Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.     

Limited flexibility of lactose detected from residual dipolar couplings using molecular dynamics simulations and steric alignment methods

The conformational flexibility of lactose in solution has been investigated by residual dipolar couplings (RDCs). One-bond carbon-proton and proton-proton coupling constants have been measured in two oriented media and interpreted in combination with molecular dynamics simulations (MD). Two different approaches, known as PALES (Zweckstetter et al., J. Am. Chem. Soc. 2000, 122, 3791-3792) and TRAMITE (Azurmendi et al., J. Am. Chem. Soc. 2002, 124, 2426-2427), have been used to determine the alignment tensor from a shape-induced alignment model with the oriented medium. The steric alignment of the structures from several MD trajectories has provided ensemble averaged RDCs that have been compared with the experimental ones. The obtained results reveal the almost exclusive presence of a major low energy region defined as syn-phi/syn-psi (> 97%), for which sampling occurs in a dynamic manner. This result satisfactorily agrees with that determined by standard NOE-based methods.     

Ru(IV)-catalyzed isomerization of allylamines in water: a highly efficient procedure for the deprotection of N-allylic amines

A general and efficient method for the deprotection of N-allylic substrates in aqueous media, using catalytic amounts of the bis(allyl)-ruthenium(IV) complexes [Ru(eta3:eta2:eta3-C12H18)Cl2] and [{Ru(eta3:eta3-C10H16)(micro-Cl)Cl}2], has been developed.     

Iron(III)-catalyzed Prins-type cyclization using homopropargylic alcohol: a method for the synthesis of 2-alkyl-4-halo-5,6-dihydro-2H-pyrans

[reaction: see text] A new Prins-type cyclization between homopropargylic alcohol and aldehydes in the presence of FeX(3) to obtain 2-alkyl-4-halo-5,6-dihydro-2H-pyrans in good yield is described. Osmium-catalyzed cis dihydroxylation provided direct access to trans-2-alkyl-3-hydroxy-tetrahydro-pyran-4-ones. Anhydrous ferric halides are also shown to be excellent catalysts for the standard Prins cyclization using homoallylic alcohol. Isolation of an intermediate acetal provides substantiation of a proposed mechanism.     

Electrochemistry of vanadium-doped tetragonal and monoclinic ZrO2 attached to graphite/polyester composite electrodes

The electrochemistry of monoclinic and tetragonal vanadium-doped zirconias (VZrO₂), prepared from gel precursors with vanadium loadings ranging from 0.5 to 15 mol%, has been studied using abrasive-conditioned graphite/polyester composite electrodes immersed in aqueous HCl and HClO₄ solutions. Isolated vanadium centers form a solid solution in the zirconia lattice with a solubility limit close to 5 mol%. Above 5 mol%, finely dispersed V₂O₅ is formed. Vanadium centers located at the boundary sites of the zirconia lattice display successive one-electron transfer processes near to +0.25 and +0.10 V vs. SCE, whereas finely dispersed V₂O₅ yields three successive reduction processes at +0.46, +0.30, and +0.16 V vs. SCE. Electrochemical data indicate the presence of both V⁵⁺ and V⁴⁺ centers in the lattice of monoclinic and tetragonal zirconias, the V⁵⁺/V⁴⁺ ratio decreasing as the vanadium loading increases. Electronic Publication     

Micellar electrokinetic capillary chromatography for the determination of Viagra and its metabolite (UK-103,320) in human serum

Micellar electrokinetic capillary chromatography (MEKC) was investigated for the determination of Viagra (sildenafil citrate, SC) and its metabolite (UK-103,320) in human serum in a concentration range of clinical interest. For MEKC, human serum samples spiked with SC and UK were obtained directly after elution with methanol from a tC18 cartridge. The extract was evaporated and regenerated in a solution 1 mM of phosphate buffer (pH 12.3) which contained a methanol percentage of 20% that was analyzed using phosphate buffer (pH 12.3, 10 mM) containing 30 mM sodium dodecyl sulfate (SDS) as separation electrolyte and a fused-silica capillary. This method gave satisfactory interday precision with respect to migration times relative standard deviation (RSD < 1%) and linear responses for the concentration ranges investigated (0.50-3.50 mg L(-1) for the compound SC and 0.90-4.60 mg L(-1) for UK). An intraday RSD (n = 5 graphs) between the slopes of the calibration graphs was acceptable (6.40%) for SC and (3.37%) for UK. A satisfactory interday precision between slopes was also obtained (RSD 4.10% for SC and a RSD 2.72% for UK) which demonstrated the ruggedness of this method. Detection limits (S/N = 3) were about 200 ng/mL for both compounds in human serum. MEKC was shown as a good method with regards to simplicity, precision and sensitivity.     

Highly diastereoselective cyanation of methyl ketimines obtained from (R)-glyceraldehyde

[reaction: see text] Addition of trimethylsilyl cyanide to ketimines derived from (R)-2,2-dimethyl-1,3-dioxolan-4-yl methyl ketone to generate a quaternary stereocenter has been achieved with high yields and excellent diastereoselectivity. The stereoselectivity was found to be temperature and solvent dependent. The beta-hydroxy-alpha-amino nitrile of syn configuration was the major compound in kinetically controlled reactions, whereas the anti stereoisomer was obtained in excess in thermodynamically controlled reactions. Double stereodifferentiation under kinetic control conditions was successful, and the cyanation reaction occurred with complete syn diastereoselectivity using the matched pair. The versatility of the resulting amino nitrile as a synthetic intermediate was tested by performing the synthesis of orthogonally protected (R)-(2-aminomethyl)alanine.     

Application of matrix solid-phase dispersion to the determination of a new generation of fungicides in fruits and vegetables

A method based on matrix solid-phase dispersion (MSPD) and gas chromatography to determine eight fungicides in fruits and vegetables is described. Fungicide residues were identified and quantified using nitrogen-phosphorus detection and electron-capture detection connected in parallel and confirmed by mass spectrometric detection. The method required 0.5 g of sample, C18 bonded silica as dispersant sorbent, silica as clean-up sorbent and ethyl acetate as eluting solvent. Recoveries from spiked orange, apple, tomato, artichoke, carrot and courgette samples ranged from 62 to 102% and relative standard deviations were less than 15% in the concentration range 0.05-10 mg kg(-1). Detection and quantitation limits ranged 3-30 microg kg(-1) and 10-100 microg kg(-1), respectively, with linear calibration curves up to 10 mg kg(-1). The analytical characteristics of MSPD compared very favourably with the results of a classical multiresidue method, which uses ethyl acetate and anhydrous sodium sulphate for the extraction.     

Asymmetric synthesis of 2H-azirines derived from phosphine oxides using solid-supported amines. Ring opening of azirines with carboxylic acids

A simple and efficient asymmetric synthesis of 2H-azirine-2-phosphine oxides 3 is described. The key step is a solid-phase bound achiral or chiral amine-mediated Neber reaction of beta-ketoxime tosylates derived from phosphine oxides 1. Reaction of 2H-azirines 3 and 11 with carboxylic acids 4 gives phosphorylated ketamides 5 and 12. Ring closure of ketamides 5 and 12 with triphenylphosphine and hexachloroethane in the presence of triethylamine leads to the formation of phosphorylated oxazoles 8 and 13.     

Synthesis of pyrazine-phosphonates and -phosphine oxides from 2H-azirines or oximes

[reaction: see text] Tetrasubstituted pyrazines containing two phosphonate groups 2 in positions 2 and 5 and trisubstituted pyrazines containing a phosphonate 5 or a phosphine oxide group 7 in position 2 are obtained by thermal treatment of 2H-azirine-2-phosphonates 1 and -phosphine oxides 6. These pyrazines can also be prepared from beta-ketoxime tosylates 9 and 10 or from oxime derived from phosphine oxide 11.