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https://www.readbyqxmd.com/read/28108896/pharmacophore-based-screening-and-drug-repurposing-exemplified-on-glycogen-synthase-kinase-3-inhibitors
#1
Luminita Crisan, Sorin Avram, Liliana Pacureanu
The current study was conducted to elaborate a novel pharmacophore model to accurately map selective glycogen synthase kinase-3 (GSK-3) inhibitors, and perform virtual screening and drug repurposing. Pharmacophore modeling was developed using PHASE on a data set of 203 maleimides. Two benchmarking validation data sets with focus on selectivity were assembled using ChEMBL and PubChem GSK-3 confirmatory assays. A drug repurposing experiment linking pharmacophore matching with drug information originating from multiple data sources was performed...
January 21, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28108663/determination-of-the-conformational-ensemble-of-the-tar-rna-by-x-ray-scattering-interferometry
#2
Xuesong Shi, Peter Walker, Pehr B Harbury, Daniel Herschlag
The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108079/preparation-and-evaluation-of-pillararene-bonded-silica-gel-stationary-phases-for-high-performance-liquid-chromatography
#3
Wenjie Zhao, Jianxiang Chu, Fuwei Xie, Qunpeng Duan, Lijun He, Shusheng Zhang
Pillararene bonded stationary phases for high performance liquid chromatography were prepared using 3-aminopropyltriethoxysilane as coupling reagent. The structure of the new materials was characterized by infrared spectroscopy, elemental analysis and thermogravimetric analysis. The chromatographic performance and retention mechanism of the new stationary phases were evaluated in reversed-phase mode compared with C18 using different solute probes including Tanaka test solutes, polycyclic aromatic hydrocarbons, phenols and aromatic positional isomers...
December 11, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28107635/atomic-number-dependent-structural-transitions-in-ordered-lanthanide-monolayers-role-of-the-hydration-shell
#4
Mitchell Miller, Miaoqi Chu, Binhua Lin, Wei Bu, Pulak Dutta
When lanthanide ions are present in the aqueous subphase of a floating monolayer (Langmuir film), the ions attracted to the interface will in many cases form commensurate and/or incommensurate two-dimensional structures. These lattices depend not only on the molecules forming the monolayer, but also on the atomic number of the lanthanide, with a sudden change between the lattice formed by lighter ions and that formed by heavier ions under a given monolayer. Since there are few other relevant differences between the lanthanides, we attribute the Z-dependent 'transition' to the number of water molecules associated with each ion...
January 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28107626/polymeric-nanofibers-with-ultrahigh-piezoelectricity-via-self-orientation-of-nanocrystals
#5
Xia Liu, Jing Ma, Xiaoming Wu, Liwei Lin, Xiaohong Wang
Piezoelectricity in macromolecule polymers has been gaining immense attention, particularly for applications in biocompatible, implantable, and flexible electronic devices. This paper introduces core-shell-structured piezoelectric polyvinylidene fluoride (PVDF) nanofibers chemically wrapped by graphene oxide (GO) lamellae (PVDF/GO nanofibers), in which the polar β-phase nanocrystals are formed and uniaxially self-oriented by the synergistic effect of mechanical stretching, high-voltage alignment, and chemical interactions...
January 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28107012/anion-caffeine-interactions-studied-by-13-c-and-1-h-nmr-and-atr-ftir-spectroscopy
#6
Nicolas O Johnson, Taylor Patrick Light, Gina MacDonald, Yanjie Zhang
This work investigates the interactions of a series of 11 anions with caffeine by utilizing (13)C and (1)H NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The aim of this study is to elucidate the molecular mechanisms of ion interactions with caffeine and to study how these interactions affect caffeine aggregation in aqueous solution. The chemical shift changes of caffeine (13)C and (1)H in the presence of salts provide a measure for anions' salting-out/salting-in abilities on individual carbon and hydrogen atoms in caffeine...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#7
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106994/enzymatic-halogenation-and-dehalogenation-reactions-pervasive-and-mechanistically-diverse
#8
Vinayak Agarwal, Zachary D Miles, Jaclyn M Winter, Alessandra S Eustáquio, Abrahim A El Gamal, Bradley S Moore
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution...
January 20, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28106979/li-ion-localization-and-energetics-as-a-function-of-anode-structure
#9
Nicholas William McNutt, Marshall T McDonnell, Orlando Rios, David J Keffer
In this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work1, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes...
January 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28106450/nontrivial-role-of-interlayer-cation-states-in-iron-based-superconductors
#10
Daniel Guterding, Harald O Jeschke, I I Mazin, J K Glasbrenner, E Bascones, Roser Valentí
Unconventional superconductivity in iron pnictides and chalcogenides has been suggested to be controlled by the interplay of low-energy antiferromagnetic spin fluctuations and the particular topology of the Fermi surface in these materials. Based on this premise, one would also expect the large class of isostructural and isoelectronic iron germanide compounds to be good superconductors. As a matter of fact, they, however, superconduct at very low temperatures or not at all. In this work we establish that superconductivity in iron germanides is suppressed by strong ferromagnetic tendencies, which surprisingly do not originate from changes in bond angles or bond distances with respect to iron pnictides and chalcogenides, but are due to changes in the electronic structure in a wide range of energies happening upon substitution of atom species (As by Ge and the corresponding spacer cations)...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106395/reactions-of-isocyanides-with-metal-carbyne-complex-isolation-and-characterization-of-metallacyclopropenimine-intermediates
#11
Ming Luo, Lipeng Long, Hong Zhang, Yuhui Yang, Yuhui Hua, Gang Liu, Zhenyang Lin, Haiping Xia
η(2)-Iminoketenyl species have often been postulated as the intermediates in nucleophile-induced carbyne-isocyanide C-C coupling processes. However, such species are elusive. In this article we report direct formation of η(2)-iminoketenyl complexes from reactions of metallapentalyne with isocyanides. Our studies show that steric effects of N-substituents of the isocyanides play an important role in the stability of the three-membered metallacycles of the η(2)-iminoketenyl complexes. Sterically bulky isocyanides, such as tert-butyl or 1-adamantyl isocyanides, inhibit bending at the isocyanide nitrogen atoms, a requirement for formation of η(2)-iminoketenyl structures...
January 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28106219/surface-and-interface-engineering-of-fept-c-nanocatalysts-for-electro-catalytic-methanol-oxidation-enhanced-activity-and-durability
#12
Junmei Wang, Zhenlei Wang, Shuai Li, Rongming Wang, Yujun Song
A methodology by coupling a microfluidic-batch process with in situ carbon-black mixing, successive annealing and de-alloying post-treatment was developed for engineering surface and interface microstructures of FePt/C nanocomposites. Ultra-small angular FePt nanocrystals rich in vertexes/terraces/steps and with Pt contents gradually increasing from the inner to the outer part can be synthesized at certain Fe/Pt atomic ratios (2/1 or 1.1/1), which can directly grow on carbon-black for enhanced nanocrystal-carbon interface interaction by introducing the in situ carbon-black mixing process...
January 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28106204/the-stabilization-of-tubular-crystals-in-mixtures-of-spherical-particles
#13
Ian Douglass, Helen Mayger, Toby Hudson, Peter Harrowell
Novel crystal structures in binary atomic mixtures arise when the attractive well is wide enough to allow double occupancy by small particles. The resulting crystals consist of ordered packings of self assembled linear structures comprised of a cylindrical tube of large particles enclosing a close packed core of small particles that corresponds to a stacking of overlapping icosahedra. We show that the stability of these structures depends on two essential features of the spherically symmetric pairwise interactions: (i) a radius ratio between 0...
January 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28106187/layer-separable-and-gap-tunable-topological-insulators
#14
Kai-Wei Chang, Wei Ji, Chao-Cheng Kaun
The way in which states of a topological insulator (TI) transform from monolayer to bulk is an important issue for applications in spintronics. However, unlike graphite, most layered materials are difficult to exfoliate. Using first-principles calculations, we predict that thallium selenide (TlSe) will be a layered TI with rather weak interlayer coupling and thus it should be exfoliated easily. The evolution of the topological states can also be driven by doping with indium (In) atoms or applying lateral strains...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106179/molecular-electronic-structure-in-one-dimensional-coulomb-systems
#15
Caleb J Ball, Pierre-François Loos, Peter M W Gill
Following two recent papers [Phys. Chem. Chem. Phys., 2015, 17, 3196; Mol. Phys., 2015, 113, 1843], we perform a larger-scale study of chemical structure in one dimension (1D). We identify a wide, and occasionally surprising, variety of stable 1D compounds (from diatomics to tetra-atomics) as well as a small collection of stable polymeric structures. We define the exclusion potential, a 1D analogue of the electrostatic potential, and show that it can be used to rationalise the nature of bonding within molecules...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106144/electronic-and-atomic-structures-of-the-sr3ir4sn13-single-crystal-a-possible-charge-density-wave-material
#16
H-T Wang, M K Srivastava, C-C Wu, S-H Hsieh, Y-F Wang, Y-C Shao, Y-H Liang, C-H Du, J-W Chiou, C-M Cheng, J-L Chen, C-W Pao, J-F Lee, C N Kuo, C S Lue, M-K Wu, W-F Pong
X-ray scattering (XRS), x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopic techniques were used to study the electronic and atomic structures of the high-quality Sr3Ir4Sn13 (SIS) single crystal below and above the transition temperature (T(*) ≈ 147 K). The evolution of a series of modulated satellite peaks below the transition temperature in the XRS experiment indicated the formation of a possible charge density wave (CDW) in the (110) plane...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106073/high-resolution-cryo-em-structure-of-the-proteasome-in-complex-with-adp-alfx
#17
Zhanyu Ding, Zhenglin Fu, Cong Xu, Yifan Wang, Yanxing Wang, Junrui Li, Liangliang Kong, Jinhuan Chen, Na Li, Rongguang Zhang, Yao Cong
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide...
January 20, 2017: Cell Research
https://www.readbyqxmd.com/read/28106054/extremely-broadband-on-chip-optical-nonreciprocity-enabled-by-mimicking-nonlinear-anti-adiabatic-quantum-jumps-near-exceptional-points
#18
Youngsun Choi, Choloong Hahn, Jae Woong Yoon, Seok Ho Song, Pierre Berini
Time-asymmetric state-evolution properties while encircling an exceptional point are presently of great interest in search of new principles for controlling atomic and optical systems. Here, we show that encircling-an-exceptional-point interactions that are essentially reciprocal in the linear interaction regime make a plausible nonlinear integrated optical device architecture highly nonreciprocal over an extremely broad spectrum. In the proposed strategy, we describe an experimentally realizable coupled-waveguide structure that supports an encircling-an-exceptional-point parametric evolution under the influence of a gain saturation nonlinearity...
January 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28105809/two-3d-cd-ii-metal-organic-frameworks-linked-by-benzothiadiazole-dicarboxylates-fantastic-s-cd6-cage-benzothiadiazole-antidimmer-and-dual-emission
#19
Qing Cheng, Xiao Han, Yue Tong, Chao Huang, Jie Ding, Hongwei Hou
On the basis of the same benzothiadiazole (BTD) ligand 2,1,3-benzothiadiazole-4,7-dicarboxylic acid (H2L), two new isomers of three-dimensional (3D) BTD-derived Cd(II) metal-organic frameworks 1-2 {[S@Cd6L6]·xH2O}n were obtained by the different solvothermal reactions, which were structurally similar. Surprisingly, structural analyses reveal that in 1 or 2, one free sulfur atom was fixed in a Cd(II) cluster cage by strong intermolecular interaction to form the secondary building unit (SBU) S@Cd6. Each SBU S@Cd6 is connected by six L(2-) ligands and further extended into the 3D porous framework...
January 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28105808/evolution-of-the-structural-and-electronic-properties-of-medium-sized-sodium-clusters-a-honeycomb-like-na20-cluster
#20
Wei Guo Sun, Jing Jing Wang, Cheng Lu, Xin Xin Xia, Xiao Yu Kuang, Andreas Hermann
Sodium is one of the best examples of a free-electron-like metal and of a certain technological interest. However, an unambiguous determination of the structural evolution of sodium clusters is challenging. Here, we performed an unbiased structure search among neutral and anionic sodium clusters in the medium size range of 10-25 atoms, using the Crystal structure AnaLYsis by Particle Swarm Optimization (CALYPSO) method. Geometries are determined by CALYPSO structure searches, followed by reoptimization of a large number of candidate structures...
January 20, 2017: Inorganic Chemistry
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