Catalysis of phosphodiester transesterification by dinuclear Cu(II) complexes: The role of the second Cu(II) ion

Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes

The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.

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.

(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. Additionally, their impact on the biological systems is also presented and discussed.

The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex

The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.

Cleavage of phosphate diesters mediated by Zn(II) complex in Gemini surfactant micelles

The cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) catalyzed by the Zn(II)-biap (biap: N,N-bis(2-ethyl-5-methylimidazole-4-ylmethyl)aminopropane) complex has been investigated spectrophotometrically in a micellar solution of cationic Gemini surfactant 16-2-16 [bis(hexadecyldimethylammonium)ethane bromide] and CTAB (hexadecyltrimethylammonium bromide) at 25+/-0.1 degrees C. The experimental results reveal that a higher rate of acceleration (about 2016-fold) of HPNP cleavage promoted by the Zn(II)-biap complex has been observed in the 16-2-16 micellar solution in comparison with the background rate (k(0)) of HPNP spontaneous cleavage at 25 degrees C. Reaction rates of HPNP cleavage in CTAB micellar solutions are only about 40% of that in Gemini 16-2-16 micelles under comparable conditions. In addition, the cleavage rates of HPNP in Gemini micelles and in CTAB micelles are respectively 29.5 times and 12 times faster than that in aqueous buffer. Especially, a "sandwich absorptive mode" has been proposed to explain the acceleration of HPNP cleavage in a cationic micellar solution.

Geometry-dependent phosphodiester hydrolysis catalyzed by binuclear copper complexes

Two isomeric binuclear ligands PBTPA and MBTPA and their copper(II) complexes were prepared and examined for hydrolysis of a model phosphodiester substrate: bis(p-nitrophenyl)phosphate. A bell-shaped pH vs rate profile, which is in agreement with one mechanism proposed for bimetallonucleases/phosphatases, was observed for the binuclear complex of copper(II) and PBTPA. At pH 8.4, a maximum rate of 1.14 x 10(-6) s(-1)--more than 10(4)-fold over uncatalyzed reactions--was achieved. However, the analogous complex of MBTPA did not show significant rate enhancement. The binuclear complex of copper(II) and PBTPA also showed 10-fold acceleration over mononuclear complex of copper(II) and tris(2-pyridylmethyl)amine (TPA) catalyzed reaction. A phage phiX174 DNA assay showed that the complex of copper(II) and PBTPA promoted supercoiled phage phiX174 DNA relaxation under both aerobic and anaerobic conditions, in contrast to the hydrolytic inactivity of the mononuclear complex of copper(II) and TPA.

Alkali metal ion catalysis in nucleophilic displacement by ethoxide ion on p-nitrophenyl phenylphosphonate: Evidence for multiple metal ion catalysis

In continuation of our studies of alkali metal ion catalysis and inhibition at carbon, phosphorus, and sulfur centers, the role of alkali metal ions in nucleophilic displacement reactions of p-nitrophenyl phenylphosphonate (PNPP) has been examined. All alkali metal ions studied acted as catalysts. Alkali metal ions added as inert salts increased the rate while decreased rate resulted on M+ complexation with 18-crown-6 ether. Kinetic analysis indicated the interaction of possibly three potassium ions, four sodium ions, and five lithium ions in the transition state of the reactions of ethoxide with PNPP. Pre-association of the anionic substrate with two metals ions in the ground state gave the best fit to the experimental data of the sodium system. Thus, the study gives evidence of the role of several metal ions in nucleophilic displacement reactions of ethoxide with anionic PNPP, both in the ground state and in the transition state. Molecular modeling of the anionic transition state implies that the size of the monovalent cation and the steric requirement of the pentacoordinate transition state are the primary limitations on the number of cations that can be brought to bear to stabilize the transition state and catalyze nucleophilic substitution at phosphorus. The bearing of the present work on metal ion catalysis in enzyme systems is discussed, in particular enzymes that catalyze phosphoryl transfer, which often employ multiple metal ions. Our results, both kinetic and modeling, reveal the importance of electrostatic stabilization of the transition state for phosphoryl transfer that may be effected by multiple cations, either monovalent metal ions or amino acid residues. The more such cations can be brought into contact with the anionic transition state, the greater the catalysis observed.Key words: alkali metal ion catalysis, nucleophilic displacement at phosphorus, multiple metal ion catalysis, phosphoryl transfer.

Acceleration of acid-catalyzed transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate by organic solvents

[structure: see text] Transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate in the presence of 0.092 M HClO4 is 50-5000 times faster in acetonitrile, 1,4-dioxane, methanol, ethanol, N,N-dimethylformamide, or dimethyl sulfoxide than in water. This demonstrates the importance of tuning the microenvironments in designing synthetic nucleases.