Evaluation of molecular mechanics calculated binding energies for isolated and monolayer organic molecules on graphite

Rybolt, Thomas R.; Wells, Christina E.; Sisson, Charles R.; Black, Claire B.; Ziegler, Katherine A.

doi:10.1016/j.jcis.2007.05.083

Cited by 21 publications

(29 citation statements)

References 37 publications

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“…In calculations for graphite 90% or more of the van der Waals (vdW) interaction is due to the first layer, 9% or less due to the second layer and only 1% or less due to the third layer [11]. Molecular energy calculated from molecular mechanics is a sum of covalent and noncovalent energies.…”

Section: Theorymentioning

confidence: 99%

“…MM2 parameters have been used to estimate the binding energies of organic molecules on carbon surfaces [11] [12] [13].…”

Section: Introductionmentioning

confidence: 99%

“…TPD experiments involve multilayer or monolayer desorption and include molecule-molecule interactions [11]. However, many GSC determinations are based on low coverage, Henry's law adsorption for isolated molecule-surface interactions.…”

Section: Introductionmentioning

confidence: 99%

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Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

Rybolt¹,

Black²

2017

Graphene

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Two-dimensional molecular recognition studies of the six polyaromatic hydrocarbons that can be formed from the combination of four benzene rings: tetracene, pyrene, 1,2-benzanthracene, 3,4-benzphenanthrene, triphenylene, and chrysene were explored for each of these six molecules interacting with six different graphene layer site-specific nanopores. Computational studies were done for the gas phase adsorption on single layer graphene, bilayer graphene, and six molecule-specific graphene bilayer nanopores. Molecular mechanics MM2 parameters have been shown previously to provide good comparisons to experimental adsorption energies for aromatic hydrocarbons adsorption on graphitic surfaces. These binding energies are dominated by van der Waals forces. Just as a jigsaw puzzle hole can accommodate only a specific piece, two-dimensional shape specific sites were created in the top layer of a graphene bilayer to match each one of the six adsorbate molecules. The purpose of this study was to examine the molecular recognition possibilities of site specific adsorption in these simple two-dimensional nanopores based on dispersion forces and molecular shape. For example, triphenylene has a calculated surface binding energy of 24.5 kcal/mol on the graphene bilayer and 30.2 kcal/mol in its own site specific pore. The interaction energy of this molecule in the other five sites ranged from 17.6 to 23.8 kcal/mol. All the molecules tetracene, pyrene, 1,2-benzanthracene, triphenylene and chrysene had higher binding energies in their matched molecule bilayer sites than on either single or double layer graphene. In addition, each one of these five molecules had a stronger binding in their own shape specific (puzzle-ene) site than any of the other molecular sites. The results suggest that two-dimensional molecular recognition based on shape specific pores may allow selectivity useful for applications such as sensors, separations, nanofabrication, or information storage.

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Section: Theorymentioning

confidence: 99%

“…MM2 parameters have been used to estimate the binding energies of organic molecules on carbon surfaces [11] [12] [13].…”

Section: Introductionmentioning

confidence: 99%

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Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

Rybolt¹,

Black²

2017

Graphene

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“…Note that a high binding energy indicates high adhesive strength between the polymer and the calcite surface. 48,49 The binding energies between calcite and the polymer were calculated from the COMPASS force field, the results of which are listed in Table 2.…”

Section: 4143-47mentioning

confidence: 99%

A Novel Approach to Controlling CaCO₃Crystalline Assembly by Changing the Concentration of Poly(aspartic acid)

Zhou¹,

Gao²,

Hwang³

et al. 2011

Bulletin of the Korean Chemical Society

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CaCO 3 crystalline structures having novel assemblies were in situ fabricated as analogs of naturally occurring proteins and polysaccharides for biomineralization. The calcite crystal was mineralized in a poly(vinyl alcohol)-Ca 2+ complex film immersed in a Na 2 CO 3 solution containing poly(aspartic acid). The morphology and size of the CaCO 3 crystals were tuned by varying the concentration of poly(aspartic acid). The mechanisms of their nucleation orientation and formation were investigated experimentally and through molecular dynamics (MD) simulations in order to obtain a better understanding of the interactions between the polymers and the crystal at the molecular level. Both the MD results and experimental results indicate that the interaction between PVA and calcite mainly depends on the concentration of the polymer. The novel approach proposed herein for the fabrication of inorganic crystalline assembly structures can be used to fabricate precise crystalline structures.

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“…These interactions may attract or repel and along with other factors, such as bond distance, bond angle, and torsion angle, can affect the most stable dihedral angle. Although not optimized for adsorption interactions, the standard augmented MM2 parameters developed by Allinger [3,4] have been found to be quite useful in prior molecule-surface binding energy studies [5][6][7] that examined the attraction of organic molecules to various carbon surfaces. VDW forces dominate the adsorption of neutral molecules on a carbon surface.…”

Section: Introductionmentioning

confidence: 99%

Binding energies for alkane molecules on a carbon surface from gas–solid chromatography and molecular mechanics

Rybolt

Wells

Thomas

et al. 2008

Journal of Colloid and Interface Science

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Evaluation of molecular mechanics calculated binding energies for isolated and monolayer organic molecules on graphite

Cited by 21 publications

References 37 publications

Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

A Novel Approach to Controlling CaCO₃Crystalline Assembly by Changing the Concentration of Poly(aspartic acid)

Binding energies for alkane molecules on a carbon surface from gas–solid chromatography and molecular mechanics

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Evaluation of molecular mechanics calculated binding energies for isolated and monolayer organic molecules on graphite

Cited by 21 publications

References 37 publications

Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

Polycyclic Aromatic Hydrocarbon Molecule-Surface Binding Energies in Site Specific Graphene Bilayer Nanopores: A Puzzle-ene Force Field Calculation

A Novel Approach to Controlling CaCO3Crystalline Assembly by Changing the Concentration of Poly(aspartic acid)

Binding energies for alkane molecules on a carbon surface from gas–solid chromatography and molecular mechanics

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Product

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A Novel Approach to Controlling CaCO₃Crystalline Assembly by Changing the Concentration of Poly(aspartic acid)