Novel antibiotics: second generation macrocyclic peptides designed to trap Holliday junctions

Described are the syntheses of 15 macrocyclic peptides designed to trap Holliday junctions (HJs) in bacteria during site-specific and homologous recombination. This leads to inhibiting bacterial growth. These second generation macrocycles were based on the C-2 symmetrical HJ. They were synthesized using a strategy that permits elucidation of the amino acid role in binding HJs. The syntheses of these macrocycles are an important step in the development of a new class of antibiotics.     

Recent advances of group 14 dimetallenes and dimetallynes in bond activation and catalysis

Since the first heavy alkene analogues of germanium and tin were isolated in 1976, followed by West''s disilene in 1981, the chemistry of stable group 14 dimetallenes and dimetallynes has advanced immensely. Recent developments in this field veered the focus from the isolation of novel bonding motifs to mimicking transition metals in their ability to activate small molecules and perform catalysis. The potential of these homonuclear multiply bonded compounds has been demonstrated numerous times in the activation of H₂, NH₃, CO₂ and other small molecules. Hereby, the strong relationship between structure and reactivity warrants close attention towards rational ligand design. This minireview provides an overview on recent developments in regard to bond activation with group 14 dimetallenes and dimetallynes with the perspective of potential catalytic applications of these compounds.

This minireview highlights the recent advances in small molecule activation and catalytic applications of homonuclear dimetallenes, dimetallynes and interconnected bismetallylenes of heavier group 14 elements.     

Reactions of the ionized enol tautomer of acetanilide: elimination of HNCO via a novel rearrangement

The reactions of ionised acetanilide, C(6)H(5)NH(=O)CH(3)(.+), and its enol, C(6)H(5)NH(OH)=CH(2)(.+), have been studied by a combination of tandem mass spectrometric and computational methods. These two isomeric radical cations have distinct chemistries at low internal energies. The keto tautomer eliminates exclusively CH(2)=C=O to give ionised aniline. In contrast, the enol tautomer loses H-N=C=O, via an unusual skeletal rearrangement, to form predominantly ionised methylene cyclohexadiene. Hydrogen atom loss also occurs from the enol tautomer, with the formation of protonated oxindole. The mechanisms for H-N=C=O and hydrogen atom loss both involve cyclisation; the former proceeds via a spiro transition state formed by attachment of the methylene group to the ipso position, whereas the latter entails the formation of a five-membered ring by attachment to the ortho position. The behaviour of labelled analogues reveals that these two processes have different site selectivities. Hydrogen atom loss involves a reverse critical energy and is subject to an isotope effect. Surprisingly, attempts to promote the enolisation of ionised acetanilide by proton-transport catalysis were unsuccessful. In a reversal of the usual situation for ionised carbonyl compounds, ionised acetanilide is actually more stable than its enol tautomer. The enol tautomer was resistant to proton-transport catalysed ketonisation to ionised acetanilide, possibly because the favoured geometry of the encounter complex with the base molecule is inappropriate for facilitating tautomerisation.     

Inelastic electron tunneling spectroscopy

Inelastic electron tunneling spectroscopy (IETS) is a relatively new form of vibrational spectroscopy which is able to address problems previously unsolved by either IR or Raman. It is particularly useful for surface analysis.     

Synthesis, characterization, and stability of Fe-MCM-41 for production of carbon nanotubes by acetylene pyrolysis

Fe-substituted MCM-41 molecular sieves with ca. 1, 2, and 3 wt % Fe were synthesized hydrothermally using different sources of colloidal silica (HiSil and Cab-O-Sil) and characterized by ICP, XRD, N2 physisorption, UV-vis, EPR, TPR, and X-ray absorption. Catalysts synthesized from Cab-O-Sil showed higher structural order and stability than those from HiSil. The local environment of Fe in the mesoporous material as studied by UV-vis reveals the dominance of framework Fe in all the as-synthesized Fe-MCM-41 samples. Dislodgement of some Fe species to extraframework location occurs upon calcination, and this effect is more severe for Fe-MCM-41 (2 wt %) and Fe-MCM-41 (3 wt %), as confirmed by EPR and X-ray absorption. These materials have been used as catalytic templates for the production of carbon nanotubes (CNTs) by acetylene pyrolysis at atmospheric pressure. A relationship between the Fe loading in MCM-41 and the carbon species produced during this reaction has been established. Using our optimized conditions for this system, Fe-MCM-41 with ca. 2 wt % Fe showed the best results with particularly high selectivity for single-wall carbon nanotube (SWNT) production. This catalyst was selective for carbon nanotubes with a low amount of amorphous carbon for a narrow range of temperatures from 1073 to 1123 K. To account for the different selectivity of these catalysts for CNTs production, the local environment and chemical state of Fe in the used catalyst was further probed by X-band EPR.     

Applications of array biosensor for detection of food allergens

Although food is a necessity, compounds within food products can be dangerous and life-threatening for people with food allergies. These allergy-causing compounds, such as proteins from eggs and milk, must be identified on the labels of commercial products. Unintentional contamination of food with these compounds occurs as a result of storage, manufacturing procedures, or cleaning procedures. A sensitive, specific, and rapid method to identify foods containing allergens is required by the food industry. The array biosensor, a rapid detection system, may provide a solution to this need. The array biosensor performs fluorescent immunoassays on the surface of a planar waveguide by first running samples, then fluorescently labeled antibodies, over a surface patterned with capture antibodies. An optical image is captured by a charged-coupled device camera and converted into fluorescence values. Signal intensity and spot location provide information on the compound and its concentration. The array biosensor has been successfully demonstrated for toxin, bacteria, and virus detection at low levels in under 20 min in food, clinical samples, and environmental matrixes. An assay for detection of ovalbumin as an indicator of egg contamination has been developed with limits of detection of 25 pg/mL in buffer and 1.3 ng/mL (13 ng/g) in non-egg pasta extract (buffer:pasta 10:1, v/w).     

Synthesis of angular triquinanes from 1-Alkynylbicyclo[3.2. 0]hept-2-en-7-ones. A tandem alkoxy-cope ring Expansion/Transannular ring closure reaction

Addition of ethenyllithium reagents to the carbonyl group of dialkyl squarate-derived 1-alkynylbicyclo[3.2.0]hept-2-ene-7-ones (15), followed by a TBAF workup, results in a low-temperature anion-accelerated alkoxy-Cope rearrangement which proceeds by way of a strained cyclic allene intermediates (e.g.,17). This leads to the formation of angularly fused triquinanes (e.g., 20) in which each of the rings is functionally differentiated. Bicyclo[6.3. 0]undecadienones (e.g., 36) are the major products when the reactions are quenched with aqueous bicarbonate rather than TBAF. Under analogous conditions 2-alkylidene-1-alkynylbicyclo[3.2. 0]heptan-7-ones also give bicyclo[6.3.0]undecadienones by a mechanism that was established to involve a 1,5-hydrgen shift in a strained allene intermediate. The synthetic scope and mechanism of these and related transformations are discussed.     

Bifunctional atomic force microscopy probes for molecular screening applications

Force mapping with the atomic force microscope (AFM) allows the simultaneous acquisition of topography and probe-sample interaction data. For example, AFM probes functionalised with an antigen can be employed to map the spatial distribution of recognition events on a substrate functionalised with its specific antibody. However, to date this method has been limited to the detection of single receptor-ligand species. Were the detection of multiple receptor-ligand interactions possible, force mapping would offer great scope as a sensitive tool for bioassay and screening applications. We have developed an immobilisation strategy, which allows two different molecular species (in this case human serum albumin and the β subunit of human chorionic gonadotropin) to be present simultaneously on an AFM probe. Single point force spectroscopy results have revealed the ability of such probes to discriminate between their corresponding recognition points (anti-HSA and anti-βhCG IgG antibodies). As a control, force measurements were re-recorded in the presence of the known antigen (free in solution) for each antibody species and a marked decrease in the frequency of specific interaction is observed. As an additional control interactions between anti-βhCG IgG and the multifunctional probe are taken in the presence of free βhCG (“true” antigen) and free HSA (“false” antigen). It is shown that measurements recorded in the presence of a non-related protein species results in no change in either the force observed or the frequency of specific interactions, further confirmation that the specificity of force observed is due to the separation of antibody-antigen complex.     

Impact of prefractionation using Gradiflow on two-dimensional gel electrophoresis and protein identification by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Prefractionation of protein samples prior to two-dimensional electrophoresis (2-DE) has the potential to increase the dynamic detection range for proteomic analysis. We evaluated a membrane-based electrophoretic separation technique (Gradiflow) for its ability to fractionate an exoproteome sample from the filamentous fungus Trichoderma reesei. The sample was separated on the basis of size and charge. Buffer optimization was found to be necessary for successful size fractionation. Fractionation by charge was used to resolve the sample into four fractions that were subjected to analysis by two-dimensional electrophoresis (2-DE). Enhanced detection of low-abundance proteins with selective removal of high-abundance species was achieved. Fractionated and unfractionated samples were examined for differences in the ability to identify proteins following 2-DE using trypsin in-gel digestion followed by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Fractionated samples showed marked improvement in protein identification ability and sequence coverage. This study demonstrates the utility of the Gradiflow for fractionation, resulting in an enhancement of resolution and characterization of a moderately complex proteome.     

De novo synthesis of 4'-ethoxy nucleoside analogues

Butenolides 5a and 13 were used as optically active templates in the de novo synthesis of 4'-disubstituted nucleoside analogues. The butenolides were reduced and acylated in situ to give acetates 10 and 14. Vorbrüggen coupling gave the protected nucleoside analogues 11 and 15. Reduction of 11 gave 4'-ethoxy-2',3'-dideoxythymidine (6) and deprotection of 15 gave 4'-ethoxy-2',3'-dideoxydidehydrothymidine (7). The cis-dihydroxylation of a variety of butenolides occurred with the major product formed from oxidation of the beta-face.