Chapter 7 The stereochemistry of vision

Floppy molecules—their internal dynamics, spectroscopy and applications

Floppy molecules can be defined as molecules performing large amplitude vibrations (LAVs). There are different types of LAVs among which the most common are inversion and internal rotation. Molecules with LAVs have been of great interest for a very long time since their dynamic, geometry and molecular spectra were very often considered as a challenge. In the review, we present an outline of the history and development of various theoretical approaches concerning molecules with LAVs. Different types of LAVs are described with the emphasis on inversion tunneling (wagging) and internal rotation (torsion). Furthermore, strategies for building explicit and effective Hamiltonians are given and explained in detail using a hydrazine molecule, which is an exemplary molecule performing three LAVs—two inversions and one internal rotation. Since floppy molecules play a significant role in numerous areas as chemistry, pharmacy, astrophysics, biology, agriculture etc., we also provide an overview of their applications.

Cyclopropyl and isopropyl derivatives of 11-cis and 9-cis retinals at C-9 and C-13: subtle steric differences with major effects on ligand efficacy in rhodopsin

Retinal is the natural ligand (chromophore) of the vertebrate rod visual pigment. It occurs in either the 11-cis (rhodopsin) or the 9-cis (isorhodopsin) configuration. In its evolution to a G protein coupled photoreceptor, rhodopsin has acquired exceptional photochemical properties. Illumination isomerizes the chromophore to the all-trans isomer, which acts as a full agonist. This process is extremely efficient, and there is abundant evidence that the C-9 and C-13 methyl groups of retinal play a pivotal role in this process. To examine the steric limits of the C-9 and C-13 methyl binding pocket of the binding site, we have prepared C-9 and C-13 cyclopropyl and isopropyl derivatives of its native ligands and of α-retinal at C-9. Most isopropyl analogues show very poor binding, except for 9-cis-13-isopropylretinal. Most cyclopropyl derivatives exhibit intermediate binding activity, except for 9-cis-13-cyclopropylretinal, which presents good binding activity. In general, the binding site shows preference for the 9-cis analogues over the 11-cis analogues. In fact, 13-isopropyl-9-cis-retinal acts as a superagonist after illumination. Another surprising finding was that 9-cyclopropylisorhodopsin is more like native rhodopsin with respect to spectral and photochemical properties, whereas 9-cyclopropylrhodopsin behaves more like native isorhodopsin in these aspects.

Study of the shape of the binding site of bovine opsin using 10-substituted retinal isomers

The 9-cis, 11-cis, 13-cis, and all-trans isomers of 10-fluoro-, 10-chloro-, 10-methyl-, and 10-ethylretinals have been prepared and characterized. Results of their interaction with bovine opsin are reported. The data have been analyzed in terms of the conformational properties of the retinal isomers and their steric compatibility with the binding site as defined by the two-dimensional map disclosed earlier. The need to expand the active zone and previously undetected restrictions in the third dimension are noted.