Author ORCID Identifier

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Physics and Astronomy

First Advisor

Dr. Gary Hastings


In photosystem I (PSI), the secondary electron acceptor is a phylloquinone (PhQ) molecule and occupies the so-called A1 binding site. PhQ, a naphthoquinone derivative with methyl and phytyl substituents, forms a single hydrogen bond (H-bond) via one carbonyl oxygen to the protein in PSI. Light-induced Fourier-transform infrared (FTIR) difference spectra corresponding to electron acceptor A1 in PSI protein complex reconstituted with non-native quinones show the influence of the quinone-protein interactions in terms of vibrational modes. However, the interpretation of FTIR difference spectra is not straightforward; in particular, the origin of two noticeable separated carbonyls vibrational modes in the anionic states has not been elucidated.

Theoretical spectra built upon the X-ray crystal structure using the multi-layer ONIOM technique have been developed to assist the assignment of FTIR bands associated with native and foreign quinones in the A1 binding site. Calculated and FTIR spectra remarkably agree when the H-bond network, including water molecules in the H-bonded carbonyl vicinity, is included in the molecular structure. The conformity suggests that the complex H-bond network between water molecules might modulate the vibrational bands of reduced PhQ (PhQ-) in the A1 binding site; consequently, quinones' observed splits between carbonyls vibrational modes in the A1 binding site are simulated. Furthermore, theoretical models along with experiments indicate that non-native quinones adopt a particular orientation with respect to the presence of the single H-bond in the protein in addition to their chemical structures and related substituents.

Comparison between vibrational bands of PhQ- in the A1 binding site in PSI and the QA binding site of purple photosynthetic bacteria indicates that the unique H-bond pattern in the anionic state is the structural feature of the A1 binding site. In comparison, the formation of two H-bond interactions via carbonyl oxygen atoms of PhQ- in the QA binding site does not lead to the noticeable split and shift between two carbonyl vibrations. In contrast to the A1 binding site, calculations show that a polar and aprotic solvent model could be appropriate to simulate PhQ- and protein interactions in the QA binding site.

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