Electronic Energy Funnels in Cis−Trans Photoisomerization of Retinal Protonated Schiff Base

Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations

A photoactive protein usually contains a unique chromophore that is responsible for the initial photoresponse and functions of the photoactive protein are determined by the interaction between the chromophore and its protein surroundings. The combined quantum mechanical and molecular mechanical (QM/MM) approach is demonstrated to be a very useful tool for exploring structures and functions of a photoactive protein with the chromophore and its protein surroundings treated by the QM and MM methods, respectively. In this review, we summarize the basic formulas of the QM/MM approach and emphasize its applications to excited states and photoreactions of chromophores in rhodopsin protein, photoactive yellow protein, and green fluorescent protein.

Temperature investigations of E/Z isomers in ketimines based of p-dibenzoylobenzene with aniline and 2,6-dimethylaniline by infrared spectroscopy

The reaction of aniline with p-dibenzoylobenzene (K1) can lead to Z/Z, Z/E and E/E isomers however the only Z/Z and E/E were formed. At room temperature these isomers may be separated, thus the corresponding FTIR spectra could be recorded. The observed bands were assigned and temperature investigations were lead to monitor the structural changes during heating Z and E forms of K1 from 20 to 240 degrees C. FTIR spectroscopy showed that the bigger changes of the Z form was observed with an increase of temperature. Similar experience was lead with the ketimine synthesized from 2,6-dimethylaniline and p-dibenzoylobenzene (K2) investigated as a mixture of isomers.

Solvent Effects on the Low-Lying Excited States of a Model of Retinal

The low-lying excited states of a solution in alcohol of a five-double-bond model of the rhodopsin protein chromophore, the protonated 11-cis-retinal Schiff base (PSB11), are studied theoretically. We combine a multireference perturbational treatment in the description of the solute molecule with molecular dynamics calculations in the description of the solvent. The geometry, charge distribution, and electronic spectra are strongly influenced by the solvent. The solvent shift values show a marked dependence on the use of relaxed geometries in solution and on the nature of the states involved in the excitation process. The dynamic correlation has a strong effect on the order of the excited states. In solution, the first two excited states almost become degenerate.

Supramolecular Assemblies and Molecular Recognition of Amphiphilic Schiff Bases with Barbituric Acid in Organized Molecular Films

A bolaform Schiff base, N,N'-bis(salicylidene)-1,10-decanediamine (BSC10), has been synthesized and its interfacial hydrogen bond formation or molecular recognition with barbituric acid was investigated in comparison with that of a single chain Schiff base, 2-hydroxybenzaldehyde-octadecylamine (HBOA). It has been found that while HBOA formed a monolayer at the air/water interface, the bolaform Schiff base formed a multilayer film with ordered layer structure on water surface. When the Schiff bases were spread on the subphase containing barbituric acid, both of the Schiff bases could form hydrogen bonds with barbituric acid in situ in the spreading films. As a result, an increase of the molecular areas in the isotherms was observed. The in situ H-bonded films could be transferred onto solid substrates, and the transferred multilayer films were characterized by various methods such as UV-vis and FT-IR spectrosopies. Spectral changes were observed for the films deposited from the barbituric acid subphase, which supported the hydrogen bond formation between the Schiff bases and barbituric acid. By measuring the MS-TOF of the deposited films dissolved in CHCl3 solution, it was concluded that a 2:1 complex of HBOA with barbituric acid and a 1:2 complex of BSC10 with barbituric acid were formed. On the other hand, when the multilayer films of both Schiff bases were immersed in an aqueous solution of barbituric acid, a similar molecular recognition through the hydrogen bond occurred. A clear conformational change of the alkyl spacer in the bolaform Schiff base was observed during the complex formation with the barbituric acid.

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.

Analysis of the mode-specific excited-state energy distribution and wavelength-dependent photoreaction quantum yield in rhodopsin

The photoreaction quantum yield of rhodopsin is wavelength dependent: phi(lambda) is reduced by up to 5% at wavelengths to the red of 500 nm but is invariant (phi = 0.65 +/- 0.01) between 450 and 500 nm (Kim et al., 2001). To understand this nonstatistical internal conversion process, these results are compared with predictions of a Landau-Zener model for dynamic curve crossing. The initial distribution of excess photon energy in the 28 Franck-Condon active vibrational modes of rhodopsin is defined by a fully thermalized sum-over-states vibronic calculation. This calculation reveals that absorption by high-frequency unreactive modes (e.g., C[double bond]C stretches) increases as the excitation wavelength is shifted from 570 to 450 nm whereas relatively less energy is deposited into reactive low-frequency modes. This result qualitatively explains the experimentally observed wavelength dependence of phi(lambda) for rhodopsin and reveals the importance of delocalized, torsional modes in the reactive pathway.

Electronic excitations of biomolecules studied by quantum chemistry

Significant methodological advances have been made over the past ten years in developing reliable quantum chemical methods for the treatment of electronically excited states. These methods can nowadays be used routinely by the experienced researcher to accurately compute excitation spectra of medium-sized organic molecules; results have been reported for several popular photobiological systems, including green fluorescent protein. First steps are currently being taken to account for the solvochromic shifts of chromophore excitations caused by particular protein environments and to dynamically simulate photochemical reactions in the excited states.