While azobenzenes readily photoswitch in solution, their photoisomerization in densely packed self-assembled monolayers (SAMs) can be suppressed. Reasons for this can be steric hindrance and/or electronic quenching, e.g., by exciton coupling. We address these possibilities by means of nonadiabatic molecular dynamics with trajectory surface hopping calculations, investigating the trans → cis isomerization of azobenzene after excitation into the ππ* absorption band. We consider a free monomer, an isolated dimer and a dimer embedded in a SAM-like environment of additional azobenzene molecules, imitating in this way the gradual transition from an unconstrained over an electronically coupled to an electronically coupled and sterically hindered, molecular switch. Our simulations reveal that in comparison to the single molecule the quantum yield of the trans → cis photoisomerization is similar for the isolated dimer, but greatly reduced in the sterically constrained situation. Other implications of dimerization and steric constraints are also discussed.

The combination of light activation and N‐heterocyclic carbene (NHC) organocatalysis has enabled the use of acid fluorides as substrates in a UVA‐light‐mediated photochemical transformation previously observed only with aromatic aldehydes and ketones. Stoichiometric studies and TD‐DFT calculations support a mechanism involving the photoactivation of an ortho‐toluoyl azolium intermediate, which exhibits “ketone‐like” photochemical reactivity under UVA irradiation. Using this photo‐NHC catalysis approach, a novel photoenolization/Diels–Alder (PEDA) process was developed that leads to diverse isochroman‐1‐one derivatives.

In blue-light sensing using flavin (BLUF) domains, the side-chain orientation of key residues close to the flavin chromophore is still under debate. We report quantum refinements of the wild-type AppA BLUF protein from Rhodobacter sphaeroides starting from two published X-ray structures (1YRX and 2IYG) with different arrangements of the residues around the chromophore. Quantum refinement uses the same experimental X-ray raw data as conventional refinement, but includes data from quantum mechanics/molecular mechanics (QM/MM) calculations as restraints, which is expected to be more reliable than the normally employed MM data. In addition to quantum refinement, pure QM/MM geometry optimizations are performed for the 1YRX and 2IYG structures and for five models derived therefrom. Vertical excitation energies are computed at the QM(DFT/MRCI)/MM level to assess the resulting structures. The experimental absorption maximum of the dark state of wild-type AppA is well reproduced for structures that contain the Gln63 residue in 1YRX-type orientation. The computed excitation energies are red-shifted for structures with a flipped Gln63 residue in 2IYG-type orientation. The calculated 1YRX- and 2IYG-type hydrogen-bonding networks are discussed in detail, particularly with regard to the orientation of the chromophore and the Gln63, Trp104, and Met106 residues.

We address the performance of the vertical and adiabatic Franck–Condon (VFC/AFC) approaches combined with time-independent or time-dependent (TI/TD) formalisms in simulating the one-photon absorption spectra of three flavin compounds with distinct structural features. Calculations were done in the gas phase and in two solvents (water, benzene) for which experimental reference measurements are available. We utilized the independent mode displaced harmonic oscillator model without or with frequency alteration (IMDHO/IMDHO-FA) and also accounted for Duschinsky mixing effects. In the initial validation on the first excited singlet state of riboflavin, the range-separated functionals, CAM-B3LYP and ωB97xD, showed the best performance, but B3LYP also gave a good compromise between peak positions and spectral topology. Large basis sets were not mandatory to obtain high-quality spectra for the selected systems. The presence of a symmetry plane facilitated the computation of vibrationally broadened spectra, since different FC variants yield similar results and the harmonic approximation holds rather well. Compared with the AFC approach, the VFC approach performed equally well or even better for all three flavins while offering several advantages, such as avoiding error-prone geometry optimization procedures on excited-state surfaces. We also explored the advantages of curvilinear displacements and of a Duschinsky treatment for the AFC spectra in cases when a rotatable group is present on the chromophore. Taken together, our findings indicate that the combination of the VFC approach with the TD formalism and the IMDHO-FA model offers the best overall performance

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It is proposed that xanthophylls, and carotenoids in general, may assist in energy transfer from the chlorophyll Soret band to the Q band. Ground-state (1Ag ) and excited-state (1Bu ) optimizations of violaxanthin (Vx) and zeaxanthin (Zx) are performed in an environment mimicking the light-harvesting complex II (LHCII), including the closest chlorophyll b molecule (Chl). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) is used in combination with a semi-empirical description to obtain the excited-state geometries, supported by additional DFT/multireference configuration interaction calculations, with and without point charges representing LHCII. In the ground state, Vx and Zx show similar properties. At the 1Bu minimum, the energy of the Zx 1Bu state is below the Chl Q band, in contrast to Vx. Both Vx and Zx may act as acceptors of Soret-state energy; transfer to the Q band seems to be favored for Vx. These findings suggest that carotenoids may generally mediate Soret-to-Q energy flow in LHCII.

We address the effects of using Cartesian or internal coordinates in the adiabatic Franck-Condon (AFC) and vertical Franck-Condon (VFC) approaches to electronic spectra. The adopted VFC approach is a simplified variant of the original approach [A. Hazra, H. H. Chang, and M. Nooijen, J. Chem. Phys. 151, 2125 (2004)], as we omit any contribution from normal modes with imaginary frequency. For our test molecules ranging from ethylene to flavin compounds, VFC offers several advantages over AFC, especially by preserving the properties of the FC region and by avoiding complications arising from the crossing of excited-state potential surfaces or from the failure of the harmonic approximation. The spectral quality for our target molecules is insensitive to the chosen approach. We also explore the effects of Duschinsky rotation and relate the need for internal coordinates to the absence of symmetry elements. When using Duschinsky rotation and treating larger systems without planar symmetry, internal coordinates are found to outperform Cartesian coordinates in the AFC spectral calculations.

Chlorophylls and bacteriochlorophylls, together with carotenoids, serve, noncovalently bound to specific apoproteins, as principal light-harvesting and energy-transforming pigments in photosynthetic organisms. In recent years, enormous progress has been achieved in the elucidation of structures and functions of light-harvesting (antenna) complexes, photosynthetic reaction centers and even entire photosystems. It is becoming increasingly clear that light-harvesting complexes not only serve to enlarge the absorption cross sections of the respective reaction centers but are vitally important in short- and long-term adaptation of the photosynthetic apparatus and regulation of the energy-transforming processes in response to external and internal conditions. Thus, the wide variety of structural diversity in photosynthetic antenna “designs” becomes conceivable. It is, however, common for LHCs to form trimeric (or multiples thereof) structures. We propose a simple, tentative explanation of the trimer issue, based on the 2D world created by photosynthetic membrane systems.