Photochemical Sciences Ph.D. Dissertations


Probing the Photochemistry of Rhodopsin Through Population Dynamics Simulations

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Photochemical Sciences

First Advisor

Massimo Olivucci (Advisor)

Second Advisor

Andrew Gregory (Other)

Third Advisor

Hong Lu (Committee Member)

Fourth Advisor

Alexey Zayak (Committee Member)


The primary event in vision is induced by the ultrafast photoisomerization of rhodopsin, the dim-light visual pigment of vertebrates. While spectroscopic and theoretical studies have identified certain vibrationally coherent atomic motions to promote the rhodopsin photoisomerization, how exactly and to what degree such coherence is biologically related with its isomerizing efficiency (i.e. the photoisomerization quantum yield) remains unknown. In fact, in the past, the computational cost limited the simulation of the rhodopsin photoisomerization dynamics, which could be carried out only for a single molecule or a small set of molecules, therefore lacking the necessary statistical description of a molecular population motion.

In this Dissertation I apply a hybrid quantum mechanics/molecular mechanics (QM/MM) models of bovine rhodopsin, the verterbrate visual pigment, to tackle the basic issues mentioned above. Accordingly, my work has been developing along three different lines comprising the development, testing and application of new tools for population dynamics simulation: (I) Development of a suitable protocol to investigate the excited state population dynamics of rhodopsins at room temperature. (II) A correlation between the phase of a hydrogen-out-of-plane (HOOP) motion at the decay point and the outcome of the rhodopsin photoisomerization. (III) A population “splitting” mechanism adopted by the protein to maximize its quantum yield and, therefore, light sensitivity.

In conclusion, my Dissertation reports, for the first time, a connection between the initial coherent motion of a population of rhodopsin molecules and the quantum efficiency of their isomerization. The photoisomerization efficiency is ultimately determined by the way in which the degree of coherence of the excited state population motion is modulated by the protein sequence and conformation.