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https://www.readbyqxmd.com/read/28817770/photoinduced-copper-catalyzed-alkylation-of-amines-a-mechanistic-study-of-the-cross-coupling-of-carbazole-with-alkyl-bromides
#1
Jun Myun Ahn, Tanvi S Ratani, Kareem Hannoun, Gregory C Fu, Jonas C Peters
We have recently reported that a variety of couplings of nitrogen, sulfur, oxygen, and carbon nucleophiles with organic halides can be achieved under mild conditions (-40 to 30 °C) through the use of light and a copper catalyst. Insight into the various mechanisms by which these reactions proceed may enhance our understanding of chemical reactivity and facilitate the development of new methods. In this report, we apply an array of tools (EPR, NMR, transient absorption, and UV-vis spectroscopy; ESI-MS; X-ray crystallography; DFT calculations; reactivity, stereochemical, and product studies) to investigate the photoinduced, copper-catalyzed coupling of carbazole with alkyl bromides...
August 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28817602/exploring-the-potential-of-a-structural-alphabet-based-tool-for-mining-multiple-target-conformations-and-target-flexibility-insight
#2
Leslie Regad, Jean-Baptiste Chéron, Dhoha Triki, Caroline Senac, Delphine Flatters, Anne-Claude Camproux
Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility...
2017: PloS One
https://www.readbyqxmd.com/read/28816445/tracking-the-progress-and-mechanism-study-of-a-solvothermal-in-situ-domino-n-alkylation-reaction-of-triethylamine-and-ammonia-assisted-by-ferrous-sulfate
#3
Jin-Ping Zhong, Bin Liu, Tao Yang, Yue-Jin Liu, Zhong-Hong Zhu, Bing-Feng Shi, Mohamedally Kurmoo, Ming-Hua Zeng
Atom economic in situ domino N-alkylation reactions of triethylamine/ammonia with 2-(hydroxymethyl)quinolin-8-ol (HL-OH) assisted by FeSO4·7H2O were realized under mild solvothermal conditions at 120 °C in acetonitrile. The resulting tripodal 2,2',2″-[nitrilotris(methylene)]tris(quinolin-8-ol) (H3L3-N) forms a linear trimer [Fe3(L3-N)2] (1). Electrospray ionization mass spectrometry of the reaction solution provides evidence for the intermediates of three steps, while crystallography and X-ray photoelectron spectroscopy characterize the trimer...
August 17, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28815951/physics-based-all-atom-modeling-of-rna-energetics-and-structure
#4
REVIEW
Louis G Smith, Jianbo Zhao, David H Mathews, Douglas H Turner
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815915/synthesis-and-characterization-of-iridium-v-coordination-complexes-with-an-n-o-donor-organic-ligand
#5
Liam Sharninghausen, Shashi Bhushan Sinha, Dimitar Y Shopov, Brandon Q Mercado, David Balcells, Gary W Brudvig, Robert H Crabtree
We have prepared and fully characterized two isomers of [IrIV(dpyp)2] (dpyp = meso-2,4-di(2-pyridynyl)-2,4-pentanediolate). These complexes can be cleanly oxidized to [IrV(dpyp)2]+, which to our knowledge represent the first coordination complexes of Ir(V) in an N,O-donor environment. One isomer has been fully characterized in the Ir(V) state, including by x-ray crystallography, XPS, and DFT calculations, all of which support metal-centered oxidation. The unprecedented stability of these Ir(V) complexes is ascribed to the exceptional donor strength of the ligands, their resistance to oxidative degradation, and the presence of four highly donor alkoxide groups in a plane, which breaks the degeneracy of the d-orbitals and favors oxidation...
August 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28815022/modeling-of-ras-complexes-supports-roles-in-cancer-for-less-studied-partners
#6
H Billur Engin, Daniel Carlin, Dexter Pratt, Hannah Carter
BACKGROUND: RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28814505/the-molecular-architecture-of-the-yeast-spindle-pole-body-core-determined-by-bayesian-integrative-modeling
#7
Shruthi Viswanath, Massimiliano Bonomi, Seung Joong Kim, Vadim A Klenchin, Keenan C Taylor, King C Yabut, Neil T Umbreit, Heather A Van Epps, Janet Meehl, Michele H Jones, Daniel Russel, Javier A Velazquez-Muriel, Mark Winey, Ivan Rayment, Trisha N Davis, Andrej Sali, Eric G Muller
Microtubule organizing centers (MTOCs) form, anchor and stabilize the polarized network of microtubules in a cell. The central MTOC is the centrosome that duplicates during the cell cycle and during mitosis assembles a bipolar spindle to capture and segregate sister chromatids. Yet, despite their importance in cell biology, the physical structure of MTOCs is poorly understood. Here we determine the molecular architecture of the core of the yeast spindle pole body (SPB) by Bayesian integrative structure modeling based on in vivo FRET, small-angle X-ray scattering (SAXS), X-ray crystallography, electron microscopy and two-hybrid analysis...
August 16, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28814078/structural-characterization-and-unique-catalytic-performance-of-silyl-group-substituted-geminal-dichromiomethane-complexes-stabilized-with-a-diamine-ligand
#8
Masahito Murai, Ryuji Taniguchi, Naoki Hosokawa, Yusuke Nishida, Hiroko Mimachi, Toshiyuki Oshiki, Kazuhiko Takai
Stabilization by a silyl group on the methylene carbon and a diamine ligand let to the isolation of gemdichromiomethane species. X-ray crystallography confirmed the identity of the structure of this rare example of reactive gemdimetalloalkane species. The isolated gem-dichromiomethane complex acted as a storable silylmethylidene carbene equivalent, with reactivity that could be changed dramatically upon addition of a Lewis acid (ZnCl2) and a base (TMEDA) to promote both silylalkylidenation of polar aldehydes and silylcyclopropanation of non-polar alkenes...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28811582/a-new-class-of-hybrid-secretion-system-is-employed-in-pseudomonas-amyloid-biogenesis
#9
Sarah L Rouse, William J Hawthorne, Jamie-Lee Berry, Dror S Chorev, Sandra A Ionescu, Sebastian Lambert, Fisentzos Stylianou, Wiebke Ewert, Uma Mackie, R Marc L Morgan, Daniel Otzen, Florian-Alexander Herbst, Per H Nielsen, Morten Dueholm, Hagan Bayley, Carol V Robinson, Stephen Hare, Stephen Matthews
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811466/time-lapse-crystallography-snapshots-of-a-double-strand-break-repair-polymerase-in-action
#10
Joonas A Jamsen, William A Beard, Lars C Pedersen, David D Shock, Andrea F Moon, Juno M Krahn, Katarzyna Bebenek, Thomas A Kunkel, Samuel H Wilson
DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PPi...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28809779/application-of-solution-nmr-to-structural-studies-on-%C3%AE-helical-integral-membrane-proteins
#11
REVIEW
Dae-Won Sim, Zhenwei Lu, Hyung-Sik Won, Seu-Na Lee, Min-Duk Seo, Bong-Jin Lee, Ji-Hun Kim
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology...
August 15, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28809555/electronic-magnetic-and-redox-properties-and-o2-reactivity-of-iron-ii-and-nickel-ii-o-semiquinonate-complexes-of-a-tris-thioether-ligand-uncovering-the-intradiol-cleaving-reactivity-of-an-iron-ii-o-semiquinonate-complex
#12
Peng Wang, Michelle M Killian, Mohamed R Saber, Tian Qiu, Glenn P A Yap, Codrina V Popescu, Joel Rosenthal, Kim R Dunbar, Thomas C Brunold, Charles G Riordan
The iron(II) semiquinonate character within the iron(III) catecholate species has been proposed by numerous studies to account for the O2 reactivity of intradiol catechol dioxygenases, but a well-characterized iron(II) semiquinonate species that exhibits intradiol cleaving reactivity has not yet been reported. In this study, a detailed electronic structure description of the first iron(II) o-semiquinonate complex, [PhTt(tBu)]Fe(phenSQ) [PhTt(tBu) = phenyltris(tert-butylthiomethyl)borate; phenSQ = 9,10-phenanthrenesemiquinonate; Wang et al...
August 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28809478/ruthenium-ii-and-ruthenium-iii-complexes-of-p-benziporphyrin-merging-equatorial-and-axial-organometallic-coordination
#13
Aneta Idec, Miłosz Pawlicki, Lechosław Latos-Grażyński
A diamagnetic ruthenium(II) complex of 5,10,15,20-tetraphenyl-p-benziporphyrin [Ru(II)(p-BzP)(CO)Cl] was obtained via the insertion of ruthenium into p-benziporphyrin using triruthenium(0) dodecacarbonyl [Ru3(CO)12] as the metal source. The procedure applying dichloro(cycloocta-1,5-diene)ruthenium(II) (polymer, [Ru(COD)Cl2]n) afforded the paramagnetic six-coordinate ruthenium(III) p-benziporphyrin [Ru(III)(p-BzP)Cl2]. As shown by X-ray crystallography, the p-phenylene ring in both complexes is sharply tilted out of the N3 plane, as reflected by the respective N3 (pyrrole)-C6 (p-phenylene) dihedral angle [Ru(II)(p-BzP)(CO)Cl, 52...
August 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28809460/quasi-dual-packed-kernelled-au49-2-4-dmbt-27-nanoclusters-and-the-influence-of-kernel-packing-on-the-electrochemical-gap
#14
Zhikun Wu
Although face-centered cubic (fcc), body-centered cubic (bcc), hexagonal close-packed (hcp) and other structured gold nanoclusters have been reported, it is still unclear if gold nanoclusters with mix-packed (e.g., fcc and non-fcc) kernels exist, and the correlation between kernel packing and the properties of gold nanoclusters is unknown. Herein, a novel Au49(2,4-DMBT)27 nanocluster with shell electron count of 22 has been synthesized and structurally resolved by single-crystal X-ray crystallography, which revealed that Au49(2,4-DMBT)27 contained a unique Au34 kernel consisting of one quasi-fcc-structured Au21 and one non-fcc-structured Au13 unit (where 2,4-DMBTH = 2,4-dimethylbenzenethiol)...
August 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28809415/stimuli-responsive-emissive-behavior-of-1-and-1-3-connectivities-in-azulene-based-imine-ligands-cycloplatination-and-pt-tl-dative-bond-formation
#15
Sirous Jamali, Narges-Alsadat Mousavi, Mojtaba Bagherzadeh, Reza Kia, Hamidreza Samouei
The preparation of two new azulene-based imine ligands N-(2,6-diisopropylphenyl)-6-(t)Bu-1-azulenylmethaneimine, 3, and N-(2,6-diisopropylphenyl)-6-(t)Bu-3-(2,6-diisopropylphenyliminomethyl)-1-azulenylmethaneimine, 4, is described. These imine ligands display stimuli responsive emissive behavior and their fluorescence can be switched on and off by protonation and neutralization with trifluoroacetic acid and trimethylamine, respectively. The cyclometalation of the monoimine ligand by platinum gave the cyclometalated complex [PtMe(SMe2)(3')], 5, (where the prime denotes the cyclometalated ligand 3)...
August 15, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28808891/nmr-backbone-resonance-assignment-of-new-delhi-metallo-beta-lactamase
#16
Chendie Yao, Qiong Wu, Guohua Xu, Conggang Li
The emerging of the New Delhi metallo-beta-lactamase (NDM-1) has become one of the greatest threats to the clinical treatment. Although the structure of NDM-1 has been determined by X-ray crystallography, the molecular mechanism and process of catalysis reaction remain elusive. NMR spectroscopy plays a unique role in the characterization of conformational dynamics. Here we report the backbone (1)H, (15)N and (13)C chemical shift assignments of NDM-1 by heteronuclear multidimensional NMR spectroscopy as well as its secondary structure in solution as predicted by TALOS+...
August 14, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28808438/atsas-2-8-a-comprehensive-data-analysis-suite-for-small-angle-scattering-from-macromolecular-solutions
#17
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries, D I Svergun
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808437/how-to-assign-a-3%C3%A2-%C3%A2-1-dimensional-superspace-group-to-an-incommensurately-modulated-biological-macromolecular-crystal
#18
Jason Porta, Jeff Lovelace, Gloria E O Borgstahl
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808433/felix-an-algorithm-for-indexing-multiple-crystallites-in-x-ray-free-electron-laser-snapshot-diffraction-images
#19
Kenneth R Beyerlein, Thomas A White, Oleksandr Yefanov, Cornelius Gati, Ivan G Kazantsev, Nicolai Fog-Gade Nielsen, Peter M Larsen, Henry N Chapman, Søren Schmidt
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808107/structure-of-psb29-thf1-and-its-association-with-the-ftsh-protease-complex-involved-in-photosystem-ii-repair-in-cyanobacteria
#20
Martina Bec Ková, Jianfeng Yu, Vendula Krynická, Amanda Kozlo, Shengxi Shao, Peter Koník, Josef Komenda, James W Murray, Peter J Nixon
One strategy for enhancing photosynthesis in crop plants is to improve their ability to repair photosystem II (PSII) in response to irreversible damage by light. Despite the pivotal role of thylakoid-embedded FtsH protease complexes in the selective degradation of PSII subunits during repair, little is known about the factors involved in regulating FtsH expression. Here we show using the cyanobacterium Synechocystis sp. PCC 6803 that the Psb29 subunit, originally identified as a minor component of His-tagged PSII preparations, physically interacts with FtsH complexes in vivo and is required for normal accumulation of the FtsH2/FtsH3 hetero-oligomeric complex involved in PSII repair...
September 26, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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