Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization' (doi:10.18419/darus-477)

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Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization'

doi:10.18419/darus-477

DaRUS

2019-12-04

2

Kraus, Hamzeh; Rybka, Julia, 2019, "Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization'", https://doi.org/10.18419/darus-477, DaRUS, V2

Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization'

doi:10.18419/darus-477

Kraus, Hamzeh (Universität Stuttgart)

Rybka, Julia (Philipps-Universität Marburg)

358283783 - SFB 1333

TA 268/11-1

TA 268/11-1

DaRUS

Kraus, Hamzeh

Kraus, Hamzeh

2019-10-15

https://doi.org/10.18419/darus-477

Chemistry

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology and simulation parameter-files are provided for two simulations - an unmodified pore with a silanol surface and a modified pore with an unpolar DMDMS surface. Furthermore each pore has two catalytic centers placed point-symmetrical towards each other. 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.

Ziegler, Felix; Teske, Johannes; Elser, Iris; Dyballa, Michael; Frey, Wolfgang; Kraus, Hamzeh; Hansen, Niels; Rybka, Julia; Tallarek, Ulrich; Buchmeiser, Michael R (2019): Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization. In: Journal of the American Chemical Society.

10.1021/jacs.9b08776

Ziegler, Felix; Teske, Johannes; Elser, Iris; Dyballa, Michael; Frey, Wolfgang; Kraus, Hamzeh; Hansen, Niels; Rybka, Julia; Tallarek, Ulrich; Buchmeiser, Michael R (2019): Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization. In: Journal of the American Chemical Society.

Label:

benzene.gro

Text:

Cartesian coordinates of a single benzene molecule in .gro format

application/octet-stream

Label:

benzene.itp

Text:

Topology file of a benzene molecule in .itp format

application/vnd.shana.informed.formtemplate

Label:

box_modified.gro

Text:

Cartesian coordinates of the simulation box of the modified pore in .gro format

application/octet-stream

Label:

box_unmodified.gro

Text:

Cartesian coordinates of the simulation box of the unmodified pore in .gro format

application/octet-stream

Label:

catabm.gro

Text:

Cartesian coordinates of a catalyst surface molecule in .gro format

application/octet-stream

Label:

catabm.itp

Text:

Topology file of a catalyst surface molecule in .itp format

application/vnd.shana.informed.formtemplate

Label:

catabmg.itp

Text:

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

application/vnd.shana.informed.formtemplate

Label:

dmdms.gro

Text:

Cartesian coordinates of a DMDMS surface molecule in .gro format

application/octet-stream

Label:

dmdms.itp

Text:

Topology file of a DMDMS surface molecule in .itp format

application/vnd.shana.informed.formtemplate

Label:

dmdmsg.itp

Text:

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

application/vnd.shana.informed.formtemplate

Label:

eductl.gro

Text:

Cartesian coordinates of a single substrate molecule in .gro format

application/octet-stream

Label:

eductl.itp

Text:

Topology file of a Substrate molecule in .itp format

application/vnd.shana.informed.formtemplate

Label:

grid_modified.itp

Text:

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

application/vnd.shana.informed.formtemplate

Label:

grid_unmodified.itp

Text:

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

application/vnd.shana.informed.formtemplate

Label:

index_modified.ndx

Text:

Index file of the simulation box of the modified pore in .ndx format

application/octet-stream

Label:

index_unmodified.ndx

Text:

Index file of the simulation box of the unmodified pore in .ndx format

application/octet-stream

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:

productmmc.gro

Text:

Cartesian coordinates of a single product molecule in .gro format

application/octet-stream

Label:

productmmc.itp

Text:

Topology file of a Product molecule in .itp format

application/vnd.shana.informed.formtemplate

Label:

run.mdp

Text:

Simulation parameter file of the production step in .mdp format

application/octet-stream

Label:

silyl.gro

Text:

Cartesian coordinates of a TMS surface molecule in .gro format

application/octet-stream

Label:

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

Label:

topol_modified.top

Text:

Main topology file of the simulation box of the modified pore in .top format

application/octet-stream

Label:

topol_unmodified.top

Text:

Main topology file of the simulation box of the unmodified pore in .top format

application/octet-stream