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https://www.readbyqxmd.com/read/28231451/disaggregation-of-human-islet-amyloid-polypeptide-fibril-formation-by-ruthenium-polypyridyl-complexes
#1
Dengsen Zhu, Gehui Gong, Wenji Wang, Weihong Du
The toxicity of amyloid proteins is associated with many degenerative and systematic diseases. The aggregation of human islet amyloid polypeptide may induce pancreatic β-cell death, which is linked to type II diabetes. Ruthenium complexes are inhibitors of various proteins and potential anticancer metallodrugs, which can also be used to disaggregate amyloid proteins. This work reported that several ruthenium polypyridyl complexes remarkably affected the peptide aggregation by predominant hydrophobic interaction and metal coordination, as reflected by thermodynamic parameters and mass spectrometry analysis...
February 13, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28231446/how-will-kinetics-and-thermodynamics-inform-our-future-efforts-to-understand-and-build-biological-systems
#2
(no author information available yet)
No abstract text is available yet for this article.
February 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28230294/asymmetric-total-syntheses-of-kopsia-indole-alkaloids
#3
Lingying Leng, Xiaohan Zhou, Qi Liao, Falu Wang, Hao Song, Dan Zhang, Xiao-Yu Liu, Yong Qin
The asymmetric total syntheses of a group of structurally complex Kopsia alkaloids, (-)-kopsine, (-)-isokopsine, (+)-methyl chanofruticosinate, (-)-fruticosine, and (-)-kopsanone, has been achieved. The key strategies for the construction of the molecular complexity in the targets included an asymmetric Tsuji-Trost rearrangement to set the first quaternary carbon center at C20, an intramolecular cyclopropanation by diazo decomposition to install the second and third quaternary carbon centers at C2 and C7, respectively, and a SmI2 -promoted acyloin condensation to assemble the isokopsine core...
February 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28230160/global-view-of-cognate-kinase-activation-by-the-human-pyruvate-dehydrogenase-complex
#4
Elena L Guevara, Luying Yang, Barbara Birkaya, Jieyu Zhou, Natalia S Nemeria, Mulchand S Patel, Frank Jordan
The human pyruvate dehydrogenase complex (PDC) comprises four multidomain components, E1, E3, E2 and an E3-binding protein (E3BP), the latter two forming the core as E2·E3BP sub-complex. Pyruvate flux through PDC is regulated via phosphorylation (inactivation) at E1 by four PDC kinases (PDKs), and reactivation by two PDC phosphatases. Up-regulation of PDK isoform gene expression is reported in several forms of cancer, while PDKs may be further activated by PDC by binding to the E2·E3BP core. Hence, the PDK: E2·E3BP interaction provides new therapeutic targets...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229352/linshom-thermodynamic-sensor-is-a-reliable-alternative-to-capnography-for-monitoring-respiratory-rate
#5
David Preiss, Benjamin A Drew, James Gosnell, Bhavani S Kodali, James H Philip, Richard D Urman
Monitoring ventilation accurately is a technically challenging, yet indispensable aspect of patient care in the intra- and post-procedural settings. A new prototypical device known as the Linshom Respiratory Monitoring Device (LRMD) has been recently designed to non-invasively, inexpensively, and portably measure respiratory rate. The purpose of this study was to measure the accuracy and variability of LRMD measurements of respiratory rate relative to the measurement of capnography. In this prospective study, participants were enrolled and individually fitted with a face mask monitored by the LRMD and capnography...
February 22, 2017: Journal of Clinical Monitoring and Computing
https://www.readbyqxmd.com/read/28229338/investigation-of-the-encapsulation-of-metal-cations-cu-2-zn-2-ca-2-and-ba-2-by-the-dipeptide-phe-phe-using-natural-bond-orbital-theory-and-molecular-dynamics-simulation
#6
Snehasis Bhunia, Ajeet Singh, Animesh K Ojha
Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28229145/oxidation-potentials-of-phenols-and-anilines-correlation-analysis-of-electrochemical-and-theoretical-values
#7
Ania S Pavitt, Eric J Bylaska, Paul G Tratnyek
Phenols and anilines have been studied extensively as reductants of environmental oxidants (such as manganese dioxide) and as reductates (e.g., model contaminants) that are transformed by environmental oxidants (ozone, triple organic matter, etc.). The thermodynamics and kinetics of these reactions have been interpreted using oxidation potentials for substituted phenols and anilines, often using a legacy experimental dataset that is of uncertain quality. Although there are many alternative oxidation potential data, there has been little systematic analysis of the relevance, reliability, and consistency of the data obtained by different methods...
February 23, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28228353/isochoric-and-isobaric-freezing-of-fish-muscle
#8
Gabriel Năstase, Chenang Lyu, Gideon Ukpai, Alexandru Șerban, Boris Rubinsky
We have recently shown that, a living organism, which succumbs to freezing to -4 °C in an isobaric thermodynamic system (constant atmospheric pressure), can survive freezing to -4 °C in an isochoric thermodynamic system (constant volume). It is known that the mechanism of cell damage in an isobaric system is the freezing caused increase in extracellular osmolality, and, the consequent cell dehydration. An explanation for the observed survival during isochoric freezing is the thermodynamic modeling supported hypothesis that, in the isochoric frozen solution the extracellular osmolality is comparable to the cell intracellular osmolality...
February 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28228041/thermodynamics-of-hydration-of-fullerols-c60-oh-n-and-hydrogen-bond-dynamics-in-their-hydration-shells
#9
Sonanki Keshri, B L Tembe
Molecular dynamics simulations of fullerene and fullerols [C60(OH)n, where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28228030/anion-photoelectron-spectroscopy-of-deprotonated-ortho-meta-and-para-methylphenol
#10
Daniel J Nelson, Wilson K Gichuhi, Elisa M Miller, Julia H Lehman, W Carl Lineberger
The anion photoelectron spectra of ortho-, meta-, and para-methylphenoxide, as well as methyl deprotonated meta-methylphenol, were measured. Using the Slow Electron Velocity Map Imaging technique, the Electron Affinities (EAs) of the o-, m-, and p-methylphenoxyl radicals were measured as follows: 2.1991±0.0014, 2.2177±0.0014, and 2.1199±0.0014 eV, respectively. The EA of m-methylenephenol was also obtained, 1.024±0.008 eV. In all four cases, the dominant vibrational progressions observed are due to several ring distortion vibrational normal modes that were activated upon photodetachment, leading to vibrational progressions spaced by ∼500 cm(-1)...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28228029/predicting-low-temperature-free-energy-landscapes-with-flat-histogram-monte-carlo-methods
#11
Nathan A Mahynski, Marco A Blanco, Jeffrey R Errington, Vincent K Shen
We present a method for predicting the free energy landscape of fluids at low temperatures from flat-histogram grand canonical Monte Carlo simulations performed at higher ones. We illustrate our approach for both pure and multicomponent systems using two different sampling methods as a demonstration. This allows us to predict the thermodynamic behavior of systems which undergo both first order and continuous phase transitions upon cooling using simulations performed only at higher temperatures. After surveying a variety of different systems, we identify a range of temperature differences over which the extrapolation of high temperature simulations tends to quantitatively predict the thermodynamic properties of fluids at lower ones...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28226784/parameter-estimation-for-gene-regulatory-networks-a-two-stage-mcmc-bayesian-approach
#12
Niannan Xue, Wei Pan, Yike Guo, Niannan Xue, Wei Pan, Yike Guo, Wei Pan, Yike Guo, Niannan Xue
Genetic regulatory networks have emerged as a useful way to elucidate the biochemical pathways for biological functions. Yet, determination of the exact parametric forms for these models remain a major challenge. In this paper, we present a novel computational approach implemented in C++ to solve this inverse problem. This takes the form of an optimization stage first after which Bayesian filtering takes place. The key advantage of such a flexible, general and robust approach is that it provides us with a joint probability distribution of the model parameters instead of single estimates, which we can propagate to final predictions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#13
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28225626/combined-experimental-and-theoretical-approach-to-the-kinetics-of-magnetite-crystal-growth-from-primary-particles
#14
Marc Widdrat, Emanuel Schneck, Victoria Reichel, Jens Baumgartner, Luca Bertinetti, Wouter Habraken, Klaas Bente, Peter Fratzl, Damien Faivre
It is now recognized that nucleation and growth of crystals can occur not only by the addition of solvated ions but also by accretion of nanoparticles, in a process called nonclassical crystallization. The theoretical framework of such processes has only started to be described, partly due to the lack of kinetic or thermodynamic data. Here, we study the growth of magnetite nanoparticles from primary particles-nanometer-sized amorphous iron-rich precursors-in aqueous solution at different temperatures. We propose a theoretical framework to describe the growth of the nanoparticles and model both a diffusion-limited and a reaction-limited pathway to determine which of these best describes the rate-limiting step of the process...
February 23, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28225613/dehydrogenation-free-energy-of-co-2-aq-from-density-functional-theory-based-molecular-dynamics
#15
Florian H Hodel, Sandra Luber
Electron and proton transfers are important steps occurring in nature and in artificial (catalytic) reaction mechanisms. The often employed approach of calculating the energy differences of those steps using methods involving geometry optimizations neglects the influence of dynamic effects such as solvent rearrangement. To further investigate this issue and inspired by recent research in water oxidation, we calculate in the present study the dehydrogenation free energy of aqueous Co(2+), which is the free energy change associated with the first step of the reaction mechanism of model Co(II)-based water oxidation catalysts...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28225608/time-dependent-markov-state-models-for-single-molecule-force-spectroscopy
#16
Susmita Ghosh, Abhijit Chatterjee, Swati Bhattacharya
This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension using a handful of molecular dynamics calculations forms the basis for generating the required TD-MSM. Changes in the network topology upon stretching is related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28225599/cubic-sr2scgao5-perovskite-structural-stability-oxygen-defect-structure-and-ion-conductivity-explored-on-single-crystals
#17
Serena Corallini, Monica Ceretti, Alain Cousson, Clemens Ritter, Marco Longhin, Philippe Papet, Werner Paulus
Oxygen-deficient Sr2ScGaO5 single crystals with a cubic perovskite structure were grown by the floating-zone technique. The transparent crystals of this pure 3D oxygen electrolyte are metastable at ambient temperature, showing one-sixth of all oxygen positions vacant. While neutron single-crystal diffraction, followed by maximum entropy analysis, revealed a strong anharmonic displacements for the oxygen atoms, a predominant formation of ScO6 octahedra and GaO4 tetrahedra is indicated by Raman spectroscopic studies, resulting in a complex oxygen defect structure with short-range order...
February 22, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28225260/investigation-of-ag-tio2-interfacial-reaction-of-highly-stable-ag-nanowire-transparent-conductive-film-with-conformal-tio2-coating-by-atomic-layer-deposition
#18
Ming-Hua Yeh, Po-Shen Chen, Yi-Ching Yang, Guang-Hong Chen, Hsueh-Shih Chen
The atomic layer deposition (ALD) technique is applied to coat Ag nanowires (NWs) with a highly uniform and conformal TiO2 layer to improve the stability and sustainability of Ag NW transparent conductive films (TCFs) at high temperatures. The TiO2 layer can be directly deposited on Ag NWs with a surface polyvinylpyrrolidone (PVP) coat that acts a bed for TiO2 seeding in the ALD process. The ALD TiO2 layer significantly enhances the thermal stability at least 100 folds when aged between 200-400 °C and also provides an extra function of violet-blue light filtration for Ag NW TCFs...
February 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28225253/glutathione-adduct-patterns-of-michael-acceptor-carbonyls
#19
Christian Slawik, Christiane Rickmeyer, Martin Brehm, Alexander Böhme, Gerrit Schüürmann
Glutathione (GSH) has so far been considered to facilitate detoxification of soft organic electrophiles through covalent binding at its cysteine (Cys) thiol group, followed by stepwise catalyzed degradation and eventual elimination along the mercapturic acid pathway. Here we show that in contrast to expectation from HSAB theory, Michael-acceptor ketones, aldehydes and esters may form also single, double and triple adducts with GSH involving β-carbon attack at the much harder N-terminus of the γ-glutamyl (Glu) unit of GSH...
February 22, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28225110/tuning-the-hydrogen-evolution-activity-of-%C3%AE-mo2c-nanoparticles-via-control-of-their-growth-conditions
#20
Timothy T Yang, Wissam A Saidi
The use of water electrocatalysis for hydrogen production is a promising, sustainable and greenhouse-gas-free process to develop disruptive renewable energy technologies. Transition metal carbides, in particular β-phase Mo2C, are garnering increased attention as hydrogen evolution reaction (HER) catalysts due to their favourable synthesis conditions, stability and high catalytic efficiency. We use a thermodynamic approach in conjunction with density functional theory and a kinetic model of exchange current density to systematically study the HER activity of β-Mo2C under different experimental conditions...
February 22, 2017: Nanoscale
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