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.

In this dissertation, we describe, implement, and test wavefunctions that describe short-range, so called dynamic correlation effects through the use of explicitly correlated geminal pair functions. We present both a single-configuration explicitly correlated analogue of a Hartree-Fock wavefunction, and a multi- configurational variant, a Geminal-augmented Complete Active Space Self Consistent Field method. These methods are designed to efficiently include dynamic correlation effects during variational optimization of the wavefunction, rather than resorting to a post hoc perturbation description. We test both methods on a number of model systems and show that the geminal-augmented wavefunction is capable of describing short-range correlation effects. In addition, we present a fully exact implementation of the algorithms necessary to evaluate the many-electron integrals that arise in explicitly correlated wavefunctions.

The movement of molecules through a condensed phase is governed by an extremely complex hierarchy of considerations and constraints on motion. This is particularly true when electric fields from ions and hydrogen bonding is involved, let alone heterogeneous structuring of the liquid. This thesis seeks, principally, to quantify the timescales of probe molecule motions and to then improve the understanding of how these motions occur. The ultimate goal is to predict how changes in the environment will affect motion both of the liquid and any dissolved solutes. The nature of molecular motions in the condensed phase was investigated using ultrafast two-dimensional infrared spectroscopy. This enabled non-perturbative interrogation of the systems in question as well as the time resolution necessary to detect changes in motion. Both the reorientation of the molecules and the spectral diffusion (which quantifies structural fluctuations) were used to better understand the motions in a number of chemical systems, focusing on the effect of salts. Both aqueous solutions of salts and room temperature ionic liquids (which are a subset of salts that remain molten at room temperature) with dissolved solutes were investigated. A number of noteworthy results were obtained and some interesting conclusions were drawn about aqueous salt solutions. It was found that, in water, some salts (particularly those with a high charge density) can slow the movement of water molecules considerably. This is primarily dependent on the anion, to which the water is directly hydrogen bonded, but the cation can play a role. However, certain salts (including borohydride) leave the dynamics of water unperturbed even when extremely concentrated. This is facilitated by the formation of hydrogen bonds with water molecules such that the hydrogen bond network remains fairly intact despite the presence of the ions. The structuring of the liquid may also play a role -- ionic liquids, which exist as liquids even without the addition of water and have internal structuring, have different dynamics than typical salts when the same amount of water is added to both. Studies were conducted on ionic liquid solutions to determine the effect of structuring. By changing the alkyl chain length of the cation, the ionic liquid adopts different configurations. This cause the dynamics of solutes to change in ways that would not necessarily be expected given the change in bulk properties like viscosity. The region of the ionic liquid that is solvating the probe molecule is found to determine the dynamics rather than the liquid as a whole. However, as was found with dissolved carbon dioxide as it is of note for carbon capture applications, the long range structuring of the ionic liquid can play a role for a subset of the motions that the probe experiences.

The properties of liquid systems confined on nanometer length scales may differ considerably from those of bulk liquids, with consequences for the dynamics of processes taking place in those systems. Proton transfer dynamics in nanoconfined aqueous environments are a topic of considerable scientific interest. A significant area of research within that topic is the influence of the confining interface on dynamics within the confined environment. Similarly, liquids that display relatively long-range structure (nanometer size scales) may show the effects of that structure in the dynamics of dissolved solutes. For example, room temperature ionic liquids (RTIL), a class of compounds that has attracted considerable interest for applications in catalysis, synthesis, and energy storage, have been shown to exhibit complicated nanoscale liquid structure with the formation of hydrophilic and hydrophobic domains. The orientational relaxation dynamics of the fluorescent probe perylene dissolved in solutions of various concentrations of lithium salts in RTILs were studied by measurement of fluorescence anisotropy. Increasing concentrations of lithium salt were found to cause both the in-plane and out-of-plane rotational diffusion of perylene to become slower as the liquid's bulk viscosity increased. However, the rotational diffusion did not slow sufficiently to track the viscosity and both of the corresponding viscosity-independent molecular friction coefficients decreased. This reveals that lithium ions, which are solvated by the ionic regions of the RTILs, change the structure of the alkyl regions of the RTIL. Another series of experiments studied excited-state proton transfer kinetics in both ionic and neutral reverse micelles. TCSPC measurements of the population decay were conducted on the fluorescent photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) in bulk water, ionic reverse micelles, and non-ionic reverse micelles, and the orientational dynamics of dissolved MPTS, the methoxy derivative of HPTS, in those systems were also investigated by time dependent fluorescence anisotropy measurements. The orientational diffusion data suggest that in ionic reverse micelles, the probe molecules are located in the water core of the reverse micelle, while in non-ionic reverse micelles, the data suggest the probes are located at the water-surfactant interface. HPTS proton transfer in ionic reverse micelles followed kinetics qualitatively like those in bulk water, albeit slower, with the power law time dependence associated with recombination of the proton with the dissociated photoacid having a smaller exponent, suggesting a modified diffusion-controlled process. In neutral reverse micelles, proton transfer kinetics did not show discernible power law behavior and were best represented by a two component model with one relatively water-like population, and a population with a faster fluorescence lifetime and negligible proton transfer. Finally, the analysis of proton transfer dynamics in bulk water resulted in a t-1.1 power law for proton recombination as opposed to the t-1.5 power law predicted by theory and some previously reported observations. The reliability of these newer observations is justified, and possible ways in which existing theory may be incomplete are discussed.

With an ever increasing global demand for energy, it is paramount that energy conversion devices become more efficient or energy consuming devices use less power. The key to making these improvements is to gain a better fundamental understanding of materials. More specifically if one is able to arrive at the structural solution for a particular material, then its various properties could be predicted and tuned. To come to this level of understanding requires tools that are equally precise in the fabrication of the materials as they are in the characterization of them. Atomic layer deposition (ALD) is a deposition technique that can create highly conformal films of varying chemistries with sub-nm precision due to its self-limiting nature. Typically, these fabricated films are characterized by X-ray photoelectron spectroscopy (XPS), ellipsometry, transmission electron microscopy (TEM), atomic force microscopy (AFM), x-ray diffraction (XRD), etc. If the films are amorphous, contain nano-crystallites or are buried in nanostructures, then even some of these characterization techniques are no longer feasible. X-ray absorption near edge structure (XANES) however, may still be used to gain detailed information of the electronic and geometric structure of the thin film. XANES is a powerful characterization technique capable of revealing oxidation states, coordination chemistry, molecular orbitals, band structures, local displacement and chemical short-range order information. It can be performed on samples that are in the solid, liquid, or gas phase and can be performed in a wide range of temperatures and pressures. In this thesis, the combination of these two techniques are used to gain unprecedented insight into several functional thin films. Together the two techniques allow one to control the bonding environment and finely characterize nanomaterials at the atomic level. I will show how this synergistic combination can lead to the fundamental understanding of properties and their link to processing parameters. Specifically, this thesis provides understanding of interface effects, composition, thickness and electrical properties as well as insight on reaction mechanisms revealed by novel in-situ measurements. For second generation solar cells, the price of electricity can be decreased either by increasing the efficiency or by increasing its lifetime. The cost of the solar cell is no longer a big advantage over the first generation Si solar cells. Si solar cell cost has gone down over the years and increases in efficiency are now negligible (the efficiency of single crystal Si solar cells sits at ≈25%). The most important parameter to reduce cost in a second generation and emerging solar cell technology is to increase the efficiency. For ALD lead sulfide (PbS) Quantum dots (QDs) in a Quantum dot sensitized solar cell (QDSSC) architecture we gain atomic level insight at junctions between PbS QDs and metal oxide nano-materials, learning that distortions away from a cubic structure induced by the interface, increases the band gap. Going into ternary oxides, we next explore Zn(O, S), a commonly used buffer layer in thin film solar cells (TFSC). Through composition, thickness, interface and ALD deposition sequence control, the role of each on efficiency will be elaborated. Not unlike in solar cells, charge transport also needs to be tuned in dielectric materials used in dynamic random access memory (DRAM) applications. To be a viable option for DRAM application the dielectric film has to be high-k, ultrathin, electrically insulating and have the ability to uniformly coat high aspect ratio structures. ALD of conventional group IV high-k metal oxides like ZrO2 and HfO2 won't be able to meet future requirements for the semiconductor industry. ALD BaTiO3 (BTO) is promising candidate due to its very high dielectric constant. Due to its amorphous nature, XANES was utilized to track changes in geometric structure as a function of cationic composition, where a structure property relationship was established to link its electrical behavior. Finally, the two techniques are combined for in-situ measurements where we study the semiconductor ZnS. In-situ ALD/XANES measurements were performed for the first time on this system, where our work led us to propose a new mechanism for ALD sulfides grown on oxide interfaces.

Room-temperature ionic liquids (RTILs), which refers to salts that are liquid at room temperature, form a class of materials that have been intensively studied in recent years. A major motivator for this explosion in research is their many special properties and proposed applications. Many of these applications rely on their properties as solvents, particularly their ability to simultaneously solvate solutes of disparate natures. These properties have been linked to the existence in certain classes of RTILs of local domains with differing properties, such as polar and apolar domains. This ordering, which occurs when one ion, usually the cation, has a large hydrophobic moiety, such as an alkyl chain, is an additional constraint imposed on both liquid ordering and the charge alternation which is observed due to the ionic nature of the material. Varying the chain length of such cations not only changes the degree of polar-apolar ordering, but also bulk properties such as viscosity. My work seeks to understand and characterize ion solvation in such ionic liquids, and especially how and to what extent the details of solvation structure and dynamics are affected by the change in bulk properties or growing influence of additional ordering. To this end, the dynamics of four 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide RTILs with carbon chain lengths 2, 4, 6, and 10 were studied by measuring the orientational and spectral diffusion dynamics of the vibrational probe SeCN‒. Vibrational absorption measurements, two-dimensional infrared (2D IR) spectroscopy, and polarization-selective pump-probe (PSPP) experiments were performed on the CN stretch of the ion. The PSPP experiments yielded triexponential anisotropy decays, which were analyzed with the wobbling-in-a-cone model. The slowest decay, the complete orientational randomization, slows with increasing chain length in a hydrodynamic trend consistent with the increasing viscosity. The shortest time scale wobbling motions are insensitive to chain length, while the intermediate time scale wobbling slows mildly as the chain length increases. Spectral diffusion from the RTIL structural fluctuations was characterized through 2D IR. The faster structural fluctuations are relatively insensitive to chain length. The slowest structural fluctuations slow substantially when going from a 2 carbon chain a 4 carbon chain and slow further, but more gradually, as the chain length is increased. The main conclusion is that there exists a complex hierarchy of motions in terms of their spatial extent and their timescale. The fastest motions, which tend to be the most local, are also the ones most insensitive to bulk properties. The largest scale motions tend to be the ones most consistent with hydrodynamics. Some intermediate scale motions can be surprisingly sensitive to details of the structure which can be related to the growth of polar-apolar ordering, where other intermediate scale motions exhibit very weak trends. A complete understanding of the structure and dynamics of these ionic liquids, especially when considering the effect of various structural modifications, must then consider the richness of motions and timescales and how they are influenced by structural differences, as well as how they relate to the specific process that is being optimized through this structural modification. In order to obtain data of sufficient quality and detail to allow such modeling to be done successfully, the way these ultrafast experiments are performed, particularly the 2D IR experiments, had to be improved in both speed and freedom from distortion. To this end, I constructed a 2D IR interferometer based on Fourier-domain pulse-shaping. The resulting phase control and stability allows the experiments to be performed free of distortions. It also allows repeating the experiment with various configurations of imparted phase, known as "phase-cycling". Phase-cycling has four immediate benefits: it permits the experiment to be performed in a semi-collinear geometry, further eliminating possible distortions; it allows many unwanted terms such as scatter to be very effectively suppressed; it allows the spectrum of the excitation pulses to be advantageously controlled; and it eliminates the need for chopping beams which alone doubles the speed of acquisition. In addition, the programmatic generation of the first two pulses via pulse-shaping eliminates moving parts from that portion of the experiment, greatly speeding acquisition. This has allowed many previously inaccessible systems to be studied using this technique and was a tremendous aid in performing the experiments described here.