Artificial Enzymes

Hydrolytic activities of crystalline cellulose nanofibers

Cellulose is commonly believed to be inactive to organic substances; this inertness is an essential requirement for raw materials in industrial products. Here we demonstrate the contradictory but promising properties, which are the hydrolytic activities of crystalline cellulose nanofibers for the ester, monophosphate, and even amide bonds of small organic substrates under extremely mild conditions (neutral pH, moderate temperature, and atmospheric pressure). The hydrolytic activities were significantly extended to decompose the coat proteins of model viruses, followed by a drastic decrease in their infection capabilities to the host cells.

Molecular assemblies of porphyrins and macrocyclic receptors: recent developments in their synthesis and applications

Metalloporphyrins which form the core of many bioenzymes and natural light harvesting or electron transport systems, exhibit a variety of selective functional properties depending on the state and surroundings with which they exist in biological systems. The specificity and ease with which they function in each of their bio-functions appear to be largely governed by the nature and disposition of the protein globule around the porphyrin reaction center. Synthetic porphyrin frameworks confined within or around a pre-organized molecular entity like the protein network in natural systems have attracted considerable attraction, especially in the field of biomimetic reactions. At the same time a large number of macrocyclic oligomers such as calixarenes, resorcinarenes, spherands, cyclodextrins and crown ethers have been investigated in detail as efficient molecular receptors. These molecular receptors are synthetic host molecules with enclosed interiors, which are designed three dimensionally to ensure strong and precise molecular encapsulation/recognition. Due to their complex structures, enclosed guest molecules reside in an environment isolated from the outside and as a consequence, physical properties and chemical reactions specific to that environment in these guest species can be identified. The facile incorporation of such molecular receptors into the highly photoactive and catalytically efficient porphyrin framework allows for convenient design of useful molecular systems with unique structural and functional properties. Such systems have provided over the years attractive model systems for the study of various biological and chemical processes, and the design of new materials and molecular devices. This review focuses on the recent developments in the synthesis of porphyrin assemblies associated with cyclodextrins, calixarenes and resorcinarenes and their potential applications in the fields of molecular encapsulation/recognition, and chemical catalysis.

Templating effect in DNA proximity ligation enables use of non-bioorthogonal chemistry in biological fluids

Here we describe the first example of selective reductive amination in biological fluids using split aptamer proximity ligation (StAPL). Utilizing the cocaine split aptamer, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of target concentrations in buffer, human blood serum and artificial urine medium. We explore the substrate binding preferences of the split aptamer and find that the cinchona alkaloids quinine and quinidine bind to the aptamer with higher affinity than cocaine. This increased affinity leads to improved detection limits for these small-molecule targets. We also demonstrate that linker length and hydrophobicity impact the efficiency of split aptamer ligation. The ability to carry out selective chemical transformations using non-bioorthogonal chemistry in media where competing reactive groups are present highlights the power of the increased effective molarity provided by DNA assembly. Obviating the need for bioorthogonal chemistry would dramatically expand the repertoire of chemical transformations available for use in templated reactions such as proximity ligation assays, in turn enabling the development of novel methods for biomolecule detection.

Synthesis and electrocatalytic properties of octaalkoxycobalt phthalocyanine for the oxidation of 2-mercaptoethanol

We report on the synthesis of cobalt 2,3,9,10,16,17,23,24-octakis(2-ethylhexyloxy)phthalocyanine. This complex, when pre-adsorbed onto graphite electrodes, is active for the electro-oxidation of 2-mercaptoethanol. Its activity is higher than that of cobalt phthalocyanine and cobalt tetrasulfonated phthalocyanine adsorbed on graphite. The voltammetric response of adsorbed cobalt 3,4-octaethylhexyl- oxyphthalocyanine exhibits both Co ( II )/ Co ( I ) and Co ( III )/ Co ( II ) reversible processes. However, the Co ( III )/ Co ( II ) couple shows a pH dependence that is different from that reported for other cobalt phthalocyanine derivatives. The much higher activity of cobalt 3,4-octaethylhexyloxyphthalocyanine compared with cobalt tetrasulfonated phthalocyanine and cobalt phthalocyanine is attributed to the electron-donating ability of the ethylhexyloxy substituents on the periphery of the phthalocyanine ligand.

Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization

The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.

Magnetic nano-Fe3O4-supported 1-benzyl-1,4-dihydronicotinamide (BNAH): synthesis and application in the catalytic reduction of α,β-epoxy ketones

A novel magnetically recoverable organic hydride compound was successfully constructed by using silica-coated magnetic nanoparticles as a support. An as-prepared magnetic organic hydride compound, BNAH (1-benzyl-1,4-dihydronicotinamide), showed efficient activity in the catalytic reduction of α,β-epoxy ketones. After reaction, the magnetic nanoparticle-supported BNAH can be separated by simple magnetic separation which made the separation of the product easier.

Metal-coordinated water-soluble cavitands act as C-H oxidation catalysts

Cavitands can be smoothly derivatized by CuAAC chemistry to incorporate ligand species at the upper rim. These species can coordinate metal species in a number of different conformations, leading to self-assembly. The metal-coordination confers water solubility on the cavitands, and the iron-bound species are capable of catalytic C-H oxidations of fluorene under mild conditions.

Noncovalent complexation of monoamine neurotransmitters and related ammonium ions by tetramethoxy tetraglucosylcalix[4]arene

The noncovalent complexation of monoamine neurotransmitters and related ammonium and quaternary ammonium ions by a conformationally flexible tetramethoxy glucosylcalix[4]arene was studied by electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry. The glucosylcalixarene exhibited highest binding affinity towards serotonin, norepinephrine, epinephrine, and dopamine. Structural properties of the guests, such as the number, location, and type of hydrogen bonding groups, length of the alkyl spacer between the ammonium head-group and the aromatic ring structure, and the degree of nitrogen substitution affected the complexation. Competition experiments and guest-exchange reactions indicated that the hydroxyl groups of guests participate in intermolecular hydrogen bonding with the glucocalixarene.

What are the differences between ascorbic acid and NADH as hydride and electron sources in vivo on thermodynamics, kinetics, and mechanism?

Ascorbic acid (AscH(2)) and dihydronicotinamide adenine dinucleotide (NADH) are two very important natural redox cofactors, which can be used as hydride, electron, and hydrogen atom sources to take part in many important bioreduction processes in vivo. The differences of the two natural reducing agents as hydride, hydrogen atom, and electron donors in thermodynamics, kinetics, and mechanisms were examined by using 5,6-isopropylidene ascorbate (iAscH(-)) and β-D-glucopyranosyl-1,4-dihydronicotinamide acetate (GluNAH) as their models, respectively. The results show that the hydride-donating ability of iAscH(-) is smaller than that of GluNAH by 6.0 kcal/mol, but the electron-donating ability and hydrogen-donating ability of iAscH(-) are larger than those of GluNAH by 20.8 and 8.4 kcal/mol, respectively, which indicates that iAscH(-) is a good electron donor and a good hydrogen atom donor, but GluNAH is a good hydride donor. The kinetic intrinsic barrier energy of iAscH(-) to release hydride anion in acetonitrile is larger than that of GluNAH to release hydride anion in acetonitrile by 6.9 kcal/mol. The mechanisms of hydride transfer from iAscH(-) and GluNAH to phenylxanthium perchlorate (PhXn(+)), a well-known hydride acceptor, were examined, and the results show that hydride transfer from GluNAH adopted a one-step mechanism, but the hydride transfer from iAscH(-) adopted a two-step mechanism (e-H(•)). The thermodynamic relation charts (TRC) of the iAscH(-) family (including iAscH(-), iAscH(•), iAsc(•-), and iAsc) and of the GluNAH family (including GluNAH, GluNAH(•+), GluNA(•), and GluNA(+)) in acetonitrile were constructed as Molecule ID Cards of iAscH(-) and of GluNAH in acetonitrile. By using the Molecule ID Cards of iAscH(-) and GluNAH, the character chemical properties not only of iAscH(-) and GluNAH but also of the various reaction intermediates of iAscH(-) and GluNAH all have been quantitatively diagnosed and compared. It is clear that these comparisons of the thermodynamics, kinetics, and mechanisms between iAscH(-) and GluNAH as hydride and electron donors in acetonitrile should be quite important and valuable to diagnose and understand the different roles and functions of ascorbic acid and NADH as hydride, hydrogen atom, and electron sources in vivo.