Molecular dynamics simulation of the dynamical behaviors of an aromatic carboxylic acid molecule with different conformations on a Au (111) surface

Ju, Shin‐Pon; Lee, Wen‐Jay; Chen, Hui-Chuan; Chang, Jee-Gong

doi:10.1063/1.2718485

Cited by 8 publications

(14 citation statements)

References 23 publications

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“…(9) and the potential of the substrate Eq. (10), which is at least two orders of magnitude smaller, it can be concluded that the right-hand sides of Eqs. (20) and (21) are at least two orders of magnitude larger than the right-hand side of Eq.…”

Section: Effective Interactionmentioning

confidence: 92%

“…The internal configuration of the molecules affects the interaction with the substrate and therefore transport (see, for instance, Refs. [9,10]). However, the deterministic internal DOF can also act as a source of noise [5,11] if their dynamics are sufficiently fast and chaotic.…”

Section: Introductionmentioning

confidence: 99%

“…The internal configuration of the molecules affects the interaction with the substrate, and therefore transport (see, for instance, Refs. [9,10]). However, the deterministic internal d.o.f.…”

Section: Introductionmentioning

confidence: 99%

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Internal degrees of freedom and transport of benzene on graphite

Wijn

2011

Phys. Rev. E

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In this paper, the chaotic internal degrees of freedom of a benzene molecule adsorbed on a graphite substrate, their interplay with thermal noise, and their effects on the diffusion and drift are investigated analytically by making use of the presence of two different time scales as well as by molecular-dynamics simulations. The effects of thermal noise are investigated, and it is found that noise does not significantly alter the dynamics of the internal degrees of freedom yet does affect the friction and diffusion of the center of mass. Qualitative and quantitative theoretical predictions for the friction and diffusion of the molecule on the substrate are made and are compared to molecular-dynamics simulations. Contributions to the friction and diffusion from the finite heat bath as well as the slow dynamics of the center of mass are formally identified. It is shown that the torsion in benzene, which dominates the nonlinear coupling, significantly affects the friction of the molecule on the surface. The results compare favorably with recent results from He-neutron spin echo experiments on this system. Based on the analytical and numerical results, some suggestions are made for experimental conditions under which the effects of internal degrees of freedom might be observable.

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Section: Effective Interactionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Internal degrees of freedom and transport of benzene on graphite

Wijn

2011

Phys. Rev. E

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“…In the case of diffusion of large molecules adsorbed on a surface, the internal dynamics of the molecules can be such a source of noise. Experimental [30] and numerical [16] evidence exists demonstrating that rotational and other internal degrees of freedom affect the diffusion. In some cases clusters of molecules have been shown to diffuse more rapidly than single particles [8,25].…”

Section: Introductionmentioning

confidence: 99%

Relating chaos to deterministic diffusion of a molecule adsorbed on a surface

Wijn

Fasolino

2009

J. Phys.: Condens. Matter

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Chaotic internal degrees of freedom of a molecule can act as noise and affect the diffusion of the molecule on a substrate. A separation of timescales between the fast internal dynamics and the slow motion of the centre of mass on the substrate makes it possible to directly link chaos to diffusion. We discuss the conditions under which this is possible, and show that in simple atomistic models with pair-wise harmonic potentials, strong chaos can arise through the geometry. Using molecular dynamics simulations, we demonstrate that a realistic model of benzene is indeed chaotic, and that the internal chaos affects the diffusion on a graphite substrate.

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“…Our previous study 41 used MD simulation to investigate the dynamic behavior of 1,3,5-triscarboxymethoxy benzene (TCMB, C 6 H 3 (OCH 2 COOH) 3 on an Au(111) substrate at a temperature of 50 K. This study determined that, when LAK geometry appeared between the aromatic ring and Au(111) surface atom, the TCMB molecule resided atop the Au atom for 1.1-1.3 ns, which is significantly longer than for other orientations of the TCMB on the Au(111). In addition, for S7 and PF8 on Au (111), the local Phe-Pro pair LAK structures were predicted to extend the time that S7 and PF8 remained stably on the Au(111) facet, enhancing the growth of the (111) facet for AuNP.…”

Section: )(Right) As Shown Inmentioning

confidence: 98%

Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches

Lin

et al. 2020

Sci Rep

Self Cite

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The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH 2 ) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH 2 ) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH 2 ) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.

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Molecular dynamics simulation of the dynamical behaviors of an aromatic carboxylic acid molecule with different conformations on a Au (111) surface

Cited by 8 publications

References 23 publications

Internal degrees of freedom and transport of benzene on graphite

Internal degrees of freedom and transport of benzene on graphite

Relating chaos to deterministic diffusion of a molecule adsorbed on a surface

Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches

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