Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181.

A computational three-layer ONIOM(QM-high:QM-low:MM) hybrid scheme has been applied to analyze the protonation state of the Glu181 amino acid residue in rhodopsin, which is vital to determining the rhodopsin photoactivation mechanism. Due to conflicting evidence from previous studies, it has yet to be conclusively resolved. In this study, we fully optimize dark-state rhodopsin model structures differing only at the 181-residue site-protonated and unprotonated Glu181-and calculate several experimentally observable properties.

Molecular mechanics-valence bond method for planar conjugated hydrocarbon cations.

We present an extension of the molecular mechanics-valence bond (MMVB) hybrid method to study ground and excited states of planar conjugated hydrocarbon cations. Currently, accurate excited state calculations on these systems are limited to expensive ab initio studies of smaller systems: up to 15 active electrons in 16 pi orbitals with complete active space self-consistent field (CASSCF) theory using high symmetry. The new MMVB extension provides a faster, cheaper treatment to investigate larger cation systems with more than 24 active orbitals.

Photostability via sloped conical intersections: a computational study of the excited states of the naphthalene radical cation.

On the basis of an extensive ab initio electronic structure study of the ground and excited-state potential energy surfaces of the naphthalene radical cation (N*+), we propose a mechanism for its ultrafast nonradiative relaxation from the second excited state (D2) down to the ground state (D0), which could explain the experimentally observed photostability [Zhao, L.; Lian, R.; Shkrob I.