Design and construction of an ultra-low-background 14-crystal germanium array for high efficiency and coincidence measurements

Physics experiments, environmental surveillance, and treaty verification techniques continue to require increased sensitivity for detecting and quantifying radionuclides of interest. This can be done by detecting a greater fraction of gamma emissions from a sample (higher detection efficiency) and reducing instrument backgrounds. A current effort for increased sensitivity in high resolution gamma spectroscopy will produce an intrinsic germanium (HPGe) array designed for high detection efficiency, ultra-low-background performance, and useful coincidence efficiencies. The system design is optimized to accommodate filter paper samples, e.g. samples collected by the Radionuclide Aerosol Sampler/Analyzer (RASA). The system will provide high sensitivity for weak collections on atmospheric filter samples, as well as offering the potential to gather additional information from more active filters using gamma cascade coincidence detection. The current effort is constructing an ultra-low-background HPGe crystal array consisting of two vacuum cryostats, each housing a hexagonal array of 7 crystals on the order of 70% relative efficiency per crystal. Traditional methods for constructing ultra-low-background detectors are used, including use of materials known to be low in radioactive contaminants, use of ultra pure reagents, clean room assembly, etc. The cryostat will be constructed mainly from copper electroformed into near-final geometry at PNNL. Details of the detector design, simulation of efficiency and coincidence performance, HPGe crystal testing, and progress on cryostat construction are presented.     

Maize kernel hardness classification by near infrared (NIR) hyperspectral imaging and multivariate data analysis

The use of near infrared (NIR) hyperspectral imaging and hyperspectral image analysis for distinguishing between hard, intermediate and soft maize kernels from inbred lines was evaluated. NIR hyperspectral images of two sets (12 and 24 kernels) of whole maize kernels were acquired using a Spectral Dimensions MatrixNIR camera with a spectral range of 960-1662 nm and a sisuChema SWIR (short wave infrared) hyperspectral pushbroom imaging system with a spectral range of 1000-2498 nm. Exploratory principal component analysis (PCA) was used on absorbance images to remove background, bad pixels and shading. On the cleaned images, PCA could be used effectively to find histological classes including glassy (hard) and floury (soft) endosperm. PCA illustrated a distinct difference between glassy and floury endosperm along principal component (PC) three on the MatrixNIR and PC two on the sisuChema with two distinguishable clusters. Subsequently partial least squares discriminant analysis (PLS-DA) was applied to build a classification model. The PLS-DA model from the MatrixNIR image (12 kernels) resulted in root mean square error of prediction (RMSEP) value of 0.18. This was repeated on the MatrixNIR image of the 24 kernels which resulted in RMSEP of 0.18. The sisuChema image yielded RMSEP value of 0.29. The reproducible results obtained with the different data sets indicate that the method proposed in this paper has a real potential for future classification uses.     

Toward uniform nanotubular compounds: synthetic approach and ab initio calculations

We propose to synthesize a new class of single-walled nanotubular compounds (SWNCs) and investigate the interplay between their structural and electronic properties using ab initio density functional calculations. SWNCs are composed of cyclacenes of variable diameter interconnected by various linker compounds. Cyclacenes map directly onto and can be viewed as the shortest segments of (n,0) zigzag carbon nanotubes. We focus on cyclacenes with n=6-12 fused benzene rings interconnected by biphenyl, tetrazine, or acetylene linkers. Depending upon the nature and the orientation of the linkers, we find it possible to change the systems from narrow-gap to wide-gap semiconductors, and to modulate the band dispersion, suggesting the possibility of band gap engineering.     

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.     

Influence of hydrogen bonding on excitonic coupling and hierarchal structure of a light-harvesting porphyrin aggregate

Helical porphyrin nanotubes of tetrakis(4-sulfonatophenyl)porphyrin (TSPP) were examined in DCl/D(2)O solution using resonance Raman and resonance light scattering spectroscopy to probe the influence of hydrogen bonding on the excitonic states. Atomic force microscopy reveals similar morphology for aggregates deposited from DCl/D(2)O and from HCl/H(2)O solution. Deuteration results in subtle changes to the aggregate absorption spectrum but large changes in the relative intensities of Raman modes in the J-band excited resonance Raman spectra, revealing relatively more reorganization along lower-frequency vibrational modes in the protiated aggregate. Depolarization ratio dispersion and changes in the relative Raman intensities for excitation wavelengths spanning the J-band demonstrate interference from overlapping excitonic transitions. Distinctly different Raman excitation profiles for the protiated and deuterated aggregates reveal that isotopic substitution influences the excitonic structure of the J-band. The deuterated aggregate exhibits a nearly two-fold increase in intensity of resonance light scattering as a result of an increase in the coherence number, attributed to decreased exciton-phonon scattering. We propose that strongly coupled cyclic N-mers, roughly independent of isotopic substitution, largely decide the optical absorption spectrum, while water-mediated hydrogen bonding influences the further coherent coupling among them when they are assembled into nanotubes. The results show that, similar to natural light-harvesting complexes such as chlorosomes, hydrogen bonding can have a critical influence on exciton dynamics.