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Hydrogen bond surrogate

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https://www.readbyqxmd.com/read/28936336/cyclohexa-1-4-dienes-in-transition-metal-free-ionic-transfer-processes
#1
REVIEW
Sebastian Keess, Martin Oestreich
Safe- and convenient-to-handle surrogates of hazardous chemicals are always in demand. Recently introduced cyclohexa-1,4-dienes with adequate substitution fulfil this role as El(+)/H(-) equivalents in B(C6F5)3-catalysed transfer reactions of El-H to π- and σ-donors (C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C/C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C and CO/CN)...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28889766/stabilized-helical-peptides-overview-of-the-technologies-and-its-impact-on-drug-discovery
#2
Mark Klein
Protein-protein interactions are predominant in the workings of all cells. Until now, there have been a few successes in targeting protein-protein interactions with small molecules. Peptides may overcome some of the challenges of small molecules in disrupting protein-protein interactions. However, peptides present a new set of challenges in drug discovery. Thus, the study of the stabilization of helical peptides has been extensive. Areas covered: Several technological approaches to helical peptide stabilization have been studied...
September 9, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28876948/thioamide-a-hydrogen-bond-acceptor-in-proteins-and-nucleic-acids
#3
V Rao Mundlapati, Sanjeev Gautam, Dipak Kumar Sahoo, Arindam Ghosh, Himansu S Biswal
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts...
September 12, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28792768/role-of-hydrogen-bonding-in-photoinduced-electron-proton-transfer-from-phenols-to-a-polypyridine-ru-complex-with-a-proton-accepting-ligand
#4
Sergei V Lymar, Mehmed Z Ertem, Anna Lewandowska-Andralojc, Dmitry E Polyansky
Electron-proton transfer (EPT) from phenols to a triplet metal-to-ligand charge transfer (MLCT)-excited Ru polypyridine complex containing an uncoordinated nitrogen site, 1(T), can be described by a kinetic model that accounts for the H-bonding of 1(T) to phenol, 1(T) to solvent, and phenol to solvent. The latter plays a major role in the kinetic solvent effect and commonly precludes simultaneous determination of the EPT rate constant and 1(T)-phenol H-bonding constant. A number of these quantities previously reported for similar systems are shown to be in error due to inconsistent data analysis...
August 15, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28654782/revisiting-blood-brain-barrier-a-chromatographic-approach
#5
Xavier Subirats, Laura Muñoz-Pascual, Michael H Abraham, Martí Rosés
Drugs designed to reach a pharmacological CNS target must be effectively transported across the blood-brain barrier (BBB), a thin monolayer of endothelial cells tightly attached together between the blood and the brain parenchyma. Because of the lipidic nature of the BBB, several physicochemical partition models have been studied as surrogates for the passive permeation of potential drug candidates across the BBB (octanol-water, alkane-water, PAMPA...). In the last years, biopartition chromatography is gaining importance as a noncellular system for the estimation of biological properties in early stages of drug development...
October 25, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28613818/efficient-removal-of-anionic-radioactive-pollutant-from-water-using-ordered-urea-functionalized-mesoporous-polymeric-nanoparticle
#6
Jian Shen, Wei Chai, Kaixuan Wang, Fang Zhang
A urea-functionalized ordered mesoporous polymeric nanoparticle for removing the perrhenate anion ReO4(-) as the surrogate of the particularly intractable anion radioactive pollutant TcO4(-) was demonstrated in the present study. This nanomaterial (denoted as urea-MPN) was produced for the first time by a surfactant-directed urea-phenol-formaldehyde resol oligomers self-assembly protocol under hydrothermal condition. The obtained urea-MPN possessed the uniform nanosized spherical morphology with a 3D interconnected ordered cubic mesoporous structure...
July 12, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28594080/structural-basis-for-expansion-of-the-genetic-alphabet-with-an-artificial-nucleobase-pair
#7
Karin Betz, Michiko Kimoto, Kay Diederichs, Ichiro Hirao, Andreas Marx
Hydrophobic artificial nucleobase pairs without the ability to pair through hydrogen bonds are promising candidates to expand the genetic alphabet. The most successful nucleobase surrogates show little similarity to each other and their natural counterparts. It is thus puzzling how these unnatural molecules are processed by DNA polymerases that have evolved to efficiently work with the natural building blocks. Here, we report structural insight into the insertion of one of the most promising hydrophobic unnatural base pairs, the dDs-dPx pair, into a DNA strand by a DNA polymerase...
September 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28576078/cf2h-a-hydrogen-bond-donor
#8
Chanan D Sessler, Martin Rahm, Sabine Becker, Jacob M Goldberg, Fang Wang, Stephen J Lippard
The CF2H group, a potential surrogate for the OH group, can act as an unusual hydrogen bond donor, as confirmed by crystallographic, spectroscopic, and computational methods. Here, we demonstrate the bioisosterism of the OH and CF2H groups and the important roles of CF2-H···O hydrogen bonds in influencing intermolecular interactions and conformational preferences. Experimental evidence, corroborated by theory, reveals the distinctive nature of CF2H hydrogen bonding interactions relative to their normal OH hydrogen bonding counterparts...
June 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28561588/protein-domain-mimics-as-modulators-of-protein-protein-interactions
#9
Nicholas Sawyer, Andrew M Watkins, Paramjit S Arora
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design...
June 20, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28558205/ruthenium-catalyzed-urea-synthesis-by-n-h-activation-of-amines
#10
Varadhan Krishnakumar, Basujit Chatterjee, Chidambaram Gunanathan
Activation of the N-H bond of amines by a ruthenium pincer complex operating via "amine-amide" metal-ligand cooperation is demonstrated. Catalytic formyl C-H activation of N,N-dimethylformamide (DMF) is observed in situ, which resulted in the formation of CO and dimethylamine. The scope of this new mode of bond activation is extended to the synthesis of urea derivatives from amines using DMF as a carbon monoxide (CO) surrogate. This catalytic protocol allows the synthesis of simple and functionalized urea derivatives with liberation of hydrogen, devoid of any stoichiometric activating reagents, and avoids the direct use of fatal CO...
May 30, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28211267/efficient-and-selective-uptake-of-tco4-by-a-cationic-metal-organic-framework-material-with-open-ag-sites
#11
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
#12
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
#13
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...
March 24, 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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