Interplay of molecular structure and photon response in select alternative nucleobases and pigments
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Interplay of molecular structure and photon response in select alternative nucleobases and pigments

  • Author(s): Gate, Gregory
  • Advisor(s): de Vries, Mattanjah
  • et al.
Abstract

The spectroscopic analyses of organic molecules relevant to genetic material and the origin of life, as well as various culturally important pigments and dyes are reported. This analysis was conducted in the cold, gas phase using resonance enhanced multiphoton ionization (REMPI). REMPI allows for structural characterization and a temporal description of the excited state dynamics. This experimental technique, when combined with state-of-the-art theoretical calculations, creates a much clearer picture of what is occurring on the molecular and electronic levels. These studies are focused on the excited state dynamics of these systems – how do they react and get rid of their electronic energy after absorption of a photon. A photon is merely a packet of energy, which a molecule then converts to electronic energy upon resonant photon absorption. How these systems react to this added energy is a function of their electronic structure, which is ultimately dependent on their molecular structure. Slight changes in the molecular structure alter the excited state dynamics. It is our goal to develop a model to connect molecular structure to photostability.Several nucleobase analogues have been studied to determine their photostability. These studies were conducted to help understand the role light hardiness played in the evolution of life’s genetic material, long before the creation of the ozone layer. Photostability is determined by a system’s excited state lifetime and the presence of any barriers along the pertinent relaxation pathways on the potential energy surfaces. Coupled with results from theoretical calculations, assignments for the relative photostabilities can be deduced. The results from these nucleobase analogues are then compared to the canonical nucleobases: adenine, cytosine, guanine, thymine, and uracil. First, the pyrimidine isocytosine was studied. Isocytosine has the same ligand substructure as guanine, helping to explain the ultrafast lifetimes of biological, keto guanine. A review of the spectroscopy of the C2 and C6 substituted purines follows. Finally, the dynamics of the purines isoguanine, 2,6-diaminopurine, xanthine, and their various tautomers are then explored. The canonical nucleobases are much more photostable than their analogues, supporting the theory that genetic material was selected, at least partially, for its enhanced photostability properties. Excited state dynamics and photostability are very subtle functions of molecular structure, but with no clear mechanism apparent. Culturally relevant pigments and dyes were also studied spectroscopically. These molecules of interest were studied for their expansive use since antiquity in works of art, due to their visible colorant properties. A study of indigo revealed competing proton transfer and hydrogen transfer relaxation mechanisms, with the mechanism dependent on the exact vibronic mode excited. With enough excess energy, the more photostable proton transfer dynamics becomes the dominant pathway. Separately, the excited state dynamics of the red dye pigments alizarin and purpurin, along with several other hydroxyanthraquinones, were studied. This study was motivated by the apparent fading of some of these compounds in bulk (e.g. paint in a work of art). A mechanism heavily dependent on their -OH substitution was resolved to help explain their resistance to fading. All the systems studied herein are noted for having undergone some form of selection process. For the nucleobases, that involved surviving the ultraviolet bombardment on an early Earth. For DNA, that meant meeting the necessary requirements for the genetic material of life. And for pigments and dyes, that required having the proper steady-state absorption properties for the artist’s purposes. Ultimately, the response to these selection pressures were determined by these compounds’ molecular structure. This work increases the understanding between molecular structure and excited state dynamics.

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