High resolution absorption spectra of the IF molecule in the X¹Σ⁺ ground state were observed with the Kitt Peak Fourier transform spectrometer in a F₂/I₂ flame. Iodine fluoride is the most unstable interhalogen compound. Accurate wavenumber measurements (±0.0002 cm⁻¹) were made for the 1-0, 2-1 and 2-0 bands and molecular constants were derived. The observation of a high resolution emission spectrum at 13 μm (750 cm⁻¹) is unusual. Seven bands (1-0 through 7-6) of the main isotopic form, ²⁸Si³²S, were observed along with three bands (1-0, 2-1 and 3-2) for each of the minor species, ²⁹Si³²S, ³⁰Si³²S and ²⁸Si³⁴S. More than 2450 lines were fitted for this important astrophysical molecule. Dunham coefficients were obtained for each isotopomer of SiS. Mass-reduced Dunham parameters, including Watson's correction due to the breakdown of the Born-Oppenheimer approximation, were also derived from the data. The first high resolution spectrum of a metal dihalides was recorded by infrared emission spectroscopy. The infrared emission spectrum of BeF₂ was observed in the region of the antisymmetric stretching mode, ν₃, and the combination band, ν₁ + ν₂. Eight vibration-rotation bands were rotationally analyzed and the spectroscopic constants are reported. The equilibrium beryllium fluoride bond distance (rₑ) was found to be 1.3729710(95)Å in BeF₂. Values of the vibrational frequencies of all the three normal modes were obtained from the spectra. The gas phase infrared spectrum of C₆₀ (buckminsterfullerine) has been observed in emission with the National Solar Observatory Fourier transform spectrometer at Kitt Peak. Bands attributable to the C₆₀ molecule are found at 527.1 cm⁻¹, 570.3 cm⁻¹, 1169.1 cm⁻¹ and 1406.9 cm⁻¹. Additional emission features are tentatively assigned to C₇₀ or combination bands of C₆₀. A new, strong emission is observed at 1010.2 cm⁻¹ belonging to an unknown molecule. A new electronic state of ³Π symmetry of PtO has been observed between 7100 cm⁻¹ and 8015 cm⁻¹ above the ground state. This new state was observed through an electronic transition to the ³Σ⁻ ground state of this free radical. Three independent electronic systems connecting the Ω = 0,1 and 2 spin components in the upper state to Ω = 1 component in the ground state have been recorded in emission with the Fourier transform spectrometer associated with the McMath Solar Telescope at Kitt Peak. (Abstract shortened with permission of author.)

This dissertation presents the results of several investigations into nonadiabatic reaction dynamics in the 0.5 to 10 K temperature regime. The free jet flow reactor technique for production of very low local temperatures and the method for extraction of reaction rate coefficients in this unique environment is reviewed. Ion-neutral reactions which exhibit nonadiabatic behavior are initiated by state selective resonantly enhanced multiphoton ionization and the reactions are subsequently studied using time of flight mass spectrometric detection. The importance of long lived collision complexes in nonadiabatic ion-neutral reactions is reemphasized. Collisional electronic spin orbit relaxation of Xe⁺(²P(½) is shown to be very inefficient for a wide variety of collision partners. A sequential two electron charge transfer mechanism is proposed to account for the high efficiency of the fine structure relaxation by methane and nitrous oxide both of which have open charge transfer channels. The results of fine structure state specific reactions of Ar⁺(²P(J)) with H₂, D₂, HD, CH₄ and CD₄ are presented as examples of nonadiabatic atom and electron transfer reactions. Preliminary results on vibrational-rotational relaxation of neutrals in the free jet at very low temperatures using a pump-probe technique are presented.

In this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute high-accuracy ground and excited electronic states. Chapters 1 and 2 should be seen as introductory Chapters, where the mathematical foundations of modern electronic structure theory necessary to understand this work are laid down. Chapters 3 and 4 covers the development of methods and algorithms relevant to ground state computations. We propose a semi-definite-based algorithm to compute ground-state Hartree-Fock energies and wave functions, that can be easily extended to Kohn-Sham density functional theory. We also propose a parametrized coupled-pair functional to compute accurate non-covalent molecular interaction energies. Chapters 3 through 7 cover methods relevant to excited state computations. We propose an explicitly time-dependent coupled-cluster framework rooted on the equation-of-motion formalism to compute linear absorption spectra of molecular systems. The method is further expanded by recasting a linear absorption line shape function in terms of Pad ́e approximants. The expanded method is shown to be an efficient tool for the simulation of near-edge X-ray absorption fine structure. Finally, we propose a time-dependent Hartree-Fock method within the framework of cavity quantum-electrodynamics that allows us to simulate the interaction of molecular systems with quantized radiation fields, such as those found on plasmonic nanoparticles and nano cavities. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester 2017. / November 15, 2017. / Includes bibliographical references. / Albert Eugene DePrince, III, Professor Directing Dissertation; Sachin Shanbhag, University Representative; Naresh Dalal, Committee Member; Oliver Steinbock, Committee Member.

This thesis presents a joint experimental and theoretical study of the state-to-state resolved rotationally inelastic scattering of NO(X) with atoms and homonuclear diatoms. Emphasis is placed on measuring the correlations between the vectors which describe the system: k and k' the initial and final relative velocities, respectively, r the initial NO bond axis orientation, and j' the final rotational angular momentum of NO. Experimentally, the initial f Δ-doublet state of NO(X) is selected using a Hexapole state selector, and the scattered NO detected using (1+1') REMPI. In the first part of this thesis the k-k' correlation in the scattering of NO(X) with O2(X) is presented. A modified onion peeling algorithm is used to extracted the (partially) pair correlated angular distributions from the experimental ion images, as well as the relative populations of O₂ rotational states populated during scattering. Strong similarities are observed between the scattering of NO with Ar and O₂. The second part of this thesis focuses on steric effects (the r - k - k' correlation); the initial orientation of the NO bond axis is controlled using a static electric field, such that the collision partner approaches either the 'ends' or the 'sides' of the NO molecule. A new quantum mechanical theory is presented to describe the scattering of a symmetric top molecule in the presence of an arbitrarily directed electric field. The scattering of NO(X) with Ar at a collision energy of E_coll = 651cm^-1 is presented for 'end-on' and 'side-on' scattering on the spin-orbit changing and conserving manifolds, respectively. In both cases good agreement with full quantum mechanical calculations is observed. Scattering resulting in only weak deflection is shown to be very sensitive to the orientation of the NO bond axis prior to collision, and is maximised for collisions at the 'side' of the molecule. The integral steric asymmetry for scattering of NO with N₂(X) and O₂(X) is also presented, and information about the potential energy surfaces for such interactions inferred.

This thesis describes the Raman and Contrast change in chemically doped and/or intercalated thin layers of graphene with halogen gases, FeCl3 and alkali metals. The first chapter introduces graphene and graphite intercalation compounds (GICs). It will also briefly explain Raman of the graphitic compounds including GICs. The second chapter presents doping status of halogen molecules doped graphene. The Raman spectra of the graphene G peak as a function of different number of layers implies the doping structure of few layers graphene. The adsorption-induced electric potential difference between surface and interior layers implies that a band gap opens in the bilayer type bands of I2 doped 3 L and 4 L. The third chapter investigates graphene enhanced raman signal of halogen molecules adsorbed onto and intercalated into graphene. We analyze and model the intramolecular electronic, charge transfer, and multiple reflection electromagnetic mechanisms responsible for the unusual sensitivity. We attribute the large Raman signal from both adsorbed iodine and intercalated bromine species to intramolecular electronic resonance enhancement. The signal evolution with varying graphene thickness is explained by multiple reflection electromagnetic calculations. The fourth chapter explains how the graphene to adjacent graphene layers decouple by expanding lattice distance with insertion of FeCl3 intercalants. Raman measurement proves that adsorbed FeCl3 can easily be washed off by acetone while intercalated FeCl3 is relatively intact by impermeable graphene layers. The fifth chapter considers alkali metal intercalated few layers graphene. We try to understand how the extreme electronic properties of alkali doped bulk graphite develops in few layer thick intercalated graphenes, as a function of the number of layers, starting from a single graphene layer with adsorbed alkali atoms to several graphene layers intercalated with alkali metals. We study both optical reflectivity and Raman scattering, as they reveal different aspects of the electronic structure of peculiar graphene intercalation compounds characters.

This thesis describes two types of interactions between zero-dimensional and two-dimensional materials: energy transfer and surface diffusion. The first chapter introduces zero-dimensional and two-dimensional materials and their unique properties. Based on emerging properties different from bulk materials', several attempts have been shown to study the interaction between these two classes of materials. The second chapter presents the study on the energy transfer between zero-dimensional and two-dimensional materials, specifically semiconductor nanocrystals (or "quantum dots") and graphene. The fluorescence quenching was observed for quantum dots on graphene compared those in the absence of graphene. The strong energy transfer is through Coulomb interaction in the way similar to Forster resonant energy transfer. Based on simple assumptions, energy transfer between quantum dots and single-layer graphene was extended to quantum dots and few-layer graphene and quantitative agreement was achieved between experimental results and calculation from theory. The third chapter investigates the surface diffusion of zero-dimensional materials on a two-dimensional material. Metal adatoms diffuse on graphene and form different nanostructures depending on the supporting substrate for graphene. As a atomically thin material, graphene is susceptible to change in underlying supporting substrates. This susceptibility will introduce surface corrugation, chemical reactivity and electron-hole puddles to graphene, and finally will lead to different morphology of metal nanoparticles on graphene. Using classical nucleation theory, different diffusion constants of Au adatoms were reported on graphene supported by different substrate. Two major factors are identified to explain the difference: surface corrugation and π electronic stabilization. In the final chapter, the characterization of zero-dimensional and two-dimensional materials is discussed. It is mainly done using Raman spectroscopy, which is a non-destructive tool. Without knowing the pristine properties of materials, their interactions with other materials are beyond reach.

This thesis harnesses the environmental sensitivity of the dark states of molecular fluorophores, both endogeneous in cells/tissue and externally introduced for mapping of chemical micro-environments including factors such as ion concentration and microviscosity. A novel technique for directly detecting the dynamics and population of dark states, such as the lowest triplet state, was developed and called FAPA, Fluorescence Anomalous Phase Advance. This technique is a sensitive and fast reporter of dark state dynamics and can be used for imaging. In addition, a genetically-encoded microviscosity and micro-environmental mapping ability with high protein-specific specificity was developed by using a TMP-tag and Fluorescence Lifetime Imaging.

This thesis investigates some diffusion related problems, in acetonitrile confined in silica nanopores, and in modeling single molecule forced rupture experiments of biomacromolecules. Based on a method used to calculate the position-dependent diffusion coefficients in inhomogeneous liquids, we apply absorbing boundary conditions in the analysis of molecular dynamics trajectories of confined acetonitrile. We show that the dynamics of acetonitrile may be described by a two population exchange model that accounts for bulk-like relaxation in the center, frustrated dynamics near the surface of the pore and the self-diffusion. We find that hydrogen-bonding interactions play a large role in engendering this behavior. We compare our method with prior techniques that do not take diffusion into account and discuss their pitfalls. We also calculate the position-dependent diffusion tensors in the center population of acetonitrile. To model single molecule forced rupture experiments under constant velocity conditions, we study the barrier crossing problem of a diffusive particle in a time-dependent potential, We develop an integral equation connecting the first passage time distribution of a Brownian diffusion process in the presence of an absorbing boundary condition and the corresponding Green's function in the absence of the absorbing boundary. We further investigate the numerical solutions of the integral equation for a diffusion process in a time-dependent potential. Our numerical procedure, based on the exact integral equation, avoids the adiabatic approximation used in the previous analytical theories and is useful for fitting the rupture force distribution data from experiments, especially at larger pulling speeds, large cantilever spring constants, and smaller reaction rates. We also propose a model based on subdiffusion to explain the anomalous rupture force distributions with positive skewness that are observed in some single molecule forced rupture experiments of ligand-receptor complexes.

This dissertation presents studies on self-organization in soft matter systems. A wide variety of systems is studied, with the goal of understanding both the nonequilibrium and the equilibrium properties of this important process. In Chapter 2, we study the self-assembly of asymmetric Janus colloidal particles. We identify and systematically describe the effect of the ratio of hydrophobic to hydrophilic surface area on the nonequilibrium processes and structure formation. In Chapter 3, we examine systems of hard, aspherical particles. We demonstrate that the thermodynamics of self-organization of a system of these aspherical particle (either a system of identical particles or a polydisperse system of different-shaped particles) is well-predicted by a simple relationship between the crystallization pressure and two measures of particle asphericity borrowed from other fields. In Chapter 4, we shift focus to systems of soft particles in two dimensions and on the surface of a sphere. Soft particles are particles with a nite interaction potential at zero distance; such particles exhibit a surprisingly large variety of ordered structures at equilibrium. A similar phenomenon is seen when the study is extended to soft particles on the surface of a sphere.In Chapter 5, we study the free energy of two-component polymer brush systems in which polymers of different length are patterned in alternating stripes of specified widths on the surface of a cylinder. We present the dependence of the free energy on the polymer lengths and stripe width and a qualitative explanation of its functional form. Finally, in Chapter 6, we approach the reverse self-assembly problem. That is, we describe an algorithm for answering the reverse (and much more dicult) question, "Given a specic desired target self-assembled structure, what interparticle interactions will yield a system which will self-assemble into that structure?" We also describe a new model of interparticle interaction which should be able to generate interparticle interaction geometries with a high degree of flexibility.

This dissertation presents studies on self-assembly of nanoparticles adsorbed onto fluid and elastic membranes. It focuses on particles that are at least one order of magnitude larger than the surface thickness, in which case all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be analyzed. We use Monte Carlo and molecular dynamics simulations to study the phase behavior of these systems, and its dependence on the mechanical and geometrical properties of the surface, the strength of the particle-surface interaction and the size and the concentration of the nanoparticles. We present scaling laws and accurate free-enegy calculations to understand the occurrence of the phases of interest, and discuss the implications of our results. Chapters 3 and 4 deal with fluid membranes. We show how fluid membranes can mediate linear aggregation of spherical nanoparticles binding to them for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We find that the key to understanding the stability of linear aggregates resides in the interplay between bending and binding energies of the nanoparticles. Furthermore, we demonstrate how linear aggregation can lead to membrane tubulation and determine how tube formation compares with the competing budding process. The development of tubular structures requires less adhesion energy than budding, pointing to a potentially unexplored route of viral infection and nanoparticle internalization in cells. In Chapters 5 - 8, we shift focus to elastic membranes and study self-assembly of nanoparticles mediated by elastic surfaces of different geometries, namely planar, cylindrical and spherical. Again, a variety of linear aggregates are obtained, but their spatial organization can be controlled by changing the stretching rigidity of the elastic membrane, the strength of the particle adhesion, the curvature of the surface, as well as by introducing surface defects. Furthermore, we show how a fully flexible filament binding to a cylindrical elastic membrane may acquire a macroscopic persistence length and a helical conformation. We find that the filaments helical pitch is completely determined by the mechanical properties of the surface, and can be easiliy tuned. Moreover, we study the collapse of unstretchable (thin) hollow nanotube due to the collective behavior of nanoparticles assembling on its surface, resulting in an ordered nanoparticle engulfment inside the collapsed structure. Our hope is that the results presented in this Dissertation will stimulate further experimental studies of the mechanical properties of fluid and cross-linked membranes, in particular the long range correlations arising due to the particle binding.