Photochemistry is the chemical response of molecules to light and drives many natural processes such as photosynthesis, vision, and bioluminescence. Nonradiative decay via intersystem crossing or internal conversion are mechanisms of particular interest due to the direct conversion of energy from light into mechanical motion. This presents unique difficulties to experiment due to the rapid time-scale on which these dynamics often occur. The involvement of multiple electronic states is a commensurate challenge to theoretical methods. Nonetheless, theoretical quantum chemistry approaches have had much success towards this objective and have been used in conjunction with experiment to produce powerful results. In particular, advancements such as GPU acceleration of electronic structure energy and gradient calculations have enabled on-the-fly simulation techniques such as ab initio multiple spawning (AIMS) to simulate these processes. In this dissertation, we use AIMS to produce one-to-one comparisons with experiment through direct modelling of experimental observables. We specifically highlight dynamics involved in photoisomerization of cis-stilbene and photodissociation of ortho-nitrophenol in comparison to time-resolved photoelectron spectra and ultrafast electron diffraction respectively. Additionally, we discuss enhancements of AIMS algorithms to address existing challenges in simulating excitations to higher lying electronic states

The remarkable properties of glassy materials arise from their complex amorphous structures and dynamics. The heterogeneity of these materials was studied on molecular length scales and picosecond time scales using a combination of polarization-selective IR pump-probe and 2D IR experiments and a vibrational chromophore that is sensitive to local chemical and electrical environments. By monitoring the restricted orientational motion of the chromophore in a polymer, the distribution of sub-nanometer pores could be explored. The same chromophore in a hydrogen-bonding system showed extreme polarization dependence in the 2D line shape, providing evidence for significant dynamical heterogeneity in the supercooled liquid phase

Knowledge of the point spread function (PSF) of a microscope allows point sources of light such as single molecules and particles to be localized in space with a precision on the order of tens of nanometers or better. Single-molecule localization microscopy (SMLM) leverages this to enable both tracking of single molecules to study their dynamics as well as super-resolution imaging of static objects labeled with fluorescent molecules to reveal their structure. Since localization entails estimating parameters of the molecule from its PSF, the precision and accuracy with which those parameters can be determined are of fundamental importance to the quality of the results in a localization experiment. The work presented in this Dissertation seeks to improve the precision and accuracy of single-molecule localization through developments in computational tools, optical design, and calibration methods. Special attention is paid to the localization of engineered PSFs, in which the PSF shape is deliberately altered to encode information such as three-dimensional (3D) molecular position or orientation of the molecular dipole. The first two Chapters in this Dissertation serve as introductions. Chapter 1 presents general background on a variety of topics relevant to single-molecule localization microscopy. In Chapter 2, the theory underlying image formation in single-molecule fluorescence microscopy is presented, with a special focus on aberrations and engineered PSFs, which play a crucial role throughout the Dissertation. Chapter 3 of this Dissertation reviews the experimental methods employed in this Dissertation. This includes the optical designs employed for illuminating molecules and detecting their fluorescence, as well as descriptions of the instrument control procedures and a detailed walkthrough of the image analysis and localization procedures employed throughout the remaining Chapters. The primary results presented in this Dissertation are the subject of Chapters 4-7. The first two of these focus on the improvement of localization precision. In Chapter 4, it is shown that models of the tetrapod PSF derived from diffraction theory calculations are not sufficient to enable precise 3D localization of single emitters. A method of phase retrieval is demonstrated which enables the determination of a more realistic PSF model, informed by experimental measurements, and allows for recovery of the localization precision to nearly its theoretical limit. Chapter 5 presents a complementary approach to improving localization precision based on illumination with a tilted light sheet excitation beam instead of conventional wide-field illumination to achieve optical sectioning of samples several microns thick. Combination of this illumination strategy with the double helix PSF is shown to improve the signal-to-background ratio and enable 3D single-molecule super-resolution imaging of large structures within mammalian cells with superior localization precision. In the final two Chapters of this Dissertation, the theme shifts from localization precision to localization accuracy. Chapter 6 describes an experimental study of the PSF near the interface between an aqueous sample medium and a glass coverslip. Refraction of collected fluorescence through this interface gives the PSF a depth-dependent shape leading to a distortion of axial position estimates as well as an apparent rescaling of the focal position, both of which limit the accuracy of 3D localization microscopy. These effects are carefully characterized using a calibration standard I developed which provides ground truth. Finally, Chapter 7 addresses an orientation-dependent lateral bias in the PSF which is induced by the anisotropy of the dipole radiation patterns of single molecules. An experimental approach based on polarization filtering is shown to remove the bias by rejecting the component of emitted light which is radially-polarized in the Fourier plane of the microscope, producing a PSF which enables unbiased estimation of the lateral position and azimuthal orientation of the molecule

This thesis describes, generally, the conception and development of the aluminum-graphite battery using chloroaluminate ionic liquid and ionic liquid analog electrolytes, with a transition to magnesium metal batteries also utilizing the tetrachloroaluminate anion in a magnesium aluminum chloride complex in ethereal solvent electrolyte system. Reversible aluminum deposition is generally achieved from liquid electrolytes that can support the Al2Cl7- anion, and was established in imidazolium-based ionic liquids in the 1982 by Wilkes. With no vapor pressure and large electrochemical stability windows, the concept of ionic liquids in general presents a scaffold for developing the ideal battery electrolyte, as they are non-flammable and have the potential to provide for highly efficient redox processes at both electrodes in the battery. Unfortunately, they tend to be rather expensive due to the use of synthetic organic cations. The majority of the work done here describes the development of ionic liquid analog electrolytes based on the asymmetric cleavage of Al2Cl6 by urea ($0.50/kg) to generate an ionic system. Furthermore, the invention and characterization of ionic liquid analogs of drastically decreased viscosity and increased ionic conductivity, using N-alkyl derivatives of urea, is presented. Additionally, more dense and even aluminum metal deposit morphologies were observed using ionic liquid analogs derived from N-alkylated derivatives of urea, making for significantly improved systems from which to deposit aluminum. Graphite has long been established as capable of forming intercalation compounds, particularly with the lithium cation upon chemical/electrochemical reduction, and is used as such for the anode of the common lithium-ion battery. An amphoteric material, graphite has become the subject of immense study for hosting both cationic and anionic species through reduction and oxidation, respectively, in the formation of lamellar intercalation compounds for use as the active material in battery electrodes. In this work, graphite is shown to highly reversibly intercalate/de-intercalate AlCl4- anions, which were derived from ionic liquids capable of reversible aluminum deposition, allowing for the development of a high-rate aluminum metal-graphite battery. Ionic liquid analog electrolytes based on urea and its N-alkylated derivatives were also incorporated successfully, with high efficiency redox reactions occurring at both electrodes, providing for an economically viable technology that (when estimated at scale) is cheaper than lead-acid batteries, which account for two-thirds of a 30 billion dollar battery industry, today. Magnesium has been shown to be able to be reversibly deposited with high efficiency from magnesium aluminum chloride complex (in ethereal solvent) electrolytes, which also contain AlCl4- anions. In theory, a battery similar in nature to the aluminum metal-graphite system should therefore be conceivable using a magnesium anode. However, despite the Lewis acid nature of the components of the electrolyte (AlCl3, MgCl2), it has been shown that in order to reversibly deposit magnesium, electrochemical conditioning of the electrolyte must take place, during which time Al3+ is removed from the electrolyte, which generates free Cl- that cannot be reversibly intercalated into the graphite used here, requiring another type of host. For this battery system, it is shown that Ag metal can act as a high capacity, highly reversible "host" for the Cl- ion when anodized to form AgCl, which can be used in conjunction with the magnesium metal anode to produce another highly efficient, dual-ion type cell. However, unlike in the case of the aluminum-based cell using ionic liquids, globular dendritic growth (not quite identical to the issues plaguing lithium metal based batteries) prevents a long cycle life, with short circuiting of the battery inevitable with the production of a high surface area magnesium deposit during recharging of the battery. Here we discuss in detail the optimization and characterization of these different electrolyte systems and the electrochemical mechanisms involved in the respective redox processes at the positive and negative electrodes during battery operation. Future avenues for improvement of these systems are discussed, and viability from an industry perspective is considered

Time-correlated single photon counting (TCPSC) is a fluorescence spectroscopy technique used to investigate the behavior of chromophores from the hundreds of picoseconds to the tens of nanoseconds time regime. This technique works by measuring the time difference between two photon events: the initial excitation and the time at which a photon is emitted by the chromophore. Each measurement increments the appropriate bin in a histogram by one. As more and more measurements are made, the time-dependent fluorescent behavior is uncovered. With a single fluorescent decay, one can extract the fluorescent lifetime of a species or measure excitation transport. However, by varying the polarization of light exciting the chromophore relative to a fixed resolving polarizer, the orientational dynamics of a probe can also be extracted. The first set of experiments described in this thesis are measurements of orientational dynamics of the fluorophore, perylene, solvated in solutions of room temperature ionic liquids (RTILs). The D2h symmetry of perylene made it possible to extract dynamical information on both in-plane and out-of-plane reorientation from time-resolved fluorescence anisotropy measurements. The RTILs were a series of 1-alkyl-3-methylimidazolium tetrafluoroborates, where alkyl chain varied from butyl to decyl in increments of two and varying the water content. From the anisotropy, the corresponding friction coefficients were determined to eliminate the influence of changes in viscosity caused by both the addition of water and the different alkyl chain lengths. As chain length increased, the addition of water had less of an effect on the local alkyl environment surrounding the perylene. The friction coefficients generally increased with higher water contents. At high water content, the shortest alkyl chain --BmimBF4, broke this general trend, with both in-plane and out-of-plane rotational friction decreasing above a water content of one water per ion pair. While a lot can be learned through the measurements of single wavelength emissions, doing so greatly limits the types of experiments one can study. With complex models, it becomes difficult to justify the difference between different models as many will fit a single trace perfectly. By the construction of time-dependent emission spectra, much more information can be extracted. This is done by collecting fluorescent decays at regular intervals across the emission band under identical experimental conditions. The next study shows proton transfer in the nanoscopic water channels of polyelectrolyte fuel cell membranes using a photoacid, 8-hydroxypyrene-1,3,6-trisulfonic acid sodium salt (HPTS) into the channels. Three fully hydrated membranes, Nafion (DuPont) and two 3M membranes, were studied to determine the impact of different pendant chains and equivalent weights on proton transfer. Measurements of the HPTS protonated and deprotonated fluorescent bands' population decays provided information on the proton transport dynamics. The decay of the protonated band from ~0.5 ns to tens of ns is in part determined by dissociation and recombination with the HPTS. The dissociation and recombination is manifested as a power law component in the protonated band fluorescence decay. Proton transfer dynamics of HPTS in the aprotic solvent 1-methylimidazole (MeIm) were also investigated using fast fluorescence measurements. Wavelength-dependent population dynamics of HPTS in MeIm, resulting from its deprotonation following optical excitation, were collected over the entire fluorescence emission window. Analysis of the time-dependent fluorescence spectra reveal four distinct fluorescence bands that appear and decay on different time scales. We assign these bands to be the conventionally considered protonated (P) and deporotonated (D) HPTS states with 2 additional associated states (A1 and A2). The protonated states decays within the instrument response, but the remaining states were all able to be measured dynamically. The simplest kinetic model, P → A1 →A2→ D, in which the protonated state feeds into a single associated state which in turn feeds into the second associated state which deprotonates provided a quite poor fit. Detailed simulations were performed and identified the most likely kinetic model as protonated feeds into A1 which in turn feeds into both A2 and D, where A¬2 can return to A1 but not D. Another type of experiment in which the time-dependent spectra are necessary for the interpretation is in solvation dynamics of the fluorescent probe coumarin 153 (C153) in polyether sulfone membranes (PES 200) with an average pore size of ~350 nm. For instance, the structural dynamics of a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (CnmimNTf2, n = 2, 4, 6, 10) room temperature ionic liquids confined in the PES 200 membranes. The solvation dynamics of C153 in the ionic liquids are multiexponential decay, and the slowest decay component of each bulk liquid matches the slowest component of the liquid dynamics measured by optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments, which is single exponential. The fact that the slowest component of the Stokes shift matches the OHD-OKE data in all four liquids identifies this component of the solvation dynamics as arising from the complete structural randomization of the liquids. Although the pores in the PES membranes are large, confinement on the mesoscopic length scale results in substantial slowing of the dynamics for short chain ionic liquids, however, in the longest chain ionic liquid there was no noticeable confinement effect. The dynamic Stokes shift measurements report on structural relaxation, driven by a dipole created in a chromophore by its excitation from the ground electronic state to the S1 state. In another experiment, we were able to demonstrate that it is also possible to have an additional contribution from orientational relaxation of the Stokes shift chromophore. This effect, called reorientation-induced Stokes shift (RISS), can be observed when the reorientation of the chromophore and the solvent structural relaxation occur on similar time scales. Through a vector interaction, the electronic transition of the chromophore couples to its environment. The orientational diffusive motions of the chromophores will have a slight bias toward reducing the transition energy (red shift) as do the solvent structural diffusive motions. RISS is manifested in the polarization-dependence of C153 in poly(methyl methacrylate) (PMMA). Expressions are derived that permit determination of the structural dynamics by accounting for the RISS contributions. Using these equations, the structural dynamics of the medium can be measured for any system in which the directional interaction is well represented by a first order Stark effect and RISS is observed. The theoretical results are applied to the PMMA data, and the structural dynamics are obtained and discussed. Finally, the time-dependent photoluminescence of a broadband white light emitting perovskite -- 2,2'-(ethylenedioxy)bis(ethylammonium) tetrabromoplumbate, (EDBE)PbBr4 -- was measured using TCSPC. Time-dependent spectra were generated over a very broad time range from 100 ps to 100 ns. The main luminescent decay is a tri-exponential with time constants, 1.20 ns, 8.48 ns, and 21.75 ns.. Analysis of the time-dependent spectra showed a distinct spectral side peak which has a decay constant of 0.6 ns. After this peak decays, the emission line shape remains constant throughout the entire photoluminescent decay, demonstrating that the emission occurring from all wavelengths arises from a single ensemble. Therefore, the white light emission does not arise from a set of subensembles with different emission wavelengths and lifetimes. However, experiments on (EDBE)PbBr4 spin coated thin films luminescence decay is different, but it is still non-exponential and, like the crystal samples, occurs from a single ensemble after the relaxation of the rapidly decay side band. The spin coated samples have faster decays than the large single crystals

A large part of chemistry is driven by localized electric fields between charged species, for example when an electron is exchanged in between a redox reaction pair, or a nucleophile attacks a positively charged part of a molecule. Ideally, scientists try to not only observe and understand these processes, but also gain control over them in order to steer reactions in a certain direction. In this thesis, the use of electric fields to influence reactions was studied in several reactive systems, including various chemical environments and two different ways to apply electric fields. The first part of this thesis work investigates the impact of an electric field generated by a focused laser pulse of nonresonant radiation, which is referred to as photon catalysis. The second part explores other ways to apply electric fields to chemical reactions: on the surface of microdroplets, and by voltage applied to a semiconductor on the nanoscale. Chapter 1 introduces the concept of photon catalysis. It outlines how a focused laser pulse of nonresonant radiation can act as a catalyst through its strong electric field: no photons are used up or changed in the interaction, but upon the application of the electric field laser, particular reaction pathways can be favored over others, resulting in a net change in the reaction dynamics. Furthermore, Chapter 1 lays the groundwork for the following chapters by characterizing the electric field generated by a nanosecond laser pulse, and by describing the experimental setup for photon catalysis on gas-phase reactions. It also presents the first studies on photon catalysis carried out in this lab, and defines which properties of a reactive system render it a good candidate to showcase the photon catalytic effect. Chapter 2 shows how the application of a nonresonant, focused laser pulse of infrared radiation changes the outcome of the dissociation of deuterium iodide. Depending on the excitation wavelength, deuterium iodide can dissociate via different reaction pathways after the excitation, yielding a product mix of two distinct deuterium (D) species. The relative product ratio at which these two species are formed is changed in the presence of the electric field supplied by the infrared laser pulse, indicating a change in the reaction dynamics. The magnitude and the direction of change are dependent on the excitation wavelength. The underlying mechanism for the change is explored both experimentally and theoretically, and there is an agreement that the observed effect is rather caused by an AC-Stark shift of the potential energy surfaces, than by molecular alignment of the reactants. Chapter 3 continues to explore photon catalysis by extending the studies to a more complex molecule, phenol. The photodissociation of phenol along the OH bond involves two well-characterized dissociation pathways, which are populated to different degrees depending on the excitation wavelength. The reaction products are phenoxy radicals and hydrogen atoms of characteristic speeds. In this study, two features in the potential energy landscape are probed: a conical intersection, and the minimum energy threshold that it requires to dissociate the molecule. Similarly to lowering an activation barrier, the conical intersection is lowered by the electric-field induced Stark-shift, generated by the focused, nonresonant laser pulse. Therefore, the pathway that lies higher in energy is opened up wider than under field-free conditions. The dissociation origin experiences a smaller Stark-shift, yet allows for phenol dissociation at a wavelength that is not sufficient to yield any dissociation under field-free conditions. The postulated mechanism is supported by theoretical calculations. Chapter 4 transfers the concept of photon catalysis from gas-phase reactions to solution-phase systems. It outlines the changes and challenges of the chemical environment that reactants and the laser beam face, and proposes potential experimental setups. Following successful setup development, the impact of the electric field on the photoisomerization of stilbene is investigated: When a solution of cis-stilbene (CS) in cyclohexane is irradiated with ultraviolet photons, photoisomerization to trans-stilbene (TS) is promoted, and an irreversible ring-closure reaction to form phenanthrene (PH) is observed. At wavelengths around the red absorption onset, the TS formation is increased by the application of the electric field laser, and at excitation wavelengths in the center of the absorption range, the CS is increasingly converted to both TS and PH. This change is partially due to local heating in the reaction solution, which can be subtracted as background at the edge wavelengths, but is overwhelming at the absorption center. Multiphoton processes are not observed in measurable amounts. The end of this chapter highlights the promising perspectives for further use and development of photon catalysis in condensed-phase systems. Chapter 5 approaches a different application of electric fields in chemistry: the conversion of low-value polycyclic aromatic hydrocarbons to compounds with higher petrochemical utility. A new method to obtain higher conversion rates is proposed, which involves two ways of how electric fields can be applied in chemical reactions. First, the reactant solution is sprayed with a sheath gas from a small nozzle, generating micron-sized liquid droplets that exhibit strong electric fields on the surface, enhanced by an electric double layer if the solution contains water. Second, these droplets subsequently hit immobilized anatase nanoparticles, which are charged with 2 kV, and continuously wetted. The applied voltage results in an electron-hole separation, where the oxidative hole converts the water to highly reactive hydroxy radicals. The combination of the electric field on the microdroplet surface with the hydroxy radicals is required to obtain high degradation yields of the sample molecule rubrene. The method is validated on selected other molecules as well.

The first optical detection of a single molecule (SM) at cryogenic temperatures 30 years ago laid the groundwork for the routine detection of SMs today at biologically relevant temperatures, thus uncovering hidden heterogeneity that might be obscured by ensemble techniques. In addition to enabling studies of the intricate photochemistry and photophysics of fluorescent labels at the SM level, SM fluorescence has also proven useful for the imaging and tracking of cellular structures and biomolecules in a non-invasive manner with high sensitivity. The ability to genetically express fluorescent protein fusions in live cells has allowed specific labeling, and thus imaging and tracking, of dynamic processes and structures in cells. This dissertation describes applications of SM-based single-particle tracking (SPT) and super-resolution (SR) microscopy for the study of spatial organization and dynamics of bacterial proteins in two and three spatial dimensions. In an SPT experiment, the position of a SM emitter at very low concentration is measured over time to generate a trajectory, allowing for observation and quantification of labeled biomolecule dynamics at the SM level. In a SR microscopy experiment, the diffraction-limited (DL) resolution of a conventional fluorescence microscope (~200 nm in xy) is circumvented by temporally separating the emission of many SM emitters decorating a structure through control of their emissive state. A "super-resolved" image, with a factor of ~5-10 resolution improvement over a conventional DL fluorescence image, is generated by estimating the positions of many non-moving SM emitters over many frames and building up an image reconstruction in a pointillist manner. Chapter 1 of this dissertation provides an introduction to fluorescence, SM imaging, SM-based SR microscopy, and SPT. Chapter 1 also gives a brief introduction to Caulobacter crescentus, the bacterium used as the model organism in the SM studies in Chapters 4 and 5. Chapter 2 describes the experimental methods used to perform quantitative SM imaging of bacterial cells. The combination of SM imaging with point spread function (PSF) engineering has enabled the accurate and precise localization of SMs in three dimensions (3D) by the intentional introduction of specifically chosen aberrations in the emission path of an SM microscope. Throughout this dissertation, the double-helix (DH) PSF, a rotating PSF composed of two lobes whose angle encodes axial position, was used to estimate 3D SM positions. Chapter 2 describes the implementation of the DH-PSF via optical Fourier processing, and Chapter 3 describes the robust and comprehensible two-color Easy-DHPSF v2 software for localizing molecules in 3D and for registering localizations from two spectral channels into the same coordinate system with nanoscale accuracy. The resolution improvement gained from SM-based techniques is particularly useful for bacteria, the sizes of which are on the order of the DL. 3D SM-based SR and SPT have enabled the observation of structures and dynamics at length scales below the DL. Caulobacter is a useful biological target where understanding of the mechanisms for asymmetric cell division need to be explored and quantified. Central to Caulobacter's asymmetric division is the dynamic spatiotemporal regulation of gene expression and protein localization. Chapters 4 and 5 describes research performed in collaboration with Prof. Lucy Shapiro's laboratory (Department of Developmental Biology, Stanford School of Medicine) to study gene expression and signaling proteins in Caulobacter. Chapter 4 describes work studying the spatial organization and dynamics of ribosomes and a RNA-degrading enzyme RNase E using 3D SR microscopy and SPT. Results showed that the organization and dynamics of RNase E and ribosomes are closely related to the transcriptional activity of the cell. Finally, Chapter 5 describes SPT studies of the membrane-bound histidine kinase and stalked cell fate determinant DivJ in an effort to probe the physical properties of the Caulobacter stalked pole. Preliminary SPT results suggest that disrupting the physical properties and interactions at the stalked pole has an influence on DivJ diffusion and signaling.

Water is one of the most important substances in the world. It is used in a wide range of technologies and is an essential ingredient in all living cells we know today. The structure of water molecule is simple, yet it can form extended and versatile hydrogen bond (HB) network. This ability gives water extraordinary properties, such as high boiling and melting point. At the same time, the hydrogen bond network is not static. The constant breaking and re-forming of hydrogen bond occurs on the picosecond timescale. This dynamic network facilitates many functions of water, including ions solvation, protein folding and electricity conduction. Understanding the structure and dynamics of these processes is therefore of great importance. Ultrafast infrared (IR) spectroscopies offer a great method for accessing the sub-picosecond to picoseconds dynamics while a system in an electronic ground state. During the past two decades, hydrogen bond dynamics has been investigated extensively using ultrafast IR spectroscopies. But many questions still exist such as the effect of ions and confinement on the hydrogen bonding dynamics and the relation between the anomalous proton diffusion in dilute solution and hydrogen bonding. In Chapter 3, we examined the nature of molecular anion hydrogen bonding. The CN stretch of selenocyanate anions (SeCN-) was used as the vibrational probe in heavy water D2O. We observed the non-Condon effect on the CN stretch whose transition dipole changes with the strength of hydrogen bonding with water. In addition, HB rearrangement dynamics reported by SeCN- is almost the same as was that of the OH stretch of HOD molecules. This result shows that this anion does not perturb the surrounding HB network significantly in the low salt concentration solution. This ionic perspective is important and complements the results using OD or OH stretch of HOD molecules, which can only probe the effect of ions in a high salt concentration condition. In Chapter 4, we used SeCN- as the probe to examine water dynamics in confinement, and I focused on the nano waterpool formed in reverse micelles. The water pool is surrounded by surfactants which are further solvated by organic hydrophobic solvents. For large reverse micelle whose diameter is larger than 4 nm, the water pool is usually divided into two regions: the core region where water dynamics is like that in pure water and the interface region where water dynamics is slowed significant due to the confinement. Here we used ultrafast IR spectroscopies to measure the orientational relaxation of SeCN-, which reflects its interaction with water molecules and how "rigid" the HB network is. Based on the comparison between linear IR decomposition and ultrafast anisotropy dynamics, we proposed a three-component model of water in large reverse micelles. The interface component should be further separated into two layers. One layer corresponds to water in contact with the surfactant head group and has very slow reorientation. The other layer corresponds to water molecules whose coordinating structure still resembles that of bulk but the dynamics is slowed down due to the perturbation from confinement. In Chapter 5 and 6, hydrogen bonding dynamics in concentrated salt and acid solutions were investigated. Through electrochemical method, it was found decades ago that proton has extraordinary ion mobility, about 6 times larger than that of cations of similar sizse, such as sodium, ammonium or lithium. The great difference between them results from the cation transport mechanism. In dilute solution, the main transport mechanism of proton is through relay mechanism where the identity of proton transfers from one water molecule to another. This minimizes the physical diffusion of the atoms and greatly increases the proton mobility. The mechanism is generally called Grotthuss mechanism, which was came up with by Grotthuss in 1806 though not on the molecular level. However, the step time of a single proton transfer event between two water molecules is difficult to observe experimentally. Here we used the CN stretch of methyl thiocyanate (MeSCN) as the vibrational probe. In concentrated hydrochloric solutions, it has two frequency resolved states. One state refers to water hydrogen bonded to the nitrogen lone pair while the other state corresponds to hydronium ion hydrogen bonded to the CN. Chemical exchange phenomenon was observed between these two states. Ab initio simulation done by our collaborator shows that the proton hopping is the dominate mechanism for chemical exchange. The comparison experiment done in lithium chloride solution provides further contrast between hydronium and other metal ions. Therefore, we were able to track proton hopping in a time-resolved manner for the first time. Extrapolation to the dilute limit demonstrates that the HB rearrangement in pure water is the driving force of proton hopping in dilute solution.

Molecular scattering experiments interrogate the forces that govern interactions at the quantum level, but the amount of detailed information that can be extracted from a scattering experiment is limited by how precisely the input and output quantum states are defined. Experimental efforts to simplify the baffling variety of different quantum states found in room temperature gases have an illustrious history extending over more than one hundred years, and yet have only recently begun to achieve the level of control over the quantum world necessary for direct detailed interrogations of molecular interaction potentials. We present here our small contribution to this long history, where we have used optical adiabatic passage to prepare internal molecular quantum states, and then studied the rotationally inelastic scattering of these state-prepared molecules at very low collision energies. Under these conditions, nearly complete control over the quantum states was achieved, allowing us to experimentally derive insight into the dynamics of molecular scattering. To prepare the internal quantum states of molecules prior to the scattering even, we have made use of the Stark-induced adiabatic Raman passage (SARP) technique. As we describe here, SARP makes use of the time-varying adiabatic eigenstates of the light-matter system to smoothly transfer population from the initially populated ground state to a selected rovibrationally eigenstate with orientational specificity. Because of SARP's adiabatic nature, the population transfer is insensitive to fluctuations in the laser power, frequency, and arrival time, making it ideal for use in scattering experiments, which require data collection over long periods of time. Additionally, SARP is capable of vibrationally exciting large numbers of simple homonuclear diatomic molecules like H2, which are important targets for scattering experiments due to their theoretical tractability, but are nearly impossible to state prepare using other techniques. Here, we expand both theoretically and experimentally on the prior work developing SARP to show that this process is capable of population transfer to highly excited vibrational levels, thus opening up the study of the dynamics of these exotic systems. We have designed and constructed an apparatus capable of generating cold (low energy) scattering of the molecules state prepared by SARP. To do so, we make use of the small relative velocity present between two different gas components in a single supersonically expanded molecular beam. In order to demonstrate the principle of state prepared scattering in the mixed molecular beam, we have first used SARP to prepare HD in a variety of different magnetic or orientational sublevels of the (v = 1, j = 2) rovibrational energy eigenstate, where v and j give the vibrational and rotational quantum numbers. We then studied the rotational relaxation of these excited HD molecules by collision with H2, D2, and He coexpanded in the same supersonic beam, which led to a wealth of stereodynamic insights into these interaction processes. In particular, nearly complete control was achieved in the HD-He scattering case, allowing us to fully realize the potential of these experiments and directly access information about the scattering matrix.

Single-molecule fluorescence methods have become a mature and powerful tool to unravel the fundamental mechanisms of biological phenomena. These approaches enable researchers to investigate individual components on the nanoscale for heterogeneous mixtures and to monitor the dynamics of single biomolecules. Unfortunately, traditional burst-based methods are often limited by short observation time, and the immobilization of single biomolecules that enables long observation time is often undesirably perturbative. To address these limitations, a solution-based technique known as the Anti-Brownian ELectrokinetic (ABEL) trap has been developed. In the ABEL trap, high-speed feedback electronics sense position and compensate Brownian motion of a single molecule by applying electrokinetic forces, which keep the molecule in the trapping region for an extended period of time. This dissertation describes my work on the investigation of single-molecule interactions and photodynamics using the ABEL trap technology. First, I show how to measure and monitor single-molecule rotational diffusivity by combining the ABEL trap and maximum likelihood analysis of time-resolved fluorescence anisotropy based on the information inherent in each detected photon. The rotational diffusivity is extremely sensitive to the size of the molecule, and thus can be used to detect and monitor size-changing events, such as association and dissociation. We demonstrate this approach by resolving a mixture of single- and double-stranded fluorescently-labeled DNA molecules at equilibrium, freely rotating in a native solution environment. Next, we investigate photosynthetic photoprotection mechanisms at the level of individual antenna complexes (LHCII), the fundamental units which green plants use to harvest sunlight. We access the intrinsic conformational dynamics of individual LHCII complexes. In addition to an unquenched state, two partially quenched states of LHCII are observed. One of the quenched conformations significantly increases in relative population under environmental conditions mimicking high light. Our results suggest that there are at least two distinct quenching sites with different molecular compositions, meaning multiple dissipative pathways in the LHCII complex. Last, we describe the theoretical basis of a new method to measure the diffusion coefficient of diffusing objects on the surface of individual nanoscale lipid vesicles. We discuss how to probe diffusion in these highly confined environments using FRET pairs and fluorescence intensity correlation, and illustrate that this method is essentially a fluorescence correlation spectroscopy (FCS) experiment with a nanometer-sized probing volume.

Molecular simulation is a useful tool for investigating the structure and dynamics of wide-ranging chemical systems and can provide information that complements experiments. The objective of this thesis is to relate experimental spectroscopic observables to the chemical structures and dynamics that give rise to them using molecular simulations that include quantum fluctuations of both the electrons and nuclei. Chapter 1 first introduces the approach employed in this thesis to relate chemical structure to vibrational spectra as well as contextualizes some of the limitations and trade-offs associated with molecular simulations. Chapter 2 applies this approach to simulations of concentrated acid solutions with the aim of elucidating recent 2D-IR experiments. Chapter 3 presents work from an experimental collaboration investigating using a vibrational probe to observe proton transfer in solution. Lastly, Chapter 4 treats the inclusion of nuclear quantum effects in the computation of optical absorption spectra of aqueous chromophores.

The hydrogen bond is a key intermolecular interaction in chemistry, biology, geology, and materials science, with its energy tuned for a perfect balance between structural rigidity and rapid dynamic rearrangements around ambient conditions. Ultrafast infrared spectroscopic methods are described that can interrogate the dynamics and intermolecular interactions of the hydroxyl stretch mode, a sensitive reporter of hydrogen bonding environments, of water and alcohols in complex environments far removed from the bulk liquids. New methodology for conducting noncollinear two-dimensional infrared experiments in a rotating frame to accelerate data acquisition is described. Water confined in polyacrylamide hydrogels is found to slow as one population as the size of the water pool decreases. The lack of any water with bulk-like dynamics is surprising and attributed to the continuity of hydrogen bond network between the water pool and confining polymer. Room temperature ionic liquids, a family of tunable, non-volatile, and non-flammable solvents composed entirely of cations and anions, are structured at the nanoscale by charge ordering as well as the possibility of other motifs, such as segregation of polar and apolar groups. Water and alcohols isolated in ionic liquids, as representative solutes or cosolvents, experience hydrogen bond interactions with the solvating ions. A rich hierarchy of dynamical processes in the randomization of their orientations and intermolecular interactions is observed, ranging from less than 100 femtoseconds to sometimes over 100 picoseconds. The hydrogen bond interactions are highly directional, leading to distinct forms in the polarization dependence of ultrafast IR measurements of structural dynamics (spectral diffusion), particularly in ionic liquids. Theory is developed to characterize these directional interactions and dynamics quantitatively and separate the reorientation-induced spectral diffusion (RISD) processes, arising through rotation of the tracer, from spectral diffusion that is due to the randomization of the surroundings. Related theories of RISD are presented that are appropriate for carbon dioxide, a highly symmetrical vibrational probe, as well as fluorescent probe molecules undergoing time-dependent Stokes shift with highly directional interactions that determine the absorption and emission frequencies. Measurements of the dynamics of water confined in the nanoscale pores of amorphous silica are presented. Several techniques to overcome the inherent scatter from silica particles (sand) were combined, including phase cycling, polarization control, and spatial filtering, and their individual merits are discussed. The slowdown in dynamics of water in the silica pore are compared to previous measurements of the dynamics of selenocyanate, an anion that H-bonds to the surrounding water in the pore.

Modern society demands smaller, more precise devices for both microelectronic and energy technologies. The development of methods and processes that can deposit reliably uniform, conformal thin films on the nanoscale is essential to fields as diverse as catalysts and solar cells. Therefore, atomic layer deposition (ALD), a thin-film deposition technique that accomplishes these goals by using self-limiting sequential reactions between alternating precursors to achieve atomic precision over the product film, is an important tool for the modern era. Combining ALD with molecular layer deposition (MLD), which follows the same principles as ALD but deposits entire organic molecules to build films, results in a powerful system that enables the deposition of inorganic, organic, and hybrid inorganic-organic materials. Understanding the nucleation mechanisms, surface reaction chemistry, and applications of these materials and ALD/MLD processes is essential to commercialization and wider use. Through in situ Fourier transform infrared (FTIR) spectroscopy, we studied the zinc-tin-oxide (ZTO) system, a ternary ALD process that is a combination of the zinc oxide and tin oxide binary ALD processes. Previous research had indicated that the ternary system is characterized by non-idealities in the ALD growth, and we identify as a potential cause of these effects incomplete removal of the ligands from the tetrakis(dimethylamino)tin precursor, which leads to a nucleation delay when depositing ZnO on SnO2. A significant fraction of the ligands remain on the surface during the ALD of SnO2 and endure when the process is switched to ZnO ALD. This result suggests that the occupation of surface reactive sites by these persisting ligands may be the cause of the observed nucleation delay with potential ramifications for many other binary and ternary systems where persisting ligands may be present. In addition, we studied the mechanism of ALD-grown MoS2 thin films. It was observed by atomic force microscopy (AFM), grazing incidence small angle X-ray scattering (GISAXS), and X-ray reflectivity (XRR) that nucleation proceeds by the formation of small islands that coalesce into a complete film in under 100 cycles, with further film growth failing to occur after coalescence. This inertness is attributed to the chemical inactivity of the basal planes of MoS2. It was found that the final thickness of the as-grown film is not determined by the number of ALD cycles as per the normal regime, but by the temperature that the film is deposited at. This self-limiting layer synthesis (SLS) has been reported in the literature for higher temperature depositions of MoS2, but this is the first report of the effect in a low temperature, amorphous MoS2 ALD system. The thickness of films growth by ALD with the precursors Mo(CO)6 and H2S was found to saturate at around 7 nm on both native oxide-covered silicon and bulk crystalline MoS2 substrates, which may indicate that the SLS behavior is inherent to the ALD process and not substantially a product of the substrate surface potential. Finally, we demonstrated a new ALD/MLD hybrid process that used the MoS2 ALD precursor Mo(CO)6 and the counter reagent 1,2-ethanedithiol to create a MoS2-like material with organic domains. This Mo-thiolate possesses many properties that link it to MoS2, such as activity towards the hydrogen evolution reaction (HER) and similar Raman modes, but has a significantly lower density, optical transparency, and higher geometric surface area. It was found that the process has a 1.3 Å growth per cycle and can catalyze the HER reaction at an overpotential of 294 mV at -10 mA/cm2 , which is superior to planar MoS2 and ranks the as-deposited catalyst with the best nanostructured MoS2-based catalysts. We propose that this activity comes from the higher surface area induced by the incorporation of organic chains into the films. In summary, we explored the mechanisms and nucleation behavior of several ALD systems of interest to energy applications using both in situ and ex situ analysis techniques. These studies demonstrated the importance of understanding ALD surface chemistry to the overall chemical composition of the resultant films, the ramifications of different nucleation regimes in determining morphologies, and the power of ALD/MLD in creating analogues to previously known species with improved physical properties.

Understanding the structure and dynamics of biological macromolecules is a central focus of biological research. To be able to study and gain insights into these systems, it is first necessary to have an accurate and informative model for the system of interest. However, such a model is often difficult to build. For example, during protein folding, many proteins collapse into transient kinetic intermediates on timescales too fast for high-resolution experimental techniques to detect, preventing structural characterization of these species. Alternatively, current algorithms for RNA design (i.e. predicting a sequence that folds into a desired target structure) cannot accurately model structure-sequence relationships and rely primarily on brute force stochastic search, leading to poor performance on complex targets. Here, we show that it is possible to improve the quality of models for biological systems by applying a common Bayesian approach to building them, i.e. incorporating prior information to impose informative constraints on the model parameters. Through this approach, it is possible to build high-resolution models of protein dynamics given limited experimental data, as well as a state-of-the-art computational RNA design agent that outperforms all currently existing algorithms.

The behavior of molecules in condensed phases involves complex considerations to fully describe the microscopic structure and dynamics. This is particularly interesting in complex liquids with inherent heterogeneity and in binary mixtures where the competition between the interactions between similar and dissimilar species greatly affects the microstructures of the liquid. The ubiquity of aqueous binary mixtures necessitates their study, particularly because the unique properties of water often manifests anomalously in the physical properties of binary mixtures. These changes in physical properties are the result of structural changes at the molecular level. In this thesis, the dynamical results from optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments are reported for a series of aqueous binary mixtures. OHD-OKE is a nonresonant pump probe technique in which the bulk orientational dynamics of a liquid are measured via the time-dependent birefringence induced in the sample by an optical pulse. The OHD-OKE setup used in this thesis has the ability to measure dynamics over seven decades of time and eight decades of signal, which is an incredible window for a single experimental technique. Ultrafast pulses, which are necessary to have sufficient resolution, are generated by a Ti:Sapphire oscillator/regenerative amplifier. Multiple techniques including heterodyne detection and phase cycling are used to improve signal to noise, particularly at long time when signals are small. The theory behind OHD-OKE and a description of the experimental setup are given here. In addition to dynamical information, microstructural changes can be extracted from OHD-OKE data using the Debye Stokes Einstein (DSE) equation. The specific structures can be elucidated using complementary techniques. The remainder of the thesis is devoted to the aqueous binary mixtures of interest and the results from OHD-OKE and complementary techniques. First, a protic ionic liquid is compared to its aprotic analogue in order to better understand the role of hydrogen bonding in ionic liquids at various hydration levels. This work is further expanded to ionic liquids of varying chain lengths and anions in order to provide a deeper understanding of hydrophilicity and water saturation in ionic liquids. Finally, the anomalous phase behavior of the nicotine/water binary system is studied in order to elucidate the dynamics and microstructures associated with the lower critical solution temperature.

A variety of unique functional materials have been invented over past decades following the development of new chemical strategies to design and synthesize the materials. These functional materials typically come in the form of films or powders, leading to the impression that the materials are static. Despite their macroscopic appearance, in many cases molecules constituting a film or powder constantly change their microscopic configurations on ultrafast time scales. The molecular dynamics are often intimately related to the functionality of the material. Probing the ultrafast dynamics of molecules in these materials is of fundamental interest. Nonlinear infrared spectroscopy has been successful in elucidating complex dynamics occurring in liquid phases, such as bulk water, room-temperature ionic liquids, and liquid crystals. Nonlinear infrared spectroscopy exploits interactions between infrared fields and molecular vibrations to infer dynamics occurring in a system of interest. In particular, polarization-selective pump-probe spectroscopy is capable of monitoring orientational motions of molecules, while two-dimensional infrared spectroscopy characterizes the interaction between a molecule and its surroundings by observing the fluctuation of the molecular vibrational frequency. These two methods are particularly informative and have been fully developed to study liquid dynamics. However, the application of these methods to functional materials such as films or powders has been severely limited due to both experimental and conceptual problems. To overcome the challenges, we developed novel nonlinear infrared spectroscopic methods and associated theoretical frameworks which can characterize molecular dynamics in films or powders. Using the newly developed methods, we obtained new insights into unique molecular dynamics occurring in a broad range of materials. First, infrared polarization-selective angle-resolved pump-probe (PSAR-PP) spectroscopy was theoretically formulated and experimentally implemented to study orientational dynamics of a catalytic head group tethered to a flat surface. Conventional polarization-selective pump-probe spectroscopy is applicable only to three-dimensionally isotropic samples such as liquids and cannot sufficiently characterize anisotropic dynamics occurring on a surface. The new method can independently address the in-plane and out-of-plane dynamics of the head group, revealing the highly anisotropic nature of the dynamics happening at the surface. A major challenge of applying two-dimensional infrared spectroscopy to a monolayer or thin film is the detection of a small signal arising from an inherently limited number of molecules. Near-Brewster's angle reflection pump-probe geometry was found to dramatically enhance the detection of signals from thin films. The enhancement was experimentally demonstrated for a molecular monolayer and subsequently extended to study two types of functional thin films, namely a lead halide perovskite film and an ionic liquid thin film. Finally, the application of two-dimensional infrared spectroscopy to powdered samples was hampered by its vulnerability to scattered pump pulses. The scattering problem was overcome by combining an acousto-optic modulator (AOM) pulse shaping system, a polarization filter, and a new phase cycling sequence involving chopping of the probe pulse. The scatter-free two-dimensional infrared spectroscopy was applied to study molecular dynamics in metal-organic frameworks (MOFs). Both the structural fluctuations of the elastic frameworks and the dynamical nature of framework-guest interactions were revealed by the new method.

Conducting polymers are organic polymers that can change their shape and size in response to an external electric stimulus. These polymers are promising for developing programmable, adjustable, spatially and temporally controllable drug delivery systems (DDSs). Drug release is evoked by application of weak voltages or currents. However, several limitations including (i) low drug loading, (ii) incompatibility with electroactive drugs, and (iii) difficulty of scale up have made thin conducting films refractory to clinical development. To overcome these difficulties, we have utilized nanoparticles of conducting polypyrrole (PPy NPs) to design a versatile DDS capable of releasing a variety of both small and large molecule therapeutics. As examples, we have shown facile release of fluorescein, a hydrophilic model compound, piroxicam, a hydrophobic small molecule used in the management of chronic arthritic pain, methotrexate, an anti-cancer drug, and insulin, a hydrophilic polypeptide used in the treatment of diabetes. The use of nanoparticles allows easy scale up and substantially increased drug loading, estimated to be as high as 51 wt%. Moreover, by modifying the synthesis and incorporating metallic elements into the polymer scaffold, it is possible to release drugs at voltages as low as - 0.05 V vs Ag/AgCl, almost an order of magnitude lower than typically used voltages for thin films. This widens the window of operating voltage and allows PPy NPs to be used in the delivery of redox sensitive drugs. Moreover, we have demonstrated that PPy NPs can be used as a generalized pH-sensitive drug delivery system, capable of releasing any charged drug preferentially at the pH range of interest. They can be tuned to release drugs at both acidic and basic pH by varying the acidity, the charge of the drug, as well as by adding small amounts of charged amphiphiles. These PPy NPs may be delivered locally by immobilizing them in a hydrogel or coupling them to an implantable chip. We have performed proof-of-principle studies demonstrating that the drug release can be triggered wirelessly. Our results demonstrate the potential of using conducting polymer nanoparticles to treat long lasting conditions such as chronic pain, diabetes and cancer by developing externally controlled, programmable implants.

This dissertation utilizes general-purpose graphical processing units (GPGPUs) to accelerate quantum chemistry computations for solvated molecules and molecules in electronic excited states. Most chemical and biological processes happen in the solution phase. However, the application of solvent models in quantum chemistry calculation of large biomolecular system is limited by the CPU computation bottleneck. In this work, we will first show our techniques to accelerate the Conductlike Polariable Continuum Models (C-PCM) at the Hartree-Fock and DFT level of theory. Then the machinery is extended to solvated molecules at electronic excited state described with time dependent density functional theory (TDDFT), with both the state-specific and linear-response approaches. Simulation of photochemistry usually involves multiple electronic states and propagation of the nuclear wavefunction on potential energy surfaces, especially near conical intersections. This requires the electronic structure methods used to be (1) able to describe multiple states in a balanced way; (2) efficient enough for the thousands of energy and gradient computations required in molecular dynamics (MD) simulation. We derived and efficiently implemented the analytical gradient of State-Interaction State-Averaged Restricted Ensemble Averaged Kohn Sham (SI-SA-REKS) method, which is an alternative to high-level multireference wavefunction based methods, thus enabling excited state MD study of larger molecules. Finally we will demonstrate an efficient computational workflow for accurately reproducing and predicting redox potential of quinones, using our GPU accelerated PCM method.

In the past decade, ultrafast two-dimensional infrared vibrational echo spectroscopy (2D IR) has matured as a powerful technique for directly observing molecular dynamics in liquids, organic and aqueous solutions with femtoseconds (fs) to picoseconds (ps) resolution. In contrast, the application of 2D IR methods on investigating surficial and interfacial molecular dynamics remains a challenging topic. Understanding the non-bulk dynamics on material surfaces or at interfaces are fundamental to fields from heterogeneous catalysis to tribology. However, the very small amount of surficial and interfacial chromophores, usually less than ~10-13 mol of molecules within the laser spot, requires us to design highly sensitive 2D IR experiments for capturing the extremely weak vibrational echo signals. Alkyl chain monolayers immobilized on oxide surfaces are among the most popular strategies for surface functionalization. In Chapter 3, I started by examining the conformational dynamics of self-assembled monolayers (SAM) immobilized on silica substrates using transmission mode 2D IR spectroscopy. The SAMs comprised of alkyl chains of which the terminal sites away from the substrate are chemically labelled with rhenium tricarbonyl headgroups. The rhenium carbonyl complex's CO symmetric stretch acts as the strong vibrational mode to generate echo signals with a long vibrational lifetime of ~20 ps. These features allow us to measure spectral diffusion dynamics in sufficiently long time ranges up to tens of picoseconds with good signal-to-noise ratios. The headgroup spectral diffusion dynamics report on the fast gauche-trans conformational dynamics of the underlying alkyl chains. The same type of headgroup was functionalized on a series of monolayers with different alkyl chain structures to determine how major structural variables, including the chain length, the chain density and the presence of interlinking siloxane network among chains (-Si-O-Si-O-) impact on the chain dynamics. To expand the scope of 2D IR measurements to SAMs organized on metallic substrates, 2D IR methods operating in external reflection mode were developed. Comparing the monolayers with the same rhenium complex headgroup and the same alkyl chain length (11 carbons), the spectral diffusion dynamics of SAMs on SiO2 surface are faster (~40 ps) than the dynamics of thiol SAMs on gold surface (~90 ps). We suggest that the slower dynamics are due to the chains in thiol SAMs packing in a more ordered nearly-all-trans conformation, while the faster dynamics of SAMs on silica originate from the less ordered chain packing that contains more gauche defects and free volumes. Collaborated molecular dynamics simulations were applied to reproduce the spectral diffusion dynamics using time-dependent Stark effect models. Simulations confirm that the spectral diffusion dynamics are induced via Stark effect mechanisms where the alkyl chain motions cause intermolecular electric fields projected by the polar headgroups to fluctuate. SAMs with higher alkyl chain gauche defect content among the C-C bonds have more frequent chain conformational fluctuations and faster dynamics. The reflection mode method was advanced to acquire direct time-dependent 2D IR spectra of Langmuir monolayers assembled at the air/water interface for the first time, without the aid of sum-frequency generation process. On the surface of a dielectric such as water, the low reflectivity leads to reducing the local oscillator and therefore enhancing the heterodyne detected vibrational echo signal. An organometallic surfactant, TReF18, with the rhenium tricarbonyl vibrational probe being the hydrophilic part and the octadecyl hydrocarbon chain monolayers acting as the hydrophobic part was spread on water surface at two surface densities, 60 Å2 and 90 Å2 per surfactant, in the liquid expanded phase. The carbonyl spectral diffusion report that water hydrogen bond rearrangement dynamics slow from 1.5 ps in bulk water to 3.1 ps for interfacial water. Another spectral diffusion term at a rate of 42.2 ps was also observed and attributed to slower fluctuations of the number of hydrogen bonds formed between water and the three carbonyls of TReF18. At the higher surface density, two types of TReF18 minor structures are observed in addition to the main structure observed in the low surface density. 2D IR chemical exchange spectroscopy further reveals these structures interconvert in 30 ps. Moreover, the population amplitudes of the minor structures are heterogeneously distributed across the water surface and can evolve through hours to reach macroscopic structural equilibrium. We demonstrate that the enhanced reflection method united with an advanced mid-infrared pulse-shaping laser system can take usable 2D IR spectra on the monolayer within 8 seconds. This enables the simultaneous monitoring of the ultrafast molecular dynamics and the ultraslow real-time structural fluctuation. In the last chapter, I utilized 2D IR methods and polarization-selective pump-probe (PSPP) spectroscopy to investigate molecular dynamics confined in rocks. The systems include water molecules confined in two types of calcium sulfate hydrate minerals, bassanite (CaSO4•0.5H2O) and gypsum (CaSO4•2H2O). The water molecules in gypsum are highly ordered. The 2D IR spectrum show mostly pure homogeneous broadening. PSPP measurements observe only inertial orientational relaxation. In contrast, water molecules in bassanite's tubular channels are dynamically disordered. 2D IR spectra contain a significant amount of temperature-dependent inhomogeneous broadening caused by different water hydrogen-bonding configurations. At 298 K, water dynamics cause spectral diffusion to sample a portion of the inhomogeneous line width on the time scale of ∼30 ps, while the rest of inhomogeneity appears as static on the tens of picoseconds timescale of the measurements. Water angular motions in bassanite exhibit temperature-dependent diffusive orientational relaxation in a restricted cone of angles with the cone half angle being 24°. The experiments were made possible by eliminating the vast amount of scattered light produced by the granulated powder samples using phase cycling methods.

Mechanistic pathways of inorganic homogeneous catalyts are determined not only by the reactive electronic structure but also the precise arrangement of the atoms within the catalyst. Furthermore, without knowing precisely how nuclear structure and electronic structure affect each other, computational methods may not be able to accurately portray the behavior of certain inorganic complexes. Ir2(dimen)4{+2} (dimen = 1,8-diisocyano-p-menthane) is such a system. X-ray crystallography has long supposed that this particular d8-d8 dimer has two thermally accessible minima on the same ground state and more recent temperature dependent solution spectra support this but, so far, computational efforts have not been able to recreate a double minimum potential energy surface. However, a simple quasi-empirical mechanical spring model has been proposed in the literature which features two minima with a shallow barrier. Herein, a combination of transient absorption (TA) and time-resolved X-ray diffuse scattering (XDS) is used to determine that the potential energy surfaces of ground and excited state follow this model. When exciting extremes of the HOMO-LUMO band which have been inferred to correspond to each ground state minima, we are able to use vibrational wavepacket analysis to qualitatively confirm that the ground state possesses two minima while the excited state has only one, as predicted in the literature model. Furthermore, we are able to observe ground state interconversion in real-time, occuring the in ~10ps regime, confirming that interconversion is thermally accessible but with a barrier height over five times larger than predicted. Furthermore, a combination of XDS and Born-Oppenheimer Molecular Dynamics is used to produce a global picture of Ir2(dimen)4{+2} in solution in which a detailed molecular solvent response is characterized for the excited state. Using this approach, it was found, both computationally and experimentally, that he methyl groups prefer to coordinate to the ground state and recoordinate via the nitrile group in the excited state which is quite unexpected and could not be predicted by continuum models or electrostatic arguments.