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Chemical crystallography

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https://www.readbyqxmd.com/read/29910924/a-three-body-problem-a-genuine-hetero-tri-metallic-molecule-vs-a-mixture-of-two-parent-hetero-bi-metallic-molecules
#1
Haixiang Han, Zheng Wei, Matthew C Barry, Jesse C Carozza, Melisa Alkan, Andrey Yu Rogachev, Alexander S Filatov, Artem M Abakumov, Evgeny V Dikarev
This work raises a fundamental question about the "real" structure of molecular compounds containing three different metals: whether they consist of genuine hetero tri metallic species or of a mixture of parent hetero bi metallic species. Heterotrimetallic complex Li2 CoNi(tbaoac)6 ( 1 , tbaoac = tert -butyl acetoacetate) has been designed based on the model tetranuclear structure featuring two transition metal sites in order to be utilized as a molecular precursor for the low-temperature preparation of the LiCo0...
June 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29906115/x-ray-emission-spectroscopy-as-an-in-situ-diagnostic-tool-for-x-ray-crystallography-of-metalloproteins-using-an-x-ray-free-electron-laser
#2
Thomas Fransson, Ruchira Chatterjee, Franklin D Fuller, Sheraz Gul, Clemens Weninger, Dimosthenis Sokaras, Thomas Kroll, Roberto Alonso Mori, Uwe Bergmann, Jan Kern, Vittal K Yachandra, Junko Yano
Serial femtosecond crystallography (SFX) using the ultra-short X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature, which also allows for following the reaction in real time after initiating the reaction with a trigger. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore monitoring and controlling the data quality by using in situ diagnostic tools is especially important...
June 15, 2018: Biochemistry
https://www.readbyqxmd.com/read/29883126/germanium-sulfide-nano-optics-probed-by-stem-cathodoluminescence-spectroscopy
#3
Peter Sutter, Christos Argyropoulos, Eli Sutter
Nano-optical studies of confined modes in planar waveguides have attracted significant interest as a means to probe exciton-polaritons and other hybrid light-matter quasiparticles in layered semiconductors, such as transition metal dichalcogenides or boron nitride. There is a need to broaden such studies to other materials and to identify alternatives to scanning near-field optical microscopy for exciting and measuring confined waveguide modes. Here, we establish an approach for probing the dispersion of traveling waveguide modes by cathodoluminescence spectroscopy excited by the focused electron beam in scanning transmission electron microscopy (STEM-CL), and apply it to solid-state resonators consisting of mesoscale monocrystalline prisms and plates composed of GeS, an anisotropic layered semiconductor with direct bandgap in the near-infrared spectral range...
June 8, 2018: Nano Letters
https://www.readbyqxmd.com/read/29879648/identification-of-tautomeric-intermediates-of-a-novel-thiazolylazonaphthol-dye-a-density-functional-theory-study
#4
N N Karaush, V A Minaeva, G V Baryshnikov, B F Minaev, H Ågren
The recently synthesized thiazolylazo dye, 1-[5-benzyl-1,3-thiazol-2-yl)diazenyl]naphthalene-2-ol called shortly BnTAN, is studied by density functional theory (DFT) in three tautomeric forms in order to explain the available 1 H NMR, UV-Vis and FTIR spectra. An experimentally observed IR band at 1678 cm-1 , assigned to the CO bond stretching vibration, supports the notion that BnTAN retains in the less stable keto-form even in the solid state due to an ultrafast single-coordinate intramolecular proton transfer...
May 29, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29861345/biophysical-characterization-of-the-tandem-fha-domain-regulatory-module-from-the-mycobacteriumtuberculosis-abc-transporter-rv1747
#5
Florian Heinkel, Leo Shen, Melissa Richard-Greenblatt, Mark Okon, Jennifer M Bui, Christine L Gee, Laurie M Gay, Tom Alber, Yossef Av-Gay, Jörg Gsponer, Lawrence P McIntosh
The Mycobacterium tuberculosis ATP-binding cassette transporter Rv1747 is a putative exporter of cell wall biosynthesis intermediates. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting Forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). The structures of FHA-1 and FHA-2 were determined by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, respectively. Relative to the canonical 11-strand β-sandwich FHA domain fold of FHA-1, FHA-2 is circularly permuted and lacking one β-strand...
May 17, 2018: Structure
https://www.readbyqxmd.com/read/29782488/insight-into-small-molecule-binding-to-the-neonatal-fc-receptor-by-x-ray-crystallography-and-100-khz-magic-angle-spinning-nmr
#6
Daniel Stöppler, Alex Macpherson, Susanne Smith-Penzel, Nicolas Basse, Fabien Lecomte, Hervé Deboves, Richard D Taylor, Tim Norman, John Porter, Lorna C Waters, Marta Westwood, Ben Cossins, Katharine Cain, James White, Robert Griffin, Christine Prosser, Sebastian Kelm, Amy H Sullivan, David Fox, Mark D Carr, Alistair Henry, Richard Taylor, Beat H Meier, Hartmut Oschkinat, Alastair D Lawson
Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG...
May 21, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29777317/using-smiles-strings-for-the-description-of-chemical-connectivity-in-the-crystallography-open-database
#7
Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases...
May 18, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29775229/synthesis-of-an-all-ferric-cuboidal-cluster-feiii%C3%A2-s%C3%A2-sar-%C3%A2
#8
Golam Moula, Tsuyoshi Matsumoto, Matthias E Miehlich, Karsten Meyer, Kazuyuki Tatsumi
An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe₄S₄(STbt)₄ (3) [Tbt = 2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)₂ (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field ⁵⁷Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all data, the electronic ground state of the cluster has been assigned to be Stot = 0...
May 18, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29771936/assigning-crystallographic-electron-densities-with-free-energy-calculations-the-case-of-the-fluoride-channel-fluc
#9
Igor Ariz-Extreme, Jochen S Hub
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious...
2018: PloS One
https://www.readbyqxmd.com/read/29757638/antinociceptive-diterpenoids-from-the-leaves-and-twigs-of-rhododendron-decorum
#10
Yu-Xun Zhu, Zhao-Xin Zhang, Hui-Min Yan, Di Lu, Huan-Ping Zhang, Li Li, Yun-Bao Liu, Yong Li
Three new leucothane-type (1-3), two new micrathane-type (4, 5), eight new grayanane-type diterpenoids (6-13), and four known compounds were obtained from the ethanol extract of the leaves and twigs of Rhododendron decorum. The structures were determined based on NMR spectra, quantum chemical calculations, and X-ray crystallography. The antinociceptive activities of compounds 1, 3, 4, 6, 8, 10-13, and 15-17 were evaluated via the acetic acid-induced writhing test. Compounds 1, 8, 11-13, and 15 exhibited significant antinociceptive activities...
May 14, 2018: Journal of Natural Products
https://www.readbyqxmd.com/read/29755750/ionic-scattering-factors-of-atoms-that-compose-biological-molecules
#11
Koji Yonekura, Rei Matsuoka, Yoshiki Yamashita, Tsutomu Yamane, Mitsunori Ikeguchi, Akinori Kidera, Saori Maki-Yonekura
Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O- . Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology...
May 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29752272/functional-profiling-and-crystal-structures-of-isothiocyanate-hydrolases-found-in-gut-associated-and-plant-pathogenic-bacteria
#12
Tijs J M van den Bosch, Kemin Tan, Andrzej Joachimiak, Cornelia U Welte
Isothiocyanates (ITCs) are produced by cruciferous plants to protect them against herbivores and infection by microbes. These compounds are of particular interest due to their antimicrobial and anticarcinogenic properties. The breakdown of ITCs in nature is catalyzed by isothiocyanate hydrolase (ITCase), a novel family within the metallo-β-lactamase-fold superfamily of proteins. saxA genes that code for ITCases are particularly widespread in insect- and plant-associated bacteria. Enzymatic characterization of seven phylogenetically related but distinct ITCases exhibited similar activities on six selected ITCs, suggesting that phylogenetic diversity does not determine the substrate specificity of ITCases...
May 11, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29745812/biomineralization-in-modern-avian-calcified-eggshells-similarity-versus-diversity
#13
Yannicke Dauphin, Gilles Luquet, Alberto Perez-Huerta, Murielle Salomé
Avian eggshells are composed of several layers made of organic compounds and a mineral phase (calcite), and the general structure is basically the same in all species. A comparison of the structure, crystallography, and chemical composition shows that despite an overall similarity, each species has its own structure, crystallinity, and composition. Eggshells are a perfect example of the crystallographic versus biological concept of the formation and growth mechanisms of calcareous biominerals: the spherulitic-columnar structure is described as "a typical case of competitive crystal growth", but it is also said that the eggshell matrix components regulate eggshell mineralization...
December 2018: Connective Tissue Research
https://www.readbyqxmd.com/read/29726882/oxidative-c-n-fusion-of-pyridinyl-substituted-porphyrins
#14
Mathieu Berthelot, Guillaume Hoffmann, Asmae Bousfiha, Julie Echaubard, Julien Roger, Hélène Cattey, Anthony Romieu, Dominique Lucas, Paul Fleurat-Lessard, Charles H Devillers
The mild (electro)chemical oxidation of pyridin-2-ylthio-meso substituted Ni(ii) porphyrins affords C-N fused cationic and dicationic pyridinium-based derivatives. These porphyrins are fully characterized and the molecular structure of one of them was confirmed by X-ray crystallography. A mechanism for the intramolecular oxidative C-N coupling is proposed based on theoretical calculations and cyclic voltammetry analyses.
May 4, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29722962/inhibition-of-14-3-3-tau-by-hybrid-small-molecule-peptides-operating-via-two-different-binding-modes
#15
Sebastian Alexandru Andrei, Femke Meijer, Joao Neves, Luc Brunsveld, Isabelle Landrieu, Christian Ottmann, Lech-Gustav Milroy
Current molecular hypotheses have yet to deliver marketable treatments for Alzheimer's disease (AD), arguably due to a lack of basic knowledge of AD biology, and an overreliance on conventional drug modalities. Protein-protein interactions (PPIs) are emerging drug targets, which show promise for the treatment of e.g. cancer, but are still underexploited for treating neurodegenerative diseases. 14-3-3 binding to phosphorylated Tau is a promising PPI drug target based on its reported destabilizing effect on microtubules, leading to enhanced neurofibrillary tangle formation as a potential cause of AD-related neurodegeneration...
May 3, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29722815/functional-analysis-of-a-missense-allele-of-karrikin-insensitive2-that-impairs-ligand-binding-and-downstream-signaling-in-arabidopsis-thaliana
#16
Inhye Lee, Kuglae Kim, Sumin Lee, Seungjun Lee, Eunjin Hwang, Kihye Shin, Dayoung Kim, Jungki Choi, Hyunmo Choi, Jeong Seok Cha, Hoyoung Kim, Rin-A Lee, Suyeong Jeong, Jeongsik Kim, Yumi Kim, Hong Gil Nam, Soon-Ki Park, Hyun-Soo Cho, Moon-Soo Soh
A smoke-derived compound, karrikin (KAR) and endogenous, as yet unidentified, KAI2 ligand (KL) are newly emerging chemical cues for higher plants, impacting on multiple aspects of growth and development. Our forward genetic screening toward light-signaling mutants identified a mutant in Arabidopsis thaliana, designated as ply2 (pleiotropic long hypocotyl2), that had pleiotropic light-response defects. Positional cloning identified the molecular lesion of ply2 as a missense mutation of KARRIKIN INSENSITIVE2 (KAI2)/HYPOSENSITIVE TO LIGHT, which causes single amino acid substitution Ala219Val...
May 2, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29717999/improved-protein-crystal-identification-by-using-2-2-2-trichloroethanol-as-a-fluorescence-enhancer
#17
Christian Pichlo, Christine Toelzer, Konrad Chojnacki, Sinan Öcal, Matthias Uthoff, Sabine Ruegenberg, Thomas Hermanns, Magdalena Schacherl, Martin S Denzel, Kay Hofmann, Karsten Niefind, Ulrich Baumann
The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29715599/lanostane-type-c-31-triterpenoid-derivatives-from-the-fruiting-bodies-of-cultivated-fomitopsis-palustris
#18
Jinzhi Zhao, Yun Yang, Mengyao Yu, Ke Yao, Xia Luo, Huayi Qi, Guolin Zhang, Yinggang Luo
Fifteen undescribed and five known lanostane-type C31 triterpenoid derivatives were isolated from the aqueous EtOH extract of the fruiting bodies of cultivated Fomitopsis palustris. Their structures were identified from the spectroscopic data and chemical degradation studies. The structures of palustrisoic acids A and H were confirmed by X-ray crystallography. Polyporenic acid B showed strong cytotoxicity against the HCT116, A549, and HepG2 cell lines with IC50 values of 8.4, 12.1, and 12.2 μM, respectively...
April 28, 2018: Phytochemistry
https://www.readbyqxmd.com/read/29714201/mx2-a-high-flux-undulator-microfocus-beamline-serving-both-the-chemical-and-macromolecular-crystallography-communities-at-the-australian-synchrotron
#19
David Aragão, Jun Aishima, Hima Cherukuvada, Robert Clarken, Mark Clift, Nathan Philip Cowieson, Daniel Jesper Ericsson, Christine L Gee, Sofia Macedo, Nathan Mudie, Santosh Panjikar, Jason Roy Price, Alan Riboldi-Tunnicliffe, Robert Rostan, Rachel Williamson, Thomas Tudor Caradoc-Davies
MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8-21 keV to a focal spot of 22 × 12 µm FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012  photons s-1 . The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules...
May 1, 2018: Journal of Synchrotron Radiation
https://www.readbyqxmd.com/read/29714013/rapid-mapping-of-protein-binding-sites-and-conformational-epitopes-by-coupling-yeast-surface-display-to-chemical-labeling-and-deep-sequencing
#20
Tariq Ahmad Najar, Shruti Khare, Raghavan Varadarajan
Delineating the precise regions on an antigen that are targeted by antibodies is important for the development of vaccines and antibody therapeutics. X-ray crystallography and NMR are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, these are labor-intensive and require purified protein at high concentration. We have recently described [1] a rapid and reliable method that overcomes these constraints, using a panel of single cysteine mutants of the protein of interest and now provide protocols to facilitate its adoption...
2018: Methods in Molecular Biology
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