OH Nucleophile Research Articles

Nucleophilic destruction of organophosphate toxins: A computational investigation

Computed reaction enthalpies, free energies, and activation barriers in vacuo are presented for the nucleophilic detoxification of the organophosphorus compounds (H)(H O)P( O)F, (H)(H 3C O)P( O)F and (H 3C)(CH(CH 3) 2 O)P( O)F via the reaction R 1 OH + (R 2)(R 3 O)P( O)F → (R 2)(R 3 O)P( O)(O R 1) + H F for a wide variety of R 1 OH nucleophiles. Density functional theory at the B3LYP/6-311++G( d, p) computational level was employed for all the calculations. A multi-step Wright-type reaction mechanism [J. B. Wright, W.E. White, J. Mol. Struct. (THEOCHEM) 454 (1998) 259], which proceeds via a proton transfer from the nucleophile to the fluorine atom through the phosphinyl oxygen atom, was consistently found to have a lower activation barrier in the gas-phase than for the corresponding mechanism that operates via a proton transfer from the nucleophile directly to the fluorine atom. Of the nucleophilic agents investigated, peroxybenzoic acid and o-iodosobenzoic acid had the lowest classical activation barrier for the Wright-type mechanism.

A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In contrast, some mechanistic studies support the role of C75 acting as general acid and thus being protonated before the reaction. We report combined quantum chemical/molecular mechanical calculations for the C75 general base pathway, utilizing the available structural data for the wild type HDV genomic ribozyme as a starting point. Several starting configurations differing in magnesium ion placement were considered and both one-dimensional and two-dimensional potential energy surface scans were used to explore plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. We identify a most likely position for the magnesium ion, which also suggests it acts as a Lewis acid. The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data.

Catalytic Strategies of Self-Cleaving Ribozymes

[Structure: see text]. Five naturally occurring nucleolytic ribozymes have been identified: the hammerhead, hairpin, glmS, hepatitis delta virus (HDV), and Varkud satellite (VS) ribozymes. All of these RNA enzymes catalyze self-scission of the RNA backbone using a chemical mechanism equivalent to that of RNase A. RNase A uses four basic strategies to promote this reaction: geometric constraints, activation of the nucleophile, transition-state stabilization, and leaving group protonation. In this Account, we discuss the current thinking on how nucleolytic ribozymes harness RNase A's four sources of catalytic power. The geometry of the phosphodiester cleavage reaction constrains the nucleotides flanking the scissile phosphate so that they are unstacked from a canonical A-form helix and thus require alternative stabilization. Crystal structures and mutational analysis reveal that cross-strand base pairing, along with unconventional stacking and tertiary hydrogen-bonding interactions, work to stabilize the splayed conformation in nucleolytic ribozymes. Deprotonation of the 2'-OH nucleophile greatly increases its nucleophilicity in the strand scission reaction. Crystal structures of the hammerhead, hairpin, and glmS ribozymes reveal the N1 of a G residue within hydrogen-bonding distance of the 2'-OH. In each case, this residue has also been shown to be important for catalysis. In the HDV ribozyme, a hydrated magnesium has been implicated as the general base. Catalysis by the VS ribozyme requires both an A and a G, but the precise role of either has not been elucidated. Enzymes can lower the energy of a chemical reaction by binding more tightly to the transition state than to the ground states. Comparison of the hairpin ground- and transition-state mimic structures reveal greater hydrogen bonding to the transition-state mimic structure, suggesting transition-state stabilization as a possible catalytic strategy. However, the hydrogen-bonding pattern in the glmS ribozyme transition-state mimic structure and the ground-state structures are equivalent. Protonation of the 5'-O leaving group by a variety of functional groups can promote the cleavage reaction. In the HDV ribozyme, the general acid is a conserved C residue. In the hairpin ribozyme, a G residue has been implicated in protonation of the leaving group. An A in the hammerhead ribozyme probably plays a similar role. In the glmS ribozyme, an exogenous cofactor may provide the general acid. This diversity is in contrast to the relatively small number of functional groups that serve as a general base, where at least three of the nucleolytic ribozymes may use the N1 of a G.

Self‐Assembly of a Cyclic Zn4O4 Tetramer by Aerobic Oxidation of a Bisoxazoline: A Molecular “Nest” for Nucleophilic OH−

Nestwärme für Hydroxidionen: Durch Koordination und aerobe Oxidation des Bisoxazolins Me2box entsteht selbstorganisiert ein hoch geordneter [(Me2box)O4Zn4]4+-Komplex. Dieser Metallamakrocyclus wirkt als nestförmiger Hydroxidrezeptor (siehe Schema, rechts) und verfügt über Phosphatase-Aktivität. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z800870_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Self‐Assembly of a Cyclic Zn4O4 Tetramer by Aerobic Oxidation of a Bisoxazoline: A Molecular “Nest” for Nucleophilic OH−

Nesting hydroxide: Coordination and aerobic oxidation of a bisoxazoline Me2box is coupled with self-assembly to form a highly ordered [(Me2box)O4Zn4]4+ complex. The metallamacrocycle acts as a nest-like hydroxide receptor (see scheme, right) and shows catalytic phosphatase activity.

Identification of Cytochrome P450 3A4 Modification Site with Reactive Metabolite Using Linear Ion Trap-Fourier Transform Mass Spectrometry

Covalent binding of reactive metabolites to cytochrome P450s (P450s) often causes their mechanism-based inactivation (MBI), resulting in drug-drug interactions or toxicity. The detection and identification of the P450 sites to which reactive metabolites bind would elucidate MBI mechanisms. We describe a proteomic approach using nano-LC/linear ion trap-Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to characterize the binding of a reactive metabolite of raloxifene, which is a known P450 3A4 inhibitor, to the P450 3A4 isozyme. LTQ-FT analyses revealed that the metabolic reaction of raloxifene in a reconstituted P450 3A4 system formed a reactive metabolite adduct to P450 3A4 apoprotein, accompanied by a mass shift of 471 Da relative to intact P450 3A4 apoprotein. The reaction mixtures were digested with trypsin, and then the tryptic digests were analyzed by nano-LC-MS/MS. This technique revealed that VWGFYDGQQPVLAITDPDMIK (position 71-91) was a tryptic peptide modified by the reactive metabolite derived from raloxifene. The site of adduction with the reactive metabolite was further postulated to be the nucleophilic OH group of Tyr-75 of P450 3A4. A proteomic approach using LTQ-FT can yield direct information on the P450 3A4 modification site without radiolabeled compounds. In addition, this information can elucidate mechanisms involved in the covalent binding of reactive metabolites and the inactivation of P450 3A4.

Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases

The rate-limiting step for nucleotide incorporation in the pre-steady state for most nucleic acid polymerases is thought to be a conformational change. As a result, very little information is available on the role of active-site residues in the chemistry of nucleotidyl transfer. For the poliovirus RNA-dependent RNA polymerase (3D(pol)), chemistry is partially (Mg(2+)) or completely (Mn(2+)) rate limiting. Here we show that nucleotidyl transfer depends on two ionizable groups with pK(a) values of 7.0 or 8.2 and 10.5, depending upon the divalent cation used in the reaction. A solvent deuterium isotope effect of three to seven was observed on the rate constant for nucleotide incorporation in the pre-steady state; none was observed in the steady state. Proton-inventory experiments were consistent with two protons being transferred during the rate-limiting transition state of the reaction, suggesting that both deprotonation of the 3'-hydroxyl nucleophile and protonation of the pyrophosphate leaving group occur in the transition state for phosphodiester bond formation. Importantly, two proton transfers occur in the transition state for nucleotidyl-transfer reactions catalyzed by RB69 DNA-dependent DNA polymerase, T7 DNA-dependent RNA polymerase and HIV reverse transcriptase. Interpretation of these data in the context of known polymerase structures suggests the existence of a general base for deprotonation of the 3'-OH nucleophile, although use of a water molecule cannot be ruled out conclusively, and a general acid for protonation of the pyrophosphate leaving group in all nucleic acid polymerases. These data imply an associative-like transition-state structure.

Structural Roles of Monovalent Cations in the HDV Ribozyme

The hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to substitute for structural, but not catalytic, divalent metal ions in the RNA. To investigate the role of monovalent cations in ribozyme structure and function, we determined the crystal structure of the precursor HDV ribozyme in the presence of thallium ions (Tl(+)). Two Tl(+) ions can occupy a previously observed divalent metal ion hexahydrate-binding site located near the scissile phosphate, but are easily competed away by cobalt hexammine, a magnesium hexahydrate mimic and potent reaction inhibitor. Intriguingly, a third Tl(+) ion forms direct inner-sphere contacts with the ribose 2'-OH nucleophile and the pro-S(p) scissile phosphate oxygen. We discuss possible structural and catalytic implications of monovalent cation binding for the HDV ribozyme mechanism.

Alterations in Linker Flexibility Suppress DNA Topoisomerase I Mutant-induced Cell Lethality

Eukaryotic DNA topoisomerase I (Top1p) catalyzes changes in DNA topology via the formation of a covalent enzyme-DNA intermediate, which is reversibly stabilized by the anticancer agent camptothecin (CPT). Crystallographic studies of the 70-kDa C terminus of human Top1p bound to duplex DNA describe a monomeric protein clamp circumscribing the DNA helix. The structures, which lack the N-terminal domain, comprise the conserved clamp, an extended linker domain, and the conserved C-terminal active site Tyr domain. CPT bound to the covalent Top1p-DNA complex limits linker flexibility, allowing structural determination of this domain. We previously reported that mutation of Ala(653) to Pro in the linker increases the rate of enzyme-catalyzed DNA religation, thereby rendering Top1A653Pp resistant to CPT (Fiorani, P., Bruselles, A., Falconi, M., Chillemi, G., Desideri, A., and Benedetti P. (2003) J. Biol. Chem. 278, 43268-43275). Molecular dynamics studies suggested mutation-induced increases in linker flexibility alter Top1p catalyzed DNA religation. To address the functional consequences of linker flexibility on enzyme catalysis and drug sensitivity, we investigated the interactions of the A653P linker mutation with a self-poisoning T718A mutation within the active site of Top1p. The A653P mutation suppressed the lethal phenotype of Top1T718Ap in yeast, yet did not restore enzyme sensitivity to CPT. However, the specific activity of the double mutant was decreased in vivo and in vitro, consistent with a decrease in DNA binding. These findings support a model where changes in the flexibility or orientation of the linker alter the geometry of the active site and thereby the kinetics of DNA cleavage/religation catalyzed by Top1p.

Effects of Modification of the Active Site Tyrosine of Human DNA Topoisomerase I

The human topoisomerase I-mediated DNA relaxation reaction was studied following modification of the enzyme at the active site tyrosine (position 723). A series of unnatural tyrosine analogues was incorporated into the active site of human topoisomerase I by utilizing misacylated suppressor tRNAs in an in vitro protein synthesizing system. The relaxation activities of the modified human topoisomerase I analogues having varied steric, electronic, and stereochemical features were all greatly diminished relative to that of the wild type. It was found that modifications involving replacement of the nucleophilic tyrosine OH group with NH2, SH, or I groups eliminated DNA relaxation activity, as did changing the orientation of the nucleophilic tyrosine OH group. Only tyrosine analogues having the phenolic OH group in the normal position with respect to the protein backbone were active; the relative activities could be rationalized in chemical terms on the basis of the H-bonding and the electronic effects of the substituents attached to the meta position of the aromatic ring. In addition, the poisoning of one of the modified human topoisomerase I analogues, as part of covalent binary complexes with DNA, by CPT and 20-thio CPT was evaluated.

Molecular orbital analysis on the dissolution of nano-ball allophane under alkaline condition

Reaction mechanism between hydroxide ion (OH - ) and pore region of nano-ball allophane was analyzed by molecular orbital method (MOPAC-PM3) with a model cluster including the pore. Many Si atoms with silanol groups (Si-OH) are exposed as broken edge at the pore region, and nucleophilic OH - may attack the positively charged Si atoms. When Na + , as a counter ion of OH - , was held on the silanol group by cation exchange reaction (Si-ONa), calculated positive charge of the Si atom increased from that of Si-O - . This may promote nucleophilic attack and adsorption of OH - toward the Si atom. In model cluster with an OH - adsorbed on the Si atom to form five-fold coordination, decreases in calculated bond orders, bond strengths, of some Si-O and Al-O bondings were observed near the OH - adsorption site. This bond weakening will lead to dissolution of one Si and three Al atoms from the pore region of fundamental allophane structure, which is consistent with experimental observation. The increase in positive charge on Si atom and decrease in bond order of Si-O and Al-O bondings were also observed in calculations with one to six water molecules added to simulate reactions in aqueous system.

Effect of modification of the electrophilic center on the α effect

We report on a nucleophilic study of esters R-C(=X)-Y-Ar in which the electrophilic center has been modified by replacing O by S in the leaving group or carbonyl center: 4-nitrophenyl acetate (1), S-4-nitrophenyl thioacetate (2), 4-nitrophenyl benzoate (3), and O-4-nitrophenyl thionobenzoate (4). The studies include O– and S– nucleophiles as well as α nucleophiles in H2O at 25.0 ± 0.1 °C. The sulfur nucleophile (4-chlorothiophenoxide, 4-ClPhS–) exhibits significant enhanced reactivity for the reactions with thiol and thione esters 2 and 4 compared with their oxygen analogues 1 and 3. On the contrary, the common nucleophile OH– is much less reactive towards 2 and 4 compared with 1 and 3. The effect of changing both the electrophilic center and the nucleofugic center on the reactivity of the other oxygen nucleophiles is not so significant: 4-chlorophenoxide (4-ClPhO–) is four to six times more reactive in the reactions with thiol and thione esters 2 and 4 compared with their oxygen analogues 1 and 3. The α effects exhibited by butan-2,3-dione monoximate (Ox–) and HOO– are strongly dependent on the nature of the electrophilic center of the substrates, indicating that the difference in the ground-state solvation energy cannot be fully responsible for the α effect. Our results clearly emphasize the strong dependence of the α effect on the substrate structure, notably, the nature of the electrophilic center. The impact of change in the nucleofuge (1→2) and the electrophilic center (3→4) on reactivity indicates that α nucleophiles will need to be “purpose built” for decontamination and nucleophilic degradation of specific biocides.Key words: α effect, nucleophilicity, nucleofuge effect, electrophilicity, polarizability.

Transition Metal Carbene Chemistry. 4. Nucleophilic Attachment of DABCO to Fischer Carbene Complexes in MeCN

Rate constants for the attachment of DABCO (1,4-diazabicyclo[2.2.2]octane) to Fischer carbene complexes of the type (CO)(5)Cr=C(XR)C(6)H(4)Z (X = O and S) in dry MeCN at 25 degrees C are reported. Hammett rho values are 2.18 +/- 0.13 and 0.89 +/- 0.07 for DABCO reactions with (CO)(5)Cr=C(OMe)C(6)H(4)Z (10-Cr-Z) and (CO)(5)Cr=C(SMe)C(6)H(4)Z (11-Cr-Z), respectively. The rho values for the reaction of 10-Cr-Z and 11-Cr-Z with CH(CN)(2)(-) in 50% MeCN-50% H(2)O (v/v) are comparable to the present reactions. The reaction of DABCO with 10-Cr-Z is more closely related to the reaction of (n-Bu)(3)P with (CO)(5)W=C(OMe)C(6)H(5)-Z (23) which also provided a rho value 2.22. The much higher rho values and hence much higher reactivity of methoxy carbene complexes over the corresponding thiomethyl derivatives fit a pattern observed previously for alkoxide ion, OH(-), amine, and thiolate ion nucleophiles, and a rational explanation comes from the consideration of the substituent effects not only on the transition state but also on the reactant. A major difference between 10-Cr-Z and 11-Cr-Z is that the pi-donor effect of the methoxy group is much stronger than that of thiomethyl group. This leads to a substantial contribution of the zwitterionic form to the structure of 10-Cr-Z with much more localized positive charge on the methoxy group than the negative charge on the (CO)(5)Cr moiety. This leads to overall destabilization by an electron-withdrawing phenyl substituents resulting an increase in reactivity. The ethoxycarbene complexes are somewhat less reactive than their methoxy counterparts due to the somewhat more ground state stabilization through its stronger pi donor effect and partly due to steric crowding exerted by the slightly larger ethoxy group in the transition state. Higher k(1)(W)/k(1)(Cr) ratios for (thiomethyl)carbene complexes than methoxy or ethoxycarbene complexes are related to the intrinsic rate constant which is higher for ((thiomethyl)carbene)tungsten complexes than the corresponding Cr ones resulting in an enhanced ratio.

Mechanistic Plasticity of DNA Topoisomerase IB: Phosphate Electrostatics Dictate the Need for a Catalytic Arginine

Four conserved amino acids of type IB topoisomerases (Arg130, Lys167, Arg223, and His265 in vaccinia topoisomerase) catalyze the attack by tyrosine on the scissile phosphodiester to form a DNA-(3'-phosphotyrosyl)-enzyme intermediate. The mechanism entails general acid catalysis (by Lys167 and Arg130) and transition-state stabilization (via contact of His265 with the pro-Sp oxygen). Here we query the function of Arg223, which accelerates transesterification by a factor of 10(5). The requirement for Arg223 is alleviated by a neutral Sp methylphosphonate (MeP) linkage at the cleavage site. Arg223 is not required for the 30,000-fold activation of the latent endonuclease activity of topoisomerase by the Sp MeP. The rate of autohydrolysis by the DNA-(3'-MeP)-topoisomerase intermediate approaches 10% of the rate of religation to a 5'-OH DNA strand. These findings underscore the importance of transition-state electrostatics in determining the composition of the active site and dictating the balance between strand transferase and hydrolase functions.

Analogues of Vaccinia Virus DNA Topoisomerase I Modified at the Active Site Tyrosine

The mechanism of type IB topoisomerase-mediated DNA relaxation was studied by modification of vaccinia topoisomerase I at the active site tyrosine (position 274) with several tyrosine analogues. These analogues had varied steric, electronic, and stereochemical features to permit assessment of those structural elements required to support topoisomerase function. Eleven tyrosine analogues were successfully incorporated into the active site of vaccinia topoisomerase I. It was found that only tyrosine analogues having the phenolic -OH group in the normal position relative to the protein backbone were active. Modifications that replaced the nucleophilic tyrosine OH (pKa approximately 10.0) group with NH2 (pKa 4.6), SH (pKa approximately 7.0), or I groups or that changed the orientation of the nucleophilic OH group essentially eliminated topoisomerase I function. For the active analogues, the electronic effects and H-bonding characteristics of substituents in the meta-position of the aromatic ring may be important in modulating topoisomerase I function. The pH profile for the functional analogues revealed a small shift toward lower pH when compared with wild-type topoisomerase I.

Reaction Pathways and Free Energy Barriers for Alkaline Hydrolysis of Insecticide 2-Trimethylammonioethyl Methylphosphonofluoridate and Related Organophosphorus Compounds: Electrostatic and Steric Effects

Reaction pathways and free energy barriers for alkaline hydrolysis of the highly neurotoxic insecticide 2-trimethylammonioethyl methylphosphonofluoridate and related organophosphorus compounds were studied by performing first-principles electronic structure calculations on representative methylphosphonofluoridates, (RO)CH3P(O)F, in which R = CH2CH2N+(CH3)3, CH3, CH2CH2C(CH3)3, CH2CH2CH(CH3)2, CH(CH3)CH2N+(CH3)3, and CH(CH3)CH2N(CH3)2. The dominant reaction pathway was found to be associated with a transition state in which the attacking nucleophile OH- and the leaving group F- are positioned on opposite sides of the plane formed by the three remaining atoms attached to the phosphorus in order to minimize the electrostatic repulsion between these two groups. The free energy barriers calculated for the rate-determining step of the dominant pathway are 12.5 kcal/mol when R = CH2CH2N+(CH3)3, 15.5 kcal/mol when R = CH3, 17.9 kcal/mol when R = CH2CH2C(CH3)3, 16.5 kcal/mol when R = CH2CH2CH(CH3)2, 13.4 kcal/mol when R = CH(CH3)CH2N+(CH3)3, and 18.7 kcal/mol when R = CH(CH(3))CH(2)N(CH(3))(2). The calculated free energy barriers are in good agreement with available experimentally derived activation free energies, i.e. 14.7 kcal/mol when R = CH(3), 13.4 kcal/mol when R = CH2CH2N+(CH3)3, and 13.9 kcal/mol when R = CH(CH3)CH2N+(CH3)3. A detailed analysis of the calculated energetic results and available experimental data suggests that the net charge of the molecule (M) being hydrolyzed is a prominent factor affecting the free energy barrier (DeltaG) for the alkaline hydrolysis of phosphodiesters, phosphonofluoridates, and related organophosphorus compounds. The electrostatic interactions between the attacking nucleophile OH- and the molecule M being hydrolyzed favor such an order of the free energy barrier: DeltaG(M(+)+OH-) < DeltaG(M0+OH-) < DeltaG(M(-)+OH-), where M+, M0, and M- represent the cationic, neutral, and anionic molecules, respectively. The change of the substituent R in (RO)CH(3)P(O)F from CH3 to CH2CH2N+(CH3)3 is associated with both the electrostatic and steric effects on the free energy barrier, but the electrostatic effect dominates the substituent shift of the free energy barrier. This helps to better understand why the alkaline hydrolysis of (RO)CH3P(O)F with R = CH2CH2N+(CH3)3 and CH(CH3)CH2N+(CH3)3 is significantly faster than that with R = CH3. The effect of electrostatic interaction also helps to understand why the rate constants for the alkaline hydrolysis of phosphodiesters, such as intramolecular second messenger adenosine 3',5'-phosphate (cAMP), are generally smaller than those for the alkaline hydrolysis of the phosphonofluoridates and related phosphotriesters.

Synthesis and X-ray structural characterisation of the tetramethylene oxonium derivative of the hydrodecaborate anion. A versatile route for derivative chemistry of [B 10H 10] 2−

The oxonium derivative P(C 6H 5) 4[2-B 10H 9O(CH 2) 4] ( 1) has been prepared from [B 10H 10] 2− by a solvent-addition reaction route, promoted by Et 2O · BF 3. Its structure has been confirmed by single crystal X-ray analysis. 1 is assumed to be a useful synthon for the derivative chemistry of [B 10H 10] 2−. As an illustration, ring-opening reaction occurred in presence of the strong nucleophilic agent OH −, giving the monoanionic derivative [P(C 6H 5) 4] 2[2-B 10H 9O(CH 2) 4OH] ( 2).

A conformational switch controls hepatitis delta virus ribozyme catalysis.

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

Synthesis, characterization and electrochemical behavior of mononuclear, binuclear nickel(II) and heterobinuclear zinc(II)nickel(II) complexes derived from novel macrobicyclic tricompartmental ligands: kinetics of the catalytic hydrolysis of 4-nitrophenyl phosphate by the complexes

Mononuclear, binuclear NiII and heterobinuclear ZnIINiII complexes have been derived from lateral macrobicyclic tricompartmental ligands embracing three different donor sets: (i) O2N2-donor set, derived from ether oxygens and tertiary amine nitrogens; (ii) N2O2-donor set, derived from tertiary amine nitrogens and phenolic oxygens; (iii) O2N2-donor set, derived from phenolic oxygens and azomethine nitrogens. Cyclic voltammograms of the mononuclear NiII complexes showed irreversible one-electron reduction processes in the −1.2 to −1.3 V region and an irreversible oxidation process in the range +0.8 V potential region. The binuclear complexes showed quasireversible two-step single electron reduction processes around the −1.3 and −1.7 V potential regions. The anodic potential region showed an irreversible oxidation process at +1.0 V. The heterobinuclear ZnIINiII complex showed an irreversible reduction of the NiII species at −1.55 V. The catalytic hydrolysis towards 4-nitrophenyl phosphate by the mononuclear, binuclear NiII complexes and the heterobinuclear complex were found to be appreciable. The pseudo-first order rate constant for the catalytic hydrolysis catalyzed by the binuclear and heterobinuclear complexes were found to be higher (9.8 × 10−4 s−1) than that of the corresponding mononuclear complexes (1.3 × 10−5 s−1), which ascertain the requirement of two metal ions in close proximity for the binding of the nucleophilic OH and the phosphate group.