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Protochlorophyllide (Pchlide) is the substrate of the light-driven reaction catalysed by the protochlorophyllide oxidoreductase (POR) enzyme. This reaction is a crucial step for chlorophyll biosynthesis in plants, it plays an important role in plant development and it has been suggested to also play a photoprotective role in plant cells. The POR reaction is one of the very few enzymatic reactions activated by light. The fact that the reaction can be triggered with a single laser pulse makes it a unique model to study enzyme catalysis. A crystal structure of POR is to date unavailable and this lack has thwarted a full elucidation of the reaction mechanism as well as the determination of the protein ternary structure and the exact active state geometry. The substrate, Pchlide, has unique excited-state properties and the decay kinetics including what was presumed to be a long-lived triplet state. We have used time-resolved absorption and electron paramagnetic resonance (EPR) spectroscopy at cryogenic temperatures to provide direct evidence of the triplet state of Pchlide and the characterisation of its EPR signature. We have found that the triplet state of Pchlide reacts with solvated oxygen, and that POR-binding reduces the triplet lifetime, supporting the theory of POR playing a photoprotective role. We were able to stabilise and characterise a highly transient reaction intermediate by means of cryo-trapping as well as identifying changes in its structure, a matter where there is currently no clear consensus. By studying substrate analogues we have been able to expand current knowledge on which and how different regions of Pchlide are important for the reaction photochemistry. The work in this thesis opens up this crucial biological system to a whole new range of experimental techniques that can prove instrumental in elucidating the still unclear reaction mechanism of light-driven POR.

Nature uses sunlight either as energy source or as information carrier. Photoreception is achieved by two groups of specialised proteins: photo-enzymes that catalyse photoreactions and photosensors that initiate physiological functions. In the present work mechanistic studies were conducted on one representative of each group by using site-directed mutagenesis as well as stationary and time-resolved spectroscopy. The photo-enzyme NADPH:Protochlorophyllide Oxidoreductase (POR) catalyses the light-dependent C17-C18 double bond reduction of protochlorophyllide, including a hydride and a proton transfer, to produce chlorophyllide, the immediate precursor of chlorophyll. POR provides a unique opportunity to study the hydride transfer mechanism in detail. Three distinct intermediates, prior to product formation, were observed that were interpreted as electron and proton-coupled electron transfer reactions from NADPH indicating a sequential hydride transfer mechanism. An active-site mutant, POR-C226S, yields distinct different intermediates compared to POR wild type but ends in the same chlorophyllide stereoisomer most likely due to an altered protochlorophyllide binding. This work provides the first direct observation of a stepwise hydride transfer mechanism in a biological system. Cryptochromes (CRY) are so far defined as flavoprotein blue-light photosensors that regulate the circadian clock throughout nature and are suggested as the candidate magnetoreceptor in animals. Animal CRY are subdivided into two classes of proteins: the light-responsive Type I (invertebrates) and the light-independent Type II (mainly vertebrates). The molecular basis of their different roles in the circadian clock is still unknown. Animal Type I CRY are suggested to undergo conformational changes - required for induction of subsequent signalling cascades - induced by the change in the FAD redox state due to light absorption. The study shows that in contrast to Type I animal Type II CRY do not bind tightly FAD as a cofactor due to the lack of structural features and therefore provide the molecular basis for their different biological roles ruling out a direct photomagnetoreceptor function. Further, detailed studies on a fruit fly (Dm)CRY reveal that it does not undergo a photocycle as FAD release and Trp decomposition were observed. Thus, it is suggested that light is a negative regulator of DmCRY stability linking the initial photochemistry to subsequent dark processes leading to signal transduction on a molecular level.

This thesis is an investigation of the photophysical processes that occur in organic photovoltaic blends in the time between light being absorbed and free charges being generated. The purpose of all solar cells is to generate a photocurrent. The free charges, as they flow out of the device, make up the photocurrent, so understanding the processes by which they are created is vitally important to organic photovoltaic research. The main experimental method used was time-resolved fluorescence spectroscopy. This technique was used to probe the exciton population with respect to time for a variety of blends of organic semiconductors, including the high performance photovoltaic materials PCDTBT, PTB7, C71-PCBM and P3HT. The main goal of the work was to characterise the exciton diffusion lengths of these materials by developing a technique called volume quenching. Volume quenching involves blending a small quantity of quenching material into a thin film of semiconducting material. These introduced quenching sites render excitons unemissive on contact. Thus, from the drop in fluorescence compared with the ‘unquenched' material, it was possible to work out what proportion of the initial excitons have encountered a quenching site in the blends. The results can then be fitted to quantify how diffusive the excitons are -i.e. how far they move. By looking at the rate constant of the quenching process and how it varies with respect to time, quencher concentration and quencher type, it was possible to generate a wealth of additional information, not just about exciton diffusion, but about all the inter-related processes that contribute to exciton harvesting. These processes included the measurement of long-range energy transfer from the donor to the acceptor, electron transfer at the interface with the acceptor and the understanding of nanomorphology of donor-acceptor heterojunctions.

This thesis describes the synthesis of polyyne rotaxanes and an investigation of their excited state photophysical properties. The threading of dumbbell-shaped carbon chains with macrocyclic components is a way to mechanically insulate and control the environment around the carbon chains. The resulting polyyne rotaxanes can serve as model compounds for insulated carbyne. Different strategies have been tested for the synthesis of polyyne rotaxanes with different topologies and structures. Study of rotaxanes in the excited states reveals strong electronic communication between an acetylenic thread and a macrocycle. Chapter 1 summarizes the field of acetylene scaffolding, introducing some recent achievements in acetylene chemistry. General synthetic methods for polyynes are discussed, and an introduction to active metal template synthesis of rotaxanes is given. Chapter 2 describes the synthesis of a family of polyyne rotaxanes with different axle lengths and macrocycles, prepared by homocoupling of terminal alkynes. Synthesis of hexayne rotaxane with functional pyridine end-group is presented and a number of crystal structures of polyyne rotaxanes are analyzed. Chapter 3 demonstrates the use of acetylene cross-coupling in the synthesis of rotaxanes. Synthesis of rotaxanes with different topological structure is provided. Chapter 4 details the excited state properties of polyynes studied by time -resolved spectroscopy. The complexes of rhenium(I) carbonyls with rotaxanes is presented and the excited state energy transfer in rotaxanes is studied. Chapter 5 explores new synthetic strategies for polyyne rotaxanes, using "masked" precursors. It also highlights the potential of carbenoid rearrangement of alkyliden es for the construction of linear and cyclic architectures. Chapter 6 is the summary of the project and general discussion of future directions. There are two appendices in the end of thesis: Appendix A covers the photophysics of rhenium tricarbonyl complex of the hexayne rotaxane with a small macrocycle and Appendix B reports work towards the synthesis of rotaxanes with platinum(II)-alkyne complexes.

Time–resolved Fourier transform infrared difference spectroscopy has been used to study photosystem I (PSI) photosynthetic reaction centers from Synechocystis sp. PCC 6803 (S6803) at cryogenic temperature (77 K) with a series of native and non-native quinones incorporated in the A1 binding site. LED-based pump-probe spectroscopy was used to study the P700+(FA/B–/A1A–) state recombination at room temperature (298 K). “Foreign minus native” double difference spectra (DDS) were constructed by subtracting TR FTIR DS for native PSI from corresponding spectra of non-native quinones. To help assess and assign bands, density functional theory based vibrational frequency calculations for quinones in solvent, or in the presence of a single asymmetric H–bond to either a water molecule or a peptide backbone NH group, were undertaken. In the study of four high-potential naphthoquinones (2-chloro-, 2-bromo-, 2,3-dichloro- and 2,3-dibromo-1,4-naphthoquinone), we conclude that the mono-substituted NQs (2ClNQ and 2BrNQ) can occupy the binding site in different orientations, with the C3 hydrogen atom being both ortho and meta to the H-bonded C4=O group. In PSI complexes at 298 K electron transfer from A1– to FX is an order of magnitude faster on the B-branch compared to the A-branch. One factor that might contribute to this branch asymmetry in time constants is TrpB673, which is located between A1B and FX. In the study of the TrpB673Phe mutant (WB673F mutant - mutation of TrpB673 to Phe) cells, photoaccumulated FTIR DS for WB673F mutant cells indicate changes in amide I and II protein vibrations upon mutation, indicating the protein environment near FX is altered upon mutation. In the WB673F mutant light sensitive PSI samples, the phylloquinone molecule is likely doubly protonated following long periods of repetitive flash illumination at 298K which can be restored by incubating the light treated mutant PSI samples in the presence of added phylloquinone. In cyanobacteria, PSI is found mainly in trimeric and slightly in monomeric form [26]. Previous x-ray structural studies indicate there are no significant differences between them. In this study, we investigated whether they are kinetically different, and we conclude that they are very similar in this aspect as well.

The topic of this doctoral thesis is the study of time-resolved phenomena in molecular systems using the novel possibilities opened by harmonic generation in gases. These systems have different \textit{sizes}, ranging from small molecules to large clusters with hundreds of molecules, and \textit{properties}, covering simple triatomic molecules through chiral molecules to hydrogen-bonded clusters representing a complex environment in which interesting processes can be studied. This broad spectrum of dynamics can be initiated and also detected using femtosecond (1~fs = $1\cdot 10^{-15}$~s) laser pulses in vacuum- and extreme-ultraviolet (VUV/XUV) spectral range. In other words, the central part of this thesis is devoted to a time-resolved perspective on molecular dynamics arising on sub-100~fs timescales. The dynamics are elucidated using a pump-probe photoelectron spectroscopy approach. The investigated systems are photo-excited and then photo-ionized. After photo-ionization, a photoelectron is detected which carries information about the parent molecule. The information is encoded in the kinetic-energy and angular distribution of the emitted photoelectron. One of the widely used experimental setups to collect this information is a velocity-map-imaging (VMI) spectrometer, which measures energy and angular distributions of these electrons simultaneously. The most complete picture about the molecular dynamics is recorded when the VMI detection is combined with temporal information obtained by precisely timed laser pulses. To achieve this goal, all experiments have been realized in a $(1 + 1^\prime)$-photon pump-probe scheme using a two-color interferometer combined with a VMI spectrometer. The novelty of the experimental setup is a low-order-harmonic generation (LOHG) source generating femtosecond pulses of radiation in the VUV/XUV region of the electromagnetic spectrum. Such a light source is a much desired extension to explore molecular dynamics of highly excited molecular or Rydberg states which were previously inaccessible by single-photon processes. Moreover, this type of VUV/XUV source is compatible with the generation of circularly polarized harmonics, opening up a new branch of study with which molecular chirality can be studied on the ultrafast timescale. The main part of the thesis describes three case studies selected such that they demonstrate the capabilities of the presented experimental setup. They are: i) femtosecond dynamics of SO2, ii) dynamics of the solvated electron in water clusters, and iii) time-resolved photoelectron circular dichroism. The first two cases belong to the realm of femtochemistry as introduced by A. Zewail in the last two decades of the last century. The last topic opens a new avenue in ultrafast science by applying femtosecond circularly polarized pulses to study the real-time evolution of chirality during photochemical reactions. Therefore the last case is opening up the new field of femtochirality. In experiments with the SO2 molecule, the excited-state dynamics in the $\tilde{\text{A}}/\tilde{\text{B}}$- and $\tilde{\text{F}}$-bands were investigated using time-resolved photoelectron imaging and photoion yield measurements. SO2 represents a small molecular system with complex non-adiabatic coupling between multiple close-lying electronic states. Moreover, it serves as a benchmark in many theoretical studies because its full-dimensional potential-energy surfaces can be calculated. The solvated electron, which can be prepared in large water clusters, is an important product during radiolysis of liquid water and as such it has attracted a lot of attention in both experimental and theoretical studies for more than two centuries. In this thesis, the solvated electron is studied by means of time-resolved photoelectron imaging. An increase of the electron binding energy together with the narrowing of the photoelectron band of the solvated electron have been observed. This is the first direct observation of the solvation dynamics from electron creation and solvation to its decay in sub-ps timescales. Moreover, anisotropy parameters as a function of binding energy and time have been measured showing a small, but persistent anisotropy of the solvated electron. The novel experimental approach is the implementation of circularly-polarized harmonics. The combination of circularly-polarized VUV radiation with an angle-resolved photoelectron detection opens up a new way to study molecular chirality in the time domain by utilizing the so-called photoelectron circular dichroism (PECD). In this thesis, the first time-resolved PECD experiments are demonstrated on time-dependent chirality associated with a photo-induced C-I bond breaking, thereby introducing a general experimental approach for chiral femtochemistry. The experimental results are supported by high-level \textit{ab initio} calculations. The broad applicability of the time-resolved PECD measurement scheme is demonstrated by studying two chiral molecules: CHFBrI and 2-iodobutane. Whereas CHFBrI displays a non-vanishing PECD at long pump-probe delays, the PECD decays to zero after the photodissociation of 2-iodobutane, reflecting the effective chirality of the product radicals on long timescales. In addition to demonstrating the broad applicability of LOHG to ultrafast molecular dynamis, these results also pave the way to attosecond time-resolved studies in the VUV/XUV domain, such as the role of electronic coherences in excited-state dynamics, the very earliest steps in photoionization of water, or the attosecond electron-scattering dynamics in chiral molecular potentials.

Time-resolved infrared and visible absorption difference spectroscopy was applied for the study of electron transfer (ET) reactions involving A1, the secondary electron acceptor in photosystem I (PSI). In PSI, the secondary electron acceptor A1 is a phylloquinone (PhQ) molecule. Flash-induced absorption changes at room and cryogenic temperatures in the infrared and visible spectral ranges were probed for PSI with a series of native and non-native quinones in the A1 binding site. Obtained kinetic and spectral data were analyzed for the functional and structural properties of A1 and PSI. Using transient absorption spectroscopy in the visible spectral range, the rates and directionality of ET processes in PSI with modified A1 were determined. A detailed kinetic simulation model was constructed and solved in the context of Marcus ET theory, and midpoint redox potentials of A1 was predicted within a tight range. The transient absorption kinetics for ten different quinones and the kinetic simulation revealed that the wasteful charge recombination process in native PSI occurs in the inverted region. Although inverted-region ET had been widely suggested to be an important mechanism contributing to photosynthetic efficiency, the mechanism had never been demonstrated in any native photosynthetic system. The result presented here is the first demonstration of inverted-region ET in a native photosynthetic reaction center in physiological conditions. Through Marcus theory-based simulation, inverted-region ET is quantitatively shown to be an important mechanism underlying the high efficiency in PSI ET. Time-resolved infrared difference spectroscopy was undertaken using step-scan FTIR technique with a microsecond temporal resolution. Highly-resolved double difference spectrum was constructed to identify infrared bands due to PhQ in the A1 binding site. Assisted by the DFT-based vibrational frequency calculations, vibrational modes due to anionic PhQ– were identified. The calculations suggest that PhQ is asymmetrically H-bonded, and that this interaction is especially strong for PhQ–, but not for PhQ. Additionally, discrepancies that previously existed between FTIR and EPR studies on PSI with plastoquinone-9 in the A1 site were resolved. A method to incorporate a benzoquinone was established, and (A1– – A1) FTIR difference spectra for a series of benzoquinones were produced for the first time.

Recent progress in ultrafast laser science has made it possible to synthesize and control complex electromagnetic waveforms down to sub-femtosecond timescales. These tailored ultrashort laser pulses can generate coherent bursts of electromagnetic radiation in the extreme ultraviolet (XUV) and terahertz spectral regions with durations reaching the attosecond regime in the XUV region. This is accomplished by coherently controlling electronic motion in gas plasma targets. With these novel radiation sources, ultrafast time-resolved spectroscopy can be performed on a large variety of materials. Knowledge of the spectral phase of an ultrashort pulse is crucial for many applications. There are a variety of ways to fully characterize the electric field but usually, involve an elaborate setup. It is highly desirable to have a method of pulse characterization without such complications. In this work, we introduce an algorithm that retrieves the electric field from the measured fundamental and two nonlinear spectra using an iterative process. This measurement technique is insensitive to optical alignment and imperfections of the beam spatial profile. The control of electronic motion enables the generation of a wide range of coherent electromagnetic radiation. In this dissertation, we have combined the fundamental laser beam with its second harmonic to simultaneously generate extreme ultraviolet (XUV) and terahertz radiation. Synchronous pulses in widely separated spectral regions opens the possibility of powerful time-resolved spectroscopy. We introduce an intuitive semi-classical model based on the well-known three-step description to explain the observed XUV and terahertz correlations. The transparency of this model provides an intuitive physical understanding of the complex features observed in the measured XUV spectra. Key insights are obtained from this model by identifying the effect of second harmonic generation efficiency and the interference of short and long electron trajectories. Ultrashort bursts of electromagnetic radiation are powerful tools for time-resolved spectroscopy. Availability of short pulse durations over a broad spectral range aids the investigation of electron transport in a large variety of materials. We have utilized ultraviolet and XUV ultrashort pulses to probe electron transport in several inorganic scintillators. Scintillators are important because they absorb high energy photons and convert this energy to visible luminescence. Excitation and conversion to visible fluorescence takes place on a timescale of tens of picoseconds. Ultrashort bursts of XUV are an ideal excitation source for these studies. The conversion to visible fluorescence is not 100% efficient as there are competing relaxation processes that can be identified from rise and decay time of the luminescence. The results from such measurements can provide guidance in the engineering of more efficient scintillators for high energy radiation detection.

Ultrafast time-resolved infrared spectroscopy provides a powerful tool for studying the photochemistry of organometallic complexes. The studies described herein focus on the mechanisms of photochemically initiated organometallic reactions with a particular emphasis on two topics: the role of spin states and spin state changes in organometallic reactions, and the primary photochemical dynamics of complexes containing metal-metal bonds (e.g. transition metal dimers and clusters). Many of these studies seek to uncover trends in reactivity based on the spin states of organometallic reaction intermediates, with the goal of being able to offer some level of predictive insight into the reactivity of complexes as classified by their spin multiplicity. The reactivity of various coordinatively unsaturated reaction intermediates are studied with respect to bond activation, electron transfer, excited state photoisomerization, and other classes of reactions important to organometallic catalysis. A second focus, which shares some degree of overlap with the topic of spin state changes, is the primary photochemistry of complexes containing metal-metal bonds. Several of the studies reported herein use time-resolved infrared spectroscopy to examine the primary photochemical processes occurring upon excitation of transition metal dimers and clusters, and often spin state changes also found to play an important role. Results of computational chemistry calculations are frequently used to facilitate interpretation of the experimental results by computation of structures, relative energies, infrared spectra, and spin-orbit coupling for the complexes studied experimentally. Additional studies outside these two primary areas of focus also investigated the ring-slippage of cyclopentadienyl ligands and the CO-delivery properties of a popular CO-Releasing Molecule.

Plants experience rapid fluctuations in light intensity due to intermittent shading. While under low light conditions, efficient absorption of light is important, under high light conditions, this efficient light harvesting can result in excess energy that leads to photodamage. To prevent this photodamage, plants have a set of mechanisms called non-photochemical quenching (NPQ) that allow the plant to dissipate the excess energy harmlessly as heat. While NPQ has been studied for decades, there is still much we do not know about how NPQ is triggered, the changes in the photosynthetic apparatus that occur during NPQ, and the photophysical mechanisms that quench excess energy. NPQ is difficult to study both because of the large number of feedback loops and processes that contribute to NPQ and because the photosynthetic apparatus changes as NPQ turns on and off. This thesis describes the development of new time-resolved spectroscopic tools to help elucidate the proteins and processes important in NPQ. One of the techniques developed is a tool to measure the chlorophyll fluorescence lifetimes of whole leaves as they acclimate to changing light conditions. Chlorophyll is the main pigment in photosynthetic organisms, and its excited state relaxation dynamics reveal information about the energy transfer network in plants. The chlorophyll fluorescence lifetime gives additional information about quenching than the most commonly used probe of NPQ, the chlorophyll fluorescence yield. This tool is able to examine both the nanosecond-timescale and seconds- to minutes-timescale of quenching in vivo.This thesis also describes the application of the fluorescence lifetime technique to study different types of NPQ. Energy-dependent quenching (qE) is the largest and fastest component of NPQ. By comparing the shape of the fluorescence decay curves for plants with and without PsbS, a key protein in qE, it is possible to demonstrate that the presence of the protein PsbS changes only the amount of qE and the speed of qE turn-on and turn-off, not the type of quenching. This suggests that PsbS catalyzes qE. In contrast, the presence of the enzyme violaxanthin de-epoxidase and the carotenoid zeaxanthin do seem to affect the type of quenching. The fluorescence lifetime technique is also applied to study a new family of mutants that lack the protein SOQ1. Here, the fluorescence lifetime measurements confirm that the lack of SOQ1 confers extra quenching as opposed to extra photobleaching. Furthermore, the technique is able to show that SOQ1 reduces the timescale of long-term quenching that normally turns on in approximately 45 minutes by a factor of two. Additionally, a new mutant in the soq1 family shows the highest quenching of any mutant previously studied, and may be a model organism to study energy transfer when Photosystem II reaction centers are open. The development of another tool, a super-resolution stimulated emission depletion (STED) fluorescence lifetime imaging (FLIM) microscope, is also discussed. The goal of this tool was to be able to image the thylakoid membrane of plants using chlorophyll fluorescence. Chlorophyll from different protein environments would be distinguished by their fluorescence lifetime, and the STED technique would provide the resolution needed to distinguish the different parts of the thylakoid membrane. However, different types of STED-based imaging were unable to achieve super-resolution with chlorophyll.Time-resolved measurements of chlorophyll fluorescence offer a way to sensitively probe the dynamics of quenching in plants. In the future, the fluorescence lifetime technique can be applied to other processes and components of NPQ. In addition, the lessons learned in the development of both the fluorescence lifetime technique and the microscopy technique can be used to inform the development of other tools.

Our goal was to develop methods to study protein dynamics on the picosecond to nanosecond time scale. We used wavelength and femtosecond resolved fluorescence and absorbance spectroscopy coupled with site-directed mutagenesis to study the heme proteins myoglobin and cytochrome c and determine protein dynamics occurring on the picosecond to nanosecond time scale. The intrinsic amino acid tryptophan was used as a local optical probe and placed one at a time with site-directed mutagenesis that allowed us to achieve a spatial resolution down to a single amino acid.We systematically characterized resonance energy transfer (RET) between a single tryptophan and the prosthetic heme group in myoglobin to develop a novel energy-transfer pair as a molecular ruler in heme proteins to study local conformation fluctuations. Using site-directed mutagenesis, we placed a single tryptophan throughout myoglobin. We observed picosecond RET in tens to hundreds of picoseconds. We also characterized steady state parameters associated with RET allowing us to determine the orientation factor between tryptophan and heme and thus examine changes at different mutation sites revealing relative local structure flexibility and conformation fluctuations. Additionally, local environment relaxation occurs on similar time scales as the RET dynamics, resulting in a nonequilibrium dynamic process. We were able to determine the time scales of such nonequilibrium energy-transfer dynamics and elucidate the mechanism of the nonexponential RET dynamics caused by local dynamic heterogeneity and/or local environment relaxation. In cytochrome c, RET between the lone intrinsic tryptophan and heme was used to study protein folding/unfolding for various states (ferric, ferrous and CO-bound ferrous) of cytochrome c. We systematic studied heme dynamics and induced protein conformational relaxations in cytochrome c and myoglobin with femtosecond transient absorption (TA). A wide range of probing wavelengths from the visible to the UV was probed to unambiguously determine the protein dynamics of the ferric and ferrous state of cytochrome c. For cytochrome c in the ferrous state, the heme undergoes ligand bond breaking and rebinding process generating proteinquakes that perturb the local heme site and shake global protein conformation which was detected by the nearby lone intrinsic tryptophan. Cytochrome c in the ferric state has dynamics that mainly occur at the local site, including ultrafast internal conversion, vibrational cooling, and complete ground-state recovery with no global conformation relaxation observed. We expanded our studies by coupling site-directed mutagenesis of tryptophan at various locations throughout cytochrome c utilizing TA studies. Ligand photolysis from heme was used to generate proteinquakes perturbing the local heme site and shakes global protein conformation and was observed by several of the tryptophan mutations. Additionally, we observed the protein dynamics as a function of denaturing agent. The region that we studied was the pre-unfolding transition region; hence the protein was “softened.” In myoglobin, we similarly characterized the heme dynamics of the ferric, ferrous and CO-bound ferrous states. We attempted to use tryptophan as a local probe of protein dynamics for CO-bound myoglobin, but concluded that the perturbation created by CO photolysis was much smaller compared to the proteinquake generated in cytochrome c.

We constructed a novel spectroscopic system to study rotationally inelastic collisions involving truly thermal molecular ions at low temperatures. This system utilizes magnetic confinement to generate abundant concentrations of ions and time-resolved double resonance (pump-probe) techniques to study rotational energy transfer. With this system, we studied chemical and physical processes involving HCO+ and CO+ molecular ions in gas mixtures containing hydrogen and carbon monoxide. We measured the relaxation cross section for the J=2 state of HCO+ in collisions with normal hydrogen at temperatures around 40 K and 77 K. The cross sections at the lower temperature are slightly below those predicted by Langevin theory, while those at the higher temperature are in good agreement with this theory. This dissertation discusses the discrepancy of the acquired data with Langevin theory at lower temperatures. We also performed rotational energy level spectroscopic studies of the methyl formate and symmetric mono-deuterated methyl formate molecules. We developed a rho-axis method (RAM) analysis to accurately model the rotational-torsional spectrum for the ground torsional state. In this work, we report the first measurement and analysis of millimeter-wave (mmw) and submillimeter-wave (submmw) rotational-torsional transitions for mono-deuterated methyl formate. Additionally, we extended the spectral analysis of methyl formate to higher angular momentum and higher spectral frequencies than previously reported.

Exposure to UV light, particularly from the sun, is the primary controllable risk factor for the development of skin cancer. The damaging effects of UV photons results from their ability to induced photochemistry in DNA bases. While the many possible photoproducts of DNA are well known, the formation mechanisms for these photoproducts are not. In order to better understand these processes, we seek to better understand the events that occur between photon absorption and photoproduct formation - the photophysics of DNA.Femtosecond UV pump/UV probe transient absorption spectroscopy was used to study the ground-state vibrational cooling of the DNA base derivative 9-methyladenine (9MA) in solution. Photoexcitation of 9MA to the lowest bright electronic excited state at 267 nm is followed by rapid (τ ≈ 0.4 ps) internal conversion to the electronic ground state, generating more than 30 000 1/cm of excess vibrational energy. Transfer of this excess vibrational energy to the solvent was monitored via changes in the ground-state electronic absorption band at 250 and 285 nm. The vibrational cooling time increases in H2O (2.4 ps), D2O (4.2 ps), methanol (4.5 ps) and acetonitrile (13.1 ps) solvents. The studies show that the initial vibrational energy transfer from the hot solute molecule to the first solvent shell determined the thermalization rate. The studies also suggest that energy transfer between high-frequency solute and solvent modes play a more important role in vibrational cooling than expected. While the majority of excitation lead to ultrafast internal conversion, in pyrimidine bases additional decay pathways exist involving long-lived, intermediate, 1nπ* and 3ππ* states. The 1nπ*, 1ππ*, 3ππ* and S0 states of single pyrimidine bases have strongly-overlapping electronic absorption spectra which complicates study of their dynamics with conventional UV and visible techniques. A UV-pump/mid-IR-probe femtosecond transient absorption spectrometer was constructed for the purpose of studying, with high resolution and specificity, the excited-state dynamics of DNA bases. Unique marker bands for the 1nπ* and 3ππ* were determined for 1-cyclohexyluracil and thymine, respectively. A marker band for the 1nπ* was observed at 1760 1/cm in acetonitrile and methanol-d1. Marker bands at 1603 and ~1714 1/cm were assigned to the 3ππ* state of thymine. This assignment is consistent with previous nanosecond TRIR measurements and theoretical calculations. The triplet state is fully formed on a timescale significantly faster than the 1nπ* lifetime, suggesting that intersystem crossing from the 1nπ* state to the 3ππ* state occurs before the excited population reaches the minimum on the 1nπ* potential surface, supporting previous conclusions from UV-visible transient absorption measurements. The excited-state dynamics of poly(A) were studied with UV and mid-IR transient absorption. Comparison with mid-IR measurements of AMP allow the quantum yield for ultrafast internal conversion in poly(A) to be estimated. Comparison of transient spectra with ground-state absorption spectrum of poly(A) provides insight into the location of absorption bands of the long-lived excimer-like state.DNA photophysics; femtosecond spectroscopy; time-resolved spectroscopy; time-resolved infrared; vibrational cooling; vibrational relaxation; excited state dynamics

The ultrafast electronic and vibrational dynamics of a model five-coordinate, high-spin heme FeIIOEP-2MeIm, following excitation in the Soret band, have been studied in a coordinated fashion using ultrafast transient absorption, time-resolved Stokes and anti-Stokes resonance Raman spectroscopies. Electronic excitation on the blue side of the Soret band region led to sub-100 fs S2→S1, followed by 800 fs nonradiative decay to a vibrationally hot, nonthermal ground state species S0*. S0* then evolved to the thermally equilibrated ground state species S0 on ~10 ps timescale. The initial accepting modes during the S1→S0 internal conversion underwent rapid vibrational relaxation evidenced by 1-3 ps decay of transient anti-Stokes signals. Comparison to other studies in heme proteins where the initial excited electronic state was prepared by ligand photolysis led to insight into the state dependence of vibrational dynamics in hemes.The ultrafast dynamics of a six-coordinate low-spin heme FeIIOEP-(Im)2 were studied following photolysis of one of the imidazole ligands upon electronic excitation. No detectable vibrationally hot six-coordinate ground state heme is observed, indicating the intrinsic quantum yield of the photolysis to be close to unity. The intramolecular vibrational relaxation is the major contribution to the photoproduct cooling on the order of 0.6 to 4.5 ps time scale. The intermolecular vibrational cooling has a lifetime of approximately 10 ps. On average 75% of the photolysed ligand geminately recombines on the time scale of 10-20 ps strongly overlapping with the vibrational cooling dynamics. In addition to the two heme compounds, the effect of methyl groups on the vibrational relaxation processes of para-nitroaniline (PNA) was studied. Minimal impact upon electronic dynamics, significant impact upon vibrational dynamics was observed in 2-methyl, 2, 6-dimethyl and N, N-dimethyl PNA compounds. NO2 group wagging overtone (~1495 cm-1) acts as the coupling and primary accepting mode during internal conversion in all four compounds. N-methyl substitution increases vibrational cooling lifetimes, phenyl ring substitution populates two new low frequency ring vibrations not present in PNA or N, N-dimethyl PNA. Anti-Stokes intensity decay and peak-shift evolution yield different lifetimes. Off-diagonal anharmonic coupling to populated low frequency motions of the phenyl are likely to be important.

Psoralens, coumarins and flavins are biologically active photosensitizers, which have been used in pathogen inactivation of blood products, cancer treatment and skin diseases. Laser flash photolysis (LFP) with UV-visible and infrared detection and Density Functional Theory (DFT) calculations were used to directly observe and identify the triplet states of the photosensitizers, and their intermediate derivatives, and to understand their chemical reactivity. The triplet-excited states of the parent psoralen as well as 8-methoxypsoralen, 5-methoxypsoralen and trimethylpsoralen were directly observed in acetonitrile using UV-visible or time-resolved infrared (TRIR) spectroscopy. TRIR spectra of trimethylpsoralen radical ions were also obtained.The vibrational spectra of triplet visnagin and khellin, and their radical ions were obtained upon 266 nm LFP in acetonitrile. Visnagin and khellin triplet excited states react with chloranil to form their radical cations and the chloranil radical anion. The excited states of khellin, visnagin and chloranil are all involved in the light induced electron transfer reaction. Khellin and visnagin triplets both react with anionic electron donors to form the related radical anions. Triplet visnagin reacts with hydroquinone to form semiquinone radicals.In the exploratory photochemistry of lumichrome and its oxides, both nanosecond and ultrafast laser flash photolysis with UV-visible and TRIR spectroscopy were used to observe the transient species generated photochemically from lumichrome (LC), lumichome-N-oxide (LCO) and lumichome-di-N-oxide (LCO2). The transient UV-vis spectra of 3LC*, 3LCO* and 3LCO2* were obtained upon 266 nm LFP in argon saturated acetonitrile and their lifetimes were determined to be about 1 µs in deoxygenated acetonitrile. The transient vibrational spectra of LC, LCO and LCO2 triplet excited states were obtained upon 266 nm and present similar features with strong IR bands assigned to the carbonyl C=O and C=N stretching vibrations as predicted by the DFT calculations. The singlet states of lumichrome, lumichome-N-oxide, lumichome-di-N-oxide, isoquinoline N-oxide and pyridine N-oxide were identified by picosecond time-resolved absorption spectroscopy. Time-correlated single photon counting (TCSPC) and fluorescence spectroscopy were used to determine the lifetimes of the singlet states and fluorescence quantum yields of these aromatic N-oxides as well as other aromatic N-oxides.

Spontaneous Raman scattering and femtosecond time-resolved pump-probe spectroscopy are used to study and characterize material properties in superconductors, bulk semiconductors and semiconducting quantum dots. Superconducting gap oscillations are observed for the first time in MgB 2 (Tc = 39 K) and 2H-NbSe2 ( Tc = 7 K). In MgB2, multiple superconducting gap oscillations are observed at 24 cm-1, 103 cm -1 and ∼44 cm-1. These frequencies are in reasonable agreement with other reported experimental results and published theoretical models. Spontaneous Raman measurements on MgB2 show a single strong resonance at 107 cm-1 near the superconducting gap. Consistent with spontaneous Raman measurement, coherent superconducting gap oscillations in 2H-NbSe2 are observed at 18 cm-1 (E symmetry) and 14 cm-1 ( A symmetry). The analysis suggests that a non-Raman mechanism or impurities are responsible for the observed oscillations in MgB2. Spontaneous Raman spectra of MgB2 show a large frequency shift in the optical E2g phonon from 580 cm-1 at 300 K to 630 cm-1 at 3 K due to anharmonicity. The resonance at the superconducting gap frequency shows a strong asymmetric lineshape near Tc, becoming Lorentzian-like near 3 K due to spectral weight gain at low frequencies. In ZnO, a study of the anharmonic properties of the low-frequency E2 optical phonon, using pump-probe spectroscopy, show an unusually long lifetime ∼2 orders of magnitude larger for most optical modes in semiconductors. At 5 K, the frequency and lifetime are (2.9787 +/- 0.0002) THz and (211 +/- 7) ps. The temperature dependence of the lifetime is determined by up-conversion decay contributions, which vanish at zero temperature. The results show that the lifetime is limited by isotopic disorder and that nanosecond lifetimes may be achievable in isotopically-pure samples. In CdTe1-xSex quantum dots, two longitudinal optical phonons and a mixed mode are identified. The amplitude of the optical modes as a function of the laser wavelength agrees with the impulsive stimulated Raman scattering mechanism. At low power densities, the frequency of the optical phonons deviates from spontaneous Raman scattering behavior, which is attributed to impurity state trapping. Size-selective excitation effects for the acoustic phonons are more noticeable in time-domain studies. The difference between the time-domain and spontaneous Raman studies is not understood. Acoustic phonons are observed in CdSe quantum dots at 37 cm-1, 22 cm-1 and 5 cm-1 at 560 nm. The linewidth of the mode at 37 cm-1 shows a strong dependence on dot size and a linear dependence with temperature.

Ultrafast transient absorption spectroscopy has been performed on two small conjugated polyenes, 1,3,5-cis-hexatriene (cHT) and 1,3-cyclohexadiene (CHD). The reaction dynamics were investigated in two solvents, cyclohexane and hexadecane. This report presents results for one and two color kinetic studies, along with picosecond resolution, time-resolved ultra-violet spectra in the 260-300 nm spectral region. Following ultra-violet excitation, both systems undergo rapid radiationless decay of the excited state on a sub-200 fs timescale. In cHT there is essentially unit quantum yield for ground state recovery. CHD undergoes ring-opening to form cHT with a quantum yield of 0.4. In both reactions, the cHT product is highly vibrationally excited, and ultrafast single-bond isomerization is observed. This results in formation of a distribution of the three rotamers of cHT that evolves as the system vibrationally relaxes. This dynamic cooling is examined and compared between the two systems, and also for both solvents. Surprisingly, it is found that the solvent viscosity has little effect on this behavior. This is attributed to high levels of excitation at early times, and only small nuclear motions required for single-bond isomerization. Vibrational cooling occurs on a similar timescale for the two solvents (10 ps in cyclohexane, 12 ps for hexadecane). Spectra of the higher energy rotamers of cHT have been deduced from the data, and the time-dependent evolution of this distribution is discussed in detail.