No abstract

Single molecules that act as light-energy transducers (e.g., converting the energy of a photon into atomic-level mechanical motion) are examples of minimal molecular devices. Here, we focus on a molecular switch designed by merging a conformationally locked diarylidene skeleton with a retinal-like Schiff base and capable of mimicking, in solution, different aspects of the transduction of the visual pigment Rhodopsin. Complementary ab initio multiconfigurational quantum chemistry-based computations and time-resolved spectroscopy are used to follow the light-induced isomerization of the switch in methanol. The results show that, similar to rhodopsin, the isomerization occurs on a 0.3-ps time scale and is followed by <10-ps cooling and solvation. The entire (2-photon-powered) switch cycle was traced by following the evolution of its infrared spectrum. These measurements indicate that a full cycle can be completed within 20 ps.CASPT2//CASSCF ͉ mid-IR ͉ photochemical switch ͉ time resolved spectroscopy ͉ UV-vis M olecular switches based on photochemical E/Z isomerizations have been used in different contexts to convert light energy into ''mechanical'' motion at the molecular level (1-3). For instance, switches based on azobenzene have been used to control ion complexation (4, 5), electronic properties (6), catalysis (7), and the folding of peptides (8-13) whereas diarylidenes have provided the framework for the construction of rotary motors and transmissions (14). The computer modeling of switches that differ in size, polarity, and isomerization mechanism represents an attractive research target (15) yielding building blocks to be used in diverse molecular environments. However, this cannot be limited to the computation of equilibrium properties but requires the description of the entire photocycle. In other words, one needs to compute the potential energy surfaces controlling the switch E 3 Z and Z 3 E excited-state evolution, its decay and ground state relaxation, and the competing thermal E/Z isomerization in the proper environment (e.g., in solution or in a biomolecule backbone). The complexity of these calculations impedes the study of candidates that are intractable with accurate quantum chemical methods (allowing comparison with spectroscopic data) or that feature, as for azobenzene and diarylidenes (16), more than 1 low-lying excited state, leading to a plethora of reaction paths to be computed.The retinal protonated Schiff-base chromophore of rhodopsins (17-19) constitutes an example of an E/Z switch shaped by biological evolution that can be modeled with quantitative computations (20). In bovine rhodopsin (Rh), a selective photoisomerization of the 11-cis chromophore (PSB11) occurs via evolution of a single 3 * excited state (S 1 ) that survives for only 150 fs and yields, upon decay, the all-trans ground state (S 0 ) product with a 67% quantum yield (16,20). Although these properties make Rh an excellent reference for the design of E/Z switches, irradiation of PSB11 in solution (26, 27) features an unselec...

A "brute-force" ab initio CASPT2//CASSCF/CHARMM computational approach is employed to investigate the properties of the emitting state of the wild-type green fluorescence protein. The results indicate that the emitting moiety corresponds to a slightly perturbed H2O- - -chromophore complex. Thus, the protein matrix seems to be designed in such a way to mimic an environment that is more similar to gas-phase than water solution.

Versatile peroxidases are heme enzymes that combine catalytic properties of lignin peroxidases and manganese peroxidases, being able to oxidize Mn 2؉ as well as phenolic and non-phenolic aromatic compounds in the absence of mediators. The catalytic process (initiated by hydrogen peroxide) is the same as in classical peroxidases, with the involvement of 2 oxidizing equivalents and the formation of the so-called Compound I. This latter state contains an oxoferryl center and an organic cation radical that can be located on either the porphyrin ring or a protein residue. In this study, a radical intermediate in the reaction of versatile peroxidase from the ligninolytic fungus Pleurotus eryngii with H 2 O 2 has been characterized by multifrequency (9.4 and 94 GHz) EPR and assigned to a tryptophan residue. Comparison of experimental data and density functional theory theoretical results strongly suggests the assignment to a tryptophan neutral radical, excluding the assignment to a tryptophan cation radical or a histidine radical. Based on the experimentally determined side chain orientation and comparison with a high resolution crystal structure, the tryptophan neutral radical can be assigned to Trp 164 as the site involved in long-range electron transfer for aromatic substrate oxidation.Different heme peroxidases are considered to be involved in the lignin biodegradation process, a key step for carbon recycling in terrestrial ecosystems. These are lignin peroxidase (LiP) 4 and manganese peroxidase (MnP), first described in Phanerochaete chrysosporium (1-3), and the versatile peroxidase (VP), more recently described in fungi from the genera Pleurotus (4 -6) and Bjerkandera (7,8). VP is characterized by combining catalytic properties of the other two ligninolytic peroxidases, MnP and LiP. This enzyme is able to oxidize Mn 2ϩ to Mn 3ϩ and also exhibits manganese-independent activity toward veratryl alcohol and p-dimethoxybenzene. Furthermore, it oxidizes hydroquinones and substituted phenols that are not efficiently oxidized by LiP or MnP in the absence of veratryl alcohol and Mn 2ϩ , respectively. VP is even able to degrade directly high redox potential dyes, which can be eventually oxidized by LiP only in the presence of veratryl alcohol (9, 10).Two genes encoding VP isoenzymes VPL and VPS1, expressed in liquid-and solid-state fermentation cultures, respectively, have been cloned from Pleurotus eryngii (11,12). The deduced amino acid sequences for both isoenzymes were used to build molecular models by homology modeling, taking advantage of sequence identity to P. chrysosporium LiP and MnP and Coprinopsis cinerea (synonym Coprinus cinereus) peroxidase (13). Very recently, the crystal structure of recombinant P. eryngii VP expressed in Escherichia coli and activated in vitro (14) has been determined at 1.33-Å resolution (Protein Data Bank code 2BOQ).Catalytically, VP would follow the classical heme peroxidase cycle, in which hydrogen peroxide is the final electron acceptor, acting as a 2-electron oxidizing substrate f...