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https://www.readbyqxmd.com/read/29328645/assessing-intermolecular-interactions-in-guest-free-clathrate-hydrate-systems
#1
Iván León-Merino, Raúl Rodríguez-Segundo, Daniel J Arismendi-Arrieta, Rita Prosmiti
Recently, empty hydrate structures sI, sII, sH and others have been proposed as low-density ice structures by both experimental observations and computer simulations. Some of them have been synthesized in the laboratory and motivates to reexamine the stability of such guest-free clathrate structures. Using empirical and ab initio-based water models, as well as dispersion-corrected density functional theory approaches, we predict their stability, including cooperative many-body effects, in comparison with reference data from converged wavefunction-based DF-MP2 electronic structure calculations...
January 12, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29215882/theoretical-models-for-quantitative-description-of-the-acid-base-equilibria-of-the-5-6-substituted-uracils
#2
Margarita G Ilyina, Edward M Khamitov, Sergey Petrovich Ivanov, Akhat G Mustafin, Sergey L Khursan
The acidities of 18 5,6-substituted uracils have been numerically estimated as pKa values in terms of three theoretical models. The first scheme includes the calculation of the gas-phase acidity of uracil with the G3MP2B3 method and taking into account the solvent effect using the polarizable continuum approximation PCM(SMD)-TPSS/aug-cc-pVTZ. The second model is one-step and implies calculating of the free Gibbs energies of the hydrate complex of uracil (and its anion) with 5 water molecules by the TPSS/aug-cc-pVTZ method...
December 7, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29184958/hydration-peculiarities-of-graphene-oxides-with-multiple-oxidation-degrees
#3
Antenor J Paulista Neto, Vitaly V Chaban, Eudes E Fileti
Hydration properties of graphene oxide (GO) are essential for most of its potential applications. In this work, we employ atomistic molecular dynamics simulations to investigate seven GO compositions with different levels of oxygenation. Two atomic charge models for GO are compared: (1, a simplified model) sp2 carbons are purely Lennard-Jones sites; (2, a CHELPG model) sp2 carbon charges are consistent with the CHELPG scheme. Structural properties were found to depend insignificantly on the charge model, whereas thermodynamics appeared very sensitive...
November 29, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29171602/the-benchmark-of-31-p-nmr-parameters-in-phosphate-a-case-study-on-structurally-constrained-and-flexible-phosphate
#4
Jiří Fukal, Ondřej Páv, Miloš Buděšínský, Jakub Šebera, Vladimír Sychrovský
A benchmark for structural interpretation of the (31)P NMR shift and the (2)JP,C NMR spin-spin coupling in the phosphate group was obtained by means of theoretical calculations and NMR measurements in diethylphosphate (DEP) and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide (cDEP). The NMR parameters were calculated employing the B3LYP, BP86, BPW91, M06-2X, PBE0, KT2, KT3, MP2, and HF methods, and the 6-31+G(d), Iglo-n (n = II, III), cc-pVnZ (n = D, T, Q, 5), aug-cc-pVnZ (n = D, T and Q), and pcS-n and pcJ-n (n = 1, 2, 3, 4) bases, including the solvent effects described with explicit water molecules and/or the implicit Polarizable Continuum Model (PCM)...
November 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28992702/open-boundary-simulations-of-proteins-and-their-hydration-shells-by-hamiltonian-adaptive-resolution-scheme
#5
Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Alejandro Giorgetti, Paolo Carloni
The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models...
October 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28831903/think-drink-campaign-gets-national-attention
#6
Kat Keogh
A hospital's award-winning scheme - which helps patients recover faster from surgery side effects by keeping them hydrated pre-operation - is being shared nationwide.
August 23, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28831152/different-route-of-hydroxide-incorporation-and-thermal-stability-of-new-type-of-water-clathrate-x-ray-single-crystal-and-raman-investigation
#7
Mateusz Dulski, Katarzyna M Marzec, Joachim Kusz, Irina Galuskina, Katarzyna Majzner, Evgeny Galuskin
Chlormayenite Ca12Al14O32[♦4Cl2] (♦-vacancy) is partially hydrated micro porouss mineral with hydroxide groups situated at various crystallographic sites. There are few mechanisms describing its hydration. The first one assumes Cl(-) substitution by OH(-) at the center of the structural cages (W-site). The second one determines the converting a T1O4 tetrahedron to a T1O3(OH)3 octahedron due to the replacement of oxygen at the O2 site by three OH-groups according to the scheme: ((O2)O(2-) +  (W) Cl(-)) → 3 ×  (O2a)OH...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28731091/developing-force-fields-when-experimental-data-is-sparse-amber-gaff-compatible-parameters-for-inorganic-and-alkyl-oxoanions
#8
Sadra Kashefolgheta, Ana Vila Verde
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham...
August 9, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28707900/aerosol-fragmentation-driven-by-coupling-of-acid-base-and-free-radical-chemistry-in-the-heterogeneous-oxidation-of-aqueous-citric-acid-by-oh-radicals
#9
Matthew J Liu, Aaron A Wiegel, Kevin R Wilson, Frances A Houle
A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity...
August 1, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#10
Viren Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
August 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28612358/%C3%AE-chymotrypsin-in-water-acetone-and-water-dimethyl-sulfoxide-mixtures-effect-of-preferential-solvation-and-hydration
#11
Vladimir A Sirotkin, Alexandra A Kuchierskaya
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin...
October 2017: Proteins
https://www.readbyqxmd.com/read/28607681/hydration-stickers-improving-oral-hydration-in-vulnerable-patients
#12
Alysha Bhatti, Javier Ash, Shyam Gokani, Suveer Singh
Dehydration is a growing problem among elderly patients in hospital wards. Incidents such as those raised in the Francis Report highlight a problem that may not have been sufficiently addressed by current schemes. This improvement project aimed to identify the barriers faced by staff in improving oral hydration and to design and implement an effective solution. A 33 patient pilot study carried out at Chelsea & Westminster Hospital NHS Trust, United Kingdom, revealed that a significant proportion of patients were reported to be dehydrated on admission, with few having their hydration needs addressed...
2017: BMJ Quality Improvement Reports
https://www.readbyqxmd.com/read/28600826/tinker-openmm-absolute-and-relative-alchemical-free-energies-using-amoeba-on-gpus
#13
Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay Ponder, Pengyu Ren
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core...
September 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28576085/lysozyme-in-water-acetonitrile-mixtures-preferential-solvation-at-the-inner-edge-of-excess-hydration
#14
Vladimir A Sirotkin, Alexandra A Kuchierskaya
Preferential solvation/hydration is an effective way for regulating the mechanism of the protein destabilization/stabilization. Organic solvent/water sorption and residual enzyme activity measurements were performed to monitor the preferential solvation/hydration of hen egg-white lysozyme at high and low water content in acetonitrile at 25 °C. The obtained results show that the protein destabilization/stabilization depends essentially on the initial hydration level of lysozyme and the water content in acetonitrile...
June 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28513645/electrode-potential-dependent-desolvation-and-resolvation-of-germanium-100-in-contact-with-aqueous-perchlorate-electrolytes
#15
Fang Niu, Rainer Schulz, Arcesio Castañeda Medina, Rochus Schmid, Andreas Erbe
The electrode potential dependence of the hydration layer on an n-Ge(100) surface was studied by a combination of in situ and operando electrochemical attenuated total reflection infrared (ATR-IR) spectroscopy and real space density functional theory (DFT) calculations. Constant-potential DFT calculations were coupled to a modified generalised Poisson-Boltzmann ion distribution model and applied within an ab initio molecular dynamics (AIMD) scheme. As a result, potential-dependent vibrational spectra of surface species and surface water were obtained, both experimentally and by simulations...
May 31, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28492328/inhibition-of-radiolytic-molecular-hydrogen-formation-by-quenching-of-excited-state-water
#16
Gregory P Horne, Simon M Pimblott, Jay A LaVerne
Comparison of experimental measurements of the yield of molecular hydrogen produced in the gamma radiolysis of water and aqueous nitrate solutions with predictions of a Monte Carlo track chemistry model shows that the nitrate anion scavenging of the hydrated electron, its precursor, and hydrogen atom cannot account for the observed decrease in the yield at high nitrate anion concentrations. Inclusion of the quenching of excited states of water (formed by either direct excitation or reaction of the water radical cation with the precursor to the hydrated electron) by the nitrate anion into the reaction scheme provides excellent agreement between the stochastic calculations and experiment demonstrating the existence of this short-lived species and its importance in water radiolysis...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28300856/halobetasol-propionate-lotion-0-05-provides-superior-hydration-compared-to-halobetasol-propionate-cream-0-05-in-a-double-blinded-study-of-occlusivity-and-hydration
#17
Gary Grove, Charles Zerweck, Tim Houser, Anthony Andrasfay, Bob Gauthier, Charles Holland, Daniel Piacquadio
BACKGROUND: This study measured skin hydration and occlusivity of two test products [halobetasol propionate lotion, 0.05% (HBP Lotion) and Ultravate® (halobetasol propionate) cream, 0.05% (HBP Cream)] at 2, 4, and 6 hours after application to skin test sites previously challenged by dry shaving, which was performed to compromise the integrity of the stratum corneum barrier. METHODS: Trans-epidermal water loss (TEWL), an indicator of skin barrier function, was measured using cyberDERM, inc...
February 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28138128/understanding-and-preventing-contrast-induced-acute-kidney-injury
#18
REVIEW
Michael Fähling, Erdmann Seeliger, Andreas Patzak, Pontus B Persson
Contrast-induced acute kidney injury (CIAKI) occurs in up to 30% of patients who receive iodinated contrast media and is generally considered to be the third most common cause of hospital-acquired AKI. Accurate assessment of the incidence of CIAKI is obscured, however, by the use of various definitions for diagnosis, the different populations studied and the prophylactic measures put in place. A deeper understanding of the mechanisms that underlie CIAKI is required to enable reliable risk assessment for individual patients, as their medical histories will determine the specific pathways by which contrast media administration might lead to kidney damage...
March 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/27992815/molecular-dynamics-study-of-micelles-properties-according-to-their-size
#19
S Lebecque, J M Crowet, M N Nasir, M Deleu, L Lins
Surfactants are molecules able to spontaneously self-assemble to form aggregates with well-defined properties, such as spherical micelles, planar bilayers, cylindrical micelles or vesicles. Micelles have notably several applications in many domains, such as drug delivery or membrane protein solubilization. In this context, the study of micelle formation in relation with the structural and physico-chemical properties of surfactants is of great interest to better control their use in the different application fields...
March 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27760249/multidirectional-in-vivo-characterization-of-skin-using-wiener-nonlinear-stochastic-system-identification-techniques
#20
Matthew D Parker, Lynette A Jones, Ian W Hunter, A J Taberner, M P Nash, P M F Nielsen
A triaxial force-sensitive microrobot was developed to dynamically perturb skin in multiple deformation modes, in vivo. Wiener static nonlinear identification was used to extract the linear dynamics and static nonlinearity of the force-displacement behavior of skin. Stochastic input forces were applied to the volar forearm and thenar eminence of the hand, producing probe tip perturbations in indentation and extension. Wiener static nonlinear approaches increased the variance accounted for by 0.1 % to 3.4 % over linear approaches, to 94 % to 97 %...
October 19, 2016: Journal of Biomechanical Engineering
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