temperature dependence, with apparent activation energies in the range ca. 60-100 kJ mole-1 at high temperature, and ca. 3 kJ mole-1 at low temperature. This low-temperature value reflects thermally assisted tunneling to a site with slightly higher energy. NMR experiments by Sarv et al. and Ernst et al. report apparent activation energies of 61 and 78 kJ mole -1, respectively, extracted from temperature ranges 298–658 and 610–640 K. Our theoretically computed apparent activation energies for these temperature ranges are 72 and 79 kJ mole-1, respectively, in quite good agreement with experiment. In the Grotthuss proton transfer and design criteria for anhydrous proton exchange membrane study, we have modeled structures and energetics of anhydrous proton-conducting wires: tethered hydrogen-bonded chains of the form ··· HX ··· HX ··· HX ···, with functional groups HX = imidazole, triazole and formamidine; formic, sulfonic and phosphonic acids. We have applied density functional theory (DFT) to model proton wires up to 19 units long, where each proton carrier is linked to an effective backbone to mimic polymer tethering. This approach allows the direct calculation of hydrogen bond strengths. The proton wires were found to be stabilized by strong hydrogen bonds (up to 50 kJ mole-1) whose strength correlates with the proton affnity of HX [related to pK b(HX)], and not to pKa(HX) as is often assumed. Proton translocation energy landscapes for imidazole-based wires are sensitive to the imidazole attachment point (head or feet) and on wire architecture (linear or interdigitated). Linear imidazole wires with head-attachment exhibit low barriers for intrawire proton motion, rivaling proton diffusion in liquid imidazole. Excess charge relaxation from the edge of wires is found to be dominated by long-range Grotthuss shuttling for distances as long as 42 Å, especially for interdigitated wires. For imidazole, we predict that proton translocation is controlled by the energetics of desorption from the proton wire, even for relatively long wires (600 imidazole units). Proton desorption energies show no correlation with functional group properties, suggesting that proton desorption is a collective process in proton wires. In the aim of mimicking water, phenolic systems were studied using LSDA/6-311G(d,p). We find using density functional theory calculations on phenolic dimers that their polymers have low re-orientation barrier 13.7 kJ mole-1 compared to the imidazole/triazole systems in which the whole group has to rotate. This study shows that the dynamical nature of the hydrogen bonds in the system is very important to consider when searching for a proton transferring functional group for anhydrous proton exchange membranes.

Ab initio calculations were utilized to demonstrate the theory behind molecular properties and were correlated to actual spectroscopic results in the infrared and Raman. Symmetrical aspects of small flexible molecules were examined to determine how symmetry coordinates mix in the potential energy distribution and whether these are infrared and Raman active. The difficulty is the spectroscopic landscape of the spectrum gets extremely complicated even in very small carbon chain dihalides. The example of 1,4-dichlorobutane is provided. The work here will provide a solid reference for future research as we have found in previous work that 1,2-dibromopropane, a sensitive compound, has in previous publications shown what looks to be degradation. Three other publications are in preparation allyldichlorosilane, n-butylgermane and n-butylsilane of which the two finial compounds have conformers with the same symmetry. Instrumentation has been updated to be continually maintained and upgraded to be viable and competitive. Times for crystallizations of spectroscopic compounds for the IR and Raman cold cells can exceed 50-60 hours of continuous annealing. Modification and development of equipment allowed a level of automation and a much more precise temperature control at lower temperatures that would not have been possible before.

<p> Over recent years, Ion Mobility&ndash;Mass Spectrometry (IMS&ndash;MS) measurements have become a widely used tool in a number of disciplines of scientific relevance, including, in particular, the structural characterization of mass-selected biomolecules such as proteins, peptides, or lipids, brought into the gas-phase using a variety of ionization methods. In these structural studies, the measured electrical mobilities are customarily interpreted in terms of a collision cross-section, based on the classic kinetic theory of ion mobility. For ideal ions interacting as smooth, rigid-elastic hard-spheres with also-spherical gas molecules, this <i>collision cross-section</i> (CCS) is identical to the <i>true</i>, geometric cross section. On the other hand, for real ions with non-perfectly spherical geometries and atomically-rough surfaces, subject to long-range interactions with the gas molecules, the expression for the CCS can become fairly intricate.</p><p> This complexity has frequently led to the use of helium as the drift gas of choice for structural studies, given its small size and mass, its low polarizability (minimizing long-range interactions), and its sphericity and lack of internal degrees of freedom, all of which contribute to reduce departures between measured and true cross-sections. Recently, however, a growing interest has arisen for using moderately-polarizable gases such as air, nitrogen, or carbon dioxide (among others) in these structural studies, due to a number of advantages they present over helium, including their higher breakdown voltages (allowing for higher instrument resolutions) and better pumping characteristics. This shift has, nevertheless, remained objectionable in the eye of those seeking to infer accurate structural information from ion mobility measurements and, accordingly, there is a critical need to study whether or not measurements carried out in such gases may be corrected for the finite size of the gas molecules and their long-range interactions with the ions, in order to provide cross-sections truly representative of ion geometry. A first step to address this matter is undertaken here for the special case of nearly-spherical, nanometer-sized ions.</p><p> In order to attain this goal, we have performed careful and accurate IMS&ndash;MS measurements of hundreds of electrospray-generated nanodrops of the ionic liquid (IL) 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF₄), in a variety of drift gases (air, CO₂, and argon), covering a wide range of temperatures (20-100 &deg;C, for both air and CO₂), and considering nanodrops of both positive and negative polarity (the latter in room-temperature air only). Thanks to the combined measurement of the mass and mobility of these nanodrops, we are able to simultaneously determine a mobility-based collision cross-section and a mass-based diameter (taking into account the finite compressibility of the IL matter) for each of them, which then allows us to establish a comparison between the two.</p><p> Over the entire range of experimental conditions investigated, our measurements show that the electrical mobilities of these nearly-spherical, multiply-charged IL nanodrops are accurately described by an adapted version of the well-known Stokes&mdash;Millikan (SM) law for the mobility of spherical ions, with the nanodrop diameter augmented by an effective gas-molecule collision diameter, and including a correction factor to account for the effect of ion&mdash;induced dipole (polarization) interactions, which result in the mobility decreasing linearly with the ratio between the polarization and thermal energies of the ion&ndash;neutral system at contact. The availability of this empirically-validated relation enables us, in turn, to determine true, geometric cross-sections for globular ions from IMS&mdash;MS measurements performed in gases other than helium, including molecular or atomic gases with moderate polarizabilities. In addition, the observed dependence of the experimentally-determined values for the effective gas-molecule collision diameter and the parameters involved in the polarization correction on drift-gas nature, temperature, and nanodrop polarity, is further evaluated in the light of the results of numerical calculations of the electrical mobilities, in the free-molecule regime, of spherical ions subject to different types of scattering with the gas molecules and interacting with the latter under an ion&ndash;induced dipole potential. Among the number of findings derived from this analysis, a particularly notable one is that nanodrop&ndash;neutral scattering seems to be of a <i>diffuse</i> (cf. elastic and specular) character in all the scenarios investigated, including the case of the monatomic argon, which therefore suggests that the atomic-level surface roughness of our nanodrops and/or the proximity between their internal degrees of freedom, rather than the sphericity (or lack of it) and the absence (or presence) of internal degrees of freedom in the gas molecules, are what chiefly determine the nature of the scattering process.</p>

<p> 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 (<i>V_oc</i>) by 160% and short circuit current (<i>J_sc</i>) 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).</p>