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https://www.readbyqxmd.com/read/28448953/electrostatic-frequency-maps-for-amide-i-mode-of-%C3%AE-peptide-comparison-of-molecular-mechanics-force-field-and-dft-calculations
#1
Kaicong Cai, Xuan Zheng, Fenfen Du
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization...
April 19, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28448147/binding-of-small-gas-molecules-by-metal-bipyridyl-monocationic-complexes-metal-cu-ag-au-and-possible-bond-activations-therein
#2
Gourhari Jana, Sudip Pan, Pratim Kumar Chattaraj
The viability of a series of small gas molecules (H2, N2, CO, CO2, H2O, H2S, C2H2, CH4, CH3Cl, C2H4, and C2H6) bound [M-(bipy)](+) (bipy = bipyridyl; M = Cu, Ag, Au) complexes is investigated at the PBE0/cc-pVTZ/cc-pVTZ-PP level with a special emphasis on the possible bond activation within the bound ligands. While the bond dissociation energy, enthalpy change, and free energy change are computed to show the stability of the complexes with respect to the dissociation into [M-(bipy)]+ and free gas molecule (L), natural bond orbital, electron density, and energy decomposition analyses in conjunction with natural orbitals for chemical valence are carried out to characterize the nature of L-M bonds...
April 27, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28448138/idp-specific-force-field-ff14idpsff-improves-the-conformer-sampling-of-intrinsically-disordered-proteins
#3
Dong Song, Ray Luo, Hai-Feng Chen
Intrinsically disordered proteins (IDPs) or intrinsically disordered regions have not fixed tertiary structure, but play key roles in signal regulation, molecule recognition, and drug target. However it is difficult to study the structure and function of IDPs by traditional experimental methods because of their diverse conformations. Limitations of current generic protein force fields and solvent models were reported in the previous simulations of IDPs. We have also explored to overcome these limitations by developing ff99IDPs and ff14IDPs force fields to correct the dihedral distribution for eight disordered promoting residues often observed in IDPs and found encouraging improvements...
April 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28447786/a-3d-mas-nmr-experiment-utilizing-through-space-15n-15n-correlations
#4
Kevin J Donovan, Robert Silvers, Sara Linse, Robert G Griffin
We demonstrate a novel 3D NNC magic angle spinning (MAS) NMR experiment that generates 15N- 15N internuclear contacts in protein systems using an optimized 15N- 15N proton assisted recoupling (PAR) mixing period and a 13C dimension for improved resolution. The optimized PAR condition permits the acquisition of high signal-to-noise 3D data that enables backbone chemical shift assignments using a strategy that is complementary to current schemes. The spectra can also provide distance constraints. The utility of the experiment is demonstrated on an M0Ab1-42 fibril sample that yields high-quality data that is readily assigned and interpreted...
April 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28446906/stratified-bacterial-diversity-along-physico-chemical-gradients-in-high-altitude-modern-stromatolites
#5
Diego M Toneatti, Virginia H Albarracín, Maria R Flores, Lubos Polerecky, María E Farías
At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28446711/chemical-roots-of-biological-evolution-the-origins-of-life-as-a-process-of-development-of-autonomous-functional-systems
#6
REVIEW
Kepa Ruiz-Mirazo, Carlos Briones, Andrés de la Escosura
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28445998/infrared-raman-and-magnetic-resonance-spectroscopic-study-of-sio2-c-nanopowders
#7
Dariya Savchenko, Vladimir Vorliček, Ekaterina Kalabukhova, Aleksandr Sitnikov, Andrii Vasin, Dmytro Kysil, Stanislav Sevostianov, Valentyn Tertykh, Alexei Nazarov
Optical and magnetic properties of SiO2:C nanopowders obtained by chemical and thermal modification of fumed silica were studied by Fourier transform infrared spectroscopy, Raman, continuous wave (CW) electron paramagnetic resonance (EPR), echo-detected EPR and pulsed electron nuclear double resonance (ENDOR) spectroscopy. Two overlapping signals of Lorentzian lineshape were detected in CW EPR spectra of the initial SiO2:C. The EPR signal at g = 2.0055(3) is due to the silicon dangling bonds, which vanishes after thermal annealing, and the second EPR signal at g = 2...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28445753/pyroglutamate-modified-amyloid-%C3%AE-3-42-shows-%C3%AE-helical-intermediates-before-amyloid-formation
#8
Christina Dammers, Kerstin Reiss, Lothar Gremer, Justin Lecher, Tamar Ziehm, Matthias Stoldt, Melanie Schwarten, Dieter Willbold
Pyroglutamate-modified amyloid-β (pEAβ) has been described as a relevant Aβ species in Alzheimer's-disease-affected brains, with pEAβ (3-42) as a dominant isoform. Aβ (1-40) and Aβ (1-42) have been well characterized under various solution conditions, including aqueous solutions containing trifluoroethanol (TFE). To characterize structural properties of pEAβ (3-42) possibly underlying its drastically increased aggregation propensity compared to Aβ (1-42), we started our studies in various TFE-water mixtures and found striking differences between the two Aβ species...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445065/neomacrophorin-x-a-4-4-3-propellane-type-meroterpenoid-from-trichoderma-sp-1212-03
#9
Kazuaki Kusakabe, Yuna Honmura, Shota Uesugi, Akio Tonouchi, Hayato Maeda, Ken-Ichi Kimura, Hiroyuki Koshino, Masaru Hashimoto
Neomacrophorin X (1) was isolated from Trichoderma sp. 1212-03. Heteronuclear multiple bond correlation (HMBC) spectral analysis indicated a unique [4.4.3]propellane framework, which was verified by the (1)H and (13)C chemical shift calculations based on density functional theory (DFT) and subsequent comparison with experimental data obtained in CDCl3. The DFT-based electronic circular dichroism (ECD) calculations were effective in not only determining the absolute configuration but also confirming the relative structure...
April 26, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28443864/planar-chiral-ferrocenylphosphine-borane-complexes-featuring-agostic-type-b-he-e-hg-sn-interactions
#10
Alain C Tagne Kuate, Roger A Lalancette, F Jäkle
The synthesis of ferrocenylphosphine-borane adducts 1,2-fc(E)(PPh2·BH3) (E = SnR2R', HgX; 1,2-fc = 1,2-ferrocenediyl) that are substituted with organotin or organomercury Lewis acid moieties in ortho-position is presented. Several compounds that feature two ferrocenylphosphine-borane moieties bridged by Sn or Hg are also introduced. The products are fully characterized by multinuclear NMR spectroscopy, high-resolution MALDI-TOF mass spectrometry and elemental analysis. The attachment of the Lewis acid substituent to the same Cp ring of the ferrocene results in planar-chirality and the close proximity between the boron hydride group and the Lewis acid is expected to allow for agostic-type B-HE (E = Sn, Hg) interactions...
April 26, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28443361/the-effect-of-alkali-on-the-product-distribution-from-black-liquor-conversion-under-supercritical-water
#11
Y Hawangchu, D Atong, V Sricharoenchaikul
Lignin in chemical pulping waste, or black liquor (BL), can be converted into various products via supercritical water gasification (SCWG). However, the inherited alkaline contents from the pulping chemicals may affect the product yields and properties. In this research, the influence of the residual alkali on the product distribution via SCWG of soda BL and kraft BL was evaluated. The SCWG was performed in a batch quartz reactor for 10 min at various temperatures (673, 773 and 873 K) and pressures (250, 300 and 400 bar)...
April 26, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28441482/the-value-of-nmr-parameters-and-dft-calculations-for-quantum-information-processing-utilizing-phosphorus-heterocycles
#12
Jessica Boreli Dos Reis Lino, Eduardo P Rocha, Teodorico Castro Ramalho
Quantum computing is the field of science that uses quantum-mechanical phenomena, such as superposition and entanglement, to perform operations on data. The fundamental information unit used in quantum computing is the quantum bit or qubit. It is well-known that quantum computers could theoretically be able to solve problems much more quickly than any classical computers. Currently, the first and still the most successful implementations of quantum information processing (QIP) have been based on nuclear spins in liquids...
April 25, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28441022/a-low-valent-lead-hydride-and-its-extreme-low-field-1h-nmr-chemical-shift
#13
Julia Schneider, Christian Patrick Sindlinger, Klaus Eichele, Hartmut Schubert, Lars Wesemann
Although hydrides of the group 14 elements are well known as versatile starting materials in many chemical transformations, a hydride of lead in oxidation state II is so far unknown. In this work we finally complete the jigsaw puzzle by reporting the isolation of the first low valent organolead hydride. The thermolabile dimeric organolead hydride was synthesized at low temperature and fea-tures a hydride 1H NMR signal (in solution 35.61 ppm; in the solid state 31.1 ppm) at the lowest field observed so far for a diamagnetic compound in agreement with quantum chemical predictions...
April 25, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28441020/general-c-h-arylation-strategy-for-the-synthesis-of-tunable-visible-light-emitting-high-stokes-shift-benzo-a-imidazo-2-1-5-c-d-indolizine-fluorophores
#14
Éric Lévesque, William Schulz Bechara, Léa Constantineau-Forget, Guillaume Pelletier, Natalie M Rachel, Joelle N Pelletier, André B Charette
Herein we report the discovery of the benzo[a]imidazo[2,1,5-c,d]indolizine motif displaying tunable emission covering most of the visible spectrum. The polycyclic core is obtained from readily available amides via a chemoselective process involving Tf2O-mediated amide cyclodehydration followed by intramolecular C-H arylation. Additionally, these fluorescent heterocycles are easily functionalized using electrophilic reagents, enabling divergent access to varied substitution. The effects of said substitution on the compounds' photophysical properties were rationalized by DFT calculations...
April 25, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28440657/aromaticity-of-non-planar-fully-benzenoid-hydrocarbons
#15
Marija Antic, Boris Furtula, Slavko Radenković
The Clar aromatic sextet theory can provide the qualitative description on the dominant modes of cyclic π-electron conjugation in benzenoid molecules, and on the relative stability among a series of isomeric benzenoid systems. In a series of non-planar fully benzenoid hydrocarbons, the predictions of the Clar theory were tested by means of several different theoretical approaches: topological resonance energy (TRE), energy effect (ef), harmonic oscillator model of aromaticity (HOMA) index, six centre delocalization index (SCI) and nucleus independent chemical shifts (NICS)...
April 25, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28440038/induced-chemical-defense-of-a-mushroom-by-a-double-bond-shifting-polyene-synthase
#16
Philip Brandt, María García-Altares, Markus Nett, Christian Hertweck, Dirk Hoffmeister
The antilarval mushroom polyenes 18-methyl-19-oxoicosaoctaenoic acid and 20-methyl-21-oxodocosanonaenoic acid appear in response to injury of the mycelium of the stereaceous mushroom BY1. We identified a polyketide synthase (PPS1) which belongs to a hitherto completely uncharacterized clade of polyketide synthases. Expression of the PPS1 gene is massively upregulated following mycelial damage. The synthesis of the above polyenes was reconstituted in the mold Aspergillus niger as a heterologous host. This demonstrates that PPS1 1) synchronously produces branched-chain polyketides of varied lengths, and 2) catalyzes the unprecedented shift of eight or nine double bonds...
April 25, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28437687/use-of-tourmaline-as-a-potential-petrogenetic-indicator-in-the-determination-of-host-magma-crs-xrd-and-ped-xrf-methods
#17
Bahattin Gullu, Yusuf Kagan Kadioglu
Tourmaline defines a group of complex borosilicate forms as accessory mineral in igneous and metamorphic rocks and they act an important role in the interpretation of the chemical composition changes of the composition of the host fluid of the magma. The variety of tourmaline can be identified by using optical microscopy, X-Ray Diffraction (XRD) and by determining its chemical composition through Polarized Energy Dispersive X-Ray Fluorescence (PED-XRF) methods. However, microscopic investigations and XRD analyses are not quite adequate for detailed determination of tourmaline sub-groups...
April 19, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28437584/high-field-95-mo-and-183-w-static-and-mas-nmr-study-of-polyoxometalates
#18
Mohamed Haouas, Julien Trébosc, Catherine Roch-Marchal, Emmanuel Cadot, Francis Taulelle, Charlotte Martineau-Corcos
The potential of high-field NMR to measure solid-state (95) Mo and (183) W NMR in polyoxometalates (POMs) is explored using some archetypical structures like Lindqvist, Keggin, and Dawson as model compounds that are well characterized in solution. NMR spectra in static and under magic angle spinning (MAS) were obtained, and their analysis allowed extraction of the NMR parameters, including chemical shift anisotropy (CSA) and quadrupolar coupling parameters. Despite the inherent difficulties of measurement in solid state of these low-gamma NMR nuclei, due mainly to the low spectral resolution and poor signal-to-noise ratio, the observed global trends compare well with the solution state NMR data...
April 24, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28436825/integrated-ecological-and-chemical-food-web-accumulation-modeling-explains-pah-temporal-trends-during-regime-shifts-in-a-shallow-lake
#19
Xiangzhen Kong, Wei He, Ning Qin, Wenxiu Liu, Bin Yang, Chen Yang, Fuliu Xu, Wolf M Mooij, Albert A Koelmans
Shallow lakes can switch suddenly from a turbid situation with high concentrations of phytoplankton and other suspended solids to a vegetated state with clear water, and vice versa. These alternative stable states may have a substantial impact on the fate of hydrophobic organic compounds (HOCs). Models that are fit to simulate impacts from these complex interactions are scarce. We developed a contaminant fate model which is linked to an ecosystem model (PCLake) for shallow lakes. This integrated model was successful in simulating long-term dynamics (1953-2012) of representative polycyclic aromatic hydrocarbons (PAHs) in the main biotic and abiotic components in a large shallow lake (Chaohu in China), which has undergone regime shifts in this period...
April 17, 2017: Water Research
https://www.readbyqxmd.com/read/28436609/a-semi-automated-approach-to-create-purposeful-mechanistic-datasets-from-heterogeneous-data-data-mining-towards-the-in-silico-predictions-for-oestrogen-receptor-modulation-and-teratogenicity
#20
M Bashir Surfraz, Adrian Fowkes, Jeffrey P Plante
The need to find an alternative to costly animal studies for developmental and reproductive toxicity testing has shifted the focus considerably to the assessment of in vitro developmental toxicology models and the exploitation of pharmacological data for relevant molecular initiating events. We hereby demonstrate how automation can be applied successfully to handle heterogeneous oestrogen receptor data from ChEMBL. Applying expert-derived thresholds to specific bioactivities allowed an activity call to be attributed to each data entry...
April 24, 2017: Molecular Informatics
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