Electrostatic effects on the reactions of cyclohexanone oxocarbenium ions

Nucleophilic substitution reactions of 4-substituted cyclohexanone acetals display different selectivities depending upon the electronic nature of the substituent. Alkyl groups favor equatorial positions in the oxocarbenium ions, but alkoxy groups prefer axial conformers. The reactions of acetals with alkoxy groups constrained to either equatorial or axial positions suggest that the presence of an axial alkoxy group distorts the oxocarbenium ion, changing its inherent preferences for facial attack.     

A general strategy for creating "inactive-conformation" abl inhibitors

Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.     

Excited-state structural dynamics of 5-fluorouracil

5-Fluorouracil is an analogue of thymine and uracil, nucleobases found in DNA and RNA, respectively. The photochemistry of thymine is significant; UV-induced photoproducts of thymine in DNA lead to skin cancer and other diseases. In previous work, we have suggested that the differences in the excited-state structural dynamics of thymine and uracil arise from the methyl group in thymine acting as a mass barrier, localizing the vibrations at the photochemical active site. To further test this hypothesis, we have measured the resonance Raman spectra of 5-fluorouracil at wavelengths throughout its 267 nm absorption band. The spectra of 5-fluorouracil and thymine are very similar. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism suggests that, at most, 81% of the reorganization energy upon excitation is directed along photochemically relevant modes. This compares well with what was found for thymine, supporting the mass barrier hypothesis.     

Temporal variability of the telluric sodium layer

The temporal variability of the telluric sodium layer is investigated by analyzing 28 nights of data obtained with the Colorado State University LIDAR experiment. The mean height power spectrum of the sodium layer was found to be well fitted by a power law over the observed range of frequencies, 10 microHz to 4 mHz. The best-fitting power law was found be be 10(beta)nu(alpha), with alpha=-1.79+/-0.02 and beta=1.12+/-0.40. Applications to wavefront sensing require knowledge of the behavior of the sodium layer at kilohertz frequencies. Direct measurements at these frequencies do not exist. Extrapolation from low-frequency behavior to high frequencies suggests that this variability may be a significant source of error for laser guide star adaptive optics in large-aperture telescopes.     

Some crystallography,chemistry, physics,and thermodynamics of B12O2, B12P2, B12As2, and related alpha-boron type crystals

This paper shows that several alpha-boron type compounds may be useful as high-temperature semiconductors with decent carrier motilities, high electrical resistivity, good optical transparency, good stability under high radiation bombardment, and possess high neutron capture cross-sections. The most promising are B₁₂O₂, B₁₂P₂, and B₁₂As₂. Their relationship to alpha-boron, B₁₃C₂, and other derivative crystals is explained. A study of their chemical and thermodynamic properties indicates how single crystals useful for electronic devices can be grown.     

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

Metabolism of xenobiotics remains a central challenge for the discovery and development of drugs, cosmetics, nutritional supplements, and agrochemicals. Metabolic transformations are frequently related to the incidence of toxic effects that may result from the emergence of reactive species, the systemic accumulation of metabolites, or by induction of metabolic pathways. Experimental investigation of the metabolism of small organic molecules is particularly resource demanding; hence, computational methods are of considerable interest to complement experimental approaches. This review provides a broad overview of structure- and ligand-based computational methods for the prediction of xenobiotic metabolism. Current computational approaches to address xenobiotic metabolism are discussed from three major perspectives: (i) prediction of sites of metabolism (SOMs), (ii) elucidation of potential metabolites and their chemical structures, and (iii) prediction of direct and indirect effects of xenobiotics on metabolizing enzymes, where the focus is on the cytochrome P450 (CYP) superfamily of enzymes, the cardinal xenobiotics metabolizing enzymes. For each of these domains, a variety of approaches and their applications are systematically reviewed, including expert systems, data mining approaches, quantitative structure-activity relationships (QSARs), and machine learning-based methods, pharmacophore-based algorithms, shape-focused techniques, molecular interaction fields (MIFs), reactivity-focused techniques, protein-ligand docking, molecular dynamics (MD) simulations, and combinations of methods. Predictive metabolism is a developing area, and there is still enormous potential for improvement. However, it is clear that the combination of rapidly increasing amounts of available ligand- and structure-related experimental data (in particular, quantitative data) with novel and diverse simulation and modeling approaches is accelerating the development of effective tools for prediction of in vivo metabolism, which is reflected by the diverse and comprehensive data sources and methods for metabolism prediction reviewed here. This review attempts to survey the range and scope of computational methods applied to metabolism prediction and also to compare and contrast their applicability and performance.     

In situ ligand formation in the synthesis of an octanuclear dysprosium 'double cubane' cluster displaying single molecule magnet features

The nucleophilic addition of methanol and water to the dicyanonitrosomethanide anion, resulting in the formation of cyano(imino(methoxy)methyl)nitrosomethanide (cmnm) and carbamoylcyanonitrosomethanide (ccnm), respectively, is used as a means of in situ ligand synthesis during the formation of [Dy(8)(OH)(6)(OMe)(6)(cmnm)(10)(ccnm)(2)(H(2)O)(2)(MeOH)(2)] (1). This is the first time these reactions have been observed to be promoted by the presence of a lanthanoid ion. The core of the octanuclear cluster consists of two cubane moieties ([Dy(4)(OH)(3)(OMe)]), bridged by four methoxide ligands to form a central [Dy(8)(OH)(6)(OMe)(6)] moiety. The complex displays magnetic properties that are indicative of probable single molecule magnet features.     

Tetradecanuclear polycarbonatolanthanoid clusters: Diverse coordination modes of carbonate providing access to novel core geometries

The synthesis of two high nuclearity lanthanoid clusters demonstrates the versatility of the carbonate anion as a robust cluster forming agent, potentially allowing for the formation of otherwise inaccessible core topologies. The complexes, [Gd(14)(CO(3))(13)(ccnm)(9)(OH)(H(2)O)(6)(phen)(13)(NO(3))](CO(3))(2.5)·(phen)(0.5) () and [Dy(14)(CO(3))(13)(ccnm)(10)(OH)(H(2)O)(6)(phen)(13)](CO(3))(2.5)·(phen)(0.5) () (ccnm = carbamoylcyanonitrosomethanide, phen = 1,10-phenanthroline), contain a [Ln(14)(CO(3))(13)(OH)] core in which the carbonate anions display four unique coordination modes. The complexes are chiral, and the ccnm ligands also display four unique coordination modes. Extensive intra- and intermolecular π-π stacking between phen ligands leads to the formation of 1D chains in the crystal structure. Both complexes display magnetic properties that are indicative of antiferromagnetic coupling, with complex displaying behaviour consistent with possible single molecule magnet properties.     

Closely stacked oligo(phenylene ethynylene)s: effect of π-stacking on the electronic properties of conjugated chromophores

In this work, a bicyclo[4.4.1]undecane scaffold is used to hold oligo(phenylene ethynylene) units in a cofacially stacked arrangement along the entire length of the conjugated units. We study the impact that the resulting strong interchain interactions have on the photophysical properties. The length of the individual oligomer branches was varied from three to five rings to investigate the effect of conjugation on the electronic properties of the stacked segments. Absorption and fluorescence spectra were recorded and compared to those of the corresponding unstacked analogues. Time-dependent density functional theory calculations were carried out and helped to rationalize the low-energy features present in the fluorescence spectra of the stacked systems. The calculations indicate that the low-energy emissions are due to the presence of excimer-like states. The stronger intensity of the low-energy fluorescence band observed in the five-ring stacked system compared to the three-ring analogue is attributed to the smaller activation barrier that separates the local intrachain state and the excimer-like state in the former compound.     

Surface enhanced Raman spectroscopy (SERS) for the discrimination of Arthrobacter strains based on variations in cell surface composition

Surface enhanced Raman spectroscopy (SERS) is a rapid and highly sensitive spectroscopic technique that has the potential to measure chemical changes in bacterial cell surface in response to environmental changes. The objective of this study was to determine whether SERS had sufficient resolution to differentiate closely related bacteria within a genus grown on solid and liquid medium, and a single Arthrobacter strain grown in multiple chromate concentrations. Fourteen closely related Arthrobacter strains, based on their 16S rRNA gene sequences, were used in this study. After performing principal component analysis in conjunction with Linear Discriminant Analysis, we used a novel, adapted cross-validation method, which more faithfully models the classification of spectra. All fourteen strains could be classified with up to 97% accuracy. The hierarchical trees comparing SERS spectra from the liquid and solid media datasets were different. Additionally, hierarchical trees created from the Raman data were different from those obtained using 16S rRNA gene sequences (a phylogenetic measure). A single bacterial strain grown on solid media culture with three different chromate levels also showed significant spectral distinction at discrete points identified by the new Elastic Net regularized regression method demonstrating the ability of SERS to detect environmentally induced changes in cell surface composition. This study demonstrates that SERS is effective in distinguishing between a large number of very closely related Arthrobacter strains and could be a valuable tool for rapid monitoring and characterization of phenotypic variations in a single population in response to environmental conditions.