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Hughes ZE, Tomásio SM, Walsh TR. Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. NANOSCALE 2014; 6:5438-5448. [PMID: 24722915 DOI: 10.1039/c4nr00468j] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
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.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, Australia.
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Kim HY, dos Santos MC, Cole MW. Wetting Transitions of Water on Graphite and Graphene. J Phys Chem A 2014; 118:8237-41. [DOI: 10.1021/jp501046r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hye-Young Kim
- Department
of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana 70402, United States
| | - Maria Cristina dos Santos
- Instituto
de Física, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
- Department
of Physics, Penn State University, 104 Davey Lab, University Park, Pennsylvania 16802, United States
| | - Milton W. Cole
- Department
of Physics, Penn State University, 104 Davey Lab, University Park, Pennsylvania 16802, United States
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Saha A, Raghavachari K. Dimers of Dimers (DOD): A New Fragment-Based Method Applied to Large Water Clusters. J Chem Theory Comput 2013; 10:58-67. [DOI: 10.1021/ct400472v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arjun Saha
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Simon A, Spiegelman F. Water clusters adsorbed on polycyclic aromatic hydrocarbons: Energetics and conformational dynamics. J Chem Phys 2013; 138:194309. [DOI: 10.1063/1.4805015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Heßelmann A. Assessment of a Nonlocal Correction Scheme to Semilocal Density Functional Theory Methods. J Chem Theory Comput 2012; 9:273-83. [DOI: 10.1021/ct300735g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl
für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr.
3, D-91058 Erlangen, Germany
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Kołaski M, Arunkumar CR, Kim KS. Aromatic Excimers: Ab Initio and TD-DFT Study. J Chem Theory Comput 2012; 9:847-56. [DOI: 10.1021/ct300350m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Kołaski
- Center for Superfunctional
Materials, Department of
Chemistry, Pohang University of Science and Technology, San 31, Hyojadong,
Namgu, 790-784 Pohang, Korea
| | - C. R. Arunkumar
- Center for Superfunctional
Materials, Department of
Chemistry, Pohang University of Science and Technology, San 31, Hyojadong,
Namgu, 790-784 Pohang, Korea
| | - Kwang S. Kim
- Center for Superfunctional
Materials, Department of
Chemistry, Pohang University of Science and Technology, San 31, Hyojadong,
Namgu, 790-784 Pohang, Korea
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Simon A, Rapacioli M, Mascetti J, Spiegelman F. Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2012; 14:6771-86. [PMID: 22495405 DOI: 10.1039/c2cp40321h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper reports structures, energetics, dynamics and spectroscopy of H2O and (H2O)2 systems adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). On-the-fly Born-Oppenheimer molecular dynamics simulations are performed for temperatures T varying from 10 to 300 K, on a potential energy surface obtained within the self-consistent-charge density-functional based tight-binding (SCC-DFTB) approach. Anharmonic infrared (IR) spectra are extracted from these simulations. We first benchmark the SCC-DFTB semi-empirical hamiltonian vs. DFT (Density Functional Theory) calculations that include dispersion, on (C6H6)(H2O)1,2 small complexes. We find that charge corrections and inclusion of dispersion contributions in DFTB are necessary to obtain consistent structures, energetics and IR spectra. Using this Hamiltonian, the structures, energetics and IR features of the low-energy isomers of (C24H12)(H2O)1,2 are found to be similar to the DFT ones, with evidence for a stabilizing edge-coordination. The temperature dependence of the motions of H2O and (H2O)2 on the surface of C24H12 is analysed, revealing ultra-fast periodic motion. The water dimer starts diffusing at a higher temperature than the water monomer (150 K vs. 10 K respectively), which appears to be consistent with the binding energies. Qualitative and quantitative analyses of the effects of T on the IR spectra are performed. Anharmonic factors in particular are derived and it is shown that they can be used as signatures for the presence of PAH-water complexes. Finally, this paper lays the foundations for the studies of larger (PAH)m(H2O)n clusters, that can be treated with the efficient computational approach benchmarked in this paper.
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Affiliation(s)
- Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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Kysilka J, Rubeš M, Grajciar L, Nachtigall P, Bludský O. Accurate Description of Argon and Water Adsorption on Surfaces of Graphene-Based Carbon Allotropes. J Phys Chem A 2011; 115:11387-93. [DOI: 10.1021/jp205330n] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Kysilka
- Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Miroslav Rubeš
- Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Lukáš Grajciar
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Petr Nachtigall
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Ota Bludský
- Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
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Jenness GR, Karalti O, Al-Saidi WA, Jordan KD. Evaluation of Theoretical Approaches for Describing the Interaction of Water with Linear Acenes. J Phys Chem A 2011; 115:5955-64. [DOI: 10.1021/jp110374b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glen R. Jenness
- Department of Chemistry and Center for Molecular and Materials Simulations and ‡Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ozan Karalti
- Department of Chemistry and Center for Molecular and Materials Simulations and ‡Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. A. Al-Saidi
- Department of Chemistry and Center for Molecular and Materials Simulations and ‡Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kenneth D. Jordan
- Department of Chemistry and Center for Molecular and Materials Simulations and ‡Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Jenness GR, Karalti O, Jordan KD. Benchmark calculations of water-acene interaction energies: Extrapolation to the water-graphene limit and assessment of dispersion-corrected DFT methods. Phys Chem Chem Phys 2010; 12:6375-81. [PMID: 20414490 DOI: 10.1039/c000988a] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a previous study (J. Phys. Chem. C, 2009, 113, 10242-10248) we used density functional theory based symmetry-adapted perturbation theory (DFT-SAPT) calculations of water interacting with benzene (C(6)H(6)), coronene (C(24)H(12)), and circumcoronene (C(54)H(18)) to estimate the interaction energy between a water molecule and a graphene sheet. The present study extends this earlier work by use of a more realistic geometry with the water molecule oriented perpendicular to the acene with both hydrogen atoms pointing down. We also include results for an intermediate C(48)H(18) acene. Extrapolation of the water-acene results gives a value of -3.0 +/- 0.15 kcal mol(-1) for the binding of a water molecule to graphene. Several popular dispersion-corrected DFT methods are applied to the water-acene systems and the resulting interacting energies are compared to results of the DFT-SAPT calculations in order to assess their performance.
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Affiliation(s)
- Glen R Jenness
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, PA 15260, USA
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