High pressure studies using two-stage diamond micro-anvils grown by chemical vapor deposition

Ultra-high static pressures have been achieved in the laboratory using a two-stage micro-ball nanodiamond anvils as well as a two-stage micro-paired diamond anvils machined using a focused ion-beam system. The two-stage diamond anvils’ designs implemented thus far suffer from a limitation of one diamond anvil sliding past another anvil at extreme conditions. We describe a new method of fabricating two-stage diamond micro-anvils using a tungsten mask on a standard diamond anvil followed by microwave plasma chemical vapor deposition (CVD) homoepitaxial diamond growth. A prototype two-stage diamond anvil with 300?µm culet and with a CVD diamond second stage of 50?µm in diameter was fabricated. We have carried out preliminary high pressure X-ray diffraction studies on a sample of rare-earth metal lutetium sample with a copper pressure standard to 86?GPa. The micro-anvil grown by CVD remained intact during indentation of gasket as well as on decompression from the highest pressure of 86?GPa.     

Molar extinction coefficients of some carbohydrates in aqueous solutions

Molar extinction coefficients of some carbohydrates viz. l-arabinose (C₅H₁₀O₅), d-glucose (C₆H₁₂O₆), d-mannose (C₆H₁₂O₆), d-galactose (C₆H₁₂O₆), d(-) fructose (C₆H₁₂O₆) and maltose (C₁₂H₂₄O₁₂) in aqueous solutions have been determined at 81, 356, 511, 662, 1173 and 1332 keV by gamma ray transmission method in a narrow beam good geometry set-up. These coefficients have been found to depend upon the photon energy following a 4-parameter polynomial. These extinction coefficients for different sugars having the same molecular formula have same values varying within experimental uncertainty. Within concentration ranges studied, Beer-Lambert law is obeyed very well.     

Structural phase transitions in yttrium under ultrahigh pressures

X-ray diffraction studies were carried out on the rare earth metal yttrium up to 177?GPa in a diamond anvil cell at room temperature. Yttrium was compressed to 37% of its initial volume at the highest pressure. The rare earth crystal structure sequence hcp?→?Sm?type?→?dhcp?→?mixed(dhcp?+?fcc)?→?distorted fcc (dfcc) is observed in yttrium below 50?GPa. The dfcc (hR24) phase has been observed to persist in the pressure range of 50-95?GPa. A structural transition from dfcc to a low symmetry phase has been observed in yttrium at 99?±?4?GPa with a volume change of -?2.6%. This low symmetry phase has been identified as a monoclinic C2/m phase, which has also been observed in other rare earth elements under high pressures. The appearance of this low symmetry monoclinic phase in yttrium shows that its electronic structure under extreme conditions resembles that of heavy rare earth metals, with a significant increase in d-band character of the valence electrons and possibly some f-electron states near the Fermi level.     

Homoconjugation in the adamantane cage: DFT/IGLO studies of the 1, 3-dehydro-5-adamantyl cation, its isoelectronic boron analogue 1, 3-dehydro-5-boraadamantane, and related systems(1)(,)

The structure of 1,3-dehydro-5-adamantyl cation and its isoelectronic boron analogue 1,3-dehydro-5-boraadamantane as well as some related adamantane systems, hitherto unknown as persistent long-lived species, were investigated by using the density functional theory (DFT) method. (13)C and (11)B NMR chemical shifts of the compounds were also calculated using the IGLO method. Stabilization of the systems due to homoconjugation is discussed.     

Theoretical study of relative width of photonic band gap for the 3-D dielectric structure

Calculations for the relative width (Δω/ω₀) as a function of refractive index and relative radius of the photonic band gap for the fcc closed packed 3-D dielectric microstructure are reported and comparison of experimental observations and theoretical predictions are given. This work is useful for the understanding of photonic crystals and occurrence of the photonic band gap.     

离子液体作为溶剂/催化剂用于卤代烃对胺的选择性烷基化反应

在三乙胺存在下,在离子液体([bmim]I和[bmim]PF6)中进行了各种卤代烃对胺类化合物中氨基的选择性烷基化反应.反应在相对温和的条件下进行,转化率和选择性优异.离子液体可以回收并重复使用.     

Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multi-disease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines for the large-scale modeling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is compared to all other signatures that are subsequently sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions used to create the drug-proteome signatures may be determined by any screening or docking method, but the primary approach used thus far has been BANDOCK, our in-house bioanalytical or similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and chem-informatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the two docking-based pipelines from which it was synthesized, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking-based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking-based signature generation methods can capture unique and useful signals for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.     

Structural and magnetic phase transitions in gadolinium under high pressures and low temperatures

High pressure structural transition studies have been carried out on rare earth metal gadolinium in a diamond anvil cell at room temperature to 169?GPa. Gadolinium has been compressed to 38% of its initial volume at this pressure. With increasing pressure, a crystal structure sequence of hcp?→?Sm-type?→?dhcp?→?fcc?→?dfcc?→?monoclinic has been observed in our studies on gadolinium. The measured equation of state of gadolinium is presented to 169?GPa at ambient temperature. Magnetic ordering temperature of gadolinium has been studied using designer diamond anvils to a pressure of 25?GPa and a temperature of 10?K. The magnetic ordering temperature has been determined from the four-point electrical resistivity measurements carried out on gadolinium. Our experiments show that the magnetic transition temperature decreases with increasing pressure to 19?GPa and then increases when gadolinium is subjected to higher pressures.     

Disease risk of missense mutations using structural inference from predicted function

Advancements in sequencing techniques place personalized genomic medicine upon the horizon, bringing along the responsibility of clinicians to understand the likelihood for a mutation to cause disease, and of scientists to separate etiology from nonpathologic variability. Pathogenicity is discernable from patterns of interactions between a missense mutation, the surrounding protein structure, and intermolecular interactions. Physicochemical stability calculations are not accessible without structures, as is the case for the vast majority of human proteins, so diagnostic accuracy remains in infancy. To model the effects of missense mutations on functional stability without structure, we combine novel protein sequence analysis algorithms to discern spatial distributions of sequence, evolutionary, and physicochemical conservation, through a new approach to optimize component selection. Novel components include a combinatory substitution matrix and two heuristic algorithms that detect positions which confer structural support to interaction interfaces. The method reaches 0.91 AUC in ten-fold cross-validation to predict alteration of function for 6,392 in vitro mutations. For clinical utility we trained the method on 7,022 disease associated missense mutations within the Online Mendelian inheritance in man amongst a larger randomized set. In a blinded prospective test to delineate mutations unique to 186 patients with craniosynostosis from those in the 95 highly variant Coriell controls and 1000 age matched controls, we achieved roughly 1/3 sensitivity and perfect specificity. The component algorithms retained during machine learning constitute novel protein sequence analysis techniques to describe environments supporting neutrality or pathology of mutations. This approach to pathogenetics enables new insight into the mechanistic relationship of missense mutations to disease phenotypes in our patients.