Catalysis of diribonucleoside monophosphate cleavage by water soluble copper(II) complexes of calix[4]arene based nitrogen ligands

Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis

Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.

Binuclear metal complexes with a novel hexadentate imidazole derivative for the cleavage of phosphate diesters and biomolecules: distinguishable mechanisms

Oxidative cleavage of phosphate diesters (HPNP, BNPP) is highly faster than the hydrolytic one by binuclear metal complexes with novel imidazole derivative, producing a non-lactone phosphate monoester due to the direct attack of free radicals.

Aromatic foldamers as scaffolds for metal second coordination sphere design

As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe-2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex-foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.

Trisulfonamide calix[6]arene-catalysed Michael addition to nitroalkenes

We describe the application of a novel family of trisulfonamide (TSA) calix[6]arenes in general acid catalysis. Hydrogen-bonding interactions between acidic TSA and methanol boosted the reactivity of the Michael addition of indoles to nitroalkene derivatives. The transformation occurs at a low catalyst loading of 5 mol%, allowing for the synthesis of nitroalkanes with good yields and functional group tolerance.

Confinement Effects in Catalysis Using Well-Defined Materials and Cages

This review focuses on the effects that confinement of molecular and heterogeneous catalysts with well-defined structure has on the selectivity and activity of these systems. A general introduction about catalysis and how the working principles of enzymes can be used as a source of inspiration for the preparation of catalysts with enhanced performance is provided. Subsequently, relevant studies demonstrate the importance of second coordination sphere effects in a broad sense (in homogeneous and heterogeneous catalysis). Firstly, we discuss examples involving zeolites, MOFs and COFs as heterogeneous catalysts with well-defined structures where confinement influences catalytic performance. Then, specific cases of homogeneous catalysts where non-covalent interactions determine the selectivity and activity are treated in detail. This includes examples based on cyclodextrins, calix[n]arenes, cucurbit[n]urils, and self-assembled container molecules. Throughout the review, the impact of confined spaces is emphasized and put into context, in order to get a better understanding of the effects of confinement on catalyst performance. In addition, this analysis intends to showcase the similarities between homogeneous and heterogeneous catalysts, which may aid the development of novel strategies.

Highly Active Dinuclear Titanium(IV) Complexes for the Catalytic Formation of a Carbon-Heteroatom Bond

A series of mononuclear titanium(IV) complexes with the general composition κ³-[R{NHPh₂P(X)}₂Ti(NMe₂)₂] [R = C₆H₄, X = Se (3b); R = trans-C₆H₁₀, X = S (4a), Se (4b)] and [{κ²-N(PPh₂Se)₂}₂Ti(NMe₂)₂] (6b) and two dinuclear titanium(IV) complexes, [C₆H₄{(NPh₂PS)(N)}Ti(NMe₂)]₂ (3c) and [{κ²-N(PPh₂Se)}Ti(NMe₂)₂]₂ (6c), are reported. Dinuclear titanium(IV) complex 6c acts as an efficient catalyst for the chemoselective addition of an E-H bond (E = N, O, S, P, C) to heterocumulenes under mild conditions. The catalytic addition of aliphatic and aromatic amines, alcohol, thiol, phosphine oxide, and acetylene to the carbodiimides afforded the corresponding hydroelemented products in high yield at mild conditions with a broader substrate scope. The catalytic efficiency of the dinuclear complex depends on the cooperative effect of the Ti^IV ions, the systematic variation of the intermetallic distance, and the ligand's steric properties of the complex, which enhances the reaction rate. Most interestingly, this is the first example of catalytic insertion of various E-H bonds into the carbodiimides using a single-site catalyst because only the titanium-mediated insertion of E-H into a C═N unsaturated bond is reported to date. The amine and alcohol insertion reaction with the carbodiimides showed first-order kinetics with respect to the titanium(IV) catalyst as well as substrates. A most plausible mechanism for hydroelementation reaction is also proposed, based on the spectroscopic data of the controlled reaction, a time-course study, and the Hammett plot.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

Chemoselective guest-triggered shaping of a polynuclear CuII calix[6]complex into a molecular host

A new calix[6]arene scaffold bearing a tris-imidazole binding site at the small rim and three tetradentate aza ligands at the large rim was synthesized. The system binds three Cu^II ions at the large rim sites and is unable to bind a fourth one, which remains in solution. The charge repulsion between the complexes, together with the flexibility of the scaffold, disorganizes the small rim site for binding and prevents its use for host-guest studies. Although the presence of MeCN or DMF guests does not alter this state, the addition of a heptylamine guest, which further displays Brønsted basicity, restores its receptor ability by stabilizing the extra Cu^II ion at the tris-imidazole site with concomitant guest encapsulation and binding of an exo hydroxo ligand. This chemoselective nuclearity switch yields a tetranuclear complex in which the guest backbone is preorganized in front of three potentially reactive Cu(ii) complexes, reminiscent of polynuclear Cu^II enzyme active sites.

Efficient active-template synthesis of calix[6]arene-based oriented pseudorotaxanes and rotaxanes

A substrate can modify its chemical features, including a change of its reactivity, as a consequence of non-covalent interactions upon inclusion within a molecular host. Since the rise of supramolecular chemistry, this phenomenon has stimulated the ingenuity of scientists to emulate the function of enzymes by designing supramolecular systems in which the energetics and selectivity of reactions can be manipulated through programmed host-guest interactions and/or steric confinement. In this paper we investigate how the engulfment of a positively charged pyridinium-based guest inside the π-rich cavity of a tris-(N-phenylureido)calix[6]arene host affects its reactivity towards a S_N2 reaction. We found that the alkylation of complexed substrates leads to the formation of pseudorotaxanes and rotaxanes with faster kinetics and higher yields with respect to the standard procedures exploited so far. More importantly, the strategy described here expands the range of efficient synthetic routes for the formation of mechanically interlocked species with a strict control of the mutual orientation of their non-symmetric molecular components.

Copper complexes bearing an NHC–calixarene unit: synthesis and application in click chemistry

Novel N-heterocyclic carbene (NHC) copper complexes supported by calix[4]arene were synthesized and showed good catalytic activity when applied in click chemistry.

Kinetic resolution of phosphoric diester by Cinchona alkaloid derivatives provided with a guanidinium unit

Cinchona alkaloid derivatives featuring a guanidinium group in diverse positions efficiently catalyze the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP).

Moulding calixarenes for biomacromolecule targeting

After their successful use as a preorganized platform for the preparation of receptors for metal ions and small neutral molecules over the last 15 years, calixarenes are enjoying a renaissance of popularity as scaffolds for ligands that are able to efficiently and selectively target macromolecules such as proteins/enzymes, nucleic acids and lipids. This feature article summarizes the peculiar factors characterizing the calixarene structure and properties, as well as outlines the main rules that can be used to turn such macrocycles into efficient and successful ligands for these classes of biomacromolecules. Factors that affect the multivalent properties of calixarenes, such as the size, conformation and stereochemical presentation of binding groups or their amphiphilicity and hybrid character, are described in detail with the use of a few selected examples from the literature. Perspectives and applications of these ligands in bionanotechnology and nanomedicine, such as protein sensing and inhibition, gene-delivery, targeted drug-delivery and cell imaging, are also discussed.

The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports

Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.

Supramolecular control of transition metal complexes in water by a hydrophobic cavity: a bio-inspired strategy

Different strategies for obtaining water-soluble cavity-appended metal complexes are described, and their resulting interlocked assets are discussed in relationship with the very specific properties of water as a solvent.

Biomimetic cavity-based metal complexes

The biomimetic association of a metal ion with a cavity allows selective recognition, unusual redox properties and new reactivity patterns.

Novel chiral (salen)Mn(III) complexes containing a calix[4]arene unit in 1,3-alternate conformation as catalysts for enantioselective epoxidation reactions of (Z)-aryl alkenes

Two new chiral calix[4]arene-salen ligands 1a,b, based on calix[4]arene platforms in 1,3-alternate conformation, have been prepared by a new general synthetic pathway. Their Mn(III) complexes, 3a,b have shown fairly good efficiency in the asymmetric epoxidation of styrene and substituted styrenes, whereas excellent catalytic activity and selectivity were observed with rigid bicyclic alkenes, namely 1,2-dihydro-naphthalene and substituted 2,2'-dimethyl-chromene. The higher catalytic properties of 3a may be ascribed to the more rigid and inherently chiral structure as proved by molecular modelling, NMR spectroscopy and X-ray data of the similarly structured UO2 complexes 2a,b.

Guanidine based self-assembled monolayers on Au nanoparticles as artificial phosphodiesterases

Gold nanoparticles passivated with a catalytic monolayer based on guanidine exhibit high cooperativity and efficiency in the cleavage of phosphodiesters.

Diguanidinocalix[4]arenes as effective and selective catalysts of the cleavage of diribonucleoside monophosphates

Upper rim diguanidino-cone-calix[4]arenes catalyze the hydrolytic cleavage of diribonucleoside monophosphates in aqueous DMSO with good substrate selectivity and rate accelerations approaching 10⁵-fold in the most favourable substrate-catalyst combinations.

Guanidine-guanidinium cooperation in bifunctional artificial phosphodiesterases based on diphenylmethane spacers; gem-dialkyl effect on catalytic efficiency

Diphenylmethane derivatives 1-3, decorated with two guanidine units, are effective catalysts of HPNP transesterification. Substitution of the methylene group of the parent diphenylmethane spacer with cyclohexylidene and adamantylidene moieties enhances catalytic efficency, with gem-dialkyl effect accelerations of 4.5 and 9.1, respectively. Activation parameters and DFT calculations of the rotational barriers around the C-Ar bonds indicate that a major contribution to the driving force for enhanced catalysis is entropic in nature.

Selection of chiral zinc catalysts for the kinetic resolution of esters via dynamic templating

Dynamic combinatorial libraries of chiral tetradentate bis-imine zinc(II) complexes have been prepared and screened for (1) their discrimination of enantiomeric picolinate esters and pyridyl phosphonate transition state analogs (TSAs) and (2) their catalytic activity and selectivity for enantioselective methanolysis of racemic picolinate esters. The zinc complexes are in equilibrium with their imine ligands as well as with the aldehyde and amine building blocks that form them, enabling the composition of the library to adapt in response to the introduction of coordinating substrates or TSAs. Binary (L)Zn(OTf)(solv)(+) complexes are generated either individually or in libraries from chiral tartrate-derived diamines (2,3) and a set of N-heterocyclic aldehydes (4-12) and the distribution of complexes established by ESI-MS analysis. Binding studies of the (diimine)Zn(OTf)(2) complex libraries with enantiomeric R- and S-2-pyridyl phosphonate TSA 13 show chiral discrimination via formation of diastereomeric LZn(R/S-13)(+) complexes with low to moderate enatioselectivity ratios, k(R)/k(S) (α), ranging from 0.5 to 5.0; corresponding templating of selected binary complexes with the enantiomeric substrates, PyrCO(2)CH(OH)Ph (1), show negligible chiral recognition. The rate constants for methanolysis of the R- and S-esters, PyrCO(2)CH(OH)Ph (1) catalyzed by several L*Zn(OTf)(2) complexes range in value several fold depending on L and with enantioselectivity ratios, k(R)/k(S) (α), ranging from 0.76 to 2.8.

Upper rim guanidinocalix[4]arenes as artificial phosphodiesterases

Calix[4]arene derivatives, blocked in the cone conformation and functionalized with two to four guanidinium units at the upper rim were synthesized and investigated as catalysts in the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate. When compared with the behavior of a monofunctional model compound, the catalytic superiority of the calix[4]arene derivatives points to a high level of cooperation between catalytic groups. Combination of acidity measurements with the pH dependence of catalytic rates unequivocally shows that a necessary requisite for effective catalysis is the simultaneous presence, on the same molecular framework, of a neutral guanidine acting as a general base and a protonated guanidine acting as an electrophilic activator. The additional guanidinium (guanidine) group in the diprotonated (monoprotonated) trifunctional calix[4]arene acts as a more or less innocent spectator. This is not the case with the tetrasubstituted calix[4]arene, whose mono-, di-, and triprotonated forms are slightly less effective than the corresponding di- and triguanidinocalix[4]arene derivatives, most likely on account of a steric interference with HPNP caused by overcrowding.

Interactions of Calix[n]arenes with Nucleic Acids

DNA interaction with artificial binders is of great interest, especially in light of the broad range of possible biomedical applications. The growing understanding of replication, transcription and translation opened the path for new approaches to target pathological effects at a very early stage. Meanwhile, the competitive binding to nucleic acids by designed molecules, which, for example, block certain sequences for natural binders, such as transcription factors, has become a promising concept in the context of gene therapy. On the other extreme, the transport of nucleic acids over the cell membrane into the nucleus by transfection agents opens the possibility to reprogram protein biosynthesis within host cells.

In the past decades several substance classes have been developed for a noncovalent specific DNA binding with predictable biological effects, such as peptide nucleic acids or polyamide ligands. Calixarenes have not received so much attention, although they consist of a compact aromatic core tuneable in size, and allow the introduction of cationic functionalities at their upper and lower rims. Formerly being utilized as receptor moieties due to the possibility of complexating guests in their cavities, calixarenes are now also used as molecular scaffolds for multivalent ligands and are, therefore, suitable tools for cooperative DNA complexation.

This review surveys specific supramolecular interactions between calixarene derivatives and nucleic acids, with an emphasis on structural elements in the calixarenes and the biological consequences of their complex formation with DNA strands.