Intrinsic Photodynamics of Organic Dyes and Alternative Nucleobases
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Intrinsic Photodynamics of Organic Dyes and Alternative Nucleobases


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.

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