Supplementary material for 'Computational study of confinement effects in molecular heterogeneous catalysis' (doi:10.18419/darus-488)

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Supplementary material for 'Computational study of confinement effects in molecular heterogeneous catalysis'

doi:10.18419/darus-488

DaRUS

2022-01-11

1

Kraus, Hamzeh; Rybka, Julia; Hansen, Niels, 2022, "Supplementary material for 'Computational study of confinement effects in molecular heterogeneous catalysis'", https://doi.org/10.18419/darus-488, DaRUS, V1

Supplementary material for 'Computational study of confinement effects in molecular heterogeneous catalysis'

doi:10.18419/darus-488

Kraus, Hamzeh (Universität Stuttgart)

Rybka, Julia (Philipps-Universität Marburg)

Hansen, Niels (Universität Stuttgart)

358283783 - SFB 1333

TA 268/11-1

TA 268/11-1

DaRUS

Kraus, Hamzeh

Hansen, Niels

Kraus, Hamzeh

2019-11-06

https://doi.org/10.18419/darus-488

Chemistry, Computer and Information Science, Molecular Dynamics Simulation, Confinement, Olefin Metathesis, Alkene Metathesis

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication.<br> Structure, topology and simulation parameter-files are provided for six simulations - two pore sizes of 9nm and 6nm, each with simulations of pure substrate, pure product and a mixture of both, each with benzene as solute. Both pore-sizes are functionalized with epoxide groups on the inside and TMS groups on the outside surface. Furthermore each pore has two catalytic centers placed point-symmetrical towards each other.<br> The simulation is divided in three steps, an energy-minimization, an NVT equilibration and finally the NVT production simulation run.

Input files for molecular dynamics simulations with GROMACS.

Kraus H., Rybka J., Tallarek U., Hansen N. (2021) Computational Study of Confinement Effects in Molecular Heterogeneous Catalysis. In: Nagel W.E., Kröner D.H., Resch M.M. (eds) High Performance Computing in Science and Engineering '20. Springer, Cham.

10.1007/978-3-030-80602-6_7

Kraus H., Rybka J., Tallarek U., Hansen N. (2021) Computational Study of Confinement Effects in Molecular Heterogeneous Catalysis. In: Nagel W.E., Kröner D.H., Resch M.M. (eds) High Performance Computing in Science and Engineering '20. Springer, Cham.

Label:

min.mdp

Text:

Simulation parameter file of the energy-minimization step in .mdp format.

application/octet-stream

Label:

nvt.mdp

Text:

Simulation parameter file of the equilibration step in .mdp format.

application/octet-stream

Label:

run.mdp

Text:

Simulation parameter file of the production step in .mdp format.

application/octet-stream

Label:

index_6nm_mixture.ndx

Text:

Index file of the simulation box of the 6nm pore containing a mixture of substrate and product in .ndx format.

application/octet-stream

Label:

index_6nm_pure_product.ndx

Text:

Index file of the simulation box of the 6nm pore containing a pure product in .ndx format.

application/octet-stream

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index_6nm_pure_substrate.ndx

Text:

Index file of the simulation box of the 6nm pore containing pure substrate in .ndx format.

application/octet-stream

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index_9nm_mixture.ndx

Text:

Index file of the simulation box of the 9nm pore containing a mixture of substrate and product in .ndx format.

application/octet-stream

Label:

index_9nm_pure_product.ndx

Text:

Index file of the simulation box of the 9nm pore containing a pure product in .ndx format.

application/octet-stream

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index_9nm_pure_substrate.ndx

Text:

Index file of the simulation box of the 9nm pore containing pure substrate in .ndx format.

application/octet-stream

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benzene.gro

Text:

Cartesian coordinates of a single benzene molecule in .gro format.

application/octet-stream

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educt.gro

Text:

Cartesian coordinates of a single substrate molecule in .gro format.

application/octet-stream

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productmc.gro

Text:

Cartesian coordinates of a single product molecule in .gro format.

application/octet-stream

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box_6nm_mixture.gro

Text:

Cartesian coordinates of the simulation box of the 6 nm pore containing a mixture of substrate and product in .gro format.

application/octet-stream

Label:

box_6nm_pure_product.gro

Text:

Cartesian coordinates of the simulation box of the 6 nm pore containing pure product in .gro format.

application/octet-stream

Label:

box_6nm_pure_substrate.gro

Text:

Cartesian coordinates of the simulation box of the 6 nm pore containing pure substrate in .gro format.

application/octet-stream

Label:

box_9nm_mixture.gro

Text:

Cartesian coordinates of the simulation box of the 9 nm pore containing a mixture of substrate and product in .gro format.

application/octet-stream

Label:

box_9nm_pure_product.gro

Text:

Cartesian coordinates of the simulation box of the 9 nm pore containing pure product in .gro format.

application/octet-stream

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box_9nm_pure_substrate.gro

Text:

Cartesian coordinates of the simulation box of the 9 nm pore containing pure substrate in .gro format.

application/octet-stream

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catabm.gro

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Cartesian coordinates of a catalyst surface molecule in .gro format.

application/octet-stream

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Catalyst.png

Text:

Catalyst structure overview.

image/png

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grid_6nm.itp

Text:

Topology file of all used grid-molecules of the 6nm pore in .itp format.

application/vnd.shana.informed.formtemplate

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grid_9nm.itp

Text:

Topology file of all used grid-molecules of the 9nm pore in .itp format.

application/vnd.shana.informed.formtemplate

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benzene.itp

Text:

Topology file of a benzene molecule in .itp format.

application/vnd.shana.informed.formtemplate

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educt.itp

Text:

Topology file of a Substrate molecule in .itp format.

application/vnd.shana.informed.formtemplate

Label:

productmc.itp

Text:

Topology file of a Product molecule in .itp format.

application/vnd.shana.informed.formtemplate

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topol_6nm_mixture.top

Text:

Main topology file of the simulation box of the 6nm pore containing a mixture of substrate and product in .top format.

application/octet-stream

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topol_6nm_pure_product.top

Text:

Main topology file of the simulation box of the 6nm pore containing pure product in .top format.

application/octet-stream

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topol_6nm_pure_substrate.top

Text:

Main topology file of the simulation box of the 6nm pore containing pure substrate in .top format.

application/octet-stream

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topol_9nm_mixture.top

Text:

Main topology file of the simulation box of the 9nm pore containing a mixture of substrate and product in .top format.

application/octet-stream

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topol_9nm_pure_product.top

Text:

Main topology file of the simulation box of the 9nm pore containing pure product in .top format.

application/octet-stream

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topol_9nm_pure_substrate.top

Text:

Main topology file of the simulation box of the 9nm pore containing pure substrate in .top format.

application/octet-stream

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cata.itp

Text:

Topology file of a catalyst surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

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catag.itp

Text:

Topology file of a geminal catalyst surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

Label:

epoxi.itp

Text:

Topology file of an epoxide-group surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

Label:

epoxig.itp

Text:

Topology file of a geminal epoxide-group surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

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silyl.itp

Text:

Topology file of a TMS surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

Label:

silylg.itp

Text:

Topology file of a geminal TMS surface molecule in .itp format.

application/vnd.shana.informed.formtemplate