Author ORCID Identifier

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Physics and Astronomy

First Advisor

Gary Hastings

Second Advisor

Gennady Cymbalyuk

Third Advisor

Samer Gozem

Fourth Advisor

Viacheslav Sadykov

Fifth Advisor

Murad Sarsour


Time–resolved Fourier transform infrared difference spectroscopy has been used to study photosystem I (PSI) photosynthetic reaction centers from Synechocystis sp. PCC 6803 (S6803) at cryogenic temperature (77 K) with a series of native and non-native quinones incorporated in the A1 binding site. LED-based pump-probe spectroscopy was used to study the P700+(FA/B/A1A) state recombination at room temperature (298 K). “Foreign minus native” double difference spectra (DDS) were constructed by subtracting TR FTIR DS for native PSI from corresponding spectra of non-native quinones. To help assess and assign bands, density functional theory based vibrational frequency calculations for quinones in solvent, or in the presence of a single asymmetric H–bond to either a water molecule or a peptide backbone NH group, were undertaken.

In the study of four high-potential naphthoquinones (2-chloro-, 2-bromo-, 2,3-dichloro- and 2,3-dibromo-1,4-naphthoquinone), we conclude that the mono-substituted NQs (2ClNQ and 2BrNQ) can occupy the binding site in different orientations, with the C3 hydrogen atom being both ortho and meta to the H-bonded C4=O group.

In PSI complexes at 298 K electron transfer from A1 to FX is an order of magnitude faster on the B-branch compared to the A-branch. One factor that might contribute to this branch asymmetry in time constants is TrpB673, which is located between A1B and FX. In the study of the TrpB673Phe mutant (WB673F mutant - mutation of TrpB673 to Phe) cells, photoaccumulated FTIR DS for WB673F mutant cells indicate changes in amide I and II protein vibrations upon mutation, indicating the protein environment near FX is altered upon mutation. In the WB673F mutant light sensitive PSI samples, the phylloquinone molecule is likely doubly protonated following long periods of repetitive flash illumination at 298K which can be restored by incubating the light treated mutant PSI samples in the presence of added phylloquinone.

In cyanobacteria, PSI is found mainly in trimeric and slightly in monomeric form [26]. Previous x-ray structural studies indicate there are no significant differences between them. In this study, we investigated whether they are kinetically different, and we conclude that they are very similar in this aspect as well.


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