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.     

Quantitative determination of sotolon, maltol and free furaneol in wine by solid-phase extraction and gas chromatography-ion-trap mass spectrometry

A method for the analytical determination of sotolon [4,5-dimethyl-3-hydroxy-2(5H)-furanone], maltol [3-hydroxy-2-methyl-4H-pyran-4-one] and free furaneol [2,5-dimethyl-4-hydroxy-3(2H)-furanone] in wine has been developed. The analytes are extracted from 50 ml of wine in a solid-phase extraction cartridge filled with 800 mg of LiChrolut EN resins. Interferences are removed with 15 ml of a pentane-dichloromethane (20:1) solution, and analytes are recovered with 6 ml of dichloromethane. The extract is concentrated up to 0.1 ml and analyzed by GC-ion trap MS. Maltol and sotolon were determined by selected ion storage of ions in the m/z ranges 120-153 and 79-95, using the ions m/z 126 and 83 for quantitation, respectively. Furaneol was determined by non-resonant fragmentation of the m/z 128 mother ion and subsequent analysis of the m/z 81 ion. The detection limits of the method are in all cases between 0.5 and 1 microg l(-1), well below the olfactory thresholds of the compounds. The precision of the method is in the 4-5% range for levels in wine around 20 microg l(-1). Linearity holds at least up to 400 microg l(-1), and is satisfactory in all cases. The recoveries of maltol and sotolon are constant (70 and 64%, respectively) and do not depend on the type of wine. On the contrary, in the case of furaneol, red wines show constant and high recoveries (97%), while the recoveries on white wines range between 30 and 80%. Different experiments showed that this behavior is probably due to the existence of complexes formed between furaneol and sulphur dioxide or catechols. Sensory experiments confirmed that the complexed forms found in white wines are not perceived by orthonasal olfaction, and that the furaneol determined by the method can be considered as the free and odor-active fraction.     

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.     

Effect of carbon nanotubes on the crystallization and properties of polypropylene

The effect of different concentrations of single‐walled carbon nanotubes (SWNTs) on the nonisothermal crystallization kinetics, morphology, and mechanical properties of polypropylene (PP) matrix composites obtained by melt compounding was investigated by means of X‐ray diffraction, differential scanning calorimetry, optical and scanning electron microscopy, and dynamic mechanical thermal analysis. Microscopy showed well‐dispersed nanotube ropes together with small and large aggregates. The modulus was found to increase by about 75% at a level of 0.5 wt % nanotubes. The SWNTs displayed a clear nucleating effect on the PP crystallization, favoring the α crystalline form rather than the β form. The crystallization kinetics analysis showed a significant increase in activation energy on incorporating nanotubes. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2445–2453, 2005     

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.     

Synthesis of 2‐Dihydrooxadiazolinyl Chromones

Reactions of the substituted 2‐formyl chromones with aroylhydrazines gave corresponding 2‐(aroylhydrazonomethylidyne) chromones. Then 2‐(3′‐acetyl‐5′‐aryl‐2′,3′‐dihydro‐1′,3′,4′‐oxadiazol‐2′‐yl) chromones were prepared by these 2‐(aroylhydrazonomethylidyne) chromones under refluxing with Ac₂O. All target compounds were characterized through elemental analysis and IR, ¹H NMR, MS.     

Polyterephthalamides with naphthoxy‐pendent groups

A series of new aromatic polyamides having pendent naphthoxy groups were synthesized by the triphenyl phosphite‐activated polycondensation of (2‐naphthoxy)terephthalic acid (NOTPA) with various aromatic diamines in a medium consisting of N‐methyl‐2‐pyrrolidone (NMP), pyridine, and calcium chloride. The diacid monomer NOTPA was prepared from the nitro displacement of dimethyl 2‐nitroterephthalate with the potassium naphthoxide of β‐naphthol, followed by base‐induced ester hydrolysis. All the resulting polymers were noncrystalline and readily soluble in aprotic polar solvents such as NMP and N,N‐dimethylacetamide. Almost all the polymers could be solution‐cast to tough, creasable amorphous films with good mechanical properties, the values of tensile strengths ranging from 90 to 124 MPa with initial moduli ranging from 1.72 to 2.51 GPa. Except for two examples, all the other polyamides displayed discernible glass transitions between 189 and 248 °C in the differential scanning calorimetric traces. These polyamides showed insignificant decomposition below 400 °C in nitrogen or air. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1781–1789, 2002     

Biomimetic Asymmetric Reduction of Quinazolinones with Chiral and Regenerable NAD(P)H Models

A facile approach to chiral dihydroquinazolinone derivatives has been described via biomimetic asymmetric reduction of quinazolinones with chiral and regenerable NAD(P)H models. The utility of this method was demonstrated by a concise synthesis of the bromodomain protein divalent inhibitor.     

Synthesis and Antimicrobial Activity of New Pyridothienopyrimidines and Pyridothienotriazines

5‐Acetyl‐3‐amino‐4‐aryl‐6‐methylthieno[2,3‐b]pyridine‐2‐carboxamides ( 5a,b ) were reacted with triethyl orthoformate or nitrous acid to give the corresponding pyrimidinones 6a,b and triazinones 7a,b . The reaction of 5a,b with acetic anhydride was carried out and its products were identified as a mixture of 8‐acetyl‐9‐aryl‐2,7‐dimethylpyrido[3′,2′:4,5]thieno[3,2‐d]pyrimidine‐4(3H)‐one ( 9a,b ) and related 5‐acetyl‐4‐aryl‐3‐biacetylamino‐6‐methylthieno[2,3‐b]pyridine‐2‐carbonitrile ( 10a,b ). Reaction of 7a with some halocompounds afforded the N‐alkylated triazinones 8a‐c . Chlorination of 6a,b and 9a,b with phosphorus oxychloride produced 4‐chloropyrimidines 11a‐d which were used as precursors for the rest of the target heterocycles. Some of the prepared compounds were tested in vitro for their antimicrobial activities.     

A convenient catalytic approach to synthesize straight boron nitride nanotubes using synergic nitrogen source

Straight boron nitride nanotubes (BNNTs) with pure hexagonal phase were conveniently prepared by heating the mixture of Mg(BO₂)₂ · H₂O, NH₄Cl, NaN₃ and Mg powder in an autoclave at 600 °C for 20–60 h. These BNNTs had diameters mainly ranging 30–300 nm and lengths up to 5 μm, and a majority of them had at least one closed end. Besides the traditional end tips, additional cone-like tips were frequently found to be attached on the BNNTs. The effects of temperature, reactants and the possible mechanism of the catalytic formation of the BNNTs are discussed.