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Hydrogen bond surrogate

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https://www.readbyqxmd.com/read/28211267/efficient-and-selective-uptake-of-tco4-by-a-cationic-metal-organic-framework-material-with-open-ag-sites
#1
Daopeng Sheng, Lin Zhu, Chao Xu, Chengliang Xiao, Yanlong Wang, Yaxing Wang, Lanhua Chen, Juan Diwu, Jing Chen, Zhifang Chai, Thomas E Albrecht-Schmitt, Shuao Wang
(99)Tc is one of the most problematic radioisotopes in used nuclear fuel owing to its combined features of high fission yield, long half-life, and high environmental mobility. There are only a handful of functional materials that can remove TcO4(-) anion from aqueous solution and identifying for new, stable materials with high anion-exchange capacities, fast kinetics, and good selectivity remains a challenge. We report here an 8-fold interpenetrated three-dimensional cationic metal-organic framework material, SCU-100, which is assembled from a tetradentate neutral nitrogen-donor ligand and two-coordinate Ag(+) cations as potential open metal sites...
March 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28195710/palladium-catalyzed-hydrohalogenation-of-1-6-enynes-hydrogen-halide-salts-and-alkyl-halides-as-convenient-hx-surrogates
#2
David A Petrone, Ivan Franzoni, Juntao Ye, José F Rodríguez, Amalia I Poblador-Bahamonde, Mark Lautens
Difficulties associated with handling H2 and CO in metal-catalyzed processes have led to the development of chemical surrogates to these species. Despite many successful examples using this strategy, the application of convenient hydrogen halide (HX) surrogates in catalysis has lagged behind considerably. We now report the use of ammonium halides as HX surrogates to accomplish a Pd-catalyzed hydrohalogenation of enynes. These safe and practical salts avoid many drawbacks associated with traditional HX sources including toxicity and corrosiveness...
February 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28192089/dynamic-phenylalanine-clamp-interactions-define-single-channel-polypeptide-translocation-through-the-anthrax-toxin-protective-antigen-channel
#3
Koyel Ghosal, Jennifer M Colby, Debasis Das, Stephen T Joy, Paramjit S Arora, Bryan A Krantz
Anthrax toxin is an intracellularly acting toxin where sufficient detail is known about the structure of its channel, allowing for molecular investigations of translocation. The toxin is composed of three proteins, protective antigen (PA), lethal factor (LF), and edema factor (EF). The toxin's translocon, PA, translocates the large enzymes, LF and EF, across the endosomal membrane into the host cell's cytosol. Polypeptide clamps located throughout the PA channel catalyze the translocation of LF and EF. Here, we show that the central peptide clamp, the ϕ clamp, is a dynamic site that governs the overall peptide translocation pathway...
February 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28100776/crystallographic-snapshots-of-class-a-%C3%AE-lactamase-catalysis-reveal-structural-changes-that-facilitate-%C3%AE-lactam-hydrolysis
#4
Xuehua Pan, Yunjiao He, Jinping Lei, Xuhui Huang, Yanxiang Zhao
β-Lactamases confer resistance to β-lactam-based antibiotics. There is great interest in understanding their mechanisms to enable the development of β-lactamase-specific inhibitors. The mechanism of class A β-lactamases has been studied extensively, revealing Lys-73 and Glu-166 as general bases that assist the catalytic residue Ser-70. However, the specific roles of these two residues within the catalytic cycle remain not fully understood. To help resolve this, we first identified an E166H mutant that is functional but is kinetically slow...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28088866/combined-experimental-and-computational-study-on-the-unimolecular-decomposition-of-jp-8-jet-fuel-surrogates-ii-n-dodecane-n-c12h26
#5
Long Zhao, Tao Yang, Ralf I Kaiser, Tyler P Troy, Musahid Ahmed, Joao Marcelo Ribeiro, Daniel Belisario-Lara, Alexander M Mebel
We investigated temperature-dependent products in the pyrolysis of helium-seeded n-dodecane, which represents a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) aviation fuel. The experiments were performed in a high temperature chemical reactor over a temperature range of 1200 K to 1600 K at a pressure of 600 Torr, with in situ identification of the nascent products in a supersonic molecular beam using single photon vacuum ultraviolet (VUV) photoionization coupled with the analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF)...
February 1, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28088860/combined-experimental-and-computational-study-on-the-unimolecular-decomposition-of-jp-8-jet-fuel-surrogates-i-n-decane-n-c10h22
#6
Long Zhao, Tao Yang, Ralf I Kaiser, Tyler P Troy, Musahid Ahmed, Daniel Belisario-Lara, Joao Marcelo Ribeiro, Alexander M Mebel
Exploiting a high temperature chemical reactor, we explored the pyrolysis of helium-seeded n-decane as a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) over a temperature range of 1100-1600 K at a pressure of 600 Torr. The nascent products were identified in situ in a supersonic molecular beam via single photon vacuum ultraviolet (VUV) photoionization coupled with a mass spectroscopic analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF). Our studies probe, for the first time, the initial reaction products formed in the decomposition of n-decane-including radicals and thermally labile closed-shell species effectively excluding mass growth processes...
February 2, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27909346/copper-i-dioxygen-adducts-and-copper-enzyme-mechanisms
#7
Jeffrey J Liu, Daniel E Diaz, David A Quist, Kenneth D Karlin
Primary copper(I)-dioxygen (O2) adducts, cupric-superoxide complexes, have been proposed intermediates in copper-containing dioxygen-activating monooxygenase and oxidase enzymes. Here, mechanisms of C-H activation by reactive copper-(di)oxygen intermediates are discussed, with an emphasis on cupric-superoxide species. Over the past 25 years, many synthetically derived cupric-superoxide model complexes have been reported. Due to the thermal instability of these intermediates, early studies focused on increasing their stability and obtaining physical characterization...
October 2016: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/27862441/heteroacene-synthesis-through-c-s-cross-coupling-5-endo-dig-cyclization
#8
Peter Oechsle, Ulrich Flörke, Hans Egold, Jan Paradies
Highly efficient, one-step synthesis of sulfur-containing heteroacenes was achieved through palladium-catalyzed C-S cross-coupling of bis-alkynes with thioacetate as hydrogen sulfide surrogate. Heteroacenes consisting of three, five, and seven fused aromatic rings were obtained in a single catalytic step by four-, six-, and eightfold C-S bond formation.
December 19, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27762555/synthesis-of-gly-%C3%AF-z-cf%C3%A2-ch-phe-a-fluoroalkene-dipeptide-isostere-and-its-incorporation-into-a-leu-enkephalin-peptidomimetic
#9
Jean-François Nadon, Kristina Rochon, Sébastien Grastilleur, Guillaume Langlois, Thi Thanh Hà Dao, Véronique Blais, Brigitte Guérin, Louis Gendron, Yves L Dory
A new Leu-enkephalin peptidomimetic designed to explore the hydrogen bond acceptor ability of the third peptide bond has been prepared and studied. This new analog is produced by replacing the third amide of Leu-enkephalin with a fluoroalkene. An efficient and innovative synthesis of the corresponding dipeptide surrogate Fmoc-Gly-ψ[(Z)CF═CH]-Phe-OH is described. The key step involves the alkylation of a tin dienolate from the less hindered face of its chiral sulfonamide auxiliary derived from camphor. Once its synthesis was complete, its incorporation into the peptidomimetic sequence was achieved on a solid support with chlorotrityl resin following the Fmoc strategy...
January 18, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/27311877/hydrogenation-and-transfer-hydrogenation-promoted-by-tethered-ru-s-complexes-from-cooperative-dihydrogen-activation-to-hydride-abstraction-proton-release-from-dihydrogen-surrogates
#10
Alice Lefranc, Zheng-Wang Qu, Stefan Grimme, Martin Oestreich
Hydrogenation and transfer hydrogenation of imines with cyclohexa-1,4-dienes, as well as with a representative Hantzsch ester dihydrogen surrogate, are reported. Both processes are catalyzed by tethered Ru-S complexes but differ in the activation mode of the dihydrogen source: cooperative activation of the H-H bond at the Ru-S bond leads to the corresponding Ru-H complex and protonation of the sulfur atom, whereas the same cationic Ru-S catalyst abstracts a hydride from a donor-substituted cyclohexa-1,4-diene to form the neutral Ru-H complex and a low-energy Wheland intermediate...
July 11, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27302426/effect-of-monoglycerides-and-fatty-acids-on-a-ceramide-bilayer
#11
Anna Akinshina, Chinmay Das, Massimo G Noro
Monoglycerides and unsaturated fatty acids, naturally present in trace amounts in the stratum corneum (top layer of skin) lipid matrix, are commonly used in pharmaceutical, cosmetic and health care formulations. However, a detailed molecular understanding of how the oil additives get incorporated into the skin lipids from topical application and, once incorporated, how they affect the properties and integrity of the lipid matrix remains unexplored. Using ceramide 2 bilayers as skin lipid surrogates, we use a series of molecular dynamics simulations with six different natural oil ingredients at multiple concentrations to investigate the effect of the oils on the properties and stability of the bilayers...
July 14, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27188873/triazole-resistance-mediated-by-mutations-of-a-conserved-active-site-tyrosine-in-fungal-lanosterol-14%C3%AE-demethylase
#12
Alia A Sagatova, Mikhail V Keniya, Rajni K Wilson, Manya Sabherwal, Joel D A Tyndall, Brian C Monk
Emergence of fungal strains showing resistance to triazole drugs can make treatment of fungal disease problematic. Triazole resistance can arise due to single mutations in the drug target lanosterol 14α-demethylase (Erg11p/CYP51). We have determined how commonly occurring single site mutations in pathogenic fungi affect triazole binding using Saccharomyces cerevisiae Erg11p (ScErg11p) as a target surrogate. The mutations Y140F/H were introduced into full-length hexahistidine-tagged ScErg11p. Phenotypes and high-resolution X-ray crystal structures were determined for the mutant enzymes complexed with short-tailed (fluconazole and voriconazole) or long-tailed (itraconazole and posaconazole) triazoles and wild type enzyme complexed with voriconazole...
May 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27155814/insights-into-rpob-clinical-mutants-in-mediating-rifampicin-resistance-in-mycobacterium-tuberculosis
#13
Ameeruddin Nusrath Unissa, Sameer Hassan, Venkatesan Indira Kumari, Ravi Revathy, Luke Elizabeth Hanna
Rifampicin (RIF) an essential first-line anti-tuberculosis (TB) drug, resistance to RIF is a potential threat to TB control program and widely considered as surrogate marker for detection of multi-drug resistant-TB (MDR-TB), molecular understanding of which is the utmost need of the hour. Mutations at RIF resistance-determining region (RRDR) of 81-bp in the rpoB gene coding for β subunit or RpoB protein is the major cause of RIF resistance in Mycobacterium tuberculosis (MTB). Mutation at positions 526 and 531 are generally associated with high-level RIF resistance and at codons 516, 521 and 533 with low-level resistance...
June 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27059179/emergence-of-function-in-p450-proteins-a-combined-quantum-mechanical-molecular-mechanical-and-molecular-dynamics-study-of-the-reactive-species-in-the-h2o2-dependent-cytochrome-p450sp%C3%AE-and-its-regio-and-enantioselective-hydroxylation-of-fatty-acids
#14
Rajeev Ramanan, Kshatresh Dutta Dubey, Binju Wang, Debasish Mandal, Sason Shaik
This work uses combined quantum mechanical/molecular mechanical and molecular dynamics simulations to investigate the mechanism and selectivity of H2O2-dependent hydroxylation of fatty acids by the P450SPα class of enzymes. H2O2 is found to serve as the surrogate oxidant for generating the principal oxidant, Compound I (Cpd I), in a mechanism that involves homolytic O-O bond cleavage followed by H-abstraction from the Fe-OH moiety. Our results rule out a substrate-assisted heterolytic cleavage of H2O2 en route to Cpd I...
June 1, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27046675/an-optimal-hydrogen-bond-surrogate-for-%C3%AE-helices
#15
Stephen T Joy, Paramjit S Arora
Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences.
April 28, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27018227/adme-properties-evaluation-in-drug-discovery-prediction-of-caco-2-cell-permeability-using-a-combination-of-nsga-ii-and-boosting
#16
Ning-Ning Wang, Jie Dong, Yin-Hua Deng, Min-Feng Zhu, Ming Wen, Zhi-Jiang Yao, Ai-Ping Lu, Jian-Bing Wang, Dong-Sheng Cao
The Caco-2 cell monolayer model is a popular surrogate in predicting the in vitro human intestinal permeability of a drug due to its morphological and functional similarity with human enterocytes. A quantitative structure-property relationship (QSPR) study was carried out to predict Caco-2 cell permeability of a large data set consisting of 1272 compounds. Four different methods including multivariate linear regression (MLR), partial least-squares (PLS), support vector machine (SVM) regression and Boosting were employed to build prediction models with 30 molecular descriptors selected by nondominated sorting genetic algorithm-II (NSGA-II)...
April 25, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/26866502/overcoming-strain-induced-rearrangement-reactions-a-mild-dehydrative-aromatization-protocol-for-synthesis-of-highly-distorted-p-phenylenes
#17
Nirmal K Mitra, Rolande Meudom, Hector H Corzo, John D Gorden, Bradley L Merner
A series of p-terphenyl-based macrocycles, containing highly distorted p-phenylene units, have been synthesized. Biaryl bonds of the nonplanar p-terphenyl nuclei were constructed in the absence of Pd-catalyzed or Ni-mediated cross-coupling reactions, using 1,4-diketones as surrogates to strained arene units. A streamlined synthetic protocol for the synthesis of 1,4-diketo macrocycles has been developed, using only 2.5 mol % of the Hoveyda-Grubbs second-generation catalyst in both metathesis and transfer hydrogenation reactions...
March 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26457527/structure-of-the-complex-of-carboxypeptidase-b-and-n-sulfamoyl-l-arginine
#18
Valery Akparov, Nikolay Sokolenko, Vladimir Timofeev, Inna Kuranova
Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps...
October 2015: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/26391081/formal-sih4-chemistry-using-stable-and-easy-to-handle-surrogates
#19
Antoine Simonneau, Martin Oestreich
Monosilane (SiH4) is far less well behaved than its carbon analogue methane (CH4). It is a colourless gas that is industrially relevant as a source of elemental silicon, but its pyrophoric and explosive nature makes its handling and use challenging. Consequently, synthetic applications of SiH4 in academic laboratories are extremely rare and methodologies based on SiH4 are underdeveloped. Safe and controlled alternatives to the substituent redistribution approaches of hydrosilanes are desirable and cyclohexa-2,5-dien-1-ylsilanes where the cyclohexa-1,4-diene units serve as placeholders for the hydrogen atoms have been identified as potent surrogates of SiH4...
October 2015: Nature Chemistry
https://www.readbyqxmd.com/read/26352022/a-reduced-2fe2s-cluster-probe-of-sulfur-hydrogen-versus-sulfur-gold-interactions
#20
Danielle J Crouthers, Shengda Ding, Jason A Denny, Ryan D Bethel, Chung-Hung Hsieh, Michael B Hall, Marcetta Y Darensbourg
The Ph3 PAu(+) cation, renowned as an isolobal analogue of H(+) , was found to serve as a proton surrogate and form a stable Au2 Fe2 complex, [(μ-SAuPPh3 )2 {Fe(CO)3 }2 ], analogous to the highly reactive dihydrosulfide [(μ-SH)2 {Fe(CO)3 }2 ]. Solid-state X-ray diffraction analysis found the two SAuPPh3 and SH bridges in anti configurations. VT NMR studies, supported by DFT computations, confirmed substantial barriers of approximately 25 kcal mol(-1) to intramolecular interconversion between the three stereoisomers of [(μ-SH)2 {Fe(CO)3 }2 ]...
September 14, 2015: Angewandte Chemie
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