Carboxamide substituted tetramethylcyclopentadiene - synthesis, characterisation and its iridium(III) complex catalysed reduction of imines.

The novel dimeric iodo-iridium(III) complex, [Ir(Cp*CONMe2)I2]2, (Cp*CONMe2 = η5-N,N-2,3,4,5-hexamethylcyclopenta-2,4-diene carboxamide) bearing an amide moiety within the tetramethylcyclopentadiene ring, has been synthesised and characterised. The ligand Cp*CONMe2 is synthesised as two regioisomers, however the 2-substituted isomer exists as two distinguishable conformers due to restricted rotation about the amide carbonyl carbon and the ring carbon. The relative acidities of Cp*CONMe2 and Cp* are compared by their relative rates of H/D exchange. The iridium complex of N,N-2,3,4,5-hexamethylcyclopenta-2-4-diene carboxamide [IrCp*CONMe2] and (R,R)-1,2-diphenyl-N'-tosylethane-1,2-diamine ((R,R)-TsDPEN) has been evaluated in the transfer hydrogenation of imines under acidic conditions - a 5 : 2 molar ratio of formic acid : triethylamine as the hydride source for the transfer hydrogenation of 1-methyl-3,4-dihydroisoquinoline (DHIQ) and its 6,7-dimethoxy derivative in acetonitrile. A decreasing enantiomeric excess with reaction progress is attributed to different kinetic orders for formation of the two product amine enantiomers. The pseudo zero-order formation of the R-amine may be due to a pre-steady-state formation of the less stable form of the diastereomeric catalyst. By contrast, both enantiomeric amines from 1-fluorinated methyl DHIQs as substrates for reduction are formed by pseudo first-order processes.

Both the mono- and di-anions of ellagic acid are effective inhibitors of the serine ß-lactamase CTX-M-15.

Ellagic acid, a δ-lactone with ionisable phenolic residues, is an efficient time-dependent inhibitor of the serine ß-lactamase enzyme CTX-M-15. The pH-dependence of the rate of inhibition shows that both the mono- and di-anionic species of ellagic acid are effective inhibitors, both with second order rate constants of ∼1.5 × 104 M-1 s-1. The structurally similar δ-lactone urolithin A, which lacks the geometrically appropriate phenolic residue, shows only modest inhibitory activity against CTX-M-15. It is proposed that this inhibition by ellagic acid anions involves acylation of the active site serine and that the negative charge on the inhibitor is required for binding to the active site.

Phosphorothioate anti-sense oligonucleotides: the kinetics and mechanism of the sulfurisation of phosphites by phenylacetyl disulfide (PADS).

In the pharmaceutical industry the sulfurisation of nucleotide-phosphites to produce more biologically stable thiophosphates is often achieved using 'aged' solutions of phenylacetyl disulfide (PADS) which consist of a mixture of polysulfides that are more efficient sulfur transfer reagents. However, both 'fresh' and 'aged' solutions of PADS are capable of the sulfurisation of phosphites. The rates of both processes in acetonitrile are first order in sulfurising agent, phosphite and a pyridine base, although with 'aged' PADS the rate becomes independent of base at high concentrations. The Brönsted ß values for sulfurisation using 'fresh' and 'aged' PADS with substituted pyridines are 0.43 and 0.26, respectively. With 'fresh' PADS the Brönsted ßnuc = 0.51 for substituted trialkyl phosphites is consistent with a mechanism involving nucleophilic attack of the phosphite on the PADS disulfide bond to reversibly generate a phosphonium intermediate, the rate-limiting breakdown of which occurs by a base catalysed elimination process, confirmed by replacing the ionisable hydrogens in PADS with methyl groups. The comparable polysulfide phosphonium ion intermediate seen with 'aged' PADS presents a more facile pathway for product formation involving S-S bond fission as opposed to C-S bond fission.

Phosphorothioate anti-sense oligonucleotides: the kinetics and mechanism of the generation of the sulfurising agent from phenylacetyl disulfide (PADS).

The synthesis of phosphorothioate oligonucleotides is often accomplished in the pharmaceutical industry by the sulfurisation of the nucleotide-phosphite using phenylacetyl disulfide (PADS) which has an optimal combination of properties. This is best achieved by an initial 'ageing' of PADS for 48 h in acetonitrile with 3-picoline to generate polysulfides. The initial base-catalysed degradation of PADS occurs by an E1cB-type elimination to generate a ketene and acyldisulfide anion. Proton abstraction to reversibly generate a carbanion is demonstrated by H/D exchange, the rate of which is greatly increased by electron-withdrawing substituents in the aromatic ring of PADS. The ketene can be trapped intramolecularly by an o-allyl group. The disulfide anion generated subsequently attacks unreacted PADS on sulfur to give polysulfides, the active sulfurising agent. The rate of degradation of PADS is decreased by less basic substituted pyridines and is only first order in PADS indicating that the rate-limiting step is formation of the disulfide anion from the carbanion.

The kinetics and mechanism of the organo-iridium catalysed racemisation of amines.

The dimeric iodo-iridium complex [IrCp*I2]2 (Cp* = pentamethylcyclopentadiene) is an efficient catalyst for the racemisation of secondary and tertiary amines at ambient and higher temperatures with a low catalyst loading. The racemisation occurs with pseudo-first-order kinetics and the corresponding four rate constants were obtained by monitoring the time dependence of the concentrations of the (R) and (S) enantiomers starting with either pure (R) or (S) and show a first-order dependence on catalyst concentration. Low temperature (1)H NMR data is consistent with the formation of a 1 : 1 complex with the amine coordinated to the iridium and with both iodide anions still bound to the metal-ion, but at the higher temperatures used for kinetic studies binding is weak and so no saturation zero-order kinetics are observed. A cross-over experiment with isotopically labelled amines demonstrates the intermediate formation of an imine which can dissociate from the iridium complex. Replacing the iodides in the catalyst by other ligands or having an amide substituent in Cp* results in a much less effective catalysts for the racemisation of amines. The rate constants for a deuterated amine yield a significant primary kinetic isotope effect kH/kD = 3.24 indicating that hydride transfer is involved in the rate-limiting step.

The kinetics and mechanism of the organo-iridium-catalysed enantioselective reduction of imines.

The iridium complex of pentamethylcyclopentadiene and (S,S)-1,2-diphenyl-N'-tosylethane-1,2-diamine is an effective catalyst for the asymmetric transfer hydrogenation of imine substrates under acidic conditions. Using the Ir catalyst and a 5 : 2 ratio of formic acid : triethylamine as the hydride source for the asymmetric transfer hydrogenation of 1-methyl-3,4-dihydroisoquinoline and its 6,7-dimethoxy substituted derivative, in either acetonitrile or dichloromethane, shows unusual enantiomeric excess (ee) profiles for the product amines. The reactions initially give predominantly the (R) enantiomer of the chiral amine products with >90% ee but which then decreases significantly during the reaction. The decrease in ee is not due to racemisation of the product amine, but because the rate of formation of the (R)-enantiomer follows first-order kinetics whereas that for the (S)-enantiomer is zero-order. This difference in reaction order explains the change in selectivity as the reaction proceeds - the rate formation of the (R)-enantiomer decreases exponentially with time while that for the (S)-enantiomer remains constant. A reaction scheme is proposed which requires rate-limiting hydride transfer from the iridium hydride to the iminium ion for the first-order rate of formation of the (R)-enantiomer amine and rate-limiting dissociation of the product for the zero-order rate of formation of the (S)-enantiomer.

Micelle Formation in Liquid Ammonia.

Perfluorinated long chain alkyl amides aggregate in liquid ammonia with increasing concentration which reflects micelle-type formation based on changes in (19)F NMR chemical shifts. The critical micelle concentrations (cmc) decrease with increasing chain length and give Kleven parameters A = 0.18 and B = 0.19. The micelles catalyze the ammonolysis of esters in liquid ammonia. The corresponding perfluorinated long chain alkyl carboxylates form ion pairs in liquid ammonia, but the equilibrium dissociation constants indicate favorable interactions between the chains in addition to the electrostatic forces. These perfluorinated carboxylates form micelles in aqueous solution, and their cmc's generate a Kleven B-value = 0.52 compared with 0.30 for the analogous alkyl carboxylates. The differences in hydrophobicity of CH2 and CF2 units in water and liquid ammonia are discussed, as is the possible relevance to life forms in liquid ammonia.

Unusual stability and carbon acidity of a dicationic carbon species.

1,1'-Methylenebis(pyridinium) dication (MDP) is an unusual ion with two formal positively charged substituents attached to a central carbon, yet it is remarkably stable to hydrolysis at pH < 8. However, above this pH it undergoes a biphasic reaction liberating two equiv of pyridine sequentially. The rate of the first phase is second order in hydroxide ion, while that of the second is pH-independent. The first phase is also accompanied by the generation of a chromophore at 366 nm, which has been identified as a pyridine-ring-opened unsaturated iminoaldehyde formed by an ANRORC-type mechanism. This intermediate then undergoes ring closure to give the second equiv of pyridine and formaldehyde. Below pD 8 there is a very slow alternative pathway for degradation that is first order in hydroxide ion, liberates only one equiv of pyridine, and forms N-(hydroxymethyl)pyridinium ion. Deuterium exchange of the central methylene in D2O is faster than the breakdown of MDP and is predominantly OD(-)-catalyzed with a small amount of buffer catalysis. The estimated pKa of MDP dication in H2O, 21.2 at 25 °C and I = 1.0 M (KCl), is unexpectedly high but is about 9 units lower than that for the monocationic N-methylpyridinium ion. Deuterium exchange also occurs at the 2 and 6 positions of the pyridinium rings, but at a lower rate that is first order in deuteroxide ion and competitive with the breakdown of MDP only below pD 11.

Copper catalysed azide-alkyne cycloaddition (CuAAC) in liquid ammonia.

Copper(I) catalysed azide-alkyne cycloaddition reactions (CuAAC) occur smoothly in liquid ammonia (LNH(3)) at room temperature to give exclusively 1,4-substituted 1,2,3-triazoles with excellent yields (up to 99%). The CuAAC reactions in liquid ammonia require relatively small amounts of copper(I) catalyst (0.5 mole%) compared with that in conventional solvents. The product can be obtained conveniently by simply evaporation of ammonia, indicating its potential application in industry. The rate of the CuAAC reaction in liquid ammonia shows a second order dependence on the copper(I) concentration and the reaction occurs only with terminal alkynes. Deuterium exchange experiments with phenyl acetylene-d(1) show that the acidity of the alkyne is increased at least 1000-fold with catalytic amounts of copper(I) in liquid ammonia. The mechanism of the CuAAC reaction in liquid ammonia is discussed.

Copper(I)-catalyzed amination of aryl halides in liquid ammonia.

The amination of aryl halides in liquid ammonia (LNH(3)) is catalyzed by a copper(I) salt/ascorbate system to yield primary aromatic amines in good to excellent yields. The low concentrations of catalyst required and the ease of product isolation suggest that this process has potential industrial applications. Commonly used ligands for analogous metal-catalyzed reactions are not effective. The rate of amination of iodobenzene in liquid ammonia is first order in copper(I) catalyst concentration. The small Hammett ρ = 0.49 for the amination of 4-substituted iodobenzenes in liquid ammonia at 25 °C indicates that the C-I bond is not significantly broken in the transition state structure and that there is a small generation of negative charge in the aryl ring, which is compatible with the oxidative addition of the copper ion being rate limiting.

Reactive intermediates in the H-phosphonate synthesis of oligonucleotides.

The formation of H-phosphonate diesters is an important step in the synthesis of oligonucleotides. Using diphenylchlorophosphate as the activator for the coupling step is often accompanied by side reactions as a result of self 'capping' and other reactions of the reactive intermediate. In the absence of base, the activation of ethyl H-phosphonate with diphenylchlorophosphate probably occurs through the intermediate formation of bis diethyl pyro-di-H-phosphonate rather than the expected diphenyl ethyl pyro-H-phosphonate. Pyridine acts as a nucleophilic catalyst converting diphenylchlorophosphate to its pyridinium adduct. Several side and unwanted reactions are quantified so that conditions to minimise these can be identified.

Organic reactivity in liquid ammonia.

Liquid ammonia is a useful solvent for many organic reactions including aliphatic and aromatic nucleophilic substitution and metal-ion catalysed reactions. The acidity of acids is modified in liquid ammonia giving rise to differences from conventional solvents. The ionisation constants of phenols and carbon acids are the product of those for ion-pair formation and dissociation to the free ions. There is a linear relationship between the pK(a) of phenols and carbon acids in liquid ammonia and those in water of slope 1.68 and 0.7, respectively. Aminium ions exist in their unprotonated free base form in liquid ammonia. The rates of solvolysis and aminolysis by neutral amines of substituted benzyl chlorides in liquid ammonia show little or no dependence upon ring substituents, in stark contrast with the hydrolysis rates of substituted benzyl halides in water which vary 10(7) fold. However, the rates of the reaction of phenoxide ions and amine anions with 4-substituted benzyl chlorides gives a Hammett ρ = 1.1 and 0.93, respectively. The second order rate constants for the substitution of benzyl chlorides by neutral and anionic amines show a single Brønsted ß(nuc) = 0.21 whereas those for substituted phenoxide ions generate a Brønsted ß(nuc) = 0.40. The rates of aromatic nucleophilic substitution reactions in liquid ammonia are much faster than those in protic solvents indicating that liquid ammonia behaves like a typical dipolar aprotic solvent in its solvent effects on organic reactions. Nitrofluorobenzenes (NFB) readily undergo solvolysis in liquid ammonia but oxygen nucleophiles, such as alkoxide and phenoxide ions, displace the fluorine of 4-NFB in liquid ammonia to give the corresponding substitution product with little or no competing solvolysis product. The Brønsted ß(nuc) for the reaction of 4-NFB with para-substituted phenoxides is 0.91, indicative that the decomposition of the Meisenheimer σ-intermediate is rate limiting. The aminolysis of 4-NFB occurs without general base catalysis by the amine and the second order rate constants generate a Brønsted ß(nuc) of 0.36, which is also interpreted in terms of rate limiting breakdown of the Meisenheimer σ-intermediate.

Ionization of carbon acids in liquid ammonia.

The acidities of various carbon acids in liquid ammonia (LNH(3)) at room temperature were determined by NMR and rates of D-exchange. There is a reasonable linear correlation of the pK(a)s in LNH(3) with those in water and DMSO of slope 0.7 and 0.8, respectively. Carbon acids with an aqueous pK(a) of less than 12 are fully ionized in liquid ammonia. Nucleophilic substitution of benzyl chloride by carbanions in liquid ammonia generates a Brønsted ß(nuc) = 0.38.

The kinetics and mechanisms of aromatic nucleophilic substitution reactions in liquid ammonia.

The rates of aromatic nucleophilic substitution reactions in liquid ammonia are much faster than those in protic solvents indicating that liquid ammonia behaves like a typical dipolar aprotic solvent in its solvent effects on organic reactions. Nitrofluorobenzenes (NFBs) readily undergo solvolysis in liquid ammonia and 2-nitrofluorobenzene is about 30 times more reactive than the 4-substituted isomer. Oxygen nucleophiles, such as alkoxide and phenoxide ions, readily displace fluorine of 4-NFB in liquid ammonia to give the corresponding substitution product with little or no competing solvolysis product. Using the pK(a) of the substituted phenols in liquid ammonia, the Brønsted ß(nuc) for the reaction of 4-NFB with para-substituted phenoxides is 0.91, indicative of the removal of most of the negative charge on the oxygen anion and complete bond formation in the transition state and therefore suggests that the decomposition of the Meisenheimer σ-intermediate is rate limiting. The aminolysis of 4-NFB occurs without general base catalysis by the amine and the second-order rate constants generate a Brønsted ß(nuc) of 0.36 using either the pK(a) of aminium ion in acetonitrile or in water, which is also interpreted in terms of rate limiting breakdown of the Meisenheimer σ-intermediate. Nitrobenzene and diazene are formed as unusual products from the reaction between sodium azide and 4-NFB, which may be due to the initially formed 4-nitroazidobenzene decomposing to give a nitrene intermediate, which may then give diazene or be trapped by ammonia to give the unstable hydrazine which then yields nitrobenzene.

Liquid ammonia as a dipolar aprotic solvent for aliphatic nucleophilic substitution reactions.

The rate constants for the reactions of a variety of nucleophiles reacting with substituted benzyl chlorides in liquid ammonia (LNH(3)) have been determined. To fully interpret the associated linear free-energy relationships, the ionization constants of phenols ions in liquid ammonia were obtained using UV spectra. These equilibrium constants are the product of those for ion-pair formation and dissociation to the free ions, which can be separated by evaluating the effect of added ammonium ions. There is a linear relationship between the pK(a) of phenols in liquid ammonia and those in water of slope 1.68. Aminium ions exist in their unprotonated free base form in liquid ammonia and their ionization constants could not be determined by NMR. The rates of solvolysis of substituted benzyl chlorides in liquid ammonia at 25 °C show a Hammett ρ of zero, having little or no dependence upon ring substituents, which is in stark contrast with the hydrolysis rates of substituted benzyl halides in water, which vary 10(7) fold. The rate of substitution of benzyl chloride by substituted phenoxide ions is first order in the concentration of the nucleophile indicative of a S(N)2 process, and the dependence of the rate constants on the pK(a) of the phenol in liquid ammonia generates a Brønsted ß(nuc) = 0.40. Contrary to the solvolysis reaction, the reaction of phenoxide ion with 4-substituted benzyl chlorides gives a Hammett ρ = 1.1, excluding the 4-methoxy derivative, which shows the normal positive deviation. The second order rate constants for the substitution of benzyl chlorides by neutral and anionic amines show a single Brønsted ß(nuc) = 0.21 (based on the aqueous pK(a) of amine), but their dependence on the substituent in substituted benzyl chlorides varies with a Hammett ρ of 0 for neutral amines, similar to that seen for solvolysis, whereas that for amine anions is 0.93, similar to that seen for phenoxide ion.

The kinetics and mechanism of the acid-catalysed detritylation of nucleotides in non-aqueous solution.

The kinetics and mechanism of the deprotection (detritylation) of 5'-O-(4,4'-dimethoxytrityl)-2'-deoxythymidine nucleoside catalysed by dichloroacetic acid to give a 4,4'-dimethoxytrityl carbocation have been studied in toluene, dichloromethane and acetonitrile. There is little or no effect of solvent polarity on the equilibrium and rate constants. Entropies of activation are highly negative approximately -105 J K(-1) mol(-1) and similarly show little variation with solvent. Addition of small amounts of water to the reaction medium reduces the detritylation rate, presumably through its effect on the solution acidity. All observations are compatible with detritylation occurring through a concerted general acid-catalysed mechanism rather than a stepwise A1 process.

The mechanism of the phosphoramidite synthesis of polynucleotides.

The mechanism of the coupling step in polynucleotide synthesis using 5'-4,4'-dimethoxytritylthymidine-3'-beta-cyanoethyl-N,N-diisopropylphosphoramidite as the phosphitylating agent and catalysed by the salt of saccharin and N-methylimidazole in acetonitrile has been studied by (31)P NMR. Pre- and post-equilibria between the activator salt and released diisopropylamine have been examined by (1)H NMR and ITC, which show that the salt between saccharin and diisopropylamine will be present in acetonitrile. Activation of the phosphoramidite by the salt of saccharin and N-methylimidazole involves nucleophilic catalysis and the formation of a reactive saccharin adduct bonded through its carbonyl oxygen to phosphorus. The rate constants for the reaction of the 4-methoxyphenol with 5'-4,4'-dimethoxytritylthymidine-3'-beta-cyanoethyl-N,N-diisopropylphosphoramidite in the presence of saccharin-N-methylimidazole salt show a non-linear dependence on phenol concentration, becoming independent at high phenol concentrations, compatible with a change in rate limiting step from the alcoholysis step to the activation step.

The mechanisms of catalysis by metallo beta-lactamases.

Class B beta-lactamases or metallo-beta-lactamases (MBLs) require zinc ions to catalyse the hydrolysis of beta-lactam antibiotics such as penicillins, cephalosporins, carbapenems, and cephamycins. There are no clinically useful inhibitors against MBLs which are responsible for the resistance of some bacteria to antibiotics. There are two metal-ion binding sites that have different zinc ligands but the exact roles of the metal-ion remain controversial, and distinguishing between their relative importance is complex. The metal-ion can act as a Lewis acid by co-ordination to the beta-lactam carbonyl oxygen to facilitate nucleophilic attack and stabilise the negative charge developed on this oxygen in the tetrahedral intermediate anion. The metal-ion also lowers the pKa of the directly co-ordinated water molecule so that the metal-bound hydroxide ion is a better nucleophile than water and is used to attack the beta-lactam carbonyl carbon. An intrinsic property of binuclear metallo hydrolytic enzymes that depend on a metal-bound water both as the attacking nucleophile and as a ligand for the second metal-ion is that this water molecule, which is consumed during hydrolysis of the substrate, has to be replaced to maintain the catalytic cycle. With MBL this is reflected in some unusual kinetic profiles.

An activated sulfonylating agent that undergoes general base-catalyzed hydrolysis by amines in preference to aminolysis.

Activated sulfonyl derivatives, similar to acyl ones, usually undergo aminolysis with amines in water as nucleophilic attack by the amine is preferred to hydrolysis. However, despite being active sulfonyl derivatives, four-membered heterocyclic sulfonamides, beta-sultams, do not undergo aminolysis in aqueous solution but preferentially react to give hydrolysis products only. The rate of the reaction of beta-sultams in buffered solutions of simple primary amines shows a first-order dependence on amine concentrations attributed to general base-catalyzed hydrolysis by the amine. Even N-benzyl-4,4-dimethyl-3-oxo-beta-sultam, which is both a beta-sultam and a beta-lactam, undergoes hydrolysis at the sulfonyl center rather than aminolysis at either the sulfonyl or acyl center. The solvent kinetic isotope effects (SKIE, k(H(2)O)/k(D(2)O)) for the amine-catalyzed hydrolyses are 1.4 and 1.9 for the hydrolysis of N-benzoyl-beta-sultam and N-benzyl-4,4-dimethyl-3-oxo-beta-sultam, respectively, compatible with a general base-catalyzed mechanism. The amine-catalyzed hydrolysis gives a Bronsted beta value of +0.9 for both N-benzoyl beta-sultam and N-benzyl-4,4-dimethyl-3-oxo-beta-sultam, indicating that the general base amine is almost fully protonated in the transition state. A general base-catalyzed mechanism for hydrolysis rather than nucleophilic attack was also deduced for the reaction of N-benzyl-4,4-dimethyl-3-oxo-beta-sultam with carboxylate anions based on a SKIE of 1.7-1.9 and rate constants which fit the Bronsted plot for amines. In contrast to acyl transfer reactions, those for sulfonyl transfer appear to show an inverse reactivity-selectivity relationshipthe most active compounds being the most selective. The lack of reactivity of beta-sultams toward amine nucleophiles appears to be related to the mechanism of ring opening of beta-sultams with a decreased reactivity toward amines relative to hydroxide ion, probably related to the expulsion of the relatively poor leaving group amide anion.

Loss of enzyme activity during turnover of the Bacillus cereus beta-lactamase catalysed hydrolysis of beta-lactams due to loss of zinc ion.

Metallo-beta-lactamases are zinc-ion-dependent and are known to exist either as mononuclear or as dinuclear enzymes. The kinetics and mechanism of hydrolysis of the native zinc Bacillus cereus metallo-beta-lactamase (BcII) have been investigated under pre-steady-state conditions at different pHs and zinc-ion concentrations. Biphasic kinetics are observed for the hydrolysis of cefuroxime and benzylpenicillin with submicromolar concentrations of enzyme and zinc. The initial burst of product formation far exceeds the concentration of enzyme and the subsequent slower rate of hydrolysis is attributed to a branched kinetic pathway. The pH and metal-ion dependence of the microscopic rate constants of this branching were determined, from which it is concluded that two enzyme species with different metal-to-enzyme stoichiometries are formed during catalytic turnover. The dizinc enzyme is responsible for the fast route but during the catalytic cycle it slowly loses the less tightly bound zinc ion via the branching route to give an inactive monozinc enzyme; the latter is only catalytic following the uptake of a second zinc ion. The rate constant for product formation from the dinuclear enzyme and the branching rate constant show a sigmoidal dependence on pH indicative of important ionizing groups with pK(a)s of 9.0+/-0.1 and 8.2+/-0.1, respectively. The rate constant for the regeneration of enzyme activity depends on zinc-ion concentration. This unusual behaviour is attributed to an intrinsic property of metallo hydrolytic enzymes that depend on a metal bound water both as a ligand for the second metal ion and as the nucleophile which is consumed during hydrolysis of the substrate and so has to be replaced to maintain the catalytic cycle.