A mesoporous metal-organic framework used to sustainably release copper(ii) into reducing aqueous media to promote the CuAAC click reaction.

The mesoporous metal-organic framework Cr-MIL-101-NH2 (MOF1) has been used to encapsulate, by a simple impregnation method, large amounts of copper sulfate. The resulting loaded material, Cu@MOF1, was successfully employed to slowly release copper(ii) into an appropriate reaction medium in which the reducing agent sodium ascorbate reduces copper(ii) to copper(i), thus allowing the well-known copper(i)-catalyzed alkyne-azide cycloaddition (CuAAC) "click" reaction to proceed in the absence of potentially high local copper(i) concentrations. The use of a MOF-based controlled copper release system such as Cu@MOF1 may be relevant for copper(i)-catalyzed reactions having substrates that could be degraded by potentially high local concentrations of copper(i). The copper chelating ligand TBTA (tris(benzyltriazolylmethyl)amine), a very useful ligand for click chemistry, has been successfully attached to the pores of MOF1. The resulting TBTA-functionalized MOF (MOF3) was compared with its non-functionalized version (MOF1). At copper loadings of ca. 3 mmol g-1, the results revealed that the performances of the two materials are strikingly similar. Upon immersion in methanol/water (95/5) containing sodium ascorbate, both materials slowly released copper encapsulated in their pores and could be recovered and reused efficiently for up to five reaction cycles without reloading with metal ion, while allowing the CuAAC reaction to proceed with excellent conversion rates and yields.

Crystal structure of a two-dimensional coordination polymer of formula [Zn(NDC)(DEF)] (H2NDC is naphthalene-2,6-di-carb-oxy-lic acid and DEF is N,N-di-ethyl-formamide).

A zinc metal-organic framework, namely poly[bis-(N,N-di-ethyl-formamide)(µ4-naphthalene-2,6-di-carboxyl-ato)(µ2-naphthalene-2,6-di-carboxyl-ato)dizinc(II)], [Zn(C12H6O4)(C15H11NO)] n , built from windmill-type secondary building units and forming zigzag shaped two-dimensional stacked layers, has been solvothermally synthesized from naphthalene-2,6-di-carb-oxy-lic acid and zinc(II) acetate as the metal source in N,N-di-ethyl-formamide containing small amounts of formic acid.

Alpha,beta-D-CNA induced rigidity within oligonucleotides.

Introduction of alpha,beta-D-CNA featuring canonical values of the torsional angles alpha and beta within oligonucleotides leads to an overall stabilization and improved rigidity of the duplex DNA as demonstrated by UV experiments, circular dichroism and corroborated by molecular dynamics simulations.

Theoretical study of specific hydrogen-bonding effects on the bridging P-OR bond strength of phosphate monoester dianions.

It has been proposed that the driving force for the initial phosphoryl transfer step of protein tyrosine phosphatases (PTPases) could be activation of the substrate ROPO32- by means of an enforced hydrogen-bonding interaction between an aspartic general acid and the bridging oxygen atom O (Zhang et al. Biochemistry 1995, 34, 16088-16096). The potential catalytic effect of this type of interaction, with regard to P-OR bond cleavage, was investigated computationally through simple model systems in which an efficient intramolecular hydrogen bond can take place between a H-bond donor group and the bridging oxygen atom of the dianionic phosphate. The dielectric effect of the environment (epsilon = 1, 4, and 78) was also explored. The results indicate that this interaction causes significant lengthenings of the scissile P-OR bond in all media but with more extreme effects observed in the low dielectric fields epsilon = 1 and epsilon = 4. It is interesting that, in all cases examined, this interaction actually contributes to stabilize the reactant state while causing its P-OR bond to lengthen. Overall, our results support the idea that this specific hydrogen-bonding situation might well be used by PTPases as an important driving force for promoting phosphoryl transfer reactions through highly dissociative transition states.

Theoretical evaluation of the substrate-assisted catalysis mechanism for the hydrolysis of phosphate monoester dianions.

Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous S(N)2(P) reactions of F- with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH- and F- can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (beta(lg)=-0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pK(a)<11 are involved, as in alkaline phosphatase, then the S(N)2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of beta(lg) (-0.95) is predicted for the substrate-assisted catalysis mechanism.

N-Sulfonyl hydroxamate derivatives as inhibitors of class II fructose-1,6-diphosphate aldolase.

Dihydroxyacetone-phosphate and phosphonate derivatives were synthesized bearing a N-sulfonyl hydroxamate moiety. The phosphate derivatives represent competitive inhibitors for the class II-FBP aldolase catalyzed reaction, while the phosphonate isosteres are comparatively weaker inhibitors.

Constrained nucleic acids (CNA). Part 2. Synthesis of conformationally restricted dinucleotide units featuring noncanonical alpha/beta/gamma or delta/epsilon/zeta torsion angle combinations.

Four dinucleotide building units of nucleic acids in which three out of six backbone torsion angles are included in a dioxaphosphorinane ring structure (D-CNA family) have been synthesized: two diastereoisomeric alpha,beta,gamma-D-CNA {cis and trans} and two diastereoisomeric delta,epsilon,zeta-D-CNA {(S(C4'),R(P)) and (S(C4'),S(P))}. The structural analysis of these conformationally restricted dinucleotides, using NMR spectroscopy and X-ray crystallography, shows that these D-CNA structural elements allow the stabilization of torsion angle combinations, alpha/beta/gamma and delta/epsilon/zeta, that are significantly different from those typically observed in canonical A- or B-form duplexes.

Theoretical studies of the hydroxide-catalyzed P-O cleavage reactions of neutral phosphate triesters and diesters in aqueous solution: examination of the changes induced by H/Me substitution.

DFT calculations and dielectric continuum methods have been employed to map out the lowest activation free-energy profiles for the alkaline hydrolysis of representative phosphate triesters and diesters, including trimethyl phosphate (TMP), dimethyl 4-nitrophenyl phosphate (DMNPP), dimethyl hydrogen phosphate (DMHP), and the dimethyl phosphate anion (DMP-). The reliability of the calculations is supported by the excellent agreement observed between the calculated and the experimentally determined activation enthalpies for phosphate triesters with poor (TMP) and good (DMNPP) leaving groups. The results obtained for the OH- + DMHP and OH- + DMP- reactions are also consistent with all the available experimental information concerning the hydrolysis reaction of dimethyl phosphate anion at pH > 5. By performing geometry optimizations in the dielectric field (epsilon = 78.39), we found that OH- can attack the phosphorus atom of DMHP without capturing its proton only if the O-H bond of DMHP is oriented opposite the attacking OH- group. In these conditions, the rate for OH- attack on DMHP was found to be approximately 10(3)-fold faster than that for OH- attack on TMP. The calculated rate acceleration induced by the phosphoryl proton corresponds to the maximum rate effect expected from kinetic studies. Overall, our calculations performed on the dimethyl phosphate ester predict that, contrary to what is generally observed for RNA and aryl phosphodiesters, the water-promoted P-O cleavage reaction of DNA should dominate the base-catalyzed reaction at pH 7. These results are suggestive that nucleases may be less proficient as catalysts than has recently been suspected.

Diastereoselective synthesis of a conformationally restricted dinucleotide with predefined alpha and beta torsional angles for the construction of alpha,beta-constrained nucleic acids (alpha,beta-CNA).

[reaction: see text] The synthesis of a diastereopure 1,3,2-dioxaphosphorinane linkage in which two, alpha and beta, out of six torsion angles of the natural phosphodiester backbone are constrained with predefined values of ca. +60 degrees (g(+)) and 180 degrees (t), respectively, is described. The stable and unstrained six-membered cyclic phosphotriester structure represents the smallest possible ring allowing the conformational locking of the alpha torsion angle at a significant positive value that is typical of many bulged regions of nucleic acids.

Reactivity of phosphate monoester monoanions in aqueous solution. 1. Quantum mechanical calculations support the existence of "anionic zwitterion" MeO(+)(H)PO(3)(2-) as a key intermediate in the dissociative hydrolysis of the methyl phosphate anion.

The dissociative hydrolysis reaction of the methyl phosphate monoanion has been studied for the reactant species CH(3)OPO(3)H(-) (1) and CH(3)OPO(3)H(-) x H(2)O (1a) in the gas and aqueous phases by density functional theory (B3LYP) calculations. Nonspecific solvation effects were taken into account with the polarizable continuum model PCM either by solvating the gas-phase reaction paths or by performing geometry searches directly in the presence of the solvation correction. In agreement with previous theoretical studies, our gas-phase calculations indicate that proton transfer to the methoxy group of 1 is concerted with P-O bond cleavage. In contrast, optimizations performed with the PCM solvation model establish the existence of the tautomeric form CH(3)O(+)(H)PO(3)(2-) (2) as an intermediate, indicating that proton transfer and P-O bond cleavage become uncoupled in aqueous solution. The dissociative pathway of 1a is energetically favored over the dissociative pathway of 1 only when the added water molecule plays an active catalytic role in the prototropic rearrangement 1 <--> 2. In that case, it is found that the collapse (via P-O bond cleavage) of the hydrated zwitterionic form CH(3)O(+)(H)PO(3)(2-) x H(2)O (2a) is rate-determining. This collapse may occur by a stepwise mechanism through a very short-lived metaphosphate intermediate (PO(3)(-)), or by a concerted S(N)2-like displacement through a loose metaphosphate-like transition state. The present calculations do not allow a distinction to be made between these two alternatives, which are both in excellent agreement with experiment. The present study also reveals that PO(3)(-) reacts selectively with CH(3)OH and H(2)O nucleophiles in aqueous solution. However, the observed selectivity of metaphosphate is governed by solvation effects, not nucleophilicity (water being much more effective than methanol in capturing PO(3)(-)). This arises from a better solvation of the addition product H(2)O(+)PO(3)(2-) as compared to CH(3)O(+)(H)PO(3)(2-).

Evidence for the Formation of alpha-Hydroxydialkylnitrosamines in the pH-Independent Solvolysis of alpha-(Acyloxy)dialkylnitrosamines.

A kinetic study of the decay of alpha-(acyloxy)dialkylnitrosamines in aqueous solutions, at 25 degrees C, ionic strength 1 M (NaClO(4)), and 4% acetonitrile by volume, is reported. Rate constants for disappearance of the N-NO chromophore or appearance of benzaldehyde product increase with the introduction of electron-withdrawing groups into the acyloxy moiety. For some compounds, in some regions of pH, the kinetics are non-first-order. For these compounds, in other regions of pH, the rate constants are coincident with those previously reported for the decay of the corresponding alpha-hydroxydialkylnitrosamines. These data provide direct evidence that alpha-hydroxydialkylnitrosamines are intermediates in the pH-independent decomposition of the alpha-(acyloxy)dialkylnitrosamines studied.