We report a combined quantum mechanical/molecular mechanical (QM/MM) study of the DsRed.M1 protein using as QM component the self-consistent charge density functional tight-binding (SCC-DFTB) method in molecular dynamics (MD) simulations and hybrid density functional theory (DFT, B3LYP functional) in QM/MM geometry optimizations. We consider different variants of the chromophore (including the cis- and trans-acylimine and peptide forms) as well as different protonation states of environmental residues. The QM/MM calculations provide insight into the role of nearby residues concerning their interactions with the chromophore and their influence on structural and spectroscopic properties. QM/MM optimizations yield a single conformer for the anionic acylimine chromophore, whereas there are distinct cis- and trans-conformers in the anionic peptide chromophore, the latter being more stable. The calculated vertical excitation energies (DFT/MRCI) for the anionic chromophores agree well with experiment. The published crystal structure of DsRed.M1 with an anionic acylimine chromophore indicates a quinoid structure, while the QM/MM calculations predict the phenolate form to be more stable.

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited-state calculations were extracted from ground-state molecular dynamics (MD) simulations using the self-consistent-charge density functional tight binding (SCC-DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited-state calculations used time-dependent density functional theory (TDDFT) and the DFT-based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto-N7H and keto-N9H guanine, with particular focus on solvent effects in the low-energy spectrum of the keto-N9H tautomer. When compared with the vertical excitation energies of gas-phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC-DFTB-based rather than B3LYP-based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas-phase and solution spectra, typically ca. 0.1-0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent-induced structural changes and from electrostatic solute-solvent interactions, the latter being dominant.

While the optical spectra of the acene series up to pentacene provide textbook examples for the annulation principle, the spectra of the larger members are much less understood. The present work provides an investigation of the optically allowed excited states of the acene series from pentacene to nonacene, the largest acene observed experimentally, using the density functional based multireference configuration method (DFT/MRCI). For this purpose, the ten lowest energy states of the B2u and B3u irreducible representations were computed. In agreement with previous computational investigations, the electronic wave functions of the acenes acquire significant multireference character with increasing acene size. The HOMO → LUMO excitation is the major contributor to the (1)La state (p band, B2u) also for the larger acenes. The oscillator strength decreases with increasing length. The (1)Lb state (α band, B3u), so far difficult to assign for the larger acenes due to overlap with photoprecursor bands, becomes almost insensitive to acene length. The (1)Bb state (β band, B3u) also moves only moderately to lower energy with increasing acene size. Excited states of B3u symmetry that formally result from double excitations involving HOMO, HOMO-1, LUMO, and LUMO+1 decrease in energy much faster with system size. One of them (D1) has very small oscillator strength but becomes almost isoenergetic with the (1)La state for nonacene. The other (D2) also has low oscillator strength as long as it is higher in energy than (1)Bb. Once it is lower in energy than the (1)Bb state, both states interact strongly resulting in two states with large oscillator strengths. The emergence of two strongly absorbing states is in agreement with experimental observations. The DFT/MRCI computations reproduce experimental excitation energies very well for pentacene and hexacene (within 0.1 eV). For the larger acenes deviations are larger (up to 0.2 eV), but qualitative agreement is observed.

The effect of substituting the intra-cyclic sulphur of thionine by oxygen (oxonine) and selenium (selenine) on the intersystem crossing (ISC) efficiency has been studied using high level quantum mechanical methods. The ISC rate constants are considerably increased when going from O towards Se while the fluorescence rate constants remain unchanged. For the three dyes, all accessible ISC channels are driven by vibronic spin-orbit coupling (SOC) between ππ* states. The interplay between the ground and low-lying excited states has been investigated in order to determine the dominant relaxation pathways. In oxonine the relaxation to the ground state after photoexcitation in water proceeds essentially via fluorescence from the S1(πHπL*) bright state (kF = 2.10 × 10(8) s(-1)), in agreement with the high experimental fluorescence quantum yield. In aqueous solution of thionine, the ISC rate constant (kISC ∼ 1 × 10(9) s(-1)) is one order of magnitude higher than fluorescence (kF = 1.66 × 10(8) s(-1)) which is consistent with its high triplet quantum yield observed in water (ϕT = 0.53). Due to a stronger vibronic SOC in selenine, the ISC rate is very high (kISC ∼ 10(10) s(-1)) and much faster than fluorescence (kF = 1.59 × 10(8) s(-1)). This suggests selenine-based dyes as very efficient triplet photosensitizers.