CASPT2//CASSCF and TDDFT//CASSCF Mapping of the Excited State Isomerization Path of a Minimal Model of the Retinal Chromophore

Photoisomerization of Disperse Red 1 Studied with Transient Absorption Spectroscopy and Quantum Chemical Calculations

The photoisomerization of the push-pull substituted azo dye Disperse Red 1 is studied using femtosecond time-resolved absorption spectroscopy and other spectroscopic and computational techniques. In comparison with azobenzene, the pipi* state is more stabilized by the effects of push-pull substitution than the npi* state, but the latter is probably still the lowest in energy. This conclusion is based on the kinetics, anisotropy of the excited state absorption spectrum, the spectra of the ground states, and quantum chemical calculations. The S(1)(npi*) state is formed from the initially excited pipi* state in <0.2 ps, and decays to the ground state with time constants of 0.9 ps in toluene, 0.5 ps in acetonitrile, and 1.4 ps in ethylene glycol. Thermal isomerization transforms the Z isomer produced to the more stable E isomer with time constants of 29 s (toluene), 28 ms (acetonitrile), and 2.7 ms (ethylene glycol). The pathway of photoisomerization is likely to be rotation about the N=N bond. Quantum chemical calculations indicate that along the inversion pathway ground and excited state energy surfaces remain well separated, whereas rotation leads to a region where conical intersections can occur. For the ground-state Z to E isomerization, conclusive evidence is lacking, but inversion is more probably the favored pathway in the push-pull substituted systems than in the parent azobenzene.

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.

Light-Driven Unidirectional Rotation in a Molecule: ROKS Simulation

We present a first-principles molecular dynamics study of the excited-state motion in a molecule that has recently been proven to exhibit light-driven unidirectional rotation. The simulations show that the directed motion is due to the complex excited-state dynamics on ultrashort timescales in the chiral system.

Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.

Mechanistic Studies on the Cyclization of (Z)-1,2,4-Heptatrien-6-yne in Methanol: A Possible Nonadiabatic Thermal Reaction

Myers et al. pyrolyzed (Z)-1,2,4-heptatrien-6-yne (1) in methanol at 100 degrees C and observed benzylmethyl ether (2) as a major product and 2-phenylethanol (3) as a minor product. If a biradical intermediate, such as the open-shell singlet state of alpha,3-didehydrotoluene (4), was the only intermediate generated by the cyclization, then reaction with methanol might be expected to afford 2-phenylethanol as the principal product. The question that has been of interest since its first discovery is the origin of the principal product of the title reaction, benzylmethyl ether. This report considers three mechanisms for formation of the benzylmethyl ether: direct methanol participation in the cyclization of the reactant, partial ether formation from the biradical 4, or involvement of the closed-shell zwitterionic state of alpha,3-didehydrotoluene (5). A fourth mechanism, involving a cyclic allene intermediate, has been ruled out by earlier studies. In the present work, the first two mechanisms are ruled out by experiment and/or calculation. The remaining one, involving the zwitterion, is shown to be consistent with experimental and computational data only if a component of the reaction follows a nonadiabatic course.

On the Low-Lying Excited States ofsym-Triazine-Based Herbicides

We report a joint computational and luminescence study on the low-lying excited states of sym-triazines, namely, 1,3,5-triazine (1) and the ubiquitous herbicides atrazine [6-chloro-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine (2)] and ametryn [6-methylthio-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine (3)]. Geometrical structures, energetics, and transition and state properties of I and 2 were computed at the TD-DFT, CASSCF, and CASPT2 levels of theory. The fluorescence and phosphorescence emission spectra, lifetimes, and fluorescence quantum yields were measured for the three compounds, and from these, the energies of the lowest excited states and their corresponding radiative rates were determined. The predictions from CASPT2 calculations are in good agreement with the experimental results obtained from the luminescence studies and allow the interpretation of different absorption and emission features.

Calculating Absorption Shifts for Retinal Proteins: Computational Challenges

Rhodopsins can modulate the optical properties of their chromophores over a wide range of wavelengths. The mechanism for this spectral tuning is based on the response of the retinal chromophore to external stress and the interaction with the charged, polar, and polarizable amino acids of the protein environment and is connected to its large change in dipole moment upon excitation, its large electronic polarizability, and its structural flexibility. In this work, we investigate the accuracy of computational approaches for modeling changes in absorption energies with respect to changes in geometry and applied external electric fields. We illustrate the high sensitivity of absorption energies on the ground-state structure of retinal, which varies significantly with the computational method used for geometry optimization. The response to external fields, in particular to point charges which model the protein environment in combined quantum mechanical/molecular mechanical (QM/MM) applications, is a crucial feature, which is not properly represented by previously used methods, such as time-dependent density functional theory (TDDFT), complete active space self-consistent field (CASSCF), and Hartree-Fock (HF) or semiempirical configuration interaction singles (CIS). This is discussed in detail for bacteriorhodopsin (bR), a protein which blue-shifts retinal gas-phase excitation energy by about 0.5 eV. As a result of this study, we propose a procedure which combines structure optimization or molecular dynamics simulation using DFT methods with a semiempirical or ab initio multireference configuration interaction treatment of the excitation energies. Using a conventional QM/MM point charge representation of the protein environment, we obtain an absorption energy for bR of 2.34 eV. This result is already close to the experimental value of 2.18 eV, even without considering the effects of protein polarization, differential dispersion, and conformational sampling.

Fast hydrogen elimination from the [Ru(PH3)3(CO)(H)2] and [Ru(PH3)4(H)2] complexes in the first singlet excited states: A diabatic quantum dynamics study

The photodissociation dynamics of [Ru(PH3)3(CO)(H)2] and cis-[Ru(PH3)4(H)2] is theoretically analyzed in the lowest two excited singlet states. Energies obtained through electronic density functional theory calculations that use the time-dependent formalism are fitted to analytical reduced two-dimensional potential energy surfaces (2D-PES). The metal-H2 (R) and H-H (r) distances are the variables of these 2D-PES, the rest of the parameters being kept frozen at the values of the minimum energy structure in the ground electronic state. The time evolution in these 2D-PES is exactly followed by means of a fast Fourier transform algorithm applied to solve the time-dependent Schrödinger equation. A simple diabatization scheme is devised to take into account the probability of transitions between both excited states. The quantum dynamics results point out that photoelimination is almost inexistent if the H2 fragment is to be expelled without further rearrangement of the rest of the complex. Conversely, when the geometries of the complex are optimized by keeping r and R frozen at the hydrogen elimination barrier coordinates, the new 2D-PES so obtained are highly dissociative, the H2 fragment being expelled in less than 100 fs. Finally the picture of the whole reaction that emerges from our theoretical results is described and the main differences between both complexes are examined.

Access to an Excited State via the Thermal Ring-Opening of a Cyclopropylidene

[reaction: see text] Thermal generation of singlet excited states is unusual in organic chemistry. The potential energy surface for the thermal ring-opening of 4-methylene-bicyclo[3.1.0]hex-2-ene-6-ylidene (1) was calculated at the CASSCF level of theory and found to produce alpha,3-didehydrotoluene in its biradical ground state (S(0)) and/or its zwitterionic excited state (S(1)).