Analysis of trajectory similarity and configuration similarity in on-the-fly surface-hopping simulation on multi-channel nonadiabatic photoisomerization dynamics.

We propose an "automatic" approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin (P Φ B) chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Fréchet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel photoisomerization dynamics. For each cluster, the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features in each reaction channel. The results show that this analysis protocol not only assigns all trajectories into different photoisomerization reaction channels but also extracts the major molecular motion without the requirement of the pre-known knowledge of the active photoisomerization site. As a side product of this analysis tool, it is also easy to find the so-called "typical" or "representative" trajectory for each reaction channel.

Bilirubin degradation in methanol induced by continuous UV-B irradiation: a UHPLC--ESI-MS study.

Degradation of bilirubin in aerobic methanol solution by continuous UV-B irradiation has been investigated in this work. The purpose of this study was to shed more light on bilirubin interaction with the UV-B component of natural sunlight, since bilirubin is a very efficient UV-B absorber located in the skin epidermis. The degradation products have been detected and studied by a combined method of Ultra High Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry (UHPLC-ESI-MS). Bilirubin, a toxic pigment which itself is a product of (hemoglobin) degradation in organisms, undergoes its own degradation under aerobic conditions of UV-B continuous irradiation (e.g. photooxidation) that can be partly self-sensitized. Two dipyrrolic structures have been identified as a result of the bilirubin degradation, not including the bilirubin derivative biliverdin whose increase in the irradiated system is synchronous with a time dynamics of bilirubin degradation. It appears that one of dipyrrolic products originates directly from bilirubin and biliverdin molecules, while the other one is probably connected to bilirubin self-sensitized degradation. The precursor role of biliverdin in the degradation process--related to the detected dipyrroles--has not been confirmed.

Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome.

Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C(15) = C(16) double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C(15) methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study.

The geometric relaxation following light absorption of the biliverdin, phycocyanobilin and phytochromobilin tetrapyrrole chromophores of bacterial, cyanobacterial and plant phytochromes has been investigated using density functional theory methods. Considering stereoisomers relevant for both red-absorbing Pr and far-red-absorbing Pfr forms of the photoreceptor, it is found that the initial excited-state evolution is dominated by torsional motion at the C10-C11 bond. This holds true for all three chromophores and irrespective of which configuration the chromophores adopt. This finding suggests that the photochromic cycling of phytochromes between their Pr and Pfr forms, which is known to be governed by Z/E photoisomerizations at the C15-C16 bond, relies on interactions between the chromophore and the protein to prevent photoisomerizations at C10-C11. Further, it is found that the uneven distribution of positive charge between the pyrrole rings is a major factor for the photochemical reactivity of the C10-C11 bond.

Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies.

We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.

The radical ions and photoionization of bile pigments.

The semireduced, semioxidized, and OH(.)-adduct radicals of bilirubin (BR) and biliverdin (BV) have been characterized using pulse radiolysis techniques. Laser flash photolysis (265-nm) of these pigments led to monophotonic photoionization with quantum yields of 0.08 for BR and 0.03 for BV. No evidence for triplet formation or for photoisomerization was found after 265-nm laser excitation. However, 347-nm excitation of BR in chloroform led to simultaneous photoisomerization and radical formation, but the radicals are thought to have originated from a pathway other than photoionization. The relevance of these observations to BR photoreactivity is discussed. BR radical ions in alkaline solution did not react with tryptophan (TrpH), but the semioxidized TrpH radical oxidized BR with k = 4.3 X 10(8) dm3 mole-1 sec-1. When human serum albumin (HSA) was oxidized using radiolytically generated azide radicals, a radical transformation involving TrpH and TyrOH residues occurred with k = 3.8 X 10(3) sec-1. When BR was complexed with the protein the transformation rate was reduced to 1.6 X 10(3) sec-1. This was interpreted in terms of a conformational change in the protein. Identification of the probable residues involved provided information about the primary BR binding site which was consistent with an earlier report.

The action spectrum and phototransformations of pterobilin (biliverdin IX gamma).

Pterobilin 1 (biliverdin IX gamma), a butterfly bile pigment, is photocyclized into phorcabilin 2 and sarpedobilin 3 by irradiation in visible light. Selective irradiations have now been performed at the absorption maxima of pterobilin 1. The 650-nm radiations are responsible for the observed photocyclizations while the 375-nm radiations lead to decomposition products. These results are discussed in connection with a hypothesis concerning the biological role of pterobilin in butterfly larvae.