On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Visual recognition of melamine in milk via selective metallo-hydrogel formation

A novel protocol allowing convenient and highly selective visual recognition of melamine in raw milk via selective metallo-hydrogel formation at a concentration as low as 10 ppm without any tedious pretreatment has been developed.     

Determination of sulfur dioxide in vitriol plant wastewater by using a polyNiMe4TAA electrochemically modified Pt microelectrode

A Pt microelectrode modified with nickel(II) polytetramethyldibenzo[b,i]tetraaza[14]annulene was prepared by electropolymerization of nickel(II) tetramethyldibenzo[b,i]tetraaza[14]annulene monomers and applied to determine sulfur dioxide in vitriol plant wastewater. For determination of SO2 with this electrochemically modified Pt microelectrode, the linear range was from 9.6 x 10(-6) to 2.4 x 10(-4) mol L-1, the sensitivity was 1.8 x 10(-4) A L mol-1, the detection limit was calculated to be 4.8 x 10(-6) mol L-1 (S/N = 3), the response time was less than 20 s and the relative standard deviation was found to be 2.1% on analyzing 4.8 x 10(-5) mol L-1 SO2 solution repeatedly (n = 7). These results demonstrated good accuracy compared with those obtained by the conventional iodimetric method.     

A novel diacetylenic bilirubin

An etiobilirubin‐IIβ analog with the central C(10) CH₂ group replaced by a diacetylene unit ( 1 ) was synthesized by base‐catalyzed condensation of bis‐[3‐methyl‐4‐ethyl‐5‐formylpyrrol‐2‐yl]‐diacetylene ( 3 ) with 3‐methyl‐4‐ethyl‐5‐p‐toluenesulfonyl‐2‐pyrrolinone ( 10 ). Diacetylenic rubin 1 is a dark red solid, giving orange solutions with uv‐visible absorption maxima near 460 nm.     

Quinine/selectfluor combination induced asymmetric semipinacol rearrangement of allylic alcohols: an effective and enantioselective approach to alpha-quaternary beta-fluoro aldehydes

A quinine/Selectfluor combination inducing rearrangement reaction of allylic alcohols was discovered, which involved a moderate yield with good enantioselective construction of alpha-quaternary carbon center and beta-fluoro aldehyde under base condition.     

Microwave-assisted solvent-free synthesis of substituted 2-quinolones

A rapid and efficient method for the preparation of a variety of substituted 2-quinolones has been developed through the reactions of o-aminoarylketones with ester compounds containing a reactive α-methylene moiety in the presence of a catalytic amount of cerium chloride heptahydrate under solvent-free conditions in high yields. The rate and yield of the reaction are considerably improved by employing microwave irradiation.     

A new class of linear tetrapyrroles: acetylenic 10,10a-didehydro-10a-homobilirubins

Novel bilirubin analogues with dipyrrinones conjoined to an acetylene rather than a methylene group were synthesized and examined spectroscopically. Despite the increased separation of the dipyrrinones forced by replacing a -CH(2)- by a -C(triple bond)C- unit, molecular dynamics calculations show that, like bilirubin, they may still engage in intramolecular hydrogen bonding to carboxylic acid groups when the propionic acid chains are slightly lengthened, e.g., butanoic acids. Unlike bilirubin, however, which is bent in the middle and has a ridge-tile shape, the acetylene orients the attached dipyrrinones along a linear path, and intramolecular hydrogen bonding preserves a twisted linear molecular shape. The extended planes of the dipyrrinones intersect along the -C(triple bond)C- axis at an angle of 136 degrees for the conformation stabilized by intramolecular hydrogen bonding in the bis-butyric acid rubin (1b). With shorter acid chains (propionic), only one CO(2)H can engage an opposing dipyrrinone in intramolecular hydrogen bonding, and in this energy-minimum conformation of the linear pigment 1a, the intersection of the extended planes of the dipyrrinones has an angle of 171 degrees. Spectroscopic evidence for such linearized and twisted structures was found in the pigments' NMR spectral data and their exciton UV-vis and induced circular dichroism spectra.     

BIOLUMINESCENCE FROM THE REACTION OF FMN, H2O2 AND LONG CHAIN ALDEHYDE WITH BACTERIAL LUCIFERASE

Abstract— The bioluminescent oxidation of reduced flavin mononucleotide by bacterial luciferase involves a long-lived flavoenzyme intermediate whose chromophore has been postulated to be the 4a-sub-stituted peroxy anion of reduced flavin. Reaction of long chain aldehyde with this intermediate results in light emission and formation of the corresponding acid. These experiments show that the typical aldehyde-dependent, luciferase-catalyzed bioluminescence can also be obtained starting with FMN and H₂O₂ instead of FMNH₂ and O₂. We postulate that the 4a-peroxy anion intermediate is formed directly by attack of H₂O₂ on FMN. The latter may be bound to luciferase. An enzyme bound intermediate is formed which by kinetic analysis, flavin specificity for luminescence, aldehyde dependence, and bioluminescent emission spectrum appears to be identical with the species generated by reaction of FMNH, and O₂ with luciferase. The quantum yield of the H₂O₂-_- and FMN-initiated biolumlnescence is low but can be enhanced by certain metal ions, which also stimulate a chemiluminescent reaction of oxidized flavin with H₂O₂. The peak of this chemiluminescence. however, appears to be at a shorter wavelength than that (490 nm) of the bioluminescence.     

Itosides A – I,New Phenolic Glycosides from Itoa orientalis

Eight new benzoylated gentisyl alcohol (=2‐(hydroxymethyl)benzene‐1,4‐diol) glucosides, itosides A–H ( 1 – 8 ), together with the new pyrocatechol (=benzene‐1,2‐diol) glycoside itoside I ( 9 ) were isolated from the bark and twigs of Itoa orientalis (Flacourtiaceae). In itosides B–D ( 2 – 4 ), the gentisyl alcohol moiety was esterified by 1‐hydroxy‐6‐oxocyclohex‐2‐ene‐1‐carboxylic acid, while itosides E–H ( 5 – 8 ) contained instead an additional 2‐hydroxybenzoic acid moiety. The compounds were accompanied by the known derivatives 4‐hydroxytremulacin ( 10 ), poliothyrsoside ( 11 ), poliothyrsin ( 12 ), homaloside D ( 13 ), tremulacin, and pyrocatechol β‐D ‐glucopyranoside. The structures of the new compounds were elucidated by spectral and chemical methods.