Reactions within fluorobenzene-ammonia heterocluster ions: experiment and theory

Reactions occurring within gas phase fluorobenenze-ammonia heterocluster cations (FC(6)H(5)-(NH(3))(n=1-4)) have been studied through the use of a triple quadrupole mass spectrometer as well as employing density functional theory (DFT). Collision induced dissociation (CID) experiments were conducted in which mass selected cluster ions are accelerated into a cell containing argon gas and the resulting products then subsequently mass analyzed. Two dominate reaction channels are observed. The first is simple evaporative loss of neutral ammonia from the cluster ion. The second involves a substitution reaction occurring within the cluster ion to form the aniline cation, C(6)H(5)NH(2)(+), where the reactivity was found to vary as a function of cluster size. DFT calculations have been performed to both help analyze the structure and the reactivity of these cluster ions. Pronounced differences in activation energies were found that provide an explanation for the observed variation of reactivity as a function of cluster size. An ad hoc model based upon the Arrhenius equation was developed to fit both the experimental collision energy dependence of the reaction and the observed lowering of the reaction barrier to aniline formation as a function of cluster size.     

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.     

Expanded scope of heterocyclic biaryl synthesis via a palladium-catalysed thermal decarboxylative cross-coupling reaction

The palladium-catalysed decarboxylative cross-coupling of heterocyclic aromatic carboxylates and aryl halides is described. The cross-coupling proceeds under relatively mild conditions using catalytic Pd(0) and tetrabutylammonium bromide (TBAB). Utilizing a mixed solvent system consisting of N,N-dimethylformamide (DMF) and N-methyl-2-pyrrolidone (NMP), the cross-coupling system operated at temperatures ranging from 80 to 140 °C.     

The mechanostability of isolated focal adhesions is strongly dependent on pH

This report demonstrates that the mechanical stability of focal adhesions exhibits a biphasic and sensitive pH dependence. These studies used isolated focal adhesions, which retain many of the properties of the intracellular structures, including protein composition and force-dependent reinforcement by cytosolic proteins. The focal adhesion structures are least stable to applied force at a pH of 6.4, and significantly more stable at slightly higher and lower pH values. This trend is consistent with previous work that characterized the pH dependence of cell migration and may therefore be relevant to controlling the invasiveness of metastatic cancer cells. This approach is significant because it allows biochemical studies of large protein complexes previously studied only in cell culture, and therefore offers new opportunities for performing mechanistic studies of a range of factors that contribute to focal adhesion stability.     

A performance study of radio-opaque personal protective fabrics for the reduction of transmittance of gamma-rays and neutrons

Commercial radio-opaque combat (CRC) fabrics, for incorporation into personal protective equipment used by first responders and armed forces, are marketed as having the ability to provide a level of protection against specific types of radiation. For a CRC material, a standard combat uniform and a multi-layered chemical, biological, radiological, nuclear (CBRN) protective material, the present work examines chemical composition and radiation protection against gamma-rays and neutron fluxes. Significant reduction in gamma-ray transmittance occurs only for the CRC fabric (46–514 keV) with gamma-ray attenuation coefficients of 3.10 to <0.10 cm² g⁻¹. Reduction in neutron transmittance, for all three fabrics, could not be assessed with certainty as the measured transmittance was obscured by large statistical uncertainties.     

Synthesis and calorimetric, spectroscopic, and structural characterization of isocyanide complexes of trialkylaluminum and tri-tert-butylgallium

Addition of tert-butylisocyanide or 2,6-dimethylphenylisocyanide to a solution of trialkylaluminum or trialkylgallium results in formation of complexes R(3)M·C≡N(t)Bu (M = Al, R = Me (1), Et (2), (i)Bu (3), (t)Bu (4); M = Ga, R = (t)Bu (9)) or R(3)M·C≡N(2,6-Me(2)C(6)H(3)) (M = Al, R = Me (5), Et (6), (i)Bu (7), (t)Bu (8); M = Ga, R = (t)Bu (10)), respectively. Complexes 1, 4, 5, and 8-10 are isolated as solids, whereas the triethylaluminum and triisobutylaluminum adducts 2, 3, 6, and 7 are viscous oils. Complexes 1-10 were characterized by NMR ((1)H, (13)C) and IR spectroscopies, and the molecular structures of 4, 5, and 8-10 were also determined by X-ray crystallography. The frequency of the C≡N stretch of the isocyanide increased by 58-91 cm(-1) upon complexation, consistent with coordination of the isocyanide as a σ donor. Enthalpies of complex formation for 1-10 were determined by isothermal titration calorimetry. Enthalpy data suggest the following order of decreasing Lewis acidity: (t)Bu(3)Al ? (i)Bu(3)Al ≥ Me(3)Al ≈ Et(3)Al ? (t)Bu(3)Ga. In the absence of oxygen and protic reagents, the reported complexes do not undergo insertion or elimination reactions upon heating their benzene-d(6) solutions to 80 °C.     

Characterizing dusky dolphin sounds from Argentina and New Zealand

Dusky dolphin (Lagenorhynchus obscurus) acoustic sounds were characterized by analyzing narrowband recordings [0-16 kHz in New Zealand (NZ) and 0-24 kHz in Argentina], and sounds in broadband recordings (0-200 kHz) were compared to their counterparts in down-sampled narrowband recordings (0-16 kHz). The most robust similarity between sounds present in broadband recordings and their counterparts in the down-sampled narrowband recordings was inter-click interval (ICI); ICI was therefore primarily used to characterize click sounds in narrowband recordings. In NZ and Argentina, distribution of ICIs was a continuum, although the distribution of ICIs in NZ had a somewhat bimodal tendency. In NZ, sounds that had smaller mean ICIs were more likely to have constant ICIs, and less likely to have increasing or decreasing ICIs. Similar to some other delphinids, dusky dolphins may use single, short duration sounds that have a constant ICI and closely spaced clicks for communication. No whistles were documented at either study site. Temporally structured sequences of burst pulses (i.e., sounds with ICI < about 10 ms) also occurred at both study sites, and these sequences contained 2-14 burst pulses that appeared closely matched aurally and in spectrograms and waveforms.     

Probing Proteins in Solution by Xe NMR Spectroscopy

The interaction of xenon with different proteins in aqueous solution is investigated by ¹²⁹Xe NMR spectroscopy. Chemical shifts are measured in horse metmyoglobin, hen egg white lysozyme, and horse cytochrome c solutions as a function of xenon concentration. In these systems, xenon is in fast exchange between all possible environments. The results suggest that nonspecific interactions exist between xenon and the protein exteriors and the data are analyzed in term of parameters which characterize the protein surfaces. The experimental data for horse metmyoglobin are interpreted using a model in which xenon forms a 1:1 complex with the protein and the chemical shift of the complexed xenon is reported (Locci et al., Keystone Symposia “Frontiers of NMR in Molecular Biology VI”, Jan. 9–15, 1999, Breckenridge, CO, Abstract E216, p. 53; Locci et al., XeMAT 2000 “Optical Polarization and Xenon NMR of Materials”, June 28–30, 2000, Sestri Levante, Italy, p. 46).     

Enhanced MRI of tumors utilizing a new nitroxyl spin label contrast agent

Nitroxyl spin labels have been shown to be effective in vivo contrast agents for magnetic resonance imaging (MRI) of the central nervous system, myocardium, and urinary tract. A new pyrrolidine nitroxyl contrast agent (PCA) with better resistance to in vivo metabolic inactivation than previously tested agents was studied for its potential to enhance subcutaneous neoplasms in an animal model. Twenty-two contrast enhancement trials were performed on a total of 15 animals 4-6 weeks after implantation with human renal adenocarcinoma. Spin echo imaging was performed using a .35 T animal imager before and after intravenous administration of PCA in doses ranging from 0.5 to 3mM/kg. The intensity of tumor tissue in the images increased an average of 35% in animals receiving a dose of 3 mM/kg. The average enhancement with smaller doses was proportionately less. Tumor intensity reached a maximum within 15 min of injection. The average intensity difference between tumor and adjacent skeletal muscle more than doubled following administration of 3 mM/kg of PCA. Well-perfused tumor tissue was more intensely enhanced than adjacent poorly perfused and necrotic tissue.     

A Multiple-criteria Approach to Dynamic Cold-ingot Substitution

Bethlehem Steel's plant at Bethlehem, Pennsylvania uses a computer-based mill-providing procedure to plan ingot requirements for the production of structural shapes and pilings. When not enough hot steel is available to meet all the ingot requirements, cold steel ingots from inventory must be substituted in order to meet the production plan. A computer system was developed that dynamically selects cold ingots to use when hot steel is not available. This system selects cold ingots based first on ingot-selection priorities, and secondly, within priorities, on several criteria. An approach was developed that assigns a penalty to each feasible cold ingot such that the priorities and multiple criteria are addressed by simply ranking the ingots based on their penalty values. Ingots are selected from the top of the ranked list, and the results are consistently acceptable to the steel-providers at the Bethlehem plant. The system improves yield and reduces material-handling costs.