Signal amplification by allosteric catalysis

In this article we unify a series of recent studies on bio- and chemosensors under a single signaling strategy: signal amplification by allosteric catalysis (SAAC). The SAAC strategy mimics biological signal transduction processes, where molecular recognition between an external signal and a protein receptor is allosterically transduced into catalytically amplified chemical information (usually second messengers). Several recent biosensing and chemosensing studies apply this nature-inspired strategy by using engineered allosteric enzymes, ribozymes, or regulatable organic catalysts. The factors pertinent to achieving high sensitivity and specificity in SAAC strategies are analyzed. The authors believe that these early studies from a variety of research groups have opened up a new venue for the development of sensing technologies where molecular recognition and catalysis can be coupled for practical purposes.     

Non-covalent allosteric regulation of capsule catalysis

Allosteric regulation is an essential biological process that allows enzymes to modulate their active site properties by binding a control molecule at the protein exterior. Here we show the first example of capsule catalysis in which activity is changed by exotopic binding. This study utilizes a simple Pd₂L₄ capsule that can partition substrates and external effectors with high fidelity. We also present a detailed, quantitative understanding of how effector interactions alter both substrate and transition state binding. Unlike other allosteric host systems, perturbations are not a consequence of large mechanical changes, rather subtle electronic effects resulting from weak, non-covalent binding to the exterior surface. This investigation paves the way to more sophisticated allosteric systems.

External effector binding allosterically regulates the catalytic properties of a simple Pd₂L₄ capsule.     

On/off regulation of catalysis by allosteric control of metal complex nuclearity

The nature of the allosteric metal ion M (Pd2+ or Pt2+) in complexes ML of a polytopic ligand controls uptake of additional Cu2+ ions; while [Cu2Pd(L-4H)]2+ is a highly active catalyst for phosphodiester cleavage, [CuPt(L-4H)] is inactive.     

Metal-free,noncovalent catalysis of diels-alder reactions by neutral hydrogen bond donors in organic solvents and in water

We examined the catalytic activity of substituted thioureas in a series of Diels-Alder reactions and 1,3-dipolar cycloadditions. The kinetic data reveal that the observed accelerations in the relative rates are more dependent on the thiourea substituents than on the reactants or solvent. Although the catalytic effectiveness is the strongest in noncoordinating, nonpolar solvents, such as cyclohexane, it is also present in highly coordinating polar solvents, such as water. In 1,3-dipolar cycloadditions, the thiourea catalysts demonstrate only very moderate selectivity for reactions with inverse electron demand. Our experiments emphasize that both hydrophobic and polar interactions can co-exist, making these catalysts active, even in highly coordinating solvents. This class of catalysts increases the reaction rates and endo-selectivities of Diels-Alder reactions, in a similar manner to weak Lewis acids, without concomitant product inhibition.     

The origins of noncovalent catalysis of intermolecular Diels-Alder reactions by cyclodextrins,self-assembling capsules,antibodies, and RNAses

The catalysis of Diels-Alder reactions by noncovalent binding by synthetic, protein, and nucleic acid hosts has been surveyed and compared. These catalysts consist of binding cavities that form complexes containing both the diene and the dienophile; the cycloaddition reaction occurs in the cavity. The binding requires no formation of covalent bonds and is driven principally by the hydrophobic (or solvophobic) effect. A molecular mechanics and dynamics study of the cyclodextrin catalysis of a Diels-Alder reaction is used to exemplify and probe this form of catalysis. Detailed kinetic data is available for catalysis by antibodies, RNA, cyclodextrins, and Rebek's tennis ball capsules. Some of these catalysts stabilize the reactants more than the transition state and consequently will only have catalytic effect under conditions of low substrate-to-catalyst ratios. None of the hosts achieve significant specific binding of transition states that is the hallmark of enzyme catalysis.     

ATP-dependent allosteric DNA enzymes

Effector-activated ribozymes that respond to small organic molecules have previously been generated by appending binding species (aptamers) to ribozymes. In order to determine if deoxyribozymes can similarly be activated by effector molecules, we have appended an anti-adenosine aptamer to a selected deoxyribozyme ligase. The resultant constructs are specifically activated by ATP. Optimization of the joining region resulted in ligases that are activated up to 460-fold by ATP. The selected deoxyribozyme catalyzes ligation largely via a templating mechanism. Effector activation is surprisingly achieved by suppression of the rate of the background, templated ligation reaction in the absence of the effector molecule, probably by misalignment of the oligonucleotide substrates. This novel allosteric mechanism has not previously been observed for nucleic-acid catalysts and is rare even in protein catalysts.     

对映选择催化 Diels-Alder 反应

本文综述了对映选择催化 Diels-Alder 反应的进展。     

Combinatorial discovery of reusable noncovalent supports for enzyme immobilization and nonaqueous catalysis

A simple and effective method is described for the preparation of enzyme-containing materials that possess excellent catalytic activity, mechanical strength, and reusability. Uniform spherical beads were produced via the colyophilization of alpha-chymotrypsin with the support materials, leaving the active enzyme entrapped within the porous "ice-templated" support matrix. The composites were assayed for catalytic activity by monitoring a nonaqueous transesterification reaction. The mechanical strength for each composite was measured using a compression assay. Initial screens identified a set of six support materials that contributed favorably to either the enzyme activity or to the mechanical strength of the composite. A design of experiments (DoE) methodology was employed to screen 80 combinations of these six "base" materials. A model representing this formulation space was constructed which could be used to predict both the catalytic activity and mechanical strength with reasonable accuracy for any combination of the six base component materials. This model was used to predict optimized materials with an enzyme activity that was 50 times greater than that of the free enzyme. The model was also used to set a minimum acceptable mechanical stability for these composites, and the resulting materials were shown to be reusable for at least ten reaction cycles.     

Single-atom catalysis for organic reactions

Metal-based catalysis, including homogeneous and heterogeneous catalysis, plays a significant role in the modern chemical industry. Heterogeneous catalysis is widely used due to the high efficiency, easy catalyst separation and recycling. However, the metal-utilization efficiency for conventional heterogeneous catalysts needs further improvement compared to homogeneous catalyst. To tackle this, the pursing of heterogenizing homogeneous catalysts has always been attractive but challenging. As a recently emerging class of catalytic material, single-atom catalysts (SACs) are expected to bridge homogeneous and heterogeneous catalytic process in organic reactions and have arguably become the most active new frontier in catalysis field. In this review, a brief introduction and development history of single-atom catalysis and SACs involved organic reactions are documented. In addition, recent advances in SACs and their practical applications in organic reactions such as oxidation, reduction, addition, coupling reaction, and other organic reactions are thoroughly reviewed. To understand structure-property relationships of single-atom catalysis in organic reactions, active sites or coordination structure, metal atom-utilization efficiency (e.g., turnover frequency, TOF calculated based on active metal) and catalytic performance (e.g., conversion and selectivity) of SACs are comprehensively summarized. Furthermore, the application limitations, development trends, future challenges and perspective of SAC for organic reaction are discussed.     

Synergistic catalysis of anthrone Diels-Alder reactions

[reaction: see text] The combination of an amine base and Lewis acid (Li+) leads to synergistic catalysis of the Diels-Alder reaction of anthrone with methyl crotonate and some other less reactive dienophiles. These cycloadditions either do not occur with the individual catalysts used separately or they are greatly accelerated by the combined catalysts. DMSO solvent allows the use of LiCl as the Lewis acid source and can provide greater control of subsequent conversion to Michael adduct.     

Water-wire catalysis in photoinduced acid-base reactions

The pronounced ability of water to form a hyperdense hydrogen (H)-bond network among itself is at the heart of its exceptional properties. Due to the unique H-bonding capability and amphoteric nature, water is not only a passive medium, but also behaves as an active participant in many chemical and biological reactions. Here, we reveal the catalytic role of a short water wire, composed of two (or three) water molecules, in model aqueous acid-base reactions synthesizing 7-hydroxyquinoline derivatives. Utilizing femtosecond-resolved fluorescence spectroscopy, we tracked the trajectories of excited-state proton transfer and discovered that proton hopping along the water wire accomplishes the reaction more efficiently compared to the transfer occurring with bulk water clusters. Our finding suggests that the directionality of the proton movements along the charge-gradient H-bond network may be a key element for long-distance proton translocation in biological systems, as the H-bond networks wiring acidic and basic sites distal to each other can provide a shortcut for a proton in searching a global minimum on a complex energy landscape to its destination.     

Ion-ion proton transfer reactions of bio-ions involving noncovalent interactions: Holomyoglobin

Multiply protonated horse skeletal muscle holomyoglobin and apomyoglobin have been subjected to ion-ion proton transfer reactions with anions derived from perfluoro-1,3-dimethylcyclohexane in a quadrupole ion trap operated with helium as a bath gas at 1 mtorr. Neither the apomyoglobin nor holomyoglobin ions show any sign of fragmentation associated with charge state reduction to the 1 + charge state. This is particularly noteworthy for the holomyoglobin ions, which retain the noncovalently bound heme group. For example, no sign of heme loss is associated with charge state reduction from the 9 + charge state of holomyoglobin to the 1 + charge state despite the eight consecutive highly exothermic proton transfer reactions required to bring about this charge change. This result is consistent with calculations that show the combination of long ion lifetime and the high ion-helium collision rate relative to the ion-ion collision rate makes fragmentation unlikely for high mass ions in the ion trap environment even for noncovalently bound complexes of moderate binding strength. The ion-ion proton transfer rates for holo- and apomyoglobin ions of the same charge state also were observed to be indistinguishable, which supports the expectation that ion-ion proton transfer rates are insensitive to ion structure and are determined primarily by the attractive Coulomb field.     

Nature-inspired cascade catalysis: reaction control through substrate concentration--double vs. quadruple domino reactions

The design of biologically inspired, multi-component cascade reactions enables the targeted synthesis of assorted structurally complex products. Similar to regulation in cells the reaction path is controlled by the substrate concentration and complex enantiopure products with high structural diversity are provided.     

Superparamagnetic nanoparticle-supported catalysis of Suzuki cross-coupling reactions

Emulsion polymerization was examined as a novel route for the synthesis of core/shell superparamagnetic nanoparticles consisting of a highly crystalline gamma-Fe2O3 core and a very thin polymeric shell wall. These nanoparticles were used as soluble supports for immobilizing Pd catalysts to promote Suzuki cross-coupling reactions. Recovery of catalysts was facilely achieved by applying a permanent magnet externally. Isolated catalysts were reused for new rounds of reactions without significant loss of their catalytic activity.     

Interrogating the thionium hydrogen bond as a noncovalent stereocontrolling interaction in chiral phosphate catalysis

CH⋯O bonds are a privileged noncovalent interaction determining the energies and geometries of a large number of structures. In catalytic settings, these are invoked as a decisive feature controlling many asymmetric transformations involving aldehydes. However, little is known about their stereochemical role when the interaction involves other substrate types. We report the results of computations that show for the first time thionium hydrogen bonds to be an important noncovalent interaction in asymmetric catalysis. As a validating case study, we explored an asymmetric Pummerer rearrangement involving thionium intermediates to yield enantioenriched N,S-acetals under BINOL-derived chiral phosphate catalysis. DFT and QM/MM hybrid calculations showed that the lowest energy pathway corresponded to a transition state involving two hydrogen bonding interactions from the thionium intermediate to the catalyst. However, the enantiomer resulting from this process differed from the originally published absolute configuration. Experimental determination of the absolute configuration resolved this conflict in favor of our calculations. The reaction features required for enantioselectivity were further interrogated by statistical modeling analysis that utilized bespoke featurization techniques to enable the translation of enantioselectivity trends from intermolecular reactions to those proceeding intramolecularly. Through this suite of computational modeling techniques, a new model is revealed that provides a different explanation for the product outcome and enabled reassignment of the absolute product configuration.

Transferable selectivity profiles allow data from intermolecular reactions using iminium substrates to be applied to predict intramolecular reactions involving thioniums.     

Physicochemical principles of ecological catalysis of gas-phase reactions

In this article we summarize and correlate results obtained in numerous studies of heterogeneous catalytic gasphase reactions with low reactant concentrations — mostly studies performed under the direction of the author at the L. V. Pisarzhevskii Institute of Physical Chemistry, National Academy of Sciences of the Ukraine. Physicochemical principles are defined for the catalysis of such reactions in the presence of solid catalysts. Examples are cited to illustrate the use of these relationships in developing effective catalysts and processes of ecological catalysis, particularly for catalytic treatment of gas emissions and the development of essentially zero-waste technologies in resource-conserving and energy-efficient versions.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 29, No. 6, pp. 482–500, November–December, 1993.