Related Experiment Video
Updated: Jun 27, 2026
10:03
Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
Published on: June 27, 2014
Bicycle-pedal isomerization in a rhodopsin chromophore model
Igor Schapiro1, Oliver Weingart, Volker Buss
1Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany.
Journal of the American Chemical Society
|December 17, 2008
Summary
Researchers achieved the first ab initio confirmation of the "bicycle-pedal mechanism" in retinal chromophore isomerization. This fundamental reaction pathway, proposed decades ago, was observed in computational simulations of molecular dynamics.
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Photochemistry
Background:
- The bicycle-pedal mechanism is a proposed reaction pathway for the isomerization of chromophores like retinal.
- Experimental and theoretical evidence for this mechanism has been sought for decades.
- Retinal chromophores are crucial in visual pigments and other biological processes.
Purpose of the Study:
- To computationally investigate the isomerization of a retinal chromophore model.
- To achieve the first *ab initio* realization of the bicycle-pedal mechanism.
- To explore the energetic landscape of two-double-bond isomerization pathways.
Main Methods:
- Generated an ensemble of 47 starting geometries using ground-state zero-point-energy sampling.
- Performed *ab initio* molecular dynamics simulations to probe reaction pathways.
- Utilized restrained optimization to analyze synchronous rotation modes.
Main Results:
- Observed a single trajectory following the bicycle-pedal mechanism from the sampled geometries.
- This represents the first *ab initio* computational realization of the proposed mechanism.
- Found that two-double-bond isomerization is barrierless for both conrotatory and disrotatory pathways under restrained optimization.
Conclusions:
- The study provides the first *ab initio* computational evidence supporting the bicycle-pedal mechanism in retinal chromophore isomerization.
- The findings validate a long-standing hypothesis in photochemistry.
- The barrierless nature of synchronous rotation pathways has significant implications for understanding chromophore dynamics.
Related Concept Videos
01:11Channel Rhodopsins
Most organisms use photoreceptors to sense and respond to light. Examples of photoreceptors include bacteriorhodopsins and bacteriophytochromes in some bacteria, phytochromes in plants, and rhodopsins in the photoreceptor cells of the vertebral retina. The light-sensitive property of these receptors is because of the bound chromophores, such as bilin in the phytochromes and retinal in the rhodopsins.
Rhodopsins belong to the family of cell surface proteins called G-protein coupled receptors,...
Rhodopsins belong to the family of cell surface proteins called G-protein coupled receptors,...
01:26Photochemical Electrocyclic Reactions: Stereochemistry
The absorption of UV–visible light by conjugated systems causes the promotion of an electron from the ground state to the excited state. Consequently, photochemical electrocyclic reactions proceed via the excited-state HOMO rather than the ground-state HOMO. Since the ground- and excited-state HOMOs have different symmetries, the stereochemical outcome of electrocyclic reactions depends on the mode of activation; i.e., thermal or photochemical.
Selection Rules: Photochemical Activation
Selection Rules: Photochemical Activation
01:29The Photochemical Reaction Center
Reaction centers are pigment-protein complexes that initiate energy conversion from photons to chemical entities. Therefore, photochemical reaction center is a more appropriate term that describes these complexes. The Nobel laureates Robert Emerson and William Arnold provided the first experimental evidence of photochemical reaction centers by demonstrating the participation of nearly 2,500 chlorophyll molecules for the release of just one molecule of oxygen. Despite thousands of photosynthetic...
01:26Thermal and Photochemical Electrocyclic Reactions: Overview
Electrocyclic reactions are reversible reactions. They involve an intramolecular cyclization or ring-opening of a conjugated polyene. Shown below are two examples of electrocyclic reactions. In the first reaction, the formation of the cyclic product is favored. In contrast, in the second reaction, ring-opening is favored due to the high ring strain associated with cyclobutene formation.
01:34Woodward–Hoffmann Selection Rules and Microscopic Reversibility
Electrocyclic reactions, cycloadditions, and sigmatropic rearrangements are concerted pericyclic reactions that proceed via a cyclic transition state. These reactions are stereospecific and regioselective. The stereochemistry of the products depends on the symmetry characteristics of the interacting orbitals and the reaction conditions. Accordingly, pericyclic reactions are classified as either symmetry-allowed or symmetry-forbidden. Woodward and Hoffmann presented the selection criteria for...
01:22Photoreceptors and Visual Pathways
At the molecular level, visual signals trigger transformations in photopigment molecules, resulting in changes in the photoreceptor cell's membrane potential. The photon's energy level is denoted by its wavelength, with each specific wavelength of visible light associated with a distinct color. The spectral range of visible light, classified as electromagnetic radiation, spans from 380 to 720 nm. Electromagnetic radiation wavelengths exceeding 720 nm fall under the infrared category, whereas...