Tethered Dinuclear Europium(III) Macrocyclic Catalysts for the Cleavage of RNA

Controlled Hydrolysis of Phosphate Esters: A Route to Calixarene-Supported Rare-Earth Clusters

Phosphate ester bonds are widely present in nature (e. g. DNA/RNA) and can be extremely stable against hydrolysis without the help of catalysts. Previously, we showed how the combination of phosphoryl and calix[4]arene moieties in the same organic framework (L_PO ) allows isolation of single lanthanide (Ln) metal ions as [Ln^III (L_PO )₂ ](O₃ SCF₃ )₃ . Here we report how by controlling the reaction conditions a new hydrolyzed phosphoryl-calix[4]arene ligand (H₃ L_HPO ) is formed as a result of Ln^III -mediated P-OEt bond cleavage in three out of the eight possible sites in L_PO . The chelating nature of H₃ L_HPO traps the Ln^III species in the form of [Ln^III (L_HPO )((EtO)₂ P(O)OH)]₂ dimers (Ln=La, Dy, Tb, Gd), where the Dy derivative shows slow magnetization relaxation. The strategy presented herein could be extended to access a broader library of hydrolyzed platforms (H_x L_HPO ; x=1-8) that may represent mimics of nuclease enzymes.

Luminescent Lanthanide Probes for Inorganic and Organic Phosphates

Inorganic and organic phosphates-including orthophosphate, nucleotides, and DNA-are some of the most fundamental anions in cellular biology, regulating numerous processes of both medical and environmental significance. The characteristic long lifetimes of emitting lanthanides, including the brighter europium(III) and terbium(III), make them ideally suited for the development of molecular probes for the detection of phosphates directly in complex aqueous media. Moreover, given their high oxophilicity and the exquisite sensitivity of their quantum yields to their hydration number, those luminescent lanthanides are perfect for the detection of phosphates. Herein we discuss the principles that have guided the recent developments of molecular probes selective for inorganic or organic phosphates and how these lanthanide complexes facilitate the study of numerous biological processes.

Series of the Largest Dish-Shaped Dysprosium Nanoclusters Formed by In Situ Reactions

A three-dimensional supermolecule structure is easily formed due to the diverse coordination modes of high-oxidation-state lanthanide metal ions. However, the design and construction of zero-dimensional (0 D) dish-shaped high-nuclearity lanthanide clusters are difficult. Herein, for the first time, we synthesized a series of the largest dish-shaped high-nuclearity lanthanide nanoclusters (1-4) by in situ tandem reactions under solvothermal one-pot conditions. The formation of 1 and 2 involved an in situ reaction of aldehydes and amines, while the condensation reactions between aldehydes occurred in 3 and 4. Based on the structural characteristics of the dish-shaped lanthanide clusters, we proposed two possible assembly mechanisms involving Dy₁ → Dy₇ → Dy₁₃ → Dy₁₉ (planar epitaxial growth mechanism) and Dy₁ → Dy₁₂ → Dy₁₈ → Dy₁₉ (planar internal growth mechanism).

Single-Crystal-to-Single-Crystal Installation of Ln4 (OH)4 Cubanes in an Anionic Metallosupramolecular Framework

Postsynthetic installation of lanthanide cubanes into a metallosupramolecular framework via a single-crystal-to-single-crystal (SCSC) transformation is presented. Soaking single crystals of K₆ [Rh₄ Zn₄ O(l-cys)₁₂ ] (K₆ [1]; l-H₂ cys=l-cysteine) in a water/ethanol solution containing Ln(OAc)₃ (Ln³⁺ =lanthanide ion) results in the exchange of K⁺ by Ln³⁺ with retention of the single crystallinity, producing Ln₂ [1] (2_Ln ) and Ln_0.33 [Ln₄ (OH)₄ (OAc)₃ (H₂ O)₇ ][1] (3_Ln ) for early and late lanthanides, respectively. While the Ln³⁺ ions in 2_Ln exist as disordered aqua species, those in 3_Ln form ordered hydroxide-bridged cubane clusters that connect [1]^6- anions in a 3D metal-organic framework through coordination bonds with carboxylate groups. This study shows the utility of an anionic metallosupramolecular framework with carboxylate groups for the creation of a series of metal cubanes that have great potential for various applications, such as magnetic materials and heterogeneous catalysts.

Nuclease Activity of Diaza-Crown Ether Complexes of Cerium(III) with Different Functional Groups as Side Arms

Cerium(III) complexes of two ligands of a diaza-crown ether with different functional groups as side arms were synthesised and characterised. The catalytic ability of the cerium(III) complexes for pUC19 DNA cleavage was investigated and compared using agarose gel electrophoresis. The results indicate that the catalytic activity of the complex CeL2 [L2 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diacetamide] with two carbamoylmethyl groups is significantly higher than the complex CeL1 [L1 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diethanol] with two hydroxyethyl groups under the same conditions. The optimum catalytic concentrations of CeL1 and CeL2 were 7.69 × 10−5 and 3.08 × 10−5 mol L−1 respectively and excessively high concentrations of the complexes can reduce their catalytic efficiency due to the formation of inactive μ-hydroxo dimers. The optimum catalytic acidities of CeL1 and CeL2 were pH 7.0 and 7.5 respectively and excessively high pH of the reaction system can reduce the catalytic efficiency of the complexes due to the formation of cerium(III) hydroxide. DNA cleavage promoted by the two complexes takes place via the same hydrolytic pathway and so the activity difference of the two complexes is attributed to the stability of the complexes, rather than the catalytic mechanism.

Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes: Solution Speciation, DFT Calculations, Luminescence Properties, and Promoted Nitrophenyl-Phosphate Hydrolysis Rates

Potentiometric speciation studies, mass spectrometry, and DFT calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (Ln^III , Ln=La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H₄ L), to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln₂ (m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y₂ LH_-1 and the Y₂ LH_-2 species tended to form structures with the respective closed- and open-form conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from the Tb^III to Eu^III ion. The internuclear distance R_TbEu values were estimated to be in the range of 9.4-11.3 Å (pH 6.7-10.6), which were comparable to those of the DFT calculated open-form conformations. Multiple linear regression analysis of the k_obs data was performed using the equation: k_obs,corr. =k_obs -k_obs,OH =kLn2LHM->1 [Ln₂ LH_-1 ]+kLn2LH-2 [Ln₂ LH_-2 ] for the observed Ln₂ L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln=Eu, Yb). The results showed that the second-order rate constants for the Eu₂ LH_-2 and Yb₂ LH_-2 species were about 50-400 times more reactive than the structural analogous Zn₂ (m-12 N₃ O-dimer) system.

Enzyme Mimics: Advances and Applications

Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.

Tri- and tetra-substituted cyclen based lanthanide(III) ion complexes as ribonuclease mimics: a study into the effect of log Ka, hydration and hydrophobicity on phosphodiester hydrolysis of the RNA-model 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP)

A series of tetra-substituted 'pseudo' dipeptide ligands of cyclen (1,4,7,10,-tetraazacyclododecane) and a tri-substituted 3'-pyridine ligand of cyclen, and the corresponding lanthanide(III) complexes were synthesised and characterised as metallo-ribonuclease mimics. All complexes were shown to promote hydrolysis of the phosphodiester bond of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP, τ1/2 = 5.87 × 10(3) h), a well known RNA mimic. The La(III) and Eu(III) tri-substituted 3'-pyridine lanthanide(III) complexes being the most efficient in promoting such hydrolysis at pH 7.4 and at 37 °C; with τ1/2 = 1.67 h for La(III) and 1.74 h for Eu(III). The series was developed to provide the opportunity to investigate the consequences of altering the lanthanide(III) ion, coordination ability and hydrophobicity of a metallo-cavity on the rate of hydrolysis using the model phosphodiester, HPNP, at 37 °C. To further provide information on the role that the log Ka of the metal bound water plays in phosphodiester hydrolysis the protonation constants and the metal ion stability constants of both a tri and tetra-substituted 3'pyridine complex were determined. Our results highlighted several key features for the design of lanthanide(III) ribonucelase mimics; the presence of two metal bound water molecules are vital for pH dependent rate constants for Eu(III) complexes, optimal pH activity approximating physiological pH (∼7.4) may be achieved if the log Ka values for both MLOH and ML(OH)2 species occur in this region, small changes to hydrophobicity within the metallo cavity influence the rate of hydrolysis greatly and an amide adjacent to the metal ion capable of forming hydrogen bonds with the substrate is required for achieving fast hydrolysis.

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).

2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine and Its Benzene Analog as Nonmetallic Cleaving Agents of RNA Phosphodiester Linkages

2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine (11a) and 1,3-bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene (11b) have been shown to accelerate at 50 mmol·L⁻¹ concentration both the cleavage and mutual isomerization of uridylyl-3′,5′-uridine and uridylyl-2′,5′-uridine by up to two orders of magnitude. The catalytically active ionic forms are the tri- (in the case of 11b) tetra- and pentacations. The pyridine nitrogen is not critical for efficient catalysis, since the activity of 11b is even slightly higher than that of 11a. On the other hand, protonation of the pyridine nitrogen still makes 11a approximately four times more efficient as a catalyst, but only for the cleavage reaction. Interestingly, the respective reactions of adenylyl-3′,5′-adenosine were not accelerated, suggesting that the catalysis is base moiety selective.

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.

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.

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.

General base-guanidinium cooperation in bifunctional artificial phosphodiesterases

Artificial phosphodiesterases that combine a guanidinium unit with a general base connected by a m-xylylene linker catalyze the transesterification of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP). The bifunctional catalysts presented in this work show varying extents of cooperation between catalytic units and a rate enhancement of 4 × 10(4) in the most favorable case.

Eu(III) complexes as anion-responsive luminescent sensors and paramagnetic chemical exchange saturation transfer agents

The Eu(III) complex of (1S,4S,7S,10S)-1,4,7,10-tetrakis(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane (S-THP) is studied as a sensor for biologically relevant anions. Anion interactions produce changes in the luminescence emission spectrum of the Eu(III) complex, in the (1)H NMR spectrum, and correspondingly, in the PARACEST spectrum of the complex (PARACEST = paramagnetic chemical exchange saturation transfer). Direct excitation spectroscopy and luminescence lifetime studies of Eu(S-THP) give information about the speciation and nature of anion interactions including carbonate, acetate, lactate, citrate, phosphate, and methylphosphate at pH 7.2. Data is consistent with the formation of both innersphere and outersphere complexes of Eu(S-THP) with acetate, lactate, and carbonate. These anions have weak dissociation constants that range from 19 to 38 mM. Citrate binding to Eu(S-THP) is predominantly innersphere with a dissociation constant of 17 μM. Luminescence emission peak changes upon addition of anion to Eu(S-THP) show that there are two distinct binding events for phosphate and methylphosphate with dissociation constants of 0.3 mM and 3.0 mM for phosphate and 0.6 mM and 9.8 mM for methyl phosphate. Eu(THPC) contains an appended carbostyril derivative as an antenna to sensitize Eu(III) luminescence. Eu(THPC) binds phosphate and citrate with dissociation constants that are 10-fold less than that of the Eu(S-THP) parent, suggesting that functionalization through a pendent group disrupts the anion binding site. Eu(S-THP) functions as an anion responsive PARACEST agent through exchange of the alcohol protons with bulk water. The alcohol proton resonances of Eu(S-THP) shift downfield in the presence of acetate, lactate, citrate, and methylphosphate, giving rise to distinct PARACEST peaks. In contrast, phosphate binds to Eu(S-THP) to suppress the PARACEST alcohol OH peak and carbonate does not markedly change the alcohol peak at 5 mM Eu(S-THP), 15 mM carbonate at pH 6.5 or 7.2. This work shows that the Eu(S-THP) complex has unique selectivity toward binding of biologically relevant anions and that anion binding results in changes in both the luminescence and the PARACEST spectra of the complex.

The Utility of 2,2′-Bipyrimidine in Lanthanide Chemistry: From Materials Synthesis to Structural and Physical Properties

This paper reviews the recent investigations undertaken on the use of 2,2′-bipyrimidine (bpm) as a ligand for designing molecular complexes as well as polymeric lanthanide materials. A special emphasis is put on the ability of this polydentate neutral ligand to yield compounds of various dimensionalities, to act as a connector between these large ions, and influence their emissive and magnetic properties. This ligand can adopt a terminal or a bridging coordination mode with lanthanide ions, thus generating a wealth of frameworks of various topologies with the 4f elements. The main focus of this review is to show the originality brought by bpm in lanthanide structural chemistry and solid-state photophysics and magnetism.

Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight

RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.

Structural and catalytic performance of a polyoxometalate-based metal-organic framework having a lanthanide nanocage as a secondary building block

A polyoxometalate-based lanthanide-organic framework was achieved using the {[Ho(4)(dpdo)(8)(H(2)O)(16)BW(12)O(40)] (H(2)O)(2)}(7+) nanocage as a secondary building block for the heterogeneous catalysis of phosphodiester cleavage in an aqueous solution.