Dissertations, Theses, and Capstone Projects

Date of Degree


Document Type


Degree Name





Marilyn R Gunner

Committee Members

Emilio Gallicchio

Stephen O'Brien

Subject Categories

Chemistry | Physics


Proton transfer pathways, Photosystem II, Proton-coupled Electron transfer reaction, Continuum Electrostatics/Monte Carlo, pKa and protonation state studies, Oxygen Evolving Complex


The mechanism of natural photosynthesis involves the use of solar energy to produce O2 we breathe and food and fuel we intake. This process results in the biological oxidation of water that takes place at room temperature, neutral pH using earth abundant elements Ca and Mn. Understanding how this challenging chemical reaction occurs in photosynthesis can be useful for designing better artificial photosynthetic complexes that can be used as biofuels. My doctoral work is to study the deprotonation and oxidation events elucidating the mechanistic details of proton coupled electron transfer reaction in a photosynthetic protein.

The O2 evolution takes place in Photosystem II (PSII), a protein-pigment complex present in higher plants, algae and cyanobacteria. The overall reaction of water being oxidized to oxygen takes place in the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic complex found in PSII. This results in the loss of four electrons and four protons, which occurs following four stages of OEC oxidation in the sequential manner known as S-state transitions or Kok Cycle. The computational methods employed to understand the reaction is combined Monte Carlo Multi Conformation Continuum Electrostatics (MCCE), Molecular Dynamics (MD) and Network analysis.

The published projects involved the study of proton transfer pathways in water channels of PSII, influence of amino acid residues and water molecules surrounding the OEC during the reaction. These water channels play an important role in the functionality of OEC assisting the reaction. The work also shows the importance of interconnected hydrogen bonding network between water channels influencing the proton egress pathways in PSII. Further work is also done on studying the pH dependence and protonation state changes of the residues upon the formation to OEC during the photoassembly process.