Photochemical Sciences Ph.D. Dissertations


Impact of Electronic State Mixing on the Photoisomerization Timescale of Natural and Synthetic Molecular Systems

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Photochemical Sciences

First Advisor

Massimo Olivucci (Advisor)

Second Advisor

Alexander Tarnovsky (Committee Member)

Third Advisor

R. Marshall Wilson (Committee Member)

Fourth Advisor

Salim Elwazani (Other)


The need for a detailed mechanistic understanding of the photoisomerization of retinal chromophore (retinal protonated Schiff base, rPSB) is becoming increasingly important, not only due to its fundamental importance in vision but also owing to the growing number of applications in various fields. The development of microbial rhodopsin based fluorescent probes and actuators essential in neuroscience, synthetic bio-mimetic molecular switches and motors useful in material science and synthetic biology are examples of such applications. The work presented in this dissertation is devoted to unveil and understand a novel mechanistic factor with significant impact on the photoisomerization of rPSB-like systems. This factor corresponds to the interaction between the first electronic excited state and higher states (usually the second excited state) occurring during the excited state lifetime or, in other words, along the excited state photoisomerization coordinate. This "electronic state mixing" effect is studied by employing different computer tools including hybrid quantum mechanics/molecular mechanics (QM/MM) methods. The investigated systems include representative animal and microbial rhodopsins, bio-mimetic N-alkyl-indanylidene-pyrrolinium (NAIP) molecular switches and a recently reported water soluble rhodopsin mimic. Our results unveil two type of effects due to changes in the electronic mixing: an impact on the excited state lifetime and an impact on vibrational coherence as we now briefly describe.

The impact on excited state lifetime is first demonstrated by uncovering the variation of rPSB photoisomerization speed in different environments is due to an increase or decrease of electronic state mixing and that this effect can be controlled by the electrostatic field of the environment. This leads us to hypothesize that animal rhodopsins, which isomerize within 200 fs, have been evolved to minimize the electronic state mixing such that biological functions are carried out in a timely manner. We then show that electronic state mixing can be used as a design principle to achieve artificial rPSBs with a longer excited state lifetime useful for producing rhodopsin based fluorescent probes. In this context, we demonstrate that minor electron donating or withdrawing chemical substitutions can cause an increase or decrease in the photoisomerization speed of rPSB. We have also investigated the photocycle and the electronic state mixing of a water-soluble artificial rhodopsin mimic. The room temperature photodynamics simulations of this system suggests that molecules of a light excited population which decay early or later is possibly modulated by electronic state mixing.

The impact of electronic state mixing on vibrational coherence is mainly investigated focusing on synthetic molecular switches. Accordingly, we show how electronic state mixing induced by steric effects can be used to control the vibrational coherence of NAIP molecular switches. On this basis, we propose that vibrational coherence may be engineered into other synthetic molecular devices by modulating steric and electronic effects.