Polymers near Metal Surfaces: Selective Adsorption and Global Conformations

Site, Luigi Delle; Abrams, Cameron F.; Alavi, Ali; Kremer, Kurt

doi:10.1103/physrevlett.89.156103

Cited by 125 publications

(157 citation statements)

References 16 publications

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“…The behavior of these molecules on Si is very different to their behavior on Ni͑111͒. The adsorption energy of benzene on Ni is 1.05 eV, 34 which is comparable to the adsorption energy of benzene on Si. The geometries, however, are very different, and on the Ni surface the benzene remains relatively undistorted at a center-of-mass distance of 2 Å.…”

Section: Summary and Discussionmentioning

confidence: 90%

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Polymer adhesion: First-principles calculations of the adsorption of organic molecules onto Si surfaces

Johnston

Nieminen

2007

Phys. Rev. B

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The structures and energetics of organic molecules adsorbed onto clean and H-passivated Si͑001͒-͑2 ϫ 1͒ surfaces have been calculated using density functional theory. For benzene adsorbed on the clean Si surface the tight-bridge structure was found to be stable and the butterfly structure metastable. Both carbonic acid, H 2 CO 3 , and propane, C 3 H 8 , dissociate on contact with the surface. Passivation of the Si surface with H atoms has a dramatic effect on the surface properties. The passivated surface is very inert and the binding energy of all the molecules is very weak.

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Section: Summary and Discussionmentioning

confidence: 90%

“…34,35 The first-principles calculations showed that benzene binds strongly to the Ni surface but that carbonic acid and propane experience significant repulsion. The behavior of these molecules on Si is very different to their behavior on Ni͑111͒.…”

Section: Summary and Discussionmentioning

confidence: 99%

Polymer adhesion: First-principles calculations of the adsorption of organic molecules onto Si surfaces

Johnston

Nieminen

2007

Phys. Rev. B

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“…In the dualresolution modeling approach for studying the behavior of polymers near metal surfaces [22,23,24], for example, polymer chain ends that interact with the metal surface are represented partially atomistically while the remaining parts of the polymers, where lower resolution is adequate, are represented as bead-spring chains. However, the switching between different levels of resolution, i.e, the atomic and mesoscopic, is not allowed during the course of that MD simulation, and therefore the initial level of detail and thereby the number of degrees of freedom in the system remain unchanged.…”

Section: Introductionmentioning

confidence: 99%

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

Praprotnik

Site

Kremer

2005

The Journal of Chemical Physics

372

514

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We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.

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“…Most simulations of the organic molecules-metal surfaces interactions are from the ab initio calculation and density functional theory (DFT) [11][12][13][14], which developed the potentials for the molecules between metals, but they are limited in a rather small scale. By MD methods, Braun et al [15] simulated multi-peptides interacting with gold of 5 ns.…”

Section: Introductionmentioning

confidence: 99%

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Yang

Zhao

2007

Engineering Analysis with Boundary Elements

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Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and Au the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. r

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Polymers near Metal Surfaces: Selective Adsorption and Global Conformations

Cited by 125 publications

References 16 publications

Polymer adhesion: First-principles calculations of the adsorption of organic molecules onto Si surfaces

Polymer adhesion: First-principles calculations of the adsorption of organic molecules onto Si surfaces

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

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