Mass spectrometric study to characterize thioisoindole derivatives of aminoglycoside antibiotics

Aminoglycoside antibiotics are widely used to treat serious Gram-negative and Gram-positive bacterial infections. The lack of a UV chromophore presents a problem in the analysis of aminoglycosides. Derivatization with 1,2-phthalic dicarboxaldehyde (OPA) in the presence of a thiol made it possible to introduce a UV chromophoric thioisoindole moiety. A qualitative mass spectrometry study was carried out to confirm the molecular identity of the products formed. The conditions described earlier to derivatize gentamicin and kanamycin yielded products in which all primary amino groups are fully derivatized. On the other hand, with tobramycin and amikacin, there was also formation of incompletely derivatized products that contained one thioisoindole group less than the fully derivatized product. This study has therefore brought an additional insight into the nature of the OPA-aminoglycoside derivatives studied.     

Synthesis, X-ray diffraction analysis and NMR studies of (Z)-2-methyl-3-triphenylstannyl-3-pentene-2-ol

The synthesis of (Z)-2-methyl-3-triphenylstannyl-3-pentene-2-ol and its characterization by an X-ray diffraction study and multinuclear NMR are reported. The tin atom exhibits a distorted tetrahedral SnC₄ geometry with the four Sn---C bond distances experimentally equivalent. The slight distortion from the ideal tetrahedral geometry is because of the presence of a weak intramolecular HO → Sn interaction of 3.012(3) Å which produces a loose four-membered ring. The title compound was characterized in solution by ¹H, ¹³C and ¹¹⁹Sn NMR, and the persistence of the weak intramolecular HO → Sn coordination in solution was revealed by ¹³C and ¹¹⁹Sn secondary isotope multiplet of partially labelled entities (SIMPLE-NMR) experiments.     

Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules

Bid is a key member of the Bcl-2 family proteins involved in the control of the apoptotic cascade in cells, leading to cell death. Uncontrolled cell death is associated with several human pathologies, such as neurodegenerative diseases and ischemic injuries. Therefore, Bid represents a potential yet unexplored and challenging target for strategies aimed at the development of therapeutic agents. Here we show that a multidisciplinary NMR-based approach that we named SAR by ILOEs (structure activity relationships by interligand nuclear Overhauser effect) allowed us to rationally design a series of 4-phenylsulfanyl-phenylamine derivatives that are capable of occupying a deep hydrophobic crevice on the surface of Bid. These compounds represent the first antiapoptotic small molecules targeting a Bcl-2 protein as shown by their ability to inhibit tBid-induced SMAC release, caspase-3 activation, and cell death.     

Mechanisms of intrinsic bioremediation of gas condensate hydrocarbons in saturated soil

Applied Biochemistry and Biotechnology - The addition of gas condensate hydrocarbons to saturated soil from a gas production site stimulated sulfate reduction under anaerobic and oxygen-limiting...     

Evaluation of multidimensional (ion-exchange/reversed-phase) protein separations using linear and step gradients in the first dimension

The performance characteristics of multidimensional liquid chromatographic protein separations were evaluated using on-line electrospray mass detection, and a novel workflow for automated LC/MS data processing. Two-dimensional ion exchange/reversed-phase LC separations of Escherichia coli cytosol were conducted using either a continuous linear or discontinuous step gradient in the first dimension. Chromatographic profiles of the top 100 most abundant components were characterized to assess overall separation reproducibility within each mode, and to characterize differences in component distribution between the two modes of operation. Analysis of the resulting data indicates that multidimensional separations of complex protein mixtures can be done reproducibly. Furthermore, under the conditions employed within this study, a linear first dimension gradient was more effective at fractionating the protein mixture, distributing fewer major components to multiple second dimension cycles than an equivalent step gradient. The application of on line mass spectrometry, and automated processing of the resulting data, proved valuable for producing component level analysis of multidimensional protein separations.     

Classification of gasoline data obtained by gas chromatography using a piecewise alignment algorithm combined with feature selection and principal component analysis

A fast and objective chemometric classification method is developed and applied to the analysis of gas chromatography (GC) data from five commercial gasoline samples. The gasoline samples serve as model mixtures, whereas the focus is on the development and demonstration of the classification method. The method is based on objective retention time alignment (referred to as piecewise alignment) coupled with analysis of variance (ANOVA) feature selection prior to classification by principal component analysis (PCA) using optimal parameters. The degree-of-class-separation is used as a metric to objectively optimize the alignment and feature selection parameters using a suitable training set thereby reducing user subjectivity, as well as to indicate the success of the PCA clustering and classification. The degree-of-class-separation is calculated using Euclidean distances between the PCA scores of a subset of the replicate runs from two of the five fuel types, i.e., the training set. The unaligned training set that was directly submitted to PCA had a low degree-of-class-separation (0.4), and the PCA scores plot for the raw training set combined with the raw test set failed to correctly cluster the five sample types. After submitting the training set to piecewise alignment, the degree-of-class-separation increased (1.2), but when the same alignment parameters were applied to the training set combined with the test set, the scores plot clustering still did not yield five distinct groups. Applying feature selection to the unaligned training set increased the degree-of-class-separation (4.8), but chemical variations were still obscured by retention time variation and when the same feature selection conditions were used for the training set combined with the test set, only one of the five fuels was clustered correctly. However, piecewise alignment coupled with feature selection yielded a reasonably optimal degree-of-class-separation for the training set (9.2), and when the same alignment and ANOVA parameters were applied to the training set combined with the test set, the PCA scores plot correctly classified the gasoline fingerprints into five distinct clusters.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

A general and convenient synthesis of N-aryl piperazines

A general and convenient synthesis of N-aryl piperazines from bis(2-chloroethyl)amine hydrochloride and a broad range of anilines in diethylene glycol monomethyl ether is described.     

Cucurbit[6]uril pseudorotaxanes: distinctive gas-phase dissociation and reactivity

Cucurbit[6]uril forms a doubly charged complex with 1,4-butanediammonium cation that is observed using electrospray ionization Fourier transform mass spectrometry. Such 1:1 complexes are not observed for the smaller cucurbit[5]uril, which forms a 2:1 ammonium:cucurbituril complex instead. The 1:1 complex with cucurbit[6]uril is difficult to fragment via collisional activation; when it does fragment, both breakup of the cucurbituril cage and loss of the amine are observed. Further, the complex reacts with tert-butylamine via slow adduction. In contrast, nonrotaxane analogues (such as doubly charged 2:1 complexes of either protonated 1,4-butanediamine or protonated ethylenediamine with cucurbit[6]uril) fragment via easy loss of the intact amine upon collisional activation and react with tert-butylamine via rapid displacement of the original amine. On the basis of stoichiometry, fragmentation behavior, and reactivity, we conclude that the doubly charged complex of cucurbit[6]uril with 1,4-butanediammonium is a gas-phase pseudorotaxane.     

Ring expansion-annulation strategy for the synthesis of substituted azulenes and oligoazulenes. 2. Synthesis of azulenyl halides, sulfonates, and azulenylmetal compounds and their application in transition-metal-mediated coupling reactions

A "ring expansion-annulation strategy" for the synthesis of substituted azulenes is described based on the reaction of beta'-bromo-alpha-diazo ketones with rhodium carboxylates. The key transformation involves an intramolecular Buchner reaction followed by beta-elimination of bromide, tautomerization, and in situ trapping of the resulting 1-hydroxyazulene as a carboxylate or triflate ester. Further synthetic elaboration of the azulenyl halide and sulfonate annulation products can be achieved by employing Heck, Negishi, Stille, and Suzuki coupling reactions. Reaction of the azulenyl triflate 84 with pinacolborane provides access to the azulenylboronate 91, which participates in Suzuki coupling reactions with alkenyl and aryl iodides. The application of these coupling reactions to the synthesis of biazulenes, terazulene 101, and related oligoazulenes is described, as well as the preparation of the azulenyl amino acid derivative 110.