A quantum chemical study of the retinal of squid rhodopsin

Abstract

The squid retinal structure obtained from the Protein Data Bank (PDB ids 2Z73 and 2ZIY) is studied in a quantum chemistry method using MOPAC2009 based on a semi-empirical method with PM6 parametrization. The interaction between retinal and light (an electromagnetic field) is effectively described by the interaction between dipoles and electromagnetic fields. Thus we investigated the dipole moment and effective charge distribution of retinal. We also looked at molecular orbitals, especially the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital). MO shifting between a double bonded site and single bonded site is seen by comparing HOMO and LUMO results. Retinal changes its conformation from cis to trans at carbon 11. This carbon's effective charge is very small so that it is free from electric interactions. Then it can change conformation with a small change in energy. Show more