Oxidative demetalation of cyclohexadienyl ruthenium(II) complexes: a net Ru-mediated dearomatization

[reaction: see text] An experimentally simple method for the demetalation of spirocyclic cyclohexadienylruthenium(II) complexes has been developed. Treatment of an alkoxy-substituted cyclohexadienyl complex with CuCl(2) affords either azaspiro[4.5]decane derivatives or heavily functionalized tetrahydroisoquinolines. The former reaction manifold completes a net Ru-mediated dearomatization as the organometallic starting materials are prepared from (eta(6)-arene)Ru(II) precursors. Both of these heterocyclic products are well suited for further synthetic elaboration.     

Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs

Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. Hexamers containing F-F pairs were found to be more dynamic, especially in the region of the mispair itself. This dynamic variability derives from greater flexibility of F-F pairs. The T-T mispairs, on the other hand, were found to be comparatively tightly bound as wobble pairs. The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. Stacking interactions were nearly identical for T-T and F-F pairs, leading to similar average structures, even though F stacking was more dynamically variable. Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules.Electronic Supplementary Material This Material consists of equilibration protocol, plots of center-of-mass stacking, water radial distribution functions, helical parameter dynamics, and dynamics data for a control AT sequence. Supplementary material is available in the online version of this article at Contribution to the Jacopo Tomasi Honorary Issue     

Precursor-directed biosynthesis of epothilone in Escherichia coli

Engineered biosynthetic pathways provide a powerful method for generating complex molecules. Precursor-directed biosynthesis, which combines chemical synthesis and enzymatic transformations, allows non-native starting materials to be incorporated into biosynthetic pathways. Using this approach, we achieved the production of the anticancer agent epothilone C in Escherichia coli. An E. coli strain was engineered to express the last three modules of the epothilone biosynthetic pathway (epoD-M6, epoE, and epoF) and the substrate required to complement the biosynthetic enzymes was obtained by chemical synthesis. Under high-density cell culture conditions, the E. coli strain processed exogenously fed synthetic substrate into epothilone C at levels comparable to the native host (1 mg/L) and at higher levels than other heterologous hosts. Importantly, this precursor-directed approach will allow chemical modifications to be introduced into the polyketide backbone and may ultimately provide access to epothilone analogues with improved pharmacological properties in quantities sufficient for clinical development.     

Investigation of the metabolic fate of 2-, 3- and 4-bromobenzoic acids in bile-duct-cannulated rats by inductively coupled plasma mass spectrometry and high-performance liquid chromatography/inductively coupled plasma mass spectrometry/electrospray mass spectrometry

Inductively coupled plasma mass spectrometry (ICPMS) has been used to determine the rate and routes of excretion of bromine following the intraperitoneal administration (50 mg kg(-1)) of 2-, 3- and 4-bromobenzoic acids to male bile-duct-cannulated rats. Analysis of urine and bile for (79/81)Br using ICPMS showed that all three bromobenzoic acids were rapidly excreted (82-98%) within 48 h of dosing, primarily via the urine. High-performance liquid chromatography/inductively coupled plasma mass spectrometry (HPLC/ICPMS) was then used to obtain metabolite profiles for bile and urine. These profiles revealed that extensive metabolism had taken place, with the unchanged bromobenzoic acids forming a minor part of the total of compound-related material detected. Concomitant MS studies, supplemented by alkaline hydrolysis, enabled the identification of the major metabolite of all three of the bromobenzoic acids as a glycine conjugate. Ester glucuronide conjugates were also identified, but formed only a small proportion of total.     

Reactions of some 2H-Chromenes and 2H-Thiochromenes with triazolinediones

Simple 2H-chromenes and 2H-thiochromenes form the [2+2]-adducts, tetrahydro[1]benzo(thio)pyrano[3,4-c] [1,2]diazeto[1,2-a][1,2,4]triazoles, with triazolinediones, whereas their 3- and 4-bromo and the corresponding cycloalkylamino derivatives undergo an overall etectrophilic substitution sequence.     

The synthesis of macrocyclic polyether-diesters incorporating 1,10-phenanthrolino and 1,8-naphthyridino subunits

The preparation of a series of macrocycles, formed by reaction of HO-(-CH₂-CH₂-O-)_nH with 1,10-phenanthroline-2,9-dicarbonyl chloride (n = 2,3,4) and 1,8-naphthyridine-2,7-dicarbonyl chloride (n = 3,4), is described. An improved synthetic route to 2,7-dimethyl-1,8-naphthyridine 9 is also reported.     

Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa

Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E₀. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor–acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.

Observing electron transfer events in individual azurin molecules, we relate the spread in transfer rates in a unique way to variations in molecular parameters.     

Further solvent-free reactions of ferrocenylaldehydes: Synthesis of 1,1′-ferrocenyldiimines and ferrocenylacrylonitriles

Grinding of 1,1′-ferrocenedicarboxaldehyde with a 2.2 molar equivalent of an aromatic amine in a solvent-free environment provided excellent yields of 1,1′-ferrocenyldiimines. After mixing the aldehyde and amines, a gum or melt formed which eventually solidified to the product. An analytically pure sample of the product was obtained by cold recrystallization. Grinding of ferrocenecarboxaldehyde and 4-substituted phenylacetonitriles under solvent-free conditions provided good yields of the corresponding ferrocenylacrylonitriles. The yield in this reaction was very low when the substituent group para to the acetonitrile group was electron-donating.     

An electron spin resonance study of radicals from chloramine-t-1 : Spin trapping of radicals produced in acid media

Under acid conditions aqueous solutions of chloramine-T form nitrogen-centred radicals via loss of the chlorine atom. The nitrogen radicals produced have been studied by ESR spectroscopy using the spintrapping method. Adducts of the spin trap phenyl-t-butyl nitrone are oxidized by chloramine-T in acid media to give a paramagnetic product in which the unpaired electron interacts with two inequivalent nitrogen atoms. The spin trap 5,5-dimethyl-2-pyrrolidine-1 -oxide is oxidized rapidly to 5,5-dimethyl-2-pyrrolidone-1-oxyl by chloramine-T under acid onditions. The water soluble trap α-4-pyridyl-1-oxide-N-t-butyl nitrone forms a stable nitroxide adduct with a nitrogen radical of chloramine-T in acid solution. Identical results were obtained with chloramine-B (sodium salt of N-chlorobenzene sulfonamide), indicating the involvement of the N-chloramine group in radical formation.     

Three-dimensional self-assembly of metallic rods with submicron diameters using magnetic interactions

Metallic rods with submicron diameters that contain disklike ferromagnetic sections self-assemble into highly stable, hexagonally close-packed arrays of rods. The rods were fabricated by electrodeposition in porous alumina membranes and comprised alternating sections of gold and nickel. The thicknesses of the ferromagnetic nickel sections were approximately one-half the diameter of the rods (400 nm); this geometry orients the "easy" axis of magnetization perpendicular to the long axis of the rod. After magnetization of the rods with a rare-earth magnet, followed by sonication of the suspension, the rods spontaneously assembled into three-dimensional (3D) bundles that, on average, contained 15-30 rods. A macroscopic model of the rods suggests that the most stable orientation of the magnetic dipoles for rods in a defect-free, hexagonally close-packed arrangement is in concentric rings with the dipoles oriented head-to-tail. This configuration minimizes the energy of the bundle and does not generate a net dipole for the structure. This work provides a simple demonstration that magnetic interactions between ferromagnetic objects can direct and stabilize the formation of ordered, 3D structures by self-assembly.