Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction.     

Equilibrium of formation of the 6-carbanion of UMP,a potential intermediate in the action of OMP decarboxylase

There has been some speculation that the C-6 position in UMP may be unusually acidic, stabilizing a carbanion that is generated at this position during OMP decarboxylation. On the basis of the rate of OH- catalyzed deuterium exchange at elevated temperatures we estimate that the pKa value for ionization at C-6 of dimethyl uracil is 34 +/- 2 in water. The same method yields a value of 37 +/- 2 for ionization at C-2 of thiophene in good agreement with the value determined by polarographic methods. The barrier to proton release (46 kcal/mol) is even higher than that for CO2 release from orotic acid derivatives.     

OMP decarboxylase: an experimental test of electrostatic destabilization of the enzyme-substrate complex

6-Methylaminouridine 5'-phosphate (MAUMP) inhibits OMP decarboxylase (Ki = 3 x 10-6 M) maximally at pH values where its amino group is uncharged. Comparison of the chemical shift of free [7-13C]-MAUMP in solutions of varying pH, with that of the enzyme-bound species confirms that this inhibitor is bound with its amino group uncharged. This enzyme's apparent lack of affinity for a cationic substituent, located near the position that would ordinarily be occupied by the scissile carboxylate group of the substrate, does not appear to support the view that the E-S complex is destabilized by electrostatic repulsion in the ground state.     

Solvolysis of 4-methylcyclohexylidenemethyliodonium salt: chirality probe approach to a primary vinyl cation intermediate

Optically active 4-methylcyclohexylidenemethyl(aryl)iodonium tetrafluoroborate (1.BF(4)(-)) was prepared and its solvolysis was carried out at 60 degrees C in various solvents. The main product is optically active 4-methylcycloheptanone (or its enol derivative) in unbuffered solvents, accompanied by the iodoarene. The rearranged product always maintains the optical purity of the starting 1. Its stereochemistry conforms to a mechanism involving the rearrangement via the sigma-bond participation in departure of the nucleofuge, followed by trapping of the resulting chiral 5-methylcyclohept-1-enyl cation with a nucleophilic solvent. That is, the achiral, primary vinyl cation is not involved during the reaction. The unrearranged substitution product is also obtained in a minor fraction in unbuffered methanol, ethanol, and acetic acid, but not in trifluoroethanol or hexafluoro-2-propanol: the methoxy product from methanolysis is largely racemized, but the acetolysis product is obtained mainly via retention of configuration. Reactions of 1 with bromide, acetate, and trifluoroacetate in chloroform give unrearranged substitution products in different degrees of inversion. These unrearranged products are concluded to be formed via the direct nucleophilic substitutions. Added bases such as sodium acetate in methanol lead to the unrearranged methoxy products of complete racemization, which is ascribed to the alpha elimination (to give an alkylidenecarbene) followed by the solvent insertion.     

Use of SDS micelles to stabilize a ternary intermediate in the reaction of ferrioxamine B and 1,10-phenanthroline

Spectrophotometric measurements of the reaction of ferrioxamine B (FeHDFB(+)) with 1,10-phenanthroline (phen) reveal the presence of a ternary intermediate complex in both aqueous solution and an aqueous solution of 0.16 M sodium dodecyl sulfate (SDS). The stoichiometry of the intermediate is Fe(H(2)DFB)(phen)(2+) on the basis of a Schwarzenbach analysis of spectrophotometric data obtained at variable pH and phen concentrations. The ternary complex formation constant for the reaction FeHDFB(+) + H(+) + phen right arrow over left arrow Fe(H(2)DFB)(phen)(2+) is log K = 6.96 in aqueous solution and log K = 8.64 in aqueous 0.16 M SDS. The enhanced stability of Fe(H(2)DFB)(phen)(2+) in micellar solution was analyzed in terms of the pseudophase ion-exchange (PPIE) model of micellar reactions. The association constants for the binding of each reactant to the micellar pseudophase were measured by ultrafiltration. According to PPIE model calculations, the enhanced stability of Fe(H(2)DFB)(phen)(2+) in micellar SDS arises from a proximity effect created by the high local concentrations of reactants in the micellar pseudophase. The calculations also indicate that an inhibitory medium or compartmentalization effect is operative since the observed micellar enhancement is much smaller than predicted by the PPIE model. The micellar stabilization of the Fe(H(2)DFB)(phen)(2+) intermediate and the overall conversion of FeHDFB(+) to Fe(phen)(3)(2+) are discussed as a possible model system for siderophore iron release in microbial organisms.     

Reversible reaction via a carbanion intermediate in the elimination of ammonia from L-histidine catalysed by histidine ammonia-lyase

L-[5'-2H2]Histidine was used as a substrate to investigate the enzymatic reaction mechanism with histidine ammonia-lyase from Pseudomonas fluorescens. The study was performed to determine the exchange rate of deuterium at C-5' of the imidazole ring with solvent hydrogen relative to the net urocanic acid production. The extent of hydrogen exchange at C-5' of histidine or urocanic acid was measured by gas chromatography-mass spectrometry-selected ion monitoring, monitoring the molecular ion intensities of the respective gas chromatographic derivatives, at m/z 380 and 379 for histidine and at m/z 267 and 266 for urocanic acid. The observed hydrogen exchange at C-5' suggested a reversible mechanism via a carbanion intermediate in the reaction with histidine ammonia-lyase.     

2-(3,5-Dinitrophenyl)-1,3-dithiane carbanion: a benzylic anion with a low energy triplet state

Calculations at the DFT level predict that benzyl anions with strong π-electron-withdrawing groups in the meta position(s) have low energy diradical or triplet electronic states. Specifically, the 2-(3,5-dinitrophenyl)-1,3-dithiane carbanion is predicted to have nearly degenerate singlet and triplet states at the (U)B3LYP level as a free anion. Its lithium ion pair is predicted to be a ground-state triplet with a substantial (26 kcal/mol) singlet-triplet energy gap. Experiments on this anion using chemical trapping, NMR, and the Evans method strongly suggest that this anion is either a triplet or a ground-state singlet with a very low energy triplet state.     

Imino-C-nucleoside synthesis: heteroaryl lithium carbanion additions to a carbohydrate cyclic imine and nitrone

Promotion by Lewis acid of the addition of some aryllithiums to a carbohydrate-based imine, which has allowed a more facile synthesis of some imino-C-nucleoside analogues, is described. Use of the corresponding nitrone does not assist in some cases, but lithiated acetonitrile adds to it efficiently to give a product from which further C-nucleoside analogues can be derived.     

Computational modeling of a binding conformation of the intermediate L-histidinal to histidinol dehydrogenase

Histidinol dehydrogenase (HDH) is one of the enzymes involved in the L-histidine biosynthesis pathway. HDH is a dimer that contains one Zn2+ ion in each identical subunit. In this study, we predicted a possible binding conformation of the intermediate L-histidinal, which is experimentally not known, using a computational modeling method and three potent HDH inhibitors whose structures are similar to that of L-histidinal. At first, a set of the most probable active conformations of the potent inhibitors was determined using two different pharmacophore mapping techniques, the active analogue approach and the distance comparison method. From the most probable active conformations of the three potent inhibitors, the common parts of the L-histidinal structure were extracted and refined by energy minimization to obtain the binding conformation of L-histidinal. This predicted conformation of L-histidinal agrees with an experimentally determined conformation of L-histidine in a single crystal, suggesting that it is an experimentally acceptable conformation. The capability in this conformation to coordinate a Zn2+ ion was examined by comparing the spatial relative geometry of its functional groups with those of ligands that coordinate with a Zn2+ ion in Zn proteins of the Protein Data Bank. This comparison supported our predicted conformation.     

Aromatization of 3,4-dihydro-β-carboline-3-qarboxylic acid and its derivatives through a carbanion intermediate : mechanistic study and use in chemical synthesis

3,4-dlhydro-β-carboline-3-carboxylic acid , its esters and amide derivatives (AH₂) undergo complete aromatization into corresponding β-carboline derivatives (A) by basic treatment under mild conditions. This, together with the easy obtention of 3,4-dihydro-β-carboline from the parent N^αformyltryptophan derivatives constitutes an attractive possibility to obtain complex molecules containing the β-carboline ring. The mechanism of the reaction was investigated by polarography, U.V.spectrometry and polarimetry. In alcaline media, (AH₂) undergoes two successive equilibria : the first yielding a C₃ carbanion occurs with suppression of the chirality while the second yields a thermodynamically preferred C₄ carbanion which undergoes aromatization through an oxidative pathway (K'_a = 2×10^-14 at 45°C).     

Arylation of a carbanion derived from a pyridazine; a route to a functionalized aren

1,4-Dichlorobenzene(cyclopentadienyl)iron(II) hexafluorophosphate reacts with the carbanion derived from 3-ethoxy-6-methylpyridazine N-oxide to give a Yanovsky-type adduct.     

Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 1: free energy of binding to a binding site

Crystallization is commonly used in a separation and purification process in the production of a wide range of materials in various industries. In industry, crystallization usually starts with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood; however, we hypothesize that there might be a possible correlation between binding affinity to a surface and enhancement of nucleation. Recent studies show that amorphous polymers can be used to control crystallization, selectively produce pharmaceutical polymorphs, and discover novel pharmaceutical polymorphs. To investigate the possible correlation between the binding affinity of one molecule to key binding sites (local binding) and heterogeneous nucleation activity as well as the possibility of using this binding affinity to help guide the selection of polymers that promote heterogeneous nucleation, we computed the free energy of binding of aspirin to four nonporous cross-linked polymers in an ethanol-water 38 v% mixture. These cross-linked polymers are poly(4-acryloylmorpholine) (PAM), poly(2-carboxyethyl acrylate) (PCEA), poly(4-hydroxylbutyl acrylate) (PHBA), and polystyrene (PS); all of them were cross-linked with divinylbenzene (DVB). These systems were used because their heterogeneous nucleation activities are available in literature, and the ranking is PAM > PCEA > PHBA ≈ PS. We generated three independent surfaces for each polymer and computed the free energy of binding of aspirin to the best binding site that we found on each surface. The average free energies of binding to the best sites of PAM, PCEA, PHBA, and PS are -20.4 ± 1.0, -16.7 ± 1.0, -14.4 ± 1.1, and -13.6 ± 1.1 kcal/mol, respectively. We found that the trend of the magnitudes of the average free energies of binding to the best sites is PAM > PCEA > PHBA ≈ PS. This trend is very similar to that of heterogeneous nucleation activity. Our results suggest the importance of the free energy of binding to key sites (local binding) and the possibility of using this quantity to help guide the selection of polymers that promote heterogeneous nucleation.     

The Cassie equation: how it is meant to be used

A review of literature shows that the majority of papers cite a potentially incorrect form of the Cassie and Cassie-Baxter equations to interpret or predict contact angle data. We show that for surfaces wet with a composite interface, the commonly used form of the Cassie-Baxter equation, cosθ(c)=f(1)cosθ-(1-f), is only correct for the case of flat topped pillar geometry without any penetration of the liquid. In general, the original form of the Cassie-Baxter equation, cosθ(c)=f(1)cosθ(1)-f(2), with f(1)+f(2)≥1, should be used. The differences between the two equations are discussed and the errors involved in using the incorrect equation are estimated to be between ~3° and 13° for superhydrophobic surfaces. The discrepancies between the two equations are also discussed for the case of a liquid undergoing partial, but increasing, levels of penetration. Finally, a general equation is presented for the transition/stability criterion between the Cassie-Baxter and Wenzel modes of wetting.     

Collisional energy transfer in the intermediate states used for optical-optical double resonance excitation of ion-pair states in I2

The optical-optical double resonance spectra of I(2) and I(2)-Xe mixtures at room temperature reported in the literature using a fixed-wavelength, broad band pump laser have now been recorded using a tuneable, narrow band source. We show that during the time of the overlapped laser pulses ( approximately 10 ns) and with 10-20 Torr of Xe there is widespread collisional energy transfer in the intermediate state and that this phenomenon offers an alternative explanation for the broad bands in the excitation spectrum, assigned to XeI(2) complexes by the authors of the earlier study (M. E. Akopyan, I. Y. Novikova, S. A. Poretsky and A. M. Pravilov, Chem. Phys., 2005, 310, 287). Dispersed emission bands, previously attributed to direct fluorescence from the ion-pair state(s) of the complexes, are re-assigned to emission from ion-pair states of the parent I(2) that are populated by collisional energy transfer out of the initially excited state.     

Alkali metal complexes of a phosphine-borane-stabilised carbanion: influence of co-ligands on structure

The adducts [[(Me(3)Si)(2){Me(2)P(BH(3))}C]K(L)(n)](m) [L = THF, n = 0.5, m = infinity (2a); L = tmeda (2b), pmdeta (2c), n = 1, m = 2] may be synthesised by treatment of solvent-free [[(Me(3)Si)(2){Me(2)P(BH(3))}C]K](infinity) (2) with the corresponding Lewis base (tmeda = N,N,N',N'-tetramethylethylenediamine; pmdeta = N,N,N',N',N'-pentamethyldiethylenetriamine). X-Ray crystallography reveals that, whereas 2 crystallises with a complex 2-dimensional sheet structure, 2a crystallises as a ribbon-type one-dimensional polymer and both 2b and 2c crystallise as dimers. The corresponding complex with 12-crown-4, [K(12-crown-4)(2)][(Me(3)Si)(2){Me(2)P(BH(3))}C] (2d) crystallises as a separated ion pair. The complexes [[(Me(3)Si)(2){Me(2)P(BH(3))}C]M(pmdeta)](n) [M = Na, n = 1 (6); M = Rb, n = 2 (7)] may be synthesised by treatment of [(Me(3)Si)(2){Me(2)P(BH(3))}C]M with pmdeta. Whereas crystallises as a discrete monomer, compound 7 crystallises as a dimer. Compounds 2, 2a-2d, 6, 7 and the corresponding caesium derivative [[(Me(3)Si)(2){Me(2)P(BH(3))}C]Cs(pmdeta)](2) () provide an opportunity to consider the influence of the ionic radius of the metal and the nature of the co-ligands on the structures of alkali metal complexes of a phosphine-borane-stabilised carbanion.     

Free energy of binding of a small molecule to an amorphous polymer in a solvent

Crystallization is a commonly used purification process in industrial practice. It usually begins with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood, but we hypothesize that a possible correlation between binding affinity to a surface and nucleation enhancement might exist. Amorphous polymers have been used in controlling crystallization. However, to our knowledge, no attempt has been made to calculate the free energy of binding of a small molecule to an amorphous polymer in a solvent, and to characterize the binding sites/conformations of this system at a molecular level. We developed a two-step approach, first using Adsorption Locator to identify probable binding sites and molecular dynamics to screen for the best binding sites and then using the Blue-Moon Ensemble method to compute the free energy of binding. A system of ethylene glycol, polyvinyl alcohol (PVA), and heavy water (D(2)O) was used for validation, since experimental data exists on a related system. Looking at four independently constructed surfaces, we found that ethylene glycol binds to an indentation on the surface or in a hole beneath the surface. We focused on the indentation binding sites because they are easily accessible and do not have large free energy barriers. The closest system for which experimental data on binding energetics exists is ethylene glycol on PVA in aqueous solutions/gels, and the magnitudes of the free energy of binding to the three best indentation binding sites are close to the experimental value, 0.4-3.7 kcal/mol higher. Our approach offers a way to compute the free energy of binding and characterize the binding sites/conformations, and is general enough to apply to other small molecule/amorphous polymer/solvent systems.