A molecular dynamics simulation of a water model with intramolecular degrees of freedom

Teleman, Olle; Jönsson, Bo; Engström, Sven

doi:10.1080/00268978700100141

Cited by 400 publications

(277 citation statements)

References 28 publications

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“…The dynamics simulation data was produced using the LAMMPS software package [6] and the CLAYFF force field [7], which uses a flexible simple point charge (SPC) water model [8][9][10]. It consists of 1 ns production runs in the microcanonical (NVE) ensemble of adsorbed and bulk water on an α-quartz (001) surface at the target temperature of 300 K. …”

Section: Simulation Datamentioning

confidence: 99%

Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

2014

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Intermolecular chemical networks defined by the hydrogen bonds formed at the α-quartz|water interface have been data-mined using graph theoretical methods so as to identify and quantify structural patterns and dynamic behavior. Using molecular-dynamics simulations data, the hydrogen bond (H-bond) distributions for the water-water and water-silanol H-bond networks have been determined followed by the calculation of the persistence of the H-bond, the dipole-angle oscillations that water makes with the surface silanol groups over time, and the contiguous H-bonded chains formed at the interface. Changes in these properties have been monitored as a function of surface coverage. Using the H-bond distribution between water and the surface silanol groups, the actual number of waters adsorbed to the surface is found to be 0.6 H 2 O/10 Å 2 , irrespective of the total concentration of waters within the system. The unbroken H-bond network of interfacial waters extends farther than in the bulk liquid; however, it is more fluxional at low surface coverages (i.e., the H-bond persistence in a monolayer of water is shorter than in the bulk) Concentrations of H 2 O at previously determined water adsorption sites have also been quantified. This work demonstrates the complementary information that can be obtained through graph theoretical analysis of the intermolecular H-bond networks relative to standard analyses of molecular simulation data.

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Section: Simulation Datamentioning

confidence: 99%

Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

2014

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“…The noncarbonato and monocarbonato uranyl species can form outer-sphere complexes on siloxane surfaces through electrostatic interaction, but the dicarbonato and tricarbonato uranyl complexes rarely adsorb on the siloxane surfaces. The ClayFF force field is used to simulate Pyrophyllite [5], while SPC water model is for water molecules [6,7].…”

Section: Pyrophyllitementioning

confidence: 99%

Application of Modified Clay for Sorption of Radionuclide Elements

Liang¹

2017

J Chromatogr Sep Tech

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The clay materials are distinguished on the basis of their different crystal structures. Due to their specific structure, they are applied in the nuclear industry for the removal of radionuclides from nuclear liquid waste as ion exchange material. This mini review presents some of the recent advances of various kinds of clay materials in this aspect. These inorganic materials continue to gain attention due to their chemical and radiation stability and effectiveness over wide range of conditions.

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“…[63]. Intermolecular potential parameters between organic guest atoms (C, H) and host water molecules (Simple Point Charge model [73]) were obtained from geometric combination rules upon which CVFF is based. CVFF has previously been shown to provide accurate structural results for methane hydrate, [49] and here we apply similar techniques to more complex trihaloethane guests.…”

Section: Classical Molecular Dynamicsmentioning

confidence: 99%

Desalination utilizing clathrate hydrates (LDRD final report).

Simmons¹,

Bradshaw²,

Dedrick³

et al. 2008

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Advances are reported in several aspects of clathrate hydrate desalination fundamentals necessary to develop an economical means to produce municipal quantities of potable water from seawater or brackish feedstock. These aspects include the following, (1) advances in defining the most promising systems design based on new types of hydrate guest molecules, (2) selection of optimal multi-phase reactors and separation arrangements, and, (3) applicability of an inert heat exchange fluid to moderate hydrate growth, control the morphology of the solid hydrate material formed, and facilitate separation of hydrate solids from concentrated brine. The rate of R141b hydrate formation was determined and found to depend only on the degree of supercooling. The rate of R141b hydrate formation in the presence of a heat exchange fluid depended on the degree of supercooling according to the same rate equation as pure R141b with 4 secondary dependence on salinity. Experiments demonstrated that a perfluorocarbon heat exchange fluid assisted separation of R141b hydrates from brine. Preliminary experiments using the guest species, difluoromethane, showed that hydrate formation rates were substantial at temperatures up to at least 12°C and demonstrated partial separation of water from brine.We present a detailed molecular picture of the structure and dynamics of R141b guest molecules within water cages, obtained from ab initio calculations, molecular dynamics simulations, and Raman spectroscopy. Density functional theory calculations were used to provide an energetic and molecular orbital description of R141b stability in both large and small cages in a structure II hydrate. Additionally, the hydrate of an isomer, 1,2-dichloro-1-fluoroethane, does not form at ambient conditions because of extensive overlap of electron density between guest and host. Classical molecular dynamics simulations and laboratory trials support the results for the isomer hydrate. Molecular dynamics simulations show that R141b hydrate is stable at temperatures up to 265K, while the isomer hydrate is only stable up to 150K. Despite hydrogen bonding between guest and host, R141b molecules rotated freely within the water cage. The Raman spectrum of R141b in both the pure and hydrate phases was also compared with vibrational analysis from both computational methods. In particular, the frequency of the C-Cl stretch mode (585 cm -1 ) undergoes a shift to higher frequency in the hydrate phase. Raman spectra also indicate that this peak undergoes splitting and intensity variation as the temperature is decreased from 4°C to -4°C. 5 AcknowledgmentsThe authors gratefully acknowledge the contributions to this study made by Bill Anderson (8758) for laboratory support modifying and operating the experimental hydrate cell and Miles Clift (8758), who performed cold-stage x-ray diffraction of R141b hydrate samples.

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A molecular dynamics simulation of a water model with intramolecular degrees of freedom

Cited by 400 publications

References 28 publications

Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

Application of Modified Clay for Sorption of Radionuclide Elements

Desalination utilizing clathrate hydrates (LDRD final report).

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