Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Hanwell, Marcus D.; Curtis, Donald; Lonie, David; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey

doi:10.1186/1758-2946-4-17

Cited by 7,336 publications

(5,105 citation statements)

References 40 publications

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“…All organic molecules used in this study were created using the Avogadro molecular editing suite. 27 In this study it has been assumed that the charge of the clay basal surface remains pH independent. Whilst it has recently been shown that the surface charge of kaolinite is pH dependent, it can be difficult to decouple how much of this effect is due to basal surfaces or clay edge sites.…”

Section: Model Setupmentioning

confidence: 99%

Wetting Effects and Molecular Adsorption at Hydrated Kaolinite Clay Mineral Surfaces

2016

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. (2016) 'Wetting e ects and molecular adsorption at hydrated kaolinite clay mineral surfaces.', Journal of physical chemistry C., 120 (21). pp. 11433-11449. Further information on publisher's website:https://doi.org/10.1021/acs.jpcc.6b00187 Publisher's copyright statement: This document is the Accepted Manuscript version of a Published Work that appeared in nal form in The Journal of Physical Chemistry C, copyright c American Chemical Society after peer review and technical editing by the publisher. To access the nal edited and published work see https://doi.org/10.1021/acs.jpcc.6b00187. Additional information:Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. do not adsorb to the silicate surface, yet adsorb to the hydroxyl surface through an anion exchange mechanism. Decanamine readily adsorbs to both silicate and hydroxyl surfaces, though the hydroxyl-amine interactions are mediated through water bridges.Once charged, the decanamine remains adsorbed to both surfaces, however, both interactions are ionically mediated, rather than through van der Waals and hydrogen bonds.Furthermore, protonated decanamine is observed to adsorb to the hydroxyl surface via anion bridges, a phenomenon that is typically associated with positively charged layered double hydroxides rather than negatively charged clay minerals.2

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Section: Model Setupmentioning

confidence: 99%

Wetting Effects and Molecular Adsorption at Hydrated Kaolinite Clay Mineral Surfaces

2016

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“…24,25 All organic molecules used in this study were created using the Avogadro molecular editing suite. 26 Periodically replicated supercells contained one layer of montmorillonite composed of 84 unit cells (12 x 7 x 1), dimensions of approximately 6 x 6 x 6 nm, and a d -spacing of approximately 5 nm. Montmorillonite structures initially occupied the region 0 < z < 0.7 nm in all models, and the clay position varied little over all timescales modelled.…”

Section: Model Constructionmentioning

confidence: 99%

Molecular Dynamic Simulations of Montmorillonite–Organic Interactions under Varying Salinity: An Insight into Enhanced Oil Recovery

et al. 2015

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Publisher's copyright statement:This document is the Accepted Manuscript version of a Published Work that appeared in nal form in Journal of physical chemistry C, copyright c 2015 American Chemical Society after peer review and technical editing by the publisher. To access the nal edited and published work see http://dx.doi.org/10.1021/acs.jpcc.5b00555Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractEnhanced oil recovery is becoming commonplace in order to maximise recovery from oilfields. One of these methods, low-salinity enhanced oil recovery (EOR) has shown promise, however the fundamental underlying chemistry requires elucidating. Here, three mechanisms proposed to account for low-salinity enhanced oil recovery in sandstone reservoirs are investigated using molecular dynamic simulations. The mechanisms probed are electric double layer expansion, multicomponent ionic exchange and pH effects arising at clay mineral surfaces. Simulations of smectite basal planes interacting with uncharged non-polar decane, uncharged polar decanoic acid and charged Nadecanoate model compounds are used to this end. Various salt concentrations of NaCl are modelled: 0% , 1% , 5% and 35% to determine the role of salinity upon the three separate mechanisms. Furthermore, the initial oil/water-wetness of the clay surface is modeled. Results show that electric double layer expansion is not able to fully explain the effects of low-salinity enhanced oil recovery. The pH surrounding a clays basal plane, and hence the protonation and charge of acid molecules is determined to be one of the dominant effects driving low-salinity EOR. Further, results present that the presence of calcium cations can drastically alter the oil wettability of a clay ⇤To whom correspondence should be addressed mineral surface. Replacing all divalent cations with monovalent cations through multicomponent cation exchange dramatically increases the water wettability of a clay surface, and will increase EOR.

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“…25 The initial distance between the feed piston and the upstream membrane was set to 5 nm in order to remove size effects in the feed. The distance between the permeate piston and the downstream membrane was initially set to 2 nm, and is expected to increase over the course of the simulation as feed water molecules move to the permeate side.…”

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confidence: 99%

Multilayer Nanoporous Graphene Membranes for Water Desalination

2016

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While single-layer nanoporous graphene (NPG) has shown promise as a reverse osmosis (RO) desalination membrane, multilayer graphene can be synthesized more economically than the single-layer material. In this work, we build upon the knowledge gained to date toward single-layer graphene to explore how multilayer NPG might serve as a RO membrane in water desalination using classical molecular dynamic simulations.We show that, while multilayer NPG exhibits similarly promising desalination properties to single-layer membranes, their separation performance can be designed by manipulating various configurational variables in the multilayer case. This work establishes an atomic-level understanding of the effects of additional NPG layers, layer separation, and pore alignment on desalination performance, providing useful guidelines for the design of multilayer NPG membranes.

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Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Cited by 7,336 publications

References 40 publications

Wetting Effects and Molecular Adsorption at Hydrated Kaolinite Clay Mineral Surfaces

Wetting Effects and Molecular Adsorption at Hydrated Kaolinite Clay Mineral Surfaces

Molecular Dynamic Simulations of Montmorillonite–Organic Interactions under Varying Salinity: An Insight into Enhanced Oil Recovery

Multilayer Nanoporous Graphene Membranes for Water Desalination

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