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https://www.readbyqxmd.com/read/29764125/analysis-of-three-phase-equilibrium-conditions-for-methane-hydrate-by-isometric-isothermal-molecular-dynamics-simulations
#1
Daisuke Yuhara, Paul E Brumby, David T Wu, Amadeu K Sum, Kenji Yasuoka
To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions...
May 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29665576/radiocesium-interaction-with-clay-minerals-theory-and-simulation-advances-post-fukushima
#2
Masahiko Okumura, Sebastien Kerisit, Ian C Bourg, Laura N Lammers, Takashi Ikeda, Michel Sassi, Kevin M Rosso, Masahiko Machida
Insights at the microscopic level of the process of radiocesium adsorption and interaction with clay mineral particles have improved substantially over the past several years, triggered by pressing social issues such as management of huge amounts of waste soil accumulated after the Fukushima Dai-ichi nuclear power plant accident. In particular, computer-based molecular modeling supported by advanced hardware and algorithms has proven to be a powerful approach. Its application can now generally encompass the full complexity of clay particle adsorption sites from basal surfaces to interlayers with inserted water molecules, to edges including fresh and weathered frayed ones...
April 14, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29569896/electrolytic-co-2-reduction-in-a-flow-cell
#3
David M Weekes, Danielle A Salvatore, Angelica Reyes, Aoxue Huang, Curtis P Berlinguette
Electrocatalytic CO2 conversion at near ambient temperatures and pressures offers a potential means of converting waste greenhouse gases into fuels or commodity chemicals (e.g., CO, formic acid, methanol, ethylene, alkanes, and alcohols). This process is particularly compelling when driven by excess renewable electricity because the consequent production of solar fuels would lead to a closing of the carbon cycle. However, such a technology is not currently commercially available. While CO2 electrolysis in H-cells is widely used for screening electrocatalysts, these experiments generally do not effectively report on how CO2 electrocatalysts behave in flow reactors that are more relevant to a scalable CO2 electrolyzer system...
March 23, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29564890/reaction-of-criegee-intermediate-with-nitric-acid-at-the-air-water-interface
#4
Manoj Kumar, Jie Zhong, Xiao Cheng Zeng, Joseph S Francisco
. The role of aqueous surfaces in promoting atmospheric chemistry is increasingly being recognized. However, the bimolecular chemistries of Criegee intermediates, which influence the tropospheric budget of OH radicals, organic acids, hydroperoxides, nitrates, sulfates and particulate material, remain less explored on an aqueous surface. Herein we have employed Born Oppenheimer molecular dynamics simulations and two-layer ONIOM(QM:MM) in electronic embedding scheme to study the reaction and the spectroscopic signal of anti-CH3CHOO with nitric acid (HNO3) at the air-water interface, which is expected to be an important reaction in the polluted urban environments...
March 22, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29489607/nephrogenic-diabetes-insipidus-in-childhood-assessment-of-volume-status-and-appropriate-fluid-replenishment
#5
Stefano Guarino, Mario Diplomatico, Rosaria Marotta, Anna Pecoraro, Daniela Furlan, Lorenzo Cerrone, Emanuele Miraglia Del Giudice, Cesare Polito, Angela La Manna, Pierluigi Marzuillo
Patients affected by nephrogenic diabetes insipidus (NDI) can present with hypernatremic dehydration, and first-line rehydration schemes are completely different from those largely applied in usual conditions determining a mild to severe hypovolemic dehydration/shock. In reporting the case of a patient affected by NDI and presenting with severe dehydration triggered by acute pharyngotonsillitis and vomiting, we want to underline the difficulties in managing this condition. Restoring the free-water plasma amount in patients affected by NDI may not be easy, but some key points can help in the first line management of these patients: (1) hypernatremic dehydration should always be suspected; (2) even in presence of severe dehydration, skin turgor may be normal and therefore the skinfold recoll should not be considered in the dehydration assessment; (3) decreased thirst is an important red flag for dehydration; (4) if an incontinent patient with NDI appears to be dehydrated, it is important to place the urethral catheter to accurately measure urine output and to be guided in parenteral fluid administration; (5) if the intravenous route is necessary, the more appropriate fluid replenishment is 5% dextrose in water with an infusion rate that should slightly exceed the urine output; (6) the 0...
February 28, 2018: Pediatric Emergency Care
https://www.readbyqxmd.com/read/29419829/ion-hydration-linking-self-diffusion-and-reorientational-motion-to-water-structure
#6
Seishi Shimizu, Nobuyuki Matubayasi
Ions affect the self-diffusion and relaxation of water. Such ion-induced changes of water dynamics have long been rationalized in terms of the change of the water structure around the ions. The aim of this paper is to establish a link between dynamics and the "water structure" on the basis of the extended jump (EJ) model for the reorientational motion of water, Eyring's transition state theory of the self-diffusion of water, and the statistical thermodynamic preferential solvation theory developed from the Kirkwood-Buff (KB) theory...
February 21, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29355023/pso-assisted-development-of-new-transferable-coarse-grained-water-models
#7
Karteek K Bejagam, Samrendra Singh, Yaxin An, Carter Berry, Sanket A Deshmukh
We have employed two-to-one mapping scheme to develop three coarse-grained (CG) water models, namely, 1-, 2-, and 3-site CG models. Here, for the first time, particle swarm optimization (PSO) and gradient descent methods were coupled to optimize the force-field parameters of the CG models to reproduce the density, self-diffusion coefficient, and dielectric constant of real water at 300 K. The CG MD simulations of these new models conducted with various timesteps, for different system sizes, and at a range of different temperatures are able to predict the density, self-diffusion coefficient, dielectric constant, surface tension, heat of vaporization, hydration free energy, and isothermal compressibility of real water with excellent accuracy...
February 15, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29345927/embedded-multireference-coupled-cluster-theory
#8
David J Coughtrie, Robin Giereth, Daniel Kats, Hans-Joachim Werner, Andreas Köhn
Internally contracted multireference coupled cluster (icMRCC) theory is embedded within multireference perturbation theory (MRPT) to calculate energy differences in large strongly correlated systems. The embedding scheme is based on partitioning the orbital spaces of a complete active space self-consistent field (CASSCF) wave function, with a truncated virtual space constructed by transforming selected projected atomic orbitals (PAOs). MRPT is applied to the environment using a subtractive embedding approach that also allows for multilayer embedding...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29339135/quantitative-monitoring-the-anti-solvent-crystallization-and-storage-process-for-nandrolone-by-near-infrared-spectroscopy
#9
Xia Zeng, Xinnuo Xiong, Hongqin Yang, Bin Tang, Qiaohong Du, Quan Hou, Zili Suo, Hui Li
A novel hydrate (SH2O ) of nandrolone was prepared by anti-solvent methods. The crystallization processes with 2 schemes (A and B) were monitored by in-line near-infrared (NIR) spectroscopy. The amounts of SH2O in powder samples obtained by the anti-solvent crystallization and storage process were quantified by NIR combined with chemometrics methods. In-line NIR spectra from 4500 to 8000 cm-1 were chosen to capture physicochemical changes during the whole crystallization process. The combination of the principal component results with offline characterization (scanning electron microscopy, powder X-ray diffraction, NIR) data showed that both schemes yielded high purity SH2O products, but the crystallization speed of scheme B was significantly accelerated...
January 12, 2018: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29328645/assessing-intermolecular-interactions-in-guest-free-clathrate-hydrate-systems
#10
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, which motivates further investigations on the stability of such guest-free clathrate structures. Using semiempirical 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 wave function-based DF-MP2 electronic structure calculations...
February 8, 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
#11
Margarita G Ilyina, Edward M Khamitov, Sergey P 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 calculation 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...
January 11, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29184958/hydration-peculiarities-of-graphene-oxides-with-multiple-oxidation-degrees
#12
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...
December 13, 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
#13
Jiří Fukal, Ondřej Páv, Miloš Buděšínský, Jakub Šebera, Vladimír Sychrovský
A benchmark for structural interpretation of the31 P NMR shift and the2 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)...
December 6, 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
#14
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...
November 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28831903/think-drink-campaign-gets-national-attention
#15
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
#16
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
#17
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
#18
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 10, 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
#19
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
#20
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
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