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Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model.
journal contributionposted on 2014-05-21, 00:00 authored by Zak Hughes, S M Tomásio, Tiffany WalshTiffany Walsh
To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.
Pagination5438 - 5448
PublisherRoyal Society of Chemistry
Publication classificationC Journal article; C1 Refereed article in a scholarly journal
Copyright notice2014, Royal Society of Chemistry
CategoriesNo categories selected
Science & TechnologyPhysical SciencesTechnologyChemistry, MultidisciplinaryNanoscience & NanotechnologyMaterials Science, MultidisciplinaryPhysics, AppliedChemistryScience & Technology - Other TopicsMaterials SciencePhysicsDISTRIBUTED MULTIPOLE ANALYSISDESIGNED SURFACTANT PEPTIDESWALL CARBON NANOTUBESWATER-ADSORPTIONFORCE-FIELDBIOMEDICAL APPLICATIONSELECTRONIC-PROPERTIESMOLECULAR SIMULATIONGRAPHENE SHEETSMETAL-SURFACES