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Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements. peerReviewed

Photoactivation in the Photoactive Yellow Protein, a bacterial blue light photoreceptor, proceeds via photo-isomerization of the double C=C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double bond photo-isomerization, the isolated chromophore and many of its analogues, can isomerize around a single C-C bond as well. Whereas double bond photo-isomerization has been observed with x-ray crystallography, experimental evidence for single bond photo-isomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring and carried out transient absorption spectroscopy experiments in combination with non-adiabatic molecular dynamics simulations to reveal that the locked chromophore isomerizes around the single bond upon photo-activation. Our work thus provides experimental evidence for single bond photo-isomerization in a photoactive yellow protein chromophore analogue and suggests that photo-isomerization is not restricted to the double bonds in conjugated systems. This insight may be useful for designing light-driven molecular switches or motors. peerReviewed

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra. peerReviewed

When photoactive molecules interact strongly with confined light modes, new hybrid light-matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Förster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations suggest that while the excitation is initially fully delocalized over all molecules and the confined light mode, it very rapidly localizes onto one of the photoreactive molecules, which then undergoes the reaction. peerReviewed

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump–probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results. peerReviewed

We report on the complex of a noble-gas hydride HXeOH with carbon monoxide. This species is prepared via the annealing-induced H + Xe + OH···CO reaction in a xenon matrix, the OH···CO complexes being produced by VUV photolysis of the H2O···CO complexes. The H–Xe stretching mode of the HXeOH···CO complex absorbs at 1590.3 cm–1 and it is blue-shifted by 12.7 cm–1 from the H–Xe stretching band of HXeOH monomer. The observed blue shift indicates the stabilization of the H–Xe bond upon complexation, which is characteristic of complexes of noble-gas hydrides. The HXeOH···CO species is the first complex of a noble-gas hydride with carbon monoxide and the second observed complex of HXeOH. On the basis of the MP2/aug-cc-pVTZ-PP calculations, the experimental complex is assigned to the structure, where the carbon atom of CO interacts with the oxygen atom of HXeOH. peerReviewed