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Ab initio methods are used to characterize the ground and first excited state of the chromophore in the rhodopsin family of proteins: retinal protonated Schiff base. Retinal protonated Schiff base has five double bonds capable of undergoing isomerization. Upon absorption of light, the chromophore isomerizes and the character of the photoproducts (e.g., 13-cis and 11-cis) depends on the environment, protein vs. solution. Our ab initio calculations show that, in the absence of any specific interactions with the environment (e.g., discrete ordered charges in a protein), energetic considerations cannot explain the observed bond selectivity. We instead attribute the origin of bond selectivity to the shape (topography) of the potential energy surfaces in the vicinity of points of true degeneracy (conical intersections) between the ground and first excited electronic states. This provides a molecular example where a competition between two distinct but nearly isoenergetic photochemical reaction pathways is resolved by a topographical difference between two conical intersections.O ne of the simplest means to convert light into mechanical motion at the atomic scale is cis-trans photoisomerization, and it is widely used in photoactive proteins. Retinal protonated Schiff base (RPSB) is the best known biological chromophore, with five double bonds capable of undergoing photoisomerization. A long-standing question has been the mechanism that selects the isomerizing bond, particularly the role of the protein environment in ''steering'' reactivity. The availability of the structures of rhodopsin (1) and bacteriorhodopsin (2-5), coupled with characterization of RPSB solution-phase photochemistry (6-11), provides a unique opportunity to identify this mechanism. Conical intersections (CIs), geometries where two electronic states are truly degenerate, providing doorways from excited to ground electronic states, are widely believed to be important in photochemistry (12)(13)(14), and their role in photoinduced isomerization has been well documented (14-22). However, their role in bond torsion selectivity has yet to be established. In this paper, we show that the topography, or shape, around CIs determines this selectivity in RPSB. This direct connection between CI topography and photochemical selectivity has significant implications for understanding protein ''steering'' and the rational design of molecular optoelectronic devices.Investigations of the photochemistry of RPSB have established that the protein is not an idle spectator; quantum yield, selectivity, and time scales are all significantly different in solution and protein environments. In the protein environment, isomerization occurs exclusively around a single bond, e.g., 11-cis 3 all-trans in rhodopsin and all-trans 3 13-cis in bacteriorhodopsin. In contrast, illumination of the all-trans chromophore in solution results in several photoproducts with 11-cis being the most dominant (6-8). The isomerization quantum yield is greater than 50% in proteins (23), but rarely excee...

A DFT-based description is given of the CO2/epoxide copolymerization with a catalyst system consisting of metal (chromium, iron, titanium, aluminum)-salen complexes (salen = N,N'-bis(3,5-di-tert-butylsalicyliden-1,6-diaminophenyl) in combination with either chloride, acetate, or dimethylamino pyridine (DMAP) as external nucleophile. Calculations indicate that initiation proceeds through nucleophilic attack at a metal-coordinated epoxide, and the most likely propagation reaction is a bimolecular process in which a metal-bound nucleophile attacks a metal-bound epoxide. Carbon dioxide insertion occurs at a single metal center and is most likely the rate-determining step at low pressure. The prevalent chain terminating/degradation-the so-called backbiting, a reaction leading to formation of cyclic carbonate from the polymer chain-would involve attack of a carbonate nucleophile rather than an alkoxide at the last unit of the growing chain. The backbiting of a free carbonato chain end is particularly efficient. Anion dissociation from six-coordinate aluminum is appreciably easier than from chromium-salen complexes, indicating the reason why in the former case cyclic carbonate is the sole product. Experimental data were gathered for a series of chromium-, aluminum-, iron-, and zinc-salen complexes, which were used in combination with external nucleophiles like DMAP and mainly (tetraalkyl ammonium) chloride/acetate. Aluminum complexes transform PO (propylene oxide) and CO2 to give exclusively propylene carbonate. This is explained by rapid carbonate anion dissociation from a six-coordinate complex and cyclic formation. CO2 insertion or nucleophilic attack of an external nucleophile at a coordinated epoxide (at higher CO2 pressure) are the rate-determining steps. Catalysis with [Cr(salen)(acetate/chloride)] complexes leads to the formation of both cyclic carbonate and polypropylene carbonate with various quantities of ether linkages. The dependence of the activity and selectivity on the CO2 pressure, added nucleophile, reaction temperature, and catalyst concentration is complex. A mechanistic description for the chromium-salen catalysis is proposed comprising a multistep and multicenter reaction cycle. PO and CO2 were also treated with mixtures of aluminum- and chromium-salen complexes to yield unexpected ratios of polypropylene carbonate and cyclic propylene carbonate.

Vectorial proton translocation through membranes is a fundamental energy conversion process in biological cells. Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven, voltage-sensitive proton pump in the purple membrane (PM) of Halobacterium salinarum and achieves its biological function by cycling through a reaction sequence that includes ultrafast (∼500 fs) events, intermediate (µs) as well as slow (∼10 ms) steps. bR is of utmost simplicity in comparison with other proton translocating bioenergetic proteins and, therefore, constitutes an ideal model for the study of this process. The PM involves a highly structured supramolecular organization and is fundamental for the in vivo functioning of bR. Over the last 10 years, crystal structures of bR have become available at increasing resolution. The most recent structures resolve many of the lipids of the PM and provide atomic level detail of bR at below 2 Å resolution. Fundamental for an understanding of the function of bR is internal water that participates in proton pumping. Several water molecules have been resolved now crystallographically in two channels, on the extracellular and on the intracellular side of bR. We show that free energy perturbation theory can place water molecules in bR, with results that compare well with the observed water molecules, and we apply the method to predict water movement during bR's photocycle. A preliminary simulation illustrates that water molecules may indeed be displaced during the photocycle, after retinal undergoes an all-trans f 13-cis isomerization, and that this displacement may constitute a mechanism for proton pumping. A key advance reported in this feature article is the integration of the available bR structures into a model for the entire PM. This hexagonally periodic, lamellar model has been hydrated and refined through a constant pressure molecular dynamics simulation. The resulting structure connects extracellular bulk water with water molecules and key side groups in the interior of bR, permitting a seamless overall description of the proton path in the PM, from intracellular to extracellular space. For the first time, a complex cellular reaction can be accounted for in full atomic detail in its complete native environment.

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