The movement of energy within a material is at the heart of numerous fundamental properties of chemistry and physics. Studying the process of photo-absorption in real time provides key insights into how energy is captured, stabilized, and dissipated within a material. The work presented in this thesis uses ultrafast time-of-flight mass spectrometry and computational modeling to observe and understand the properties of photo-excited states within molecules and clusters. Experimental results provide direct measurement of excited state lifetimes, while computational modeling provides a more thorough understanding of the movement of energy within an excited state. Excited state dynamics in covalent molecules such as n-butyl bromide (C4H9Br), presented in Chapter 4, demonstrate the significance of IVR of photo-excited states. Exciting to the high energy Rydberg manifold leads to predissociation into fragments of various lengths and degrees of saturation but the predissociation process is disrupted by energy redistribution into hot vibrational states. Experimental lifetimes show that IVR occurs over rapidly (~ 600 fs) leaving less energy for bond dissociation. Additionally, a long-lived feature in the dynamics of C4H9+ shows evidence of ion-pair formation – a known phenomenon which creates a stable A+/B- pair separated by several angstroms and occurring at energies lower than direct ionization. The results of this research show the dynamics of energy transfer into bond fragmentation, kinetic energy, and vibrational motion. Metal-oxide clusters are unique materials which are representative of bulk materials but with quantized excited states instead of bands and as such can be used as atomically precise analogs to semiconducting materials. Excited state lifetimes and theoretical descriptors of electron-hole interactions of titanium oxide clusters, presented in Chapter 5, shows the significance of structure and oxidation of charge-transfer materials. Modeling the excited states of the photo-generated electrons and holes provides a window into the dynamics of charge-transfer and electron-hole separation and recombination in bulk materials. Furthermore, changes in the oxidation of the cluster have a dramatic impact on the nature of excited states and overall cluster properties. Such changes are analogous to oxygen defects in bulk materials and are critical for understanding reaction chemistry at defect sites.

Molecular structures and dynamics in amorphous materials present unique experimental challenges compared with the characterization of crystalline solids. Liquids and glassy solids have many applications in industry such as ionic liquids for fuel cells or biomolecule stabilizing agents, enhancing pharmaceuticals dissolution rates, and modified high performance biopolymers like silk for textile, biomedical, drug delivery, among many others. Amorphous materials are metastable, with kinetic profiles of phase transitions depending on relaxation dynamics, thermal history, plus factors such as temperature, pressure, and humidity. Understanding molecular structure and phase transitions of amorphous states of small molecules and biopolymers is broadly important for realizing their applications. The structure of liquid and glassy states of the drugs carbamazepine (CBZ) and indomethacin (IMC) were studied with solid-state nuclear magnetic resonance (ssNMR) spectroscopy, high energy X-ray diffraction, Fourier Infrared Transform Spectroscopy (FTIR), differential scanning calorimetry (DSC), and Empirical Potential Structure Refinement (EPSR). Both drugs have multiple crystalline polymorphs with slow dissolution kinetics, necessitating stable glassy or polymer dispersed formulations. More hydrogen bonds per CBZ molecule and a larger distribution of oligomeric states in the glass versus the liquid than expected. The chlorobenzyl ring of crystalline and glassy IMC measured with ssNMR were surprisingly found to have similar mobility. Crucially, humidity strongly affects glass structure, highlighting the importance of combining modeling techniques like EPSR with careful sample preparation for proper interpretation. Highly basic protic ionic liquids with low ∆pKa were synthesized with metathesis rather than proton transfer and characterized using NMR and dielectric spectroscopy. Finally, the protein secondary structure of spider egg sac silk was studied using ssNMR, FTIR, and scanning electron microscopy. Tubuliform silk found in spider egg sacs has extensive β-sheet domains which form nanocrystallites within an amorphous matrix. Structural predictions and spectroscopic measurements of tubuliform silk solution are mostly α-helical, with the mechanism of structural rearrangement to the β-sheet rich fiber unknown. The movement of spiders during egg silk spinning make in situ experiments difficult practically. This work is the first observation that tubuliform silk of Argiope aurantia after liquid crystalline spinning exits the spinneret as a predominantly (~70%) β-sheet fiber.

In the developing field of nonlinear plasmonics, it is important to understand the nonlinear responses of the metallic nanostructures. In the present thesis, rigorous electrodynamical simulations based on the fully vectorial three-dimensional nonlinear hydrodynamic Drude model describing metal coupled to Maxwell's equations are performed to investigate linear and nonlinear responses of the plasmonic materials and their coupling with quantum emitters.The first part of this thesis is devoted to analyzing properties of the localized surface plasmon resonances of metallic nanostructures and their nonlinear optical responses. The behavior of the second harmonic is investigated as a function of various physical parameters at different plasmonic interfaces, revealing highly complex dynamics. By collaborating with several research teams, simulations are proven to be in close agreement with experiments, both quantitative and qualitative. The second part of the thesis explores the strong coupling regime and its influence on the second harmonic generation. Considering plasmonic systems of molecules and periodic nanohole arrays on equal footing in the nonlinear regime is done for the first time. The results obtained are supported by a simple analytical model.

An Exciton is an excited state of an atom that can move between atoms in a lattice, and can be viewed as a quasi-particle. I studied the dynamics of an Exciton wave packet traveling along a line of atoms, and how the medium the wave packet travels in affects said dynamics, via numerical simulation.

Time-resolved serial femtosecond crystallography is an emerging method that allows for structural discovery to be performed on biomacromolecules during their dynamic trajectory through a reaction pathway after activation. This is performed by triggering a reaction on an ensemble of molecules in nano- or microcrystals and then using femtosecond X-ray laser pulses produced by an X-ray free electron laser to collect near-instantaneous data on the crystal. A full data set can be collected by merging a sufficient number of these patterns together and multiple data sets can be collected at different points along the reaction pathway by manipulating the delay time between reaction initiation and the probing X-rays. In this way, these ‘snapshot’ structures can be viewed in series to make a molecular movie, allowing for atomic visualization of a molecule in action and, thereby, a structural basis for the mechanism and function of a given biomacromolecule.

This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.

Industrial interest in electrocatalytic production of hydrogen has stimulated considerable research in understanding hydrogenases, the biological catalysts for proton reduction, and related synthetic mimics. Structurally closely related complexes are often synthesized to define structure-function relationships and optimize catalysis. However, this process can also lead to drastic and unpredictable changes in the catalytic behavior. In this paper, we use density functional theory calculations to identify changes in the electronic structure of [Ni(bdt)(dppf)] (bdt = 1,2-benzenedithiolate, dppf = 1,1ʹ-bis(diphenylphosphino)ferrocene) relative to [Ni(tdt)(dppf)] (tdt = toluene-3,4-dithiol) as a means to explain the substantially reduced electrocatalytic activity of the tdt complex. An increased likelihood of protonation at the sulfur sites of the tdt complex relative to the Ni is revealed. This decreased propensity of metal protonation may lead to less efficient metal-hydride production and subsequently catalysis.

The addition of aminoalkyl-substituted α-diimine (DI) ligands to bis(1,5 cyclooctadiene) nickel (or (COD)2Ni) resulted in the formation of two new nickel complexes with the general formula of (Me2NPrDI)2Ni and (PyEtDI)2Ni. Investigation of these complexes by 1H NMR spectroscopy revealed diimine coordination but also the absence of amine arm coordination. Using the 1H NMR spectra in conjunction with structures determined through single crystal X-ray diffraction, the electronic structure of both complexes was described as having a Ni(II) metal center that is antiferromagnetically coupled to 2 DI radical monoanions. A greater ligand field was sought by replacing the pendant amines with phosphine groups on the DI ligands. This yielded ligands with the general formula (Ph2PPrDI) and (Ph2PEtDI). Upon addition to (COD)2Ni, each ligand immediately displaced both COD ligands from the Ni0 center to produce new κ4 N,N,P,P complexes, (Ph2PPrDI)Ni and (Ph2PEtDI)Ni, as observed via single crystal X-ray diffraction and NMR spectroscopy. Reduction of the DI backbone was observed in both complexes, with both complexes being described as having a Ni(I) metal center that is antiferromagnetically coupled to a DI radical monoanion. In addition to alkylphosphine substituted DI ligands, the coordination of a pyridine diimine (PDI) ligand featuring pendant alkylphosphines was also investigated. The addition of (Ph2PPrPDI) to (COD)2Ni produced a new paramagnetic (μeff = 1.21 μB), κ4-N,N,N,P complex identified as (Ph2PPrPDI)Ni. Reduction of the PDI chelate was observed through single crystal X-ray diffraction with the electronic structure described as having a low-spin Ni(I) metal center that is weakly coupled to a PDI radical monoanion (SNi = 1/2). The ability of the three Ni complexes to mediate the hydrosilylation of several unsaturated organic substrates was subsequently investigated. Using a range of catalyst loadings, the hydrosilylation of various substituted ketones afforded a mixture of both the mono- and di-hydrosilylated products within 24 hours, while the hydrosilylation of various substituted aldehydes afforded the mono-hydrosilylated product almost exclusively within hours. (Ph2PEtDI)Ni and (Ph2PPrPDI)Ni were identified as the most effective catalysts for the hydrosilylation of aldehydes at ambient temperature using catalyst loadings of 1 mol%.