Date of Award

Summer 8-7-2018

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Physics and Astronomy

First Advisor

Gary Hastings

Second Advisor

Vadym Apalkov

Third Advisor

Gennady Cymbalyuk

Fourth Advisor

Mukesh Dhamala

Fifth Advisor

Brian Thoms


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.