A motif for reversible nitric oxide interactions in metalloenzymes.

Nitric oxide (NO) participates in numerous biological processes, such as signalling in the respiratory system and vasodilation in the cardiovascular system. Many metal-mediated processes involve direct reaction of NO to form a metal-nitrosyl (M-NO), as occurs at the Fe(2+) centres of soluble guanylate cyclase or cytochrome c oxidase. However, some copper electron-transfer proteins that bear a type 1 Cu site (His2Cu-Cys) reversibly bind NO by an unknown motif. Here, we use model complexes of type 1 Cu sites based on tris(pyrazolyl)borate copper thiolates [Cu(II)]-SR to unravel the factors involved in NO reactivity. Addition of NO provides the fully characterized S-nitrosothiol adduct [Cu(I)](κ(1)-N(O)SR), which reversibly loses NO on purging with an inert gas. Computational analysis outlines a low-barrier pathway for the capture and release of NO. These findings suggest a new motif for reversible binding of NO at bioinorganic metal centres that can interconvert NO and RSNO molecular signals at copper sites.

An asymmetric pericyclic cascade approach to 3-alkyl-3-aryloxindoles: generality, applications and mechanistic investigations.

The reaction of L-serine derived N-arylnitrones with alkylarylketenes generates asymmetric 3-alkyl-3-aryloxindoles in good to excellent yields (up to 93%) and excellent enantioselectivity (up to 98% ee) via a pericyclic cascade process. The optimization, scope and applications of this transformation are reported, alongside further synthetic and computational investigations. The preparation of the enantiomer of a Roche anti-cancer agent (RO4999200) 1 (96% ee) in three steps demonstrates the potential utility of this methodology.

Copper(I) nitrosyls from reaction of copper(II) thiolates with S-nitrosothiols: mechanism of NO release from RSNOs at Cu.

S-nitrosothiols (RSNOs) serve as ready sources of biological nitric oxide activity, especially in conjunction with copper centers. We report a novel pathway for the generation of NO within the coordination sphere of copper model complexes from reaction of copper(II) thiolates with S-nitrosothiols. Reaction of tris(pyrazolyl)borate copper(II) thiolates (iPr2)TpCu-SR (R = C6F5 or CPh3) with (t)BuSNO leads to formation of (iPr2)TpCu(NO) and the unsymmetrical disulfide RS-S(t)Bu. Quantum mechanical investigations with B3LYP-D3/6-311G(d) suggest formation of a κ(1)-N-RSNO adduct (iPr2)TpCu(SR)(R'SNO) that precedes release of RSSR' to deliver (iPr2)TpCu(NO). This process is reversible; reaction of (iPr2)TpCu(NO) (but not (iPr2)TpCu(NCMe)) with C6F5S-SC6F5 forms (iPr2)TpCu-SC6F5. Coupled with the facile, reversible reaction between (iPr2)TpCu(NO) and C6F5SNO to give (iPr2)TpCu-SC6F5 and 2 equiv NO, we outline a new, detailed catalytic cycle for NO generation from RSNOs at Cu.

Computational enzyme design.

Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.

Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction.

The Morita-Baylis-Hillman reaction forms a carbon-carbon bond between the α-carbon of a conjugated carbonyl compound and a carbon electrophile. The reaction mechanism involves Michael addition of a nucleophile catalyst at the carbonyl ß-carbon, followed by bond formation with the electrophile and catalyst disassociation to release the product. We used Rosetta to design 48 proteins containing active sites predicted to carry out this mechanism, of which two show catalytic activity by mass spectrometry (MS). Substrate labeling measured by MS and site-directed mutagenesis experiments show that the designed active-site residues are responsible for activity, although rate acceleration over background is modest. To characterize the designed proteins, we developed a fluorescence-based screen for intermediate formation in cell lysates, carried out microsecond molecular dynamics simulations, and solved X-ray crystal structures. These data indicate a partially formed active site and suggest several clear avenues for designing more active catalysts.

Spiroligozymes for transesterifications: design and relationship of structure to activity.

Transesterification catalysts based on stereochemically defined, modular, functionalized ladder-molecules (named spiroligozymes) were designed, using the "inside-out" design strategy, and mutated synthetically to improve catalysis. A series of stereochemically and regiochemically diverse bifunctional spiroligozymes were first synthesized to identify the best arrangement of a pyridine as a general base catalyst and an alcohol nucleophile to accelerate attack on vinyl trifluoroacetate as an electrophile. The best bifunctional spiroligozyme reacted with vinyl trifluoroacetate to form an acyl-spiroligozyme conjugate 2.7 × 10(3)-fold faster than the background reaction with a benzyl alcohol. Two trifunctional spiroligozymes were then synthesized that combined a urea with the pyridine and alcohol to act as an oxyanion hole and activate the bound acyl-spiroligozyme intermediate to enable acyl-transfer to methanol. The best trifunctional spiroligozyme carries out multiple turnovers and acts as a transesterification catalyst with k(1)/k(uncat) of 2.2 × 10(3) and k(2)/k(uncat) of 1.3 × 10(2). Quantum mechanical calculations identified the four transition states of the catalytic cycle and provided a detailed view of every stage of the transesterification reaction.

Rapid catalyst identification for the synthesis of the pyrimidinone core of HIV integrase inhibitors.

A microscale chemistry improvement engine: a pre-dosed microscale high-throughput experimentation additives platform enables rapid, serendipitous reaction improvement. This platform allowed one chemist to set up 475 experiments and analyze the results using MISER chromatography in a single day, thus resulting in two high-quality catalytic systems for the construction of the title compound 1. Support for a single-electron transfer mechanism was obtained.

Origins of the diastereoselectivity in hydrogen bonding directed Diels-Alder reactions of chiral dienes with achiral dienophiles: a computational study.

In this study, the origins of diastereoselectivity in the hydrogen bonding assisted Diels-Alder reactions of chiral dienes with achiral dienophiles have been investigated with density functional methods. The distortion/interaction model has been applied to shed light on the origins of selectivity. C9-Substituted chiral anthracene templates (R = (CH(3))(OCH(3))(H), R = (CH(3))(OH)(H), R = (CH(3))(CH(2)CH(3))(H) and R = (-CH(2)-C(CH(3))(OCH(3))(H)) are used to rationalize the role of a stereogenic center and H-bonding on the product distribution ratio. Even though hydrogen bonding increases the reactivity of the diene, the stereoselectivity is reduced because of the hydrogen bonding capacity of both diastereomeric transition states. The interaction energies of the studied anthracene templates with N-methyl maleimide at the transition state correlate linearly with an increase in reactivity. The selectivity is determined by both favorable distortion and interaction energies. The π-facial selectivity induced by the presence of a chiral auxiliary in 1-substituted 1,3-pentadienes (R1 = (CH(3))(OCH(3))(H) and R1 = (CH(3))(OH)(H)) has also been modeled in order to rationalize the role of the stereogenic center and H-bonding on the stereoselectivity of an aliphatic diene. In both parts, the product distribution ratios calculated from Boltzmann distributions based on Gibbs free energies are in reasonable agreement with the experimental results. Finally the role of OH-substituted five-membered pyrrolidine on C9 of anthracene is investigated since the successful usage of the conformationally rigid pyrrolidines in asymmetric synthesis is well known. Overall, both in the acyclic system and in anthracene, the facilitation due to H-bonding is reflected in the interaction energies: the higher the difference in interaction energies in the transition structures of the two diastereomers, the more selective the H-bonding assisted Diels-Alder reaction is.

Why do some Fischer indolizations fail?

The mechanisms of the Fischer indole synthesis and competing cleavage pathways were explored with SCS-MP2/6-31G(d) and aqueous solvation calculations. Electron-donating substituents divert the reaction pathway to heterolytic N-N bond cleavage and preclude the acid-promoted [3,3]-sigmatropic rearrangement.

Mechanism and selectivity of cinchona alkaloid catalyzed [1,3]-shifts of allylic trichloroacetimidates.

Density functional theory calculations were used to investigate the [3,3]- and [1,3]-shifts of O-allylic trichloroacetimidates in the presence of cinchona alkaloids. Thermal [1,3]- and [3,3]-rearrangements proceed through concerted pseudopericyclic transition states to give the corresponding rearranged products. [1,3]-Rearrangement is catalyzed via a double S(N)2' mechanism in which syn addition of the nucleophile is exclusively preferred in both steps. The catalyzed mechanism is favored by a 6.3 kcal/mol free energy difference compared to the alternative [3,3]-rearrangement pathway. The fast-reacting enantiomer is predicted to be determined by the availability of the H-bonding interaction between the catalyst and the substrate.

Understanding the stereoselection induced by chiral anthracene templates in Diels-Alder cycloaddition: a DFT study.

Recyclable chiral anthracene templates have emerged as an effective and well-designed approach in preparing complex biologically active molecules such as butenolides, alpha,beta-unsaturated lactams, and related compounds in their enantiomerically pure forms. Highly diastereoselective initial cycloaddition serves as the key element of the total process, as it determines the final stereochemistry of the product. The diastereoselectivity of chiral anthracene templates is explored by using density functional theory (DFT) methods, and the reliability and applicability of the previously proposed models, mostly based on steric arguments, are tested by mechanistic means. The diastereomers A and B are identified according to the stereochemistry around the formed stereocenter on the dienophile attached to C9, as being R or S, respectively. The reactions of (R)-9-(1-methoxyethyl)anthracene and (S)-9-(1-methoxy-2,2,2-trifluoroethyl)anthracene with maleic anhydride both give exclusively diastereomer A via a similar transition state in which the CH(3)/CF(3) group is antiperiplanar to the approaching dienophile. The major product of the reaction between (R)-9-(1-phenylethyl)aminoanthracene and maleic anhydride is diastereomer B. The geometry around nitrogen is close to planar in the transition state (10-25 degrees out of plane), and the nitrogen lone pair is antiperiplanar to the incoming dienophile. Both of the lowest energy diastereomeric transition states giving A and B benefit from the favorable interaction between the carbonyl oxygen and the amine hydrogen; this interaction does not play a substantial role in the selectivity of the reaction as previously proposed. The diastereomeric transition states leading to A and B for the reaction between (R)-9-acyloxyanthracene and maleic anhydride have very similar interactions around the reaction center, leading to a very small energy difference between the diastereomeric transition states. The product distribution ratios for all templates calculated from Boltzmann distributions agree very well with the experimental results.

Effect of Lewis acid catalysts on Diels-Alder and hetero-Diels-Alder cycloadditions sharing a common transition state.

The thermal and Lewis acid catalyzed cycloadditions of beta,gamma-unsaturated alpha-ketophosphonates and nitroalkenes with cyclopentadiene have been explored by using density functional theory (DFT) methods. In both cases, only a single highly asynchronous bis-pericyclic transition state yielding both Diels-Alder and hetero-Diels-Alder cycloadducts could be located. Stepwise pathways were found to be higher in energy. On the potential energy surface, the bis-pericyclic cycloaddition transition state is followed by the Claisen rearrangement transition state. No intermediates were located between these transition states. Claisen rearrangement transition states are also highly asynchronous, but bond lengths are skewed in the opposite direction compared to the bis-pericyclic transition states. The relative positions of the bis-pericyclic and Claisen rearrangement transition states may control periselectivity due to the shape of the potential energy surface and corresponding dynamical influences. Inspection of the thermal potential energy surface (PES) indicates that a majority of downhill paths after the bis-pericyclic transition state lead to the Diels-Alder cycloadducts, whereas a smaller number of downhill paths reach the hetero-Diels-Alder products with no intervening energy barrier. Lewis acid catalysts alter the shape of the surface by shifting the cycloaddition and the Claisen rearrangement transition states in opposite directions. This topographical change qualitatively affects the branching ratio after the bis-pericyclic transition state and ultimately reverses the periselectivity of the cycloaddition giving a preference for hetero-Diels-Alder cycloadducts.

Bifurcations on potential energy surfaces of organic reactions.

A single transition state may lead to multiple intermediates or products if there is a post-transition-state reaction pathway bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects, rather than transition-state energetics, control selectivity. This Minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions.