Interionic potentials in alkali halides and their use in simulations of the molten salts

Sangster, M J L; Dixon, M.

doi:10.1080/00018737600101392

Cited by 636 publications

(236 citation statements)

References 125 publications

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“…The MD simulations were started at 0 K and heated to 300 K in 10 ps using temperature rescaling. The simulations were then run for 10 ps with temperature rescaling to allow the average kinetic and potential energies to equilibrate at this temperature, then for a further 10 ps with no temperature rescaling to allow the temperature fluctuations (which are proportional to specific heat) [19] to equilibrate. After equilibration, the simulations were run for a further 40 ps during which time structural and thermodynamic data were periodically written onto hard disk for later analysis.…”

Section: Methodsmentioning

confidence: 99%

Secondary and tertiary structures involving chondroitin and chondroitin sulphates in solution, investigated by rotary shadowing/electron microscopy and computer simulation

Scott

Chen

Brass

1992

European Journal of Biochemistry

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Rotary shadowing/electron microscopy of chondroitin 6-sulphate (CS6) and 4-sulphate (CS4) showed that the former, but not the latter, aggregated to mesh works. Preparations made from salt (ammonium acetate) solutions showed enhanced aggregation. Computer modelling, using molecular mechanics and dynamics, was applied to secondary structures (twofold helices) derived from NMR studies, to determine geometric and energetic constraints on duplex and higher-aggregate formation. The calculations suggested that chondroitin, CS6 and undersulphated CS4 could form duplexes, while CS4 could not, thus bridging the gap between atomic dimensions (NMR) and high polymer scale (clcctron microscopy). Calculations suggested that water structure helped to stabilise the twofold helix. It is proposed that the twofold helical, flat, tape-like molecules aggregate via hydrophobic bonding between the very extensive hydrophobic patches (9 CH units) repeated on alternating sides of the polymers. The negative charge of the polyanions opposes aggregate formation. Calculations showed that duplexes were formed with decreasing stability as the charge density increased, and as the charge was concentrated towards the centre line of the polymer (i.e. in CS4). The unsulphated polymer chondroitin could form duplexes and higher aggregates as readily as hyaluronan. Hyaluronan was calculated to form stable heteroduplexes with CS6 and CS4. The frequency and positioning of the sulphate-ester group within the polymer thus determines whether the molecule participates in duplex formation.The extra-cellular matrix of mammalian connective tissues is based on two structural elements: (a) insoluble fibres, predominantly collagenous ; (b) soluble polyanions, of a largely carbohydrate nature. The former resist or transmit tensile stresses, whereas the latter resist and absorb compressive Forces [I]. The two elements interact with each other in a very specific manner [2], implying that there are complementary binding sites, with the corollary that the shapes of the interactants must be at least semipermanent. The tertiary structures of collagen molecules, and to some extent the quaternary structure of collagen fibrils, are established [3], but the soluble polyanions have not been investigated as extensively, partly because they function in aqueous solution. There was doubt that they had stable secondary structures, or formed tertiary structures based on glycan/glycan interactions.The soluble carbohydrate polyanions are of two types, the proteoglycans, consisting of a polypeptide core with long polyanionic glycosaminoglycan (GAG) side chains, and hyaluronan (HA), a GAG that is not covalently attached to protein. [2], corresponded to characteristic differences in appearance in electron microscopy, after rotary shadowing [4-61. HA and the proteoglycan GAG chondroitin sulphate (CS), keratan sulphatc and dermatan sulphate consist of repeating disaccharide units, comprising glucosamine or galactosamine, and a uronic acid (glucuronic or iduronic) except in the case of k...

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Section: Methodsmentioning

confidence: 99%

Secondary and tertiary structures involving chondroitin and chondroitin sulphates in solution, investigated by rotary shadowing/electron microscopy and computer simulation

Scott

Chen

Brass

1992

European Journal of Biochemistry

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“…Two different simulation methods can be distinguished in statistical mechanics (see e.g. Sangster andDixon, 1976, andHansen andMcDonald, 1975):…”

Section: Discussionmentioning

confidence: 99%

Design and Implementation of the Delft Molecular-Dynamics Processor

Bakker

Bruin

1988

Special Purpose Computers

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“…By using the RIM and PIM described above, we simulated molten CuCl at 773 K, the same temperature as the HEXRD measurements of this work and ND data of Shirakawa et al, 9 and close to the 733 K of ND data of Drewitt et al 11 The ionic density was set as 0.041 ions/Å 3 , 44 (1) up to L/2 instead of . At low k this method gives spurious oscillations due to truncation errors, and therefore we computed S ab (k) directly, up to 4 Å -1 and slightly beyond, by using Eq (2).…”

Section: B Polarizable Ion Model and MD Simulationsmentioning

confidence: 99%

The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

Alcaraz

Trullàs

Tahara

et al. 2016

The Journal of Chemical Physics

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The results of the structural properties of molten copper chloride are reported from high-energy Xray diffraction measurements, reverse Monte Carlo modeling method and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å -1 related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.2

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Interionic potentials in alkali halides and their use in simulations of the molten salts

Cited by 636 publications

References 125 publications

Secondary and tertiary structures involving chondroitin and chondroitin sulphates in solution, investigated by rotary shadowing/electron microscopy and computer simulation

Secondary and tertiary structures involving chondroitin and chondroitin sulphates in solution, investigated by rotary shadowing/electron microscopy and computer simulation

Design and Implementation of the Delft Molecular-Dynamics Processor

The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

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