Electroenzymatic reactions. Investigation of a reductive dehalogenase by means of electrogenerated redox cosubstrates

As an illustration of how cyclic voltammetry can be used to unravel the mechanisms and kinetics of redox enzymes, the reductive dechlorination of trichloroethylene and tetrachloroethylene by a typical reductive dehalogenase, the tetrachloroethene reductive dehalogenase of Sulfurospirillum multivorans (formerly called Dehalospirillum multivorans), was investigated by means of several electrochemically generated cosubstrates. They comprised the monocation and the neutral form of methylviologen, the neutral form of benzylviologen, and cobaltocene. Cyclic voltammetry is used to produce the active form of the cosubstrate under controlled potential conditions. It shows large plateau-shaped catalytic responses, which are used to measure the kinetics of the enzymatic reaction as a function of the substrate and cosubstrate concentrations. The variation of the rate constant for the cosubstrate reaction with its standard potential shows the transition between two asymptotic behaviors, one in which the reaction is under diffusion control and the other in which it is under counter-diffusion control. Simple fitting of this plot allows an estimation of the standard potential of the electron acceptor center in the enzyme (E degrees = -0.57 V vs NHE).     

Ligand discrimination in the reaction of nitrones with [PtCl2(PhCN)2]. Selective formation of mono-oxadiazoline and mixed bis-oxadiazoline complexes under thermal and microwave conditions

[2+3] Cycloaddition of nitrones to the nitrile ligands in the complexes cis- or trans-[PtCl2(PhCN)2] occurs under ligand differentiation and allows for selective synthesis of complexes of the type cis- or trans-[PtCl2(oxadiazoline)(PhCN)]. Microwave irradiation enhances the reaction rates of the cycloaddition considerably and further favours the selectivity towards the mono-cycloadduct with respect to thermal conditions, because the first cycloaddition is accelerated to a higher extent than the second one. Reaction of the trans-substituted mono-oxadiazoline complexes with a nitrone different from the one used for the first cycloaddition step gives access to mixed bis-oxadiazoline compounds of the composition trans-[PtCl2(oxadiazoline-a)(oxadiazoline-b)]. The corresponding cis-configured complexes, however, do not undergo further cycloaddition. All reactions described occur without isomerisation of the stereochemistry around the platinum center, independently of whether thermal or microwave heating is applied.     

Production of octadienal in the marine diatom Skeletonema costatum

[reaction: see text] Marine diatoms produce alpha,beta,gamma,delta-unsaturated aldehydes that have detrimental effects on the reproduction of their natural predators. The production of these defensive metabolites is suggested to involve enzymatic oxidation of polyunsaturated fatty acids. In this paper, feeding experiments with labeled precursor provide clear evidence in support of the origin of octadienals 1 and 2 from 6,9,12-hexadecatrienoic acid (5), thus proving the involvement of novel lipoxygenase/lyase activity for the oxidation of C(16) fatty acids.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

The chemistry of (1-azabuta-1,3-diene)tricarbonyliron(0) complexes

In this review, an overview of synthetic and structural aspects of 1-azabuta-1,3-diene complexes of iron is given and the reactivity of these complexes is discussed with regard to inorganic, organometallic, organic and stereochemical aspects of their chemistry. Their application in the synthesis of organic and organometallic target compounds, or as transfer reagents of the tricarbonlyiron(0) moiety is demonstrated.     

Vibrational spectroscopy of aqueous solutions at high concentrations: Raman and inelastic neutron scattering

We review work performed by our group on vibrational spectroscopy of water and aqueous solutions of strong II-I electrolytes at high concentrations. Evidence shall be presented for the existence of intermediate range, solute-connected, ordered patches, whose collective vibrational modes yield a continuous vibrational density of states, as in amorphous solids. We shall review Raman and inelastic neutron scattering results, obtained for electrolytes such as ZnCl₂, NiCl₂, CuBr₂, CdCl₂. Other results, such as EXAFS, viscosity and ultrasonic attenuation will also be discussed.     

Electronic and Steric Influence of Axial and Equatorial Ligands in Vitamin B12 Model Complexes Derived from Cobaloxime: Electrochemical and 59Co-NMR Studies

In four series of strictly related organocobalt complexes, derived from cobaloximes by replacement of the O…H…O with O…-BF₂…O and/or (CH₂)₃ groups, the trends of ⁵⁹Co-NMR shielding and electrochemical data are discussed. A largely parallel behaviour of the plots of E_1/2(I) values for the first Co(III)/Co(II) electron transfer vs. the ₅₉Co chemical shifts reflects the similar sensitivity of the two parameters to a change in electron affinity of the central metal ion due to a variation of the organic group R. E_1/2(II) values for the second Co(II)/CO(I) electron transfer are less sensitive to the change of R, but the trend of the plot vs. δ(₅₉Co) is still parallel in the four series. Consistent deviations from a roughly linear dependence of E_1/2(I) on pK_a of the hydrocarbon acid corresponding to R, on Taft constant s?_* and on ⁵⁹Co shielding are noticed for the isopropyl derivatives and attributed to a steric effect. This was confirmed in a series of R? Co(DMG)pyridine complexes in which ⁵⁹Co shielding decreases steadily with increasing steric parameter E_s (Taft) of the alkyl group. There is experimental evidence from X-ray data that δ(⁵⁹Co) decreases with an increase of the Co? C bond length, illustrating steric hindrance in alkyl coordination to be responsible for the decreased shielding of the ⁵⁹Co nucleus. The relative displacements of the graphic displays for the different series reflect the effect of changes in electron affinity of the redox center, due to the equatorial ligand, which, in turn, is caused by variations in the electron-withdrawing power due to the introduction of the BF₂ group and by the change from ?2 to ?1 valence of the (CH₂)₃-capped ligands.     

Säurekatalysierte Umlagerungen von 1,5-Dimethyl-6-methyliden-tricyclo[3.2.1.02,7]oct-3-en-8endo-olen

Acid Catalysed Rearrangement of 1,5-Dimethyl-6-methyliden-tricyclo[3.2.1.0^2,7]oct-3-en-8endo-ols The tricyclic alcohols 2,3,4 and 6 (Scheme 1) are synthesized by the reaction of the tricyclic ketone 1 with sodiumborohydrid or metalloorganic reagents. Their configuration at C(8) is determined by NMR. in the presence of Eu(fod)₃. The exo-attack of 1 by the nucleophil forming the endo-alcohol is favored, the π-electrons of C(3) = C(4) hindering the endo-attack. On treatment with sulfuric acid in dioxane/water at 25° the tertiary alcohols yield aryl-substituted ketones. 3 gives in 78.5% yield a mixture of the 3-(dimethylphenyl)-2-butanones 12 and 13 , in addition to 16.5% of (2,3,4-trimethylphenyl)-2-propanon ( 14 ) (Scheme 2). The alcohols 4 and 6 yield mixtures of the 2-(dimethylphenyl)-3-pentanones 19 and 20 (72%), and 2-(dimethylphenyl)-propiophenones 21 and 22 (68%), respectively (Scheme 2). In the case of the secondary alcohol 2 mainly products derived from hydration at the C(6), C(9) double bond are formed, namely the mixture of diols 23 and 24 (21%), and the mixture of the isomeric 2-(dimethylphenyl)propanals 25, 26 and 27 (3%) (Scheme 3). - The structures of 12–14, 19/20, 21/22, 23/24 and 25/26/27 were established by spectroscopic data. In the case of 12 and 13 the degradation of their mixture to the known 1-(dimethylphenyl)ethanols 17/18 confirmed the assignment. - The most probable mechanism for the rearrangement of 3 is shown in Schemes 4 and 5. The reaction proceeds from 3 through a, b and g to 12 and 13; 14 is formed via e, f and i . In the case of 4 and 6 only the reaction analogue to 3 → a → b → g ?12/13 takes place. The isomeric aldehyds 25–27 formed from 2 could have the structures s, t , and v . The former two could be generated in a similar way as 12/13 from 3 , the latter one as shown in Scheme 8.