A system combining laser desorption, jet-cooling, resonant 2-photon ionization (R2PI) spectroscopy, and time-of-flight mass spectrometry (TOF-MS) generates exceptionally well resolved vibronic spectroscopy and fragment free mass spectrometry for molecules within a complex matrix. Following laser desorption, gas-phase molecules are entrained in a supersonic molecular beam of argon. This causes extremely efficient jet-cooling of the internal degrees of freedom within the molecules and makes it possible to perform high resolution spectroscopy. The cold molecule is resonantly excited to the first electronic excited state by a tunable dye laser, and subsequently ionized by another photon before being detected in the TOF-MS. The result is the ability to selectively ionize a single target molecule within an extremely complex matrix.

The advantages of R2PI spectroscopy have been extended to include nanoscale proximal probe thermal desorption, allowing detection of organic paint pigments in situ within microscopic paint cross sections. These organic paints are often present as part of complex mixtures within thin layers, well below the spatial resolution of many instruments. We also report the first high resolution spectroscopy of chromophores within madder dye, an historically significant organic colorant, allowing for the unambiguous identification of the molecule within the intrinsically complex nature of ancient paintings.

Additionally, pottery sherds from Maya vessels (600-900 CE) and Mississippian vessels (1100-1200 CE) were examined for three molecular markers (theobromine, theophylline and caffeine) using R2PI spectroscopic techniques. The data obtained supports the existence of a previously unknown trade network between Mesoamerican and North American civilizations.

Excited state intramolecular proton transfer (ESIPT). To elucidate the mechanism of ESIPT and reaction barrier of tunneling mechanism in indigo, a combination of laser desorption, jet cooling, resonance enhanced multiphoton ionization (REMPI), time-of-flight mass spectrometry is employed to produce vibronically resolved spectra of deuterium substituted indigo. The picosecond two color REMPI spectrum of indigo displayed a red shift and peak splitting upon deuterium substitution on and above the barrier, as well as no shift or blue shift below the barrier, where the barrier corresponds to the separation of the proton transfer and hydrogen transfer forms of the keto-enol tautomer in the S1 state. In pump probe measurements, deuterium substitution induces a longer excited state lifetime with a kh/kd ratio of 2.5, indicating that tunnel effect takes place in the ESIPT of the non-deuterated system.

Environmental conditions such as solar irradiation can induce biochemical reactions and pose a threat to organic molecules necessary in life. How DNA responds to radiation is relevant to human health because radiation damage can affect genetic propagation and lead to cancer. A detailed photochemistry is unraveled by studying the intrinsic properties of individual DNA/RNA building blocks, followed by extrapolation to larger systems such as base pairs via gas phase laser spectroscopy. Moreover, the photodynamics of nucleobases may further our understanding of prebiotic chemistry and its role in developing life as we know it. Electronic structure and excited state dynamics of nucleobases and base pairs have been studied in the past; however, detailed spectroscopy has not been reported for all of them. Moreover, some nucleobase analogues were never studied in the gas phase. As a result, we attempt to build on what was previously established on nucleobases and base pairs and then take a step further to explore a nucleobase analogue.

This work reports studies of electronic structure and excited state dynamics of biological molecules via resonance-enhanced multiphoton ionization in the gas phase. First, we measured well-resolved vibronic spectra of all the molecules we studied by resonant two-photon ionization. Then, we performed double-resonance spectroscopy to further elucidate the structure and excited state dynamics of the target molecules. Because biomolecules typically exist in several tautomeric forms which are isolated under gas phase jet-cooled conditions, we used UV-UV double resonance spectroscopy to determine the number of tautomers present and their origins. We used IR-UV double resonance spectroscopy to obtain tautomer-specific IR spectra. We measured excited state lifetimes of tautomer-selected nucleobases by nanosecond and picosecond pump-probe spectroscopy. Using these methods, we were able to draw a new picture for the dynamics of bare nucloebases thymine and uracil in the gas phase. In the gas phase jet expansion, both molecules were present in the keto form and exhibited long lived excited states. These long lived states have been implicated in the formation of DNA photolesions by causing the formation of a cyclobutane pyrimidine dimer, which can lead to cancers such as melanoma and carcinoma. We also determined that replacing the oxygen in guanine with sulfur results in drastically different dynamics due to the heavy atom effect.

With the use of a free-electron laser, we were able to collect IR spectra for multiple base pairs in the far-IR region (<880 cm-1). Although the far IR region has been difficult to access both experimentally and computationally, we were able to structurally characterize the molecules with the help of Born–Oppenheimer Molecular Dynamics (BOMD). This far-IR region yields new information because it is characterized by large-scale delocalized vibrations that cannot be observed in the mid-IR region.

Finally, we used R2PI in combination with supersonic jet cooling and mass spectrometry to examine archaeological samples. We studies organic residues within pottery sherds from Maya vessels (600−900 CE) and Mississippian vessels (1100−1200 CE), successfully detecting three molecular markers, caffeine, theobromine, and theophylline, associated with the use of cacao.

What does a molecule do after it absorbs a photon? This dissertation contains a compilation of my published work on this very question on dye molecules and alternative nucleobases, as well as notes on laboratory operation. All experimental work presented is done with some variation of Resonance Enhanced Multi-Photon Ionization (REMPI) on neutral gas phase molecules around 10 K prepared by laser desorption and entrained into a supersonic molecular beam. Detection is achieved with a time of flight mass spectrometer. When a molecule absorbs a photon, it must find a way to deal with that energy. Pigments in paintings must absorb light as part of their function, otherwise they would have no color. DNA bases absorb in the UV region because they are aromatic, which provides them the rigidity needed for a pairing structure. In both cases, some of these compounds deal with radiation better than others, displaying superior photostability. The ones that do well use some pathway that safely and rapidly converts the energy to heat, which can then be safely dissipated to the environment. Those pathways are a function of the potential energy surface, which is acutely dependent on the molecular structure. As a result, isomers, and even tautomers of a molecule can display very different dynamics. The experiment performed allows for a separation of tautomers and isomers, and as such can provide a benchmark to state-of-the-art calculations. In the first two chapters, examples of visible absorbing pigments and alternative DNA bases will be presented. In the first chapter, two papers on visible absorbing dyes are presented, with examination of the excited state intramolecular proton transfer mechanism in each system. In the first paper, we find that the indigo dye molecule is quite extraordinary in that both a hydrogen transfer and proton transfer geometry are populated following excitation. The dominant geometry varies depending on the vibronic mode excited, with each geometry displaying different characteristic lifetimes. The different lifetimes for each of these geometries allows some estimates of their yields as a function of vibronic band excitation. At high enough energy excitation, there is an interconversion between the two geometries, allowing indigo to use the fastest path available and safely dissipate the energy following excitation. The second paper analyzes a series of hydroxyanthraquinone molecules, which are red dyes or pigments. By studying a series of these dyes and comparing with high levels of calculations, the reason for the lack of photostability for hydroxyanthraquinones substituted with a 1,4- motif becomes clear; the proton transfer geometry is destabilized relative to the Frank-Condon region for molecules bearing this motif, and as such they cannot use this efficient relaxation pathway. The next chapter contains a pair of articles on a pair of alternative nucleobases, isocytosine and isoguanine. These articles seek to identify if there was a photochemical reason for cytosine and guanine to be chosen over isocytosine and isoguanine. Interestingly, we find that isocytosine bears some similarity in dynamics to guanine, while isoguanine bears some similarities to cytosine. The lower photostability of the biologically relevant tautomeric form of isoguanine is suggested to be a reason for the exclusion of isocytosine and isoguanine from biology. In the last chapter, the focus shifts from studying photophysics to analyzing mass spectra of Poly-Aromatic Hydrocarbons (PAHs) prepared in a plasma jet. These molecules are found in a wide variety of settings, from soots and combustion products to the interstellar media. In this paper, the early stages and mechanism of carbon growth are explored in a simulation of space conditions.

Organic photovoltaics have received a large amount of attention in recent years due to their potential for relatively low cost fabrication, light weight and flexible devices, and because of their high solubility, inkjet printing and roll-to-roll processing. Thanks to the new development of novel materials and methods for controlling self-assembly, organic photovoltaics have achieved over 10% efficiencies. One issue that has received relatively little attention is the types of solvents used for processing, mainly their toxicity and sustainability. Recently we discovered the use of a green solvent, 2-MeTHF, from which to process the semiconducting layer. Here we further investigate the feasibility of using 2-MeTHF as a processing solvent for a wide array of molecular donors by device fabrication, electrical and morphological characterization. We also investigated the processing of two novel non-fullerene acceptors from 2-MeTHF, and characterized their morphologies and evaluated their efficiencies.