A combined parallel synthesis and screening of macrocyclic lanthanide complexes for the cleavage of phospho di- and triesters and double-stranded DNA

DNA binding and cleavage properties of the Ce (III) complex of a diaza-crown ether

The hydrolytic cleavage of pUC19 DNA as promoted by the trivalent cerium complex (CeL) of diaza-crown ether ligand L (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane) was examined in detail. The interaction of CeL with calf thymus DNA was investigated by UV-Vis spectroscopy. Furthermore, studies on the effects of pH, reaction time, and the concentration of CeL on cleavage of pUC19 DNA were carried out by gel electrophoresis. The results indicate that CeL can bind to DNA electrostatically with a binding constant of 2.18x104 M−1; CeL can promote the cleavage of plasmid pUC19 DNA from supercoiled to the nicked form under the appropriate conditions, and the optimal pH value is 7.54. The lack of effect of radical scavengers indicates that the cleavage involves hydrolytic cleavage.

Development of the aza-crown ether metal complexes as artificial hydrolase

Hydrolases play a crucial role in the biochemical process, which can catalyze the hydrolysis of various compounds like carboxylic esters, phosphoesters, amides, nucleic acids, peptides, and so on. The design of artificial hydrolases has attracted extensive attention due to their scientific significance and potential applications in the field of gene medicine and molecular biology. Numerous macrocyclic metal complexes have been used as artificial hydrolase in the catalytic hydrolysis of the organic substrate. Aza-crown ether for this comment is a special class of the macrocyclic ligand containing both the nitrogen atoms and oxygen atoms in the ring. The studies showed that the aza-crown complexes exhibited high activity of hydrolytic enzyme. However, the aza-crown ether metal complex as artificial hydrolase is still very limited because of its difficulty in synthesis. This review summarizes the development of the aza-crown ether metal complexes as the artificial hydrolase, including the synthesis and catalysis of the transition metal complexes and lanthanide metal complexes of aza-crown ethers. The purpose of this review is to highlight: (1) the relationship between the structure and hydrolytic activity of synthetic hydrolase; (2) the synergistic effect of metal sites and ligands in the course of organic compound hydrolysis; and (3) the design strategies of the aza-crown ethers as hydrolase.

Nucleic Acid and Phosphoester Hydrolytic Cleavage Catalysed by Aza-Crown Ether Metal Complexes as Synthetic Nucleases

Aza-crown ethers are ligands in which the oxygen atoms are replaced by nitrogen atoms in the crown ether ring systems. This type of ligand possesses specific complexation with metal ions, such as those of transition-metals, rare earths, alkali metals and alkaline earths, which form metal complexes whose structures are similar to those of some biological enzymes. In recent decades, research on aza-crown ethers and their metal complexes as mimics of nucleases in hydrolysing nucleic acids has attracted increasing attention. These studies illuminate the mechanism of nucleic acid hydrolytic cleavage as catalysed by natural nucleases. In order to assist the design and synthesis of highly active, selective and stable mimic nucleases, this paper reviews recent progress in the investigation of aza-crown ether metal complexes as mimic nucleases, including: the relationship between the structures and activities of synthetic metallonucleases; multicentre synergistic catalysis of metal ions in multinuclear complexes; bifunctional cooperative catalysis of the branches and ions in the complexes; and especially, the structural characteristic and catalytic mechanism of aza-crown ether metal complexes as mimic nucleases.

Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes

Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.

Synthesis of Platinum(II) Chiral Tetraamine Coordination Complexes

The individual and combinatorial syntheses of individual as well as a mixture-based diversity of 195 112 platinum(II) coordination complexes of chiral tetraamines are described. The use of both solid-phase synthesis and solution phase follow-on approaches were found to best afford the title compounds.

Mechanistic studies of La3+ and Zn2+-catalyzed methanolysis of O-ethyl O-aryl methylphosphonate esters. An effective solvolytic method for the catalytic destruction of phosphonate CW simulants

The kinetics of methanolysis of six O-ethyl O-aryl methylphosphonates (6a-f) promoted by methoxide, La3+ and 1,5,9-triazacyclododecane complex of Zn2+(-OCH3) (5:Zn2+(-OCH3)) were studied as simulants for chemical warfare (CW) agents, and analyzed through the use of Brønsted plots. The beta(lg) values are, respectively, -0.76, -1.26 and -1.06, pointing to significant weakening of the P-OAr bond in the transition state. For the metal-catalyzed reactions the data are consistent with a concerted process where the P-OAr bond rupture has progressed to the extent of 84% in the La3+ reaction and ca. 70% in the Zn2+ catalyzed reaction. The catalysis afforded by the metal ions is remarkable, being about 10(6)-fold and 10(8)-fold for poor and good leaving groups, respectively, relative to the background reactions at pH 9.1. Solvent deuterium kinetic isotope studies for two of the substrates promoted by 5:Zn2+(-OCH3) give kH/kD = 1.0 +/- 0.1, consistent with a nucleophilic mechanism. A unified mechanism for the metal-catalyzed reactions is presented which involves pre-equilibrium coordination of the substrate to the metal ion followed by intramolecular delivery of a coordinated methoxide.

Kinetics and Mechanism of Hydrolysis of a Model Phosphate Diester by [Cu(Me3tacn)(OH2)2]2+ (Me3tacn = 1,4,7-Trimethyl-1,4,7-triazacyclononane)

The kinetics of hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) by [Cu(Me3tacn)(OH2)2]2+ has been studied by spectrophotometrical monitoring of the release of the p-nitrophenylate ion from BNPP. The reaction was followed for up to 8000 min at constant BNPP concentration (15 microM) and ionic strength (0.15 M) and variable concentration of complex (1.0-7.5 mM) and temperature (42.5-65.0 degrees C). Biphasic kinetic traces were observed, indicating that the complex promotes the cleavage of BNPP to NPP [(p-nitrophenyl)phosphate] and then cleavage of the latter to phosphate, the two processes differing in rate by 50-100-fold. Analysis of the more amenable cleavage of BNPP revealed that the rate of BNPP cleavage is among the highest measured for mononuclear copper(II) complexes and is slightly higher than that reported for the close analogue [Cu(iPr3tacn)(OH2)2]2+. Detailed analysis required the determination of the pKa for [Cu(Me3tacn)(OH2)2]2+ and the constant for the dimerization of the conjugate base to [(Me3tacn)Cu(OH)2Cu(Me3tacn)]2+ (Kdim). Thermodynamic parameters derived from spectrophotometric pH titration and the analysis of the kinetic data were in reasonable agreement. Second-order rate constants for cleavage of BNPP by [Cu(Me3tacn)(OH2)(OH)]+ and associated activation parameters were obtained from initial rate analysis (k = 0.065 M(-1) s(-1) at 50.0 degrees C, deltaH = 56+/-6 kJ mol(-1), deltaS = -95+/-18 J K(-1) mol(-1)) and biphasic kinetic analysis (k = 0.14 M(-1) s(-1) at 50.0 degrees C, deltaH = 55+/-6 kJ mol(-1), deltaS = -92+/-20 J K(-1) mol(-1)). The negative entropy of activation is consistent with a concerted mechanism with considerable associative character. The complex was found to catalyze the cleavage of BNPP with turnover rates of up to 1 per day. Although these turnover rates can be considered low from an application point of view, the ability of the complexes to catalyze phosphate ester cleavage is clearly demonstrated.

Solvent deuterium kinetic isotope effects for the methanolyses of neutral CO, PO and PS esters catalyzed by a triazacyclododecane : Zn2+-methoxide complex

The methanolyses of several organophosphate/phosphonate/phosphorothioate esters (O,O-diethyl O-(4-nitrophenyl) phosphate, paraoxon, ; O,O-diethyl S-(3,5-dichlorophenyl) phosphorothioate, ; O-ethyl O-(2-nitro-4-chlorophenyl) methylphosphonate, ; O,O-dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate, fenitrothion, ; O-ethyl S-(3,5-dichlorophenyl) methylphosphonothioate ) and a carboxylate ester (p-nitrophenyl acetate, ) catalyzed by methoxide and the Zn(2+)((-)OCH(3)) complex of 1,5,9-triazacyclododecane ( : Zn(2+)((-)OCH(3))) were studied in methanol and d(1)-methanol at 25 degrees C. In the case of the methoxide reactions inverse skie's were observed for the series with values ranging from 2 to 1.1, except for where the k(D)/k(H) = 0.90 +/- 0.02. The inverse k(D)/k(H) values are consistent with a direct nucleophilic methoxide attack involving desolvation of the nucleophile with varying extents of resolvation of the TS. With the : Zn(2+)((-)OCH(3)) complex all the skie values are k(D)/k(H) = 1.0 +/- 0.1 except for where the value is 0.79 +/- 0.06. Arguments are presented that the fractionation factors associated with complex : Zn(2+)((-)OCH(3)) are indistinguishable from unity. The skie's for all the complex-catalyzed methanolyses are interpreted as being consistent with an intramolecular nucleophilic attack of the Zn(2+)-coordinated methoxide within a pre-equilibrium metal : substrate complex.

Artificial metallonucleases

The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is a fascinating challenge that will show the way to obtaining artificial nucleases able to compete with the natural enzymes. This Feature Article highlights the progress reported toward the realization of synthetic nucleases with particular attention to the strategies that can be pursued to improve efficiency and sequence selectivity.

Mechanistic studies of La3+- and Zn2+-catalyzed methanolysis of aryl phosphate and phosphorothioate triesters. Development of artificial phosphotriesterase systems

The methanolyses of a series of O,O-diethyl O-aryl phosphates (2,5) and O,O-diethyl S-aryl phosphorothioates (6) promoted by methoxide and two metal ion systems, (La3+)2(-OCH3)2 and 4:Zn2+:-OCH3 (4 = 1,5,9-triazacyclododecane) has been studied in methanol at 25 degrees C. Brønsted plots of the logk2 values vs. pKa for the phenol leaving groups give beta(lg) values of -0.70, -1.43 and -1.12 for the methanolysis of the phosphates and -0.63, -0.87 and -0.74 for the methanolysis of the phosphorothioates promoted by the methoxide, La3+ and Zn2+ systems respectively. The kinetic data for the metal-catalyzed reactions are analyzed in terms of a common mechanism where there is extensive cleavage of the P-XAr bond in the rate-limiting transition state. The relevance of these findings to the mechanism of action of the phosphotriesterase enzyme is discussed.

Zn2+-Catalyzed Methanolysis of Phosphate Triesters: A Process for Catalytic Degradation of the Organophosphorus Pesticides Paraoxon and Fenitrothion

The methanolyses of two neutral phosphorus triesters, paraoxon (1) and fenitrothion (3), were investigated as a function of added Zn(OTf)(2) or Zn(ClO(4))(2) in methanol at 25 degrees C either alone or in the presence of equimolar concentrations of the ligands phenanthroline (4), 2,9-dimethylphenanthroline (5), and 1,5,9-triazacyclododecane (6). The catalysis requires the presence of methoxide, and when studied as a function of added NaOCH(3), the rate constants (k(obs)) for methanolysis of Zn(2+) alone or in the presence of equimolar 4 or 5 maximize at different [(-)OCH(3)]/[Zn(2+)](total) ratios of 0.3, 0.5, and 1.0, respectively. Plots of k(obs) vs [Zn(2+)](total) either alone or in the presence of equimolar ligands 4 and 5 at the [(-)OCH(3)]/[Zn(2+)](total) ratios corresponding to the rate maxima are curved and show a nonlinear dependence on [Zn(2+)](total). In the cases of 4 and 5, this is explained as resulting from formation of a nonactive dimer, formulated as a bis-mu-methoxide-bridged form (L:Zn(2+)((-)OCH(3))(2)Zn(2+):L) in equilibrium with an active monomeric form (L:Zn(2+)((-)OCH(3))). In the case of the Zn(2+):6 system, no dimeric forms are present as can be judged by the strict linearity of the plots of k(obs) vs [Zn(2+)](total) in the presence of equimolar 6 and (-)OCH(3). Analysis of the potentiometric titration curves for Zn(2+) alone and in the presence of the ligands allows calculation of the speciation of the various Zn(2+) forms and shows that the binding to ligands 4 and 6 is very strong, while the binding to ligand 5 is weaker. Overall the best catalytic system is provided by equimolar Zn(2+), 5, and (-)OCH(3), which exhibits excellent turnover of the methanolysis of paraoxon when the substrate is in excess. At a concentration of 2 mM in each of these components, which sets the pH of the solution at 9.5, the acceleration of the methanolysis of paraoxon and fenitrothion relative to the methoxide reaction is 1.8 x 10(6)-fold and 13 x 10(6)-fold, respectively. A mechanism for the catalyzed reactions is proposed which involves a dual role for the metal ion as a Lewis acid and source of nucleophilic Zn(2+)-bound (-)OCH(3).

Cu(ii)-Mediated decomposition of phosphorothionate PS pesticides. Billion-fold acceleration of the methanolysis of fenitrothion promoted by a simple Cu(ii)–ligand system

The kinetics of methanolysis of the title compound (3) were studied in the presence of Cu(2+), introduced as Cu(OTf), in the presence of 0.5-1.0 eq. of methoxide and in the presence of 1.0 eq. of a ligand such as bipyridyl (5), phenanthroline (6) or 1,5,9-triazacyclododecane (4). In all cases the active species involve Cu(2+)((-)OCH(3)). In the case of added strong-binding ligands 5 or 6, a plot of the observed rate constant for methanolysis of 3 vs. [Cu(2+)](total) gives a curved line modelled by a process having a [Cu(2+)](1/2) dependence consistent with an active monomeric species in equilibrium with an inactive dimer i.e.[LCu(2+)((-)OCH(3))](2) <==> 2LCu(2+)((-)OCH(3)). In the case of the added strong binding ligand 4, the plot of the observed rate constant for methanolysis of 3 vs.[Cu(2+)](total) gives a straight line consistent with the catalytically active species being Cu(2+)(OCH(3)) which shows no propensity to form inactive dimers. Turnover experiments where the [3] > [Cu(2+)](total) indicate that the systems are truly catalytic. In the optimum case a catalytic system comprising 1 mM of the complex 4Cu(2+)((-)OCH(3)) catalyzes the methanolysis of 3 with a t(1/2) of approximately 58 s accounting for a 1.7 x 10(9)-fold acceleration relative to the background reaction at near neutral (s)(s)pH (8.75).

Billion-fold acceleration of the methanolysis of paraoxon promoted by La(OTf)3 in methanol

The methanolysis of the insecticide paraoxon (2) was investigated in methanol solution containing varying [La(OTf)(3)] (OTf = (-)OS(O)(2)CF(3)) as a function of at 25 degrees C. Plots of the pseudo-first-order rate constants (k(obs)) for methanolysis as a function of [La(OTf)(3)](total) were obtained under buffered conditions from 5.15 to 10.97, and the slopes of the linear parts of these were used to determine the second-order rate constants (k(2)(obs)) for the La(3+)-catalyzed methanolysis of 2. Detailed analysis of the potentiometric titration data of La(OTf)(3) in methanol through fits to a multicomponent equilibrium mixture of dimers of general stoichiometry La(3+)(2)((-)OCH3)n, where n assumes values of 1-5, gives the equilibrium distribution of each as a function of. These data, when fit to a second expression describing k(2)(obs) in terms of a linear combination of individual rate constants k(2)(2:1), k(2)(2:2).k(2)(2:)n for the dimers, allow one to describe the overall catalytic profile in terms of the individual contributions. The most catalytically important species are the three dimers La(3+)(2)((-)OCH3)1, La(3+)(2)((-)OCH3)2, and La(3+)(2)((-)OCH3)3. The catalysis of the methanolysis of 2 is spectacular: a 2 x 10(-3) M solution of [La(3+)](total), at neutral, affords a 10(9)-fold acceleration relative to the base reaction (t(1/2) approximately 20 s at 8.2) with excellent turnover. A mechanism of the catalyzed reaction involving the La(3+)(2)((-)OCH3)2 species is proposed.

High-throughput analytical techniques for reaction optimization

This review describes recent developments in approaches to high-throughput reaction optimization, as well as the associated analytical techniques. The studies discussed include the use of UV-visible, IR-thermographic and mass spectrometric methods for application in catalyst development, process optimization and materials science. Other methods of potential use in a high-throughput format are also discussed.

Hydrolysis of linear DNA duplex catalyzed by Co(III) complex of cyclen attached to polystyrene

To design artificial restriction enzymes, synthetic catalytic centers that effectively hydrolyze linear double-stranded polydeoxyribonucleotides are needed. The Co(III) complex of cyclen (CoCyc) attached to polystyrene derivatives hydrolyzes linearized pUC18 DNA with half-lives as short as 30 min at 25 degrees C. The catalytic activity of CoCyc is enhanced by >150 times on attachment to the resin.

Hydrolysis of plasmid DNA catalyzed by Co(III) complex of cyclen attached to polystyrene

Reactivity of the Co(III) complex of cyclen (CoCyc) in the hydrolytic cleavage of supercoiled pUC18 DNA leading to the formation of the corresponding open circular form was enhanced by >200 times upon attachment of CoCyc to cross-linked polystyrenes. Thus, half-lives as short as 40 min were achieved by the resin-based CoCyc in cleavage of the supercoiled DNA at 4 degrees C.

Lanthanide-mediated DNA hydrolysis

Lanthanide ions are remarkably effective catalysts for the hydrolytic cleavage of phosphate ester bonds, including the robust bonds of DNA. This makes Ln(III) and Ce(IV) ions attractive candidates for developing selective and efficient artificial nucleases, which could have many biochemical and clinical applications. Both small-molecule-based and biopolymer-based lanthanide complexes are being pursued.

Combinatorial approaches as a component of high-throughput experimentation (HTE) in catalysis research

We consider the application of high-throughput experimentation (HTE), including combinatorial methods, to catalyst discovery and early-phase optimization. While combinatorial- and parallel-testing methods have an already substantial history in catalysis, recent work by several groups promises significant efficiency gains. In molecular catalysis, progress is noted in library design, library synthesis by pooled, parallel, and discrete formats, catalyst testing and reaction optimization; the prime constraint for organometallic catalysts is the limited scope of synthesis procedures for non-peptide-based ligand libraries. Routes described for the synthesis of heterogeneous catalysts include hydrothermal synthesis, arraying of solution precursors, automated impregnation and precipitation, and arraying of solid precursors. The key challenge in applying HTE to heterogeneous catalysis is testing; we distinguish here between Stage 1, or "discovery" testing and Stage 2, optimization testing, and describe techniques with potential in each case. Recent examples from the literature and our own work are used to illustrate these principles and the prospects for HTE applied to catalysis.