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The first examples of cross-metathesis between two different allenes is disclosed. First- and second-generation Ru complexes were found to be ineffective, at most affording only oligomeric products. The exception was a first-generation complex bearing a bidentate phenyl isopropoxy ligand (i.e., PCy3 is not released upon initiation), reactions with which afforded a 1,3-disubstituted allenyl boronate in 22% yield. On the basis of mechanistic studies designed to gain deeper understanding of the reasons for the ineffectiveness of different Ru catalysts, it was discovered that phosphine-free Ru-CAAC complexes have the steric and electronic attributes to be highly effective. The results of these investigations pave the way for development of additional olefin metathesis reactions that generate allenes.

Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.

The conversion of light energy into work is essential to life on earth. Bacteriorhodopsin (bR), a light-activated proton pump in Archae, has served for many years as a model system for the study of...

We report an experimental discovery and computational investigation of the first photochemical stereoselective [1,3]-sigmatropic silyl shift of an allylsilane. An organocatalytic enantioselective cascade annulation generates a trimethylsilyl-o-isotoluene reactant in >99:1 e.r., and this trimethylsilyl-o-isotoluene contains an allylic silane moiety that undergoes a stereoselective photochemical [1,3]-silyl shift to form a benzylsilane with 96:4 e.r. The mechanism of this unprecedented [1,3]-silyl shift has been elucidated by a series of experimental studies and CASSCF, DFT, and TD-DFT calculations on model systems and the experimental system. The highly stereoselective photoreaction is proposed to occur via a singlet silyl/allyl conical intersection. This is a new demonstration of the role of conical intersections in selective photochemistry.

Oxidative rearrangements play key roles in introducing structural complexity and biological activities of natural products biosynthesized by type II polyketide synthases (PKSs). Chartreusin (1) is a potent antitumor polyketide that contains a unique rearranged pentacyclic aromatic bilactone aglycone derived from a type II PKS. Herein, we report an unprecedented dioxygenase, ChaP, that catalyzes the final α-pyrone ring formation in 1 biosynthesis using flavin-activated oxygen as an oxidant. The X-ray crystal structures of ChaP and two homologues, docking studies, and site-directed mutagenesis provided insights into the molecular basis of the oxidative rearrangement that involves two successive C-C bond cleavage steps followed by lactonization. ChaP is the first example of a dioxygenase that requires a flavin-activated oxygen as a substrate despite lacking flavin binding sites, and represents a new class in the vicinal oxygen chelate enzyme superfamily.

Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, w...

This Communication details the implementation of a new concept for the design of high-performance optoelectronic materials: three-dimensional (3D) graphene nanostructures. This general strategy is showcased through the synthesis of a three-bladed propeller nanostructure resulting from the coupling and fusion of a central triptycene hub and helical graphene nanoribbons. Importantly, these 3D graphene nanostructures show remarkable new properties that are distinct from the substituent parts. For example, the larger nanostructures show an enhancement in absorption and decreased contact resistance in optoelectronic devices. To show these enhanced properties in a device setting, the nanostructures were utilized as the electron-extracting layers in perovskite solar cells. The largest of these nanostructures achieved a PCE of 18.0%, which is one of the highest values reported for non-fullerene electron-extracting layers.

The cycloadditions of benzene and ten different azabenzenes (pyridine, three diazines, three triazines, and three tetrazines) with the ethylene dienophile have been explored with density functional theory (M06-2X) and analyzed with the distortion/interaction model. Activation barriers correlate closely with both distortion energies and interaction energies over an activation energy range of 45 kcal/mol. The replacement of CH with N increases Diels-Alder reactivity due not only to the more favorable orbital interaction, but also to a decrease in distortion energy. The rates of reactions are greatly influenced by the nature of the bonds being formed: two C-C bonds > one C-C bond, and one C-N bond > two C-N bonds. The activation energy of Diels-Alder reactions correlates very well with reaction energies and with the NICS(0) values of the aromatic dienes. The distortion energy of the Diels-Alder reaction transition states mostly arises from the diene out-of-plane distortion energy.

A new class of bioorthogonal reagents, 1,2,4-triazines, is described. These scaffolds are stable in biological media and capable of robust reactivity with trans-cyclooctene (TCO). The enhanced stability of the triazine scaffold enabled its direct use in recombinant protein production. The triazine-TCO reaction can also be used in tandem with other bioorthogonal cycloaddition reactions. These features fill current voids in the bioorthogonal toolkit.

The cycloadditions of tetrazines with cyclopropenes and other strained alkenes have become among the most valuable bioorthogonal reactions. These reactions lead to bicyclic Diels-Alder adducts that spontaneously lose N2. We report quantum mechanical (QM) and quasiclassical trajectory simulations on a number of these reactions, with special attention to stereoelectronic and dynamic effects on spontaneous N2 loss from these adducts. QM calculations show that the barrier to N2 loss is low, and molecular dynamics calculations show that the intermediate is frequently bypassed dynamically. There is a large preference for N2 loss anti to the cyclopropane moiety rather than syn from adducts formed from reactions with cyclopropenes. This is explained by the interactions of the Walsh orbitals of the cyclopropane group with the breaking C-N bonds in N2 loss. Dynamical effects opposing the QM preferences have also been discovered involving the coupling of vibrations associated with the formation of the new C-C bonds in the cycloaddition step, and those of the breaking C-N bonds during subsequent N2 loss. This dynamic matching leads to pronounced nonstatistical effects on the lifetimes of Diels-Alder intermediates. An unusual oscillatory behavior of the intermediate decay rate has been identified and attributed to specific vibrational coupling.

We have investigated the gas-phase production of isoquinoline by performing collisional activation on benzalaminoacetal, the first intermediate in the classic solution-phase Pomeranz-Fritsch synthesis of isoquinoline. We have elucidated the reaction pathways in the gas phase using tandem mass spectrometry. Unlike the corresponding condensed-phase reaction, where catalytic proton exchange between intermediate(s) and solvent (Brønsted-Lowry base) is known to drive the reaction, the gas-phase reaction follows the "mobile proton model" to form the products via a number of intermediates, some the same as in their condensed-phase counterparts. Energy-resolved mass spectrometry, deuterium labeling experiments, and theoretical calculations (B3LYP/6-31G**) identified 27 different reaction routes in the gas phase, forming a complex interlinked reaction network. The experimental measurements and theoretical calculations confirm the proton hopping onto different basic sites of the precursors and intermediates to transform them ultimately into isoquinoline.

The Diels-Alder reactions of seven 1,2,4,5-tetrazines with unstrained and strained alkenes and alkynes were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The higher reactivities of alkenes compared to alkynes in the Diels-Alder reactions with tetrazines arise from the differences in both interaction and distortion energies. Alkenes have HOMO energies higher than those of alkynes and therefore stronger interaction energies in inverse-electron-demand Diels-Alder reactions with tetrazines. We have also found that the energies to distort alkenes into the Diels-Alder transition-state geometries are smaller than for alkynes in these reactions. The strained dienophiles, trans-cyclooctene and cyclooctyne, are much more reactive than unstrained trans-2-butene and 2-butyne, because they are predistorted toward the Diels-Alder transition structures. The reactivities of substituted tetrazines correlate with the electron-withdrawing abilities of the substituents. Electron-withdrawing groups lower the LUMO+1 of tetrazines, resulting in stronger interactions with the HOMO of dienophiles. Moreover, electron-withdrawing substituents destabilize the tetrazines, and this leads to smaller distortion energies in the Diels-Alder transition states.

The azide-dibenzocyclooctyne and trans-cyclooctene-tetrazine cycloadditions are both bioorthogonal and mutually orthogonal: trans-cyclooctene derivatives greatly prefer to react with tetrazines rather than azides, while dibenzocyclooctyne derivatives react with azides but not with tetrazines under physiological conditions. DFT calculations used to identify the origins of this extraordinary selectivity are reported, and design principles to guide discovery of new orthogonal cycloadditions are proposed. Two new bioorthogonal reagents, methylcyclopropene and 3,3,6,6-tetramethylthiacycloheptyne, are predicted to be mutually orthogonal in azide and tetrazine cycloadditions.

A shell−core cluster 2 produced by depositing a self-assembled monolayer (SAM) of 6-thiohexyl-3-nitro-4-(4‘-stilbenoxymethyl)-benzoate (1) on a nanoparticulate gold colloid preserves normal solution-phase photoreactivity of the trans-stilbene and o-nitrobenzyl ether moieties, but shows quenched fluorescence. Nearest-neighbor aggregation is weaker for 1 bound to the roughly spherical colloidal gold particle (in cluster 2) than for analogous stilbenoids bound to a planar gold surface. Unlike the observed photochemical reactivity of stilbenylalkyl sulfides appended as SAMs on planar gold surfaces, the chromophores present in these shell−core nanocomposites 2 exhibit efficient trans-to-cis photoisomerization and blocked [2 + 2] photodimerization. Wavelength selectivity for photoisomerization and photocleavage proved to be elusive, but triplet sensitization of the geometric isomerization took place without photorelease of the attached group.

The carbon-13 chemical shift tensors of pentaerythritol (C(CH2OH)4, tetrakis(hydroxymethyl)methane) are measured with use of the two-dimensional chemical shift correlation technique. The results are interpreted with quantum-chemical ab initio gauge invariant atomic orbital computations of the nuclear shielding tensors based on X-ray and neutron diffraction structures, and on corresponding structures modified by optimizing the CH2 proton positions with the Gaussian 94 program. The X-ray based computations correlate with the experimental tensors with a root-mean-square deviation of 4.45 ppm, while the neutron structure gives a root-mean-square deviation of 0.86 ppm. After optimizing the CH2 proton positions for the X-ray and neutron structures, root-mean-square deviations of 1.19 and 0.84 ppm, respectively, are calculated. Tensor computations for the central carbon were done with hypothetical structures obtained by altering the C−C−C angle. The difference between the two computed principal values of this ax...

Complete carbon-13 chemical shift tensors are measured in single crystals of methyl α-d-galactopyranoside monohydrate, methyl α-d-glucopyranoside, methyl α-d-mannopyranoside, methyl β-d-galactopyranoside, methyl β-d-glucopyranoside hemihydrate, and methyl β-d-xylopyranoside. The fits of the experimental data to the second-rank form of shift tensors reflect the accuracy of the measured tensors and yield standard deviations that range between 0.27 and 0.75 ppm. Ab initio gauge-invariant atomic orbital (GIAO) computations using the D-95 double-ζ basis set are used to assign the experimental tensors to the carbons in the unit cell. The root-mean-square (rms) deviation of the diffraction-structure-based GIAO shieldings fitted to all of the experimental shifts is 4.99 ppm. By optimizing the ring and methyl proton positions with the Gaussian-92 program and repeating the GIAO computations, the root-mean-square deviation is reduced to 2.40 ppm. These results illustrate that complete 13C chemical shift tensors meas...

We have used a variety of physical methods to investigate the ways by which copper phenanthrolines bind to B-form DNA. To vary the composition of the DNA, we have employed poly(dG-dC)-poly(dG-dC), M. lysodeikticus DNA, salmon testes DNA, and poly(dA-dT)-poly(dA-dT) as hosts. The specific copper complexes we have studied are Cu(dmp) 2 + and Cu(bcp) 2 + where dmp and bcp denote 2,9-dimethyl- 1,10-phenanthroline and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline, respectively. The results indicate that the dmp complex binds externally in a solvent-accessible site. However, the solvent cannot access the metal center as readily in the case of the bcp complex because Cu(bcp) 2 + is emissive in the presence of DNA

The isotopic 13 C labeled 1-decanols at positions 1, 5, and 9 have been synthesized and their dynamics in (CD 3 O-CD 2 CD 2 ) 2 O, CD 3 CD 2 OD, and CD 2 Cl 2 solvents have been studied by 13 C-coupled relaxation methods. The experiments were performed in the temperature range of 245-298 K. The data were fitted the Redfield theory of nuclear spin relaxation to yield dipolar spectral densities which were then transformed into Cartesian correlation times. The Cartesian correlation times obtained experimentally have a strong bearing on local anisotropic motion and suggests that the size of groups attached to agiven carbon and also hydrogen between 1-decanol and the various solvent molecules have a profound efect on local segmental motion