Theoretical and applied studies of rhodopsin and bacteriorhodopsin

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)




Robert R. Birge


Retinal, Holographic memory, Rhodopsin, Bacteriorhodopsin

Subject Categories

Biochemistry, Biophysics, and Structural Biology | Biophysics | Chemistry | Life Sciences | Physical Sciences and Mathematics


Part I . The conformational and electronic properties of the 12-s-cis and 12-s-trans conformers of 11-cis retinal are analyzed. Our models confirm that the 12-s-cis isomer is more stable in vacuum and the 12-s-trans conformer is more stable in polar and nonpolar solvent environments due to dispersive and electrostatic interactions. Electronic analysis indicates that the features in the absorption spectrum are due to a complex set of overlapping transitions. Assignments are made for all four band systems.

Ground- and excited-state surfaces connecting rhodopsin and bathorhodopsin along the [Special characters omitted.] dihedral reaction path are partially adiabatically mapped. Forward and reverse photochemistry is simulated via molecular dynamics. The activated complex is reached in ∼375 fs following excitation. Best results for quantum yields and product formation times are obtained by including both dynamic and phased (partitioned) nonadiabatic coupling: [Special characters omitted.] ps; [Special characters omitted.] ps. The lower quantum yield of the B [arrow right] R isomerization is due to a sign change in the nonadiabatic coupling term at [Special characters omitted.] = 92° and to the rapid arrival of the trajectory into the activated complex which prevents equilibration of the excited state and lowers the dynamic coupling term. The [Special characters omitted.] excited singlet state spectrum is calculated as a function of time following excitation of rhodopsin.

A model of thermal noise in rods is proposed whereby thermal isomerization occurs when the retinal Schiff base is unprotonated. This model accounts for the low activation energy of 23-27 kcal mol -1 and is supported by both molecular models and experimental measurements.

Part II . A prototype holographic memory is described which demonstrates simultaneous storage and retrieval of ten holographic images in the same volume of a bacteriorhodopsin(BR)/polyvinylalcohol(PVA) film. The suitability of BR as a volume holographic memory medium is discussed.

Photochemistry in dried PVA films of the blue membrane form of BR is demonstrated. As in solution, blue[Lef-right arrow]pink interconversion occurs, but with much lower quantum yield. Additionally, a species absorbing maximally at 450 nm appears as a photoproduct of blue membrane.


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