The dinuclear Zn(II) complex catalyzed cyclization of a series of 2-hydroxypropyl aryl phosphate RNA models: progressive change in mechanism from rate-limiting P-O bond cleavage to substrate binding

A methoxide-bridged dinuclear Zn(II) complex of 1,3-[N,N'-bis(1,5,9-triazacyclododecane)]propane (1-Zn(II)2:(-OCH3)) was prepared, and its catalysis of the cyclization of a series of 2-hydroxypropyl aryl phosphates (4a-g) was investigated in methanol at pH 9.8, T = 25degreesC by stopped-flow spectrophotometry. An X-ray diffraction structure of the hydroxide analogue of 1-Zn(II)2:(-OCH3), namely 1-Zn(II)2:(-OH), reveals that each of the Zn(II) ions is coordinated by the three N's of the triazacyclododecane units and a bridging hydroxide. The cyclizations of substrates 4a-g reveal a progressive change in the observed kinetics from Michaelis-Menten saturation kinetics for the poorer substrates (4-OCH3 (4g); 4-H (4f); 3-OCH3 (4e); 4-Cl (4d); 3-NO2, (4c)) to second-order kinetics (linear in 1-Zn(II)2:(-OCH3)) for the better substrates (4-NO2,3-CH3 (4b); 4-NO2, (4a)). The data are analyzed in terms of a multistep process whereby a first formed complex rearranges to a reactive complex with a doubly activated phosphate coordinated to both metal ions. The kinetic behavior of the series is analyzed in terms of change in rate-limiting step for the catalyzed reaction whereby the rate-limiting step for the poorer substrates (4g-c) is the chemical step of cyclization of the substrate, while for the better substrates (4b,a) the rate-limiting step is binding. The catalysis of the cyclization of these substrates is extremely efficient. The kcat/KM values for the catalyzed reactions range from 2.75 x 10(5) to 2.3 x 10(4) M-1 s-1, providing an acceleration of 1 x 10(8) to 4 x 10(9) relative to the methoxide reaction (k2OCH3, which ranges from 2.6 x 10(-3) to 5.9 x 10(-6) M-1 s-1 for 4a-g). At a pH of 9.8 where the catalyst is maximally active, the acceleration for the substrates ranges from (1 - 4) x 10(12) relative to the background reaction at the same pH. Detailed energetics calculations show that the transition state for the catalyzed reaction comprising 1-Zn(II)2, methoxide, and 4 is stabilized by about -21 to -23 kcal/mol relative to the transition state for the methoxide reaction. The pronounced catalytic activity is attributed to a synergism between a positively charged catalyst that has high affinity for the substrate and for the transition state for cyclization, and a medium effect involving a reduced polarity/dielectric constant that complements a reaction where an oppositely charged reactant and catalyst experience charge dispersal in the transition state.     

A reductionist biomimetic model system that demonstrates highly effective Zn(II)-catalyzed cleavage of an RNA model

The cyclization of the RNA model 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP, 1) promoted by Zn2+ alone and the 1,5,9-triazacyclododecane complex of Zn2+ (Zn2+:[12]aneN3) is studied in ethanol in the presence of 0.5 equiv of -OEt/Zn2+ to investigate the effect of a low polarity/dielectric medium on a metal-catalyzed reaction of biological relevance. Ethanol exerts a medium effect that promotes strong binding of HPNPP to Zn2+, followed by a dimerization to form a catalytically active complex (HPNPP:Zn2+)2 in which the phosphate undergoes cyclization with a rate constant of kcat = 2.9 s(-1) at s(s)pH 7.1. In the presence of the triaza ligand:Zn2+ complex, the change from water to methanol and then to ethanol brings about a mechanism where two molecules of the complex, suggested as EtOH:Zn2+:[12]aneN3 and its basic form, EtO-:Zn2+:[12]aneN3, bind to HPNPP and catalyze its decomposition with a rate constant of kcat of 0.13 s(-1) at s(s)pH 7.1. Overall, the acceleration exhibited in these two situations is 4 x 10(14)-fold and 1.7 x 10(12)-fold relative to the background ethoxide-promoted reactions at the respective s(s)pH values. The implications of these findings are discussed within the context of the idea that enzymatic catalysis is enhanced by a reduced effective dielectric constant within the active site.     

Potentiometric titration of metal ions in ethanol

The potentiometric titrations of Zn2+, Cu2+ and 12 Ln3+ metal ions were obtained in ethanol to determine the titration constants (defined as the at which the [-OEt]/[Mx+]t ratios are 0.5, 1.5, and 2.5) and in two cases (La3+ and Zn2+) a complete speciation diagram. Several simple monobasic acids and aminium ions were also titrated to test the validity of experimental titration measurements and to establish new constants in this medium that will be useful for the preparation of buffers and standard solutions. The dependence of the titration constants on the concentration and type of metal ion and specific counterion effects is discussed. In selected cases, the titration profiles were analyzed using a commercially available fitting program to obtain information about the species present in solution, including La3+ for which a dimer model is proposed. The fitting provides the microscopic values for deprotonation of one to four metal-bound ethanol molecules. Kinetics for the La3+-catalyzed ethanolysis of paraoxon as a function of are presented and analyzed in terms of La3+ speciation as determined by the analysis of potentiometric titration curves. The stability constants for the formation of Zn2+ and Cu2+ complexes with 1,5,9-triazacyclododecane as determined by potentiometric titration are presented.     

Combination of a dinuclear Zn2+ complex and a medium effect exerts a 10(12)-fold rate enhancement of cleavage of an RNA and DNA model system

The catalytic ability of a dinuclear Zn2+ complex of 1,3-bis-N1-(1,5,9-triazacyclododecyl)propane (3) in promoting the cleavage of an RNA model, 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP, 1), and a DNA model, methyl p-nitrophenyl phosphate (MNPP, 4), was studied in methanol solution in the presence of added CH3O- at 25 degrees C. The di-Zn2+ complex (Zn2 :3), in the presence of 1 equiv of added methoxide, exhibits a second-order rate constant of (2.75 +/- 0.10) x 10(5) M(-1) s(-1) for the reaction with 1 at s(s)pH 9.5, this being 10(8)-fold larger than the k2 value for the CH3O- promoted reaction (kOCH3 = (2.56 +/- 0.16) x 10(-3) M(-1) s(-1)). The complex is also active toward the DNA model 4, exhibiting Michaelis-Menten kinetics with a KM and kmax of 0.37 +/- 0.07 mM and (4.1 +/- 0.3) x 10(-2) s(-1), respectively. Relative to the background reactions at s(s)pH 9.5, Zn2 :3 accelerates cleavage of each phosphate diester by a remarkable factor of 1012-fold. A kinetic scheme common to both substrates is discussed. The study shows that a simple model system comprising a dinuclear Zn2+ complex and a medium effect of the alcohol solvent achieves a catalytic reactivity that approaches enzymatic rates and is well beyond anything seen to date in water for the cleavage of these phosphate diesters.     

Cu(II)-promoted methanolysis of N,N-dipicolylacetamide. multistep activation by decoupling of > ̈̈N-C═O resonance via Cu(II)-N binding, delivery of the Cu(II):((-)OCH3) nucleophile, and metal ion assistance of the departure of the leaving group

The methanolysis of the Cu(II) complex of N-acetyl-N,N-bis(2-picolyl)amine (2) was investigated by a kinetic study as a function of pH in methanol at 25 °C and computationally by DFT calculations. The active species is the basic form of the complex (3(-)), or (1:Cu(II))((-)OCH(3))(HOCH(3))), and the rate constant for its solvolysis is k(max) = 1.5 × 10(-4) s(-1). The mechanism involves Cu(II) binding to the amide N lone pair, decoupling it from >N-C═O resonance, concomitant with Cu(II):((-)OCH(3)) delivery to the adjacent >N-C═O unit, followed by Cu(II)-assisted departure of the N,N-bis(2-picolyl)amide from a tetrahedral intermediate.     

Effect of Optical Excitation on the Band Structure and X-Ray Absorption Spectra of BaBiO3-Based High-Temperature Superconductors: Ab Initio Calculation

JETP Letters - The band structure, densities of states, and O K-edge X-ray absorption spectra have been calculated by the density functional theory method for BaBiO3-based perovskite...     

Europium ion catalyzed methanolysis of esters at neutral pH and ambient temperature. catalytic Involvement of Eu3+(CH3O-)(CH3OH)x

The Eu(3+)-promoted methanolysis of three esters, p-nitrophenyl acetate (1), phenyl acetate (2), and ethyl acetate (3) is reported, as well as the potentiometric titration of Eu(3+) in MeOH at various [Eu(SO(3)CF(3))(3)] (SO(3)CF(3) = OTf). The titration data are analyzed in terms of two ionizations corresponding to macroscopic and values, which are respectively defined as the values at which the [CH(3)O(-)]/[Eu(3+)] = 0.5 and 1.5. As a function of increasing [Eu(OTf)(3)], increases slightly due to a proposed Eu(3+)/(-)OTf ion pairing effect, which tends to reduce the acidity of the metal-coordinated CH(3)OH, while decreases due to the formation of Eu(3+) dimers and oligomers which stabilize the (Eu(3+)(CH(3)O(-))(2))(n)forms through bridging of the methoxides between two or more metal ions. For ester 1, a detailed kinetic analysis of the reaction rates as a function of both [Eu(OTf)(3)] and in buffered methanol reveals that the /second-order rate constant (k(2)) plot for the catalyzed reaction follows a bell-shaped profile, suggesting that the active form is a Eu(3+)(CH(3)O(-)) monomer with a kinetic of 6.33 +/- 0.06 for formation and a of 8.02 +/- 0.10 for its conversion into the inactive (Eu(3+)(CH(3)O(-))(2))(n)oligomeric form. At higher values, plots of k(obs) vs [Eu(OTf)(3)] are linear at low metal concentration and plateau at higher metal concentration due to the formation of inactive higher order aggregates. The Eu(3+)(CH(3)O(-)) catalysis of the methanolysis of esters 1, 2, and 3 is substantial. Solutions of 10(-2) M of the catalyst at 7.12 accelerate the reaction relative to the methoxide reaction at that by 8 530 000-, 195 000 000- and 7 813 000-fold, respectively.     

An ortho-palladated dimethylbenzylamine complex as a highly efficient turnover catalyst for the decomposition of P=S insecticides. Mechanistic studies of the methanolysis of some P=S-containing phosphorothioate triesters

An ortho-palladated complex Pd(dmba)(py)(OTf) (9), or Pd(N,N-dimethylbenzylamine)(pyridine)(trifluoromethanesulfonate), was synthesized and its solution properties in methanol studied as a function of pH. In neutral solution the triflate dissociates from the complex to give a dominant form Pd(dmba)(py)(HOCH3), and in acid the pyridine dissociates to give Pyr-H+ and Pd(dmba)(HOCH3)(HOCH3). Under basic conditions, Pd(dmba)(py)(HOCH3) ionizes to give Pd(dmba)(py)(-OCH3) from which the pyridine can dissociate to yield a mixture of a bis-methoxy-bridged dimer (Pd(dmba)(-OCH3))2 (15-dimer), and its monomer Pd(dmba)(HOCH3)(-OCH3). Kinetic studies under buffered conditions reveal that 9 is an effective catalyst for the methanolysis of fenitrothion and other P=S pesticides. The active form of the catalyst is a basic one having one associated methoxide generated with an apparent (s)(s)pK(a) of 10.8. Analysis of the change in the UV/vis spectrum as a function of pH generates a spectrophotometric (s)(s)pK(a) of 10.8 +/- 0.1. This catalytic system is shown to promote the methanolysis of fenitrothion (3), diazinon (4), quinalphos (5), coumaphos (10) and dichlofenthion (11) at 0.05 mol dm(-3) triethyl amine buffer, (s)(s)pH 10.8, 25 degrees C, under turnover conditions where the [phosphorothioate]/[9] ratio is 48.6, 13.4, 13.4, 18.6, and 48.6 respectively. In all cases, the products were derived from displacement of the leaving group by methoxide, the second-order turnover rate constants being 36.9, 0.45, 0.12, >146.7 and 44.3 dm3 mol(-1) s(-1) respectively. An associative mechanism for the catalyzed methanolysis of the P=S pesticides is proposed where a transiently coordinated S=P substrate is intramolecularly attacked by the Pd(II)-coordinated methoxide.