Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L<-->M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.
Molecular dynamics--coarse grained to the level of hydrophobic and hydrophilic interactions--shows that small hydrophobic graphene sheets pierce through the phospholipid membrane and navigate the double layer, intermediate size sheets pierce the membrane only if a suitable geometric orientation is met, and larger sheets lie mainly flat on the top of the bilayer where they wreak havoc with the membrane and create a patch of upturned phospholipids. The effect arises in order to maximize the interaction between hydrophobic moieties and is quantitatively explained in terms of flip-flops by the analysis of the simulations. Possible severe biological consequences are discussed.
Integrating carbon nanoparticles (CNPs) with proteins to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science. The comprehension of CNP-protein interactions requires the still-missing identification and characterization of the 'binding pocket' for the CNPs. Here, using Lysozyme and C60 as model systems and NMR chemical shift perturbation analysis, a protein-CNP binding pocket is identified unambiguously in solution and the effect of the binding, at the level of the single amino acid, is characterized by a variety of experimental and computational approaches. Lysozyme forms a stoichiometric 1:1 adduct with C60 that is dispersed monomolecularly in water. Lysozyme maintains its tridimensional structure upon interaction with C60 and only a few identified residues are perturbed. The C60 recognition is highly specific and localized in a well-defined pocket.
Three radiationless decay pathways for the photochemical decomposition of diazirine and diazomethane have been characterized using the MC-SCF method with a 6-31G* basis. From diazirine, two almost barrierless paths exist on SI. One leads, via a diradicaloid IDur conical intersection at a bent, in-plane, diazomethane-like structure, to ground-state diazomethane; the other leads, via another I D . . conical intersection at a ring-opened diazirine diradicaloid geometry, directly to lCH2 + Nz. The triplet pathway starts at a )u-u* diazirine minimum, passing over a 9 kcal mol-' barrier to a %-7r* ' D, bent diazomethane-like minimum from which the barrier to Nz extrustion is 7 kea1 mol-'. In the absence of sensitizers, this triplet path can be entered from the singlet manifold via intersystem crossing at a point that has been characterized by finding the lowest energy point on the singlet-triplet crossing surface. This crossing point occurs at a geometry that is very similar to the transition state that occurs on the singlet path between diazirine and ground-state diazomethane. However, the efficiency of intersystem crossing (spin-orbit coupling) is predicted to be low. These data rationalize the temperature dependence of the fluorescence, the fact that diazomethanes and diazirines are observed as products of photolysis of diazirines and diazomethanes, respectively, the fact that there is CHz + N2 formation from both diazirines and diazomethanes, and the fact that no triplet states seem to be involved in the reaction.
A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle of the carbonic anhydrase. A model system including the Glu106 and Thr199 residues and the "deep" water molecule has been used. It has been found that the nucleophilic attack of the zinc-bound OH on the CO2 molecule has a negligible barrier (only 1.2 kcal mol -1 ). This small value is due to a hydrogenbond network involving Glu106, Thr199, and the deep water molecule. The two usually proposed mechanisms for the internal bicarbonate rearrangement have been carefully examined. In the presence of the two Glu106 and Thr199 residues, the direct proton transfer (Lipscomb mechanism) is a two-step process, which proceeds via a proton relay network characterized by two activation barriers of 4.4 and 9.0 kcal mol -1 . This pathway can effectively compete with a rotational mechanism (Lindskog mechanism), which has a barrier of 13.2 kcal mol -1 . The fast proton transfer found here is basically due to the effect of the Glu106 residue, which stabilizes an intermediate situation where the Glu106 fragment is protonated. In the absence of Glu106, the barrier for the proton transfer is much larger (32.3 kcal mol -1 ) and the Lindskog mechanism becomes favored.
An experimental investigation of the enantioselective oxidation of aryl benzyl sulfides by tert-butyl hydroperoxide in the presence of a titanium/hydrobenzoin catalyst has shown that these sulfides are ideal substrates for this catalytic system, with negligible interference by the substituents on the aryl groups. A reaction mechanism based on DFT computations has been proposed. The DFT MPWB1K functional was used in the theoretical investigation to account for weak hydrogen-bonding and pi interactions. The computed reaction profile explains the experimentally observed enantioselectivity, which is determined by the thermodynamics of the first phase of the reaction. A detailed discussion of the hydrogen-bonding and pi interactions that drive the reaction along the observed stereochemical path is given.
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