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Part 1: Document Description
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Citation |
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Title: |
Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization' |
Identification Number: |
doi:10.18419/darus-477 |
Distributor: |
DaRUS |
Date of Distribution: |
2019-12-04 |
Version: |
2 |
Bibliographic Citation: |
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 |
Citation |
|
Title: |
Supplementary material for 'Olefin metathesis in confined geometries: a biomimetic approach towards selective macrocyclization' |
Identification Number: |
doi:10.18419/darus-477 |
Authoring Entity: |
Kraus, Hamzeh (Universität Stuttgart) |
Rybka, Julia (Philipps-Universität Marburg) |
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Grant Number: |
358283783 - SFB 1333 |
Grant Number: |
TA 268/11-1 |
Grant Number: |
TA 268/11-1 |
Distributor: |
DaRUS |
Access Authority: |
Kraus, Hamzeh |
Depositor: |
Kraus, Hamzeh |
Date of Deposit: |
2019-10-15 |
Holdings Information: |
https://doi.org/10.18419/darus-477 |
Study Scope |
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Keywords: |
Chemistry |
Abstract: |
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. |
Kind of Data: |
Input files for molecular dynamics simulations with GROMACS. |
Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
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. |
Identification Number: |
10.1021/jacs.9b08776 |
Bibliographic Citation: |
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 |
Notes: |
application/octet-stream |
Label: |
benzene.itp |
Text: |
Topology file of a benzene molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
box_modified.gro |
Text: |
Cartesian coordinates of the simulation box of the modified pore in .gro format |
Notes: |
application/octet-stream |
Label: |
box_unmodified.gro |
Text: |
Cartesian coordinates of the simulation box of the unmodified pore in .gro format |
Notes: |
application/octet-stream |
Label: |
catabm.gro |
Text: |
Cartesian coordinates of a catalyst surface molecule in .gro format |
Notes: |
application/octet-stream |
Label: |
catabm.itp |
Text: |
Topology file of a catalyst surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
catabmg.itp |
Text: |
Topology file of a geminal catalyst surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
dmdms.gro |
Text: |
Cartesian coordinates of a DMDMS surface molecule in .gro format |
Notes: |
application/octet-stream |
Label: |
dmdms.itp |
Text: |
Topology file of a DMDMS surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
dmdmsg.itp |
Text: |
Topology file of a geminal DMDMS surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
eductl.gro |
Text: |
Cartesian coordinates of a single substrate molecule in .gro format |
Notes: |
application/octet-stream |
Label: |
eductl.itp |
Text: |
Topology file of a Substrate molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
grid_modified.itp |
Text: |
Topology file of all used grid-molecules of the modified pore in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
grid_unmodified.itp |
Text: |
Topology file of all used grid-molecules of the unmodified pore in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
index_modified.ndx |
Text: |
Index file of the simulation box of the modified pore in .ndx format |
Notes: |
application/octet-stream |
Label: |
index_unmodified.ndx |
Text: |
Index file of the simulation box of the unmodified pore in .ndx format |
Notes: |
application/octet-stream |
Label: |
min.mdp |
Text: |
Simulation parameter file of the energy-minimization step in .mdp format |
Notes: |
application/octet-stream |
Label: |
nvt.mdp |
Text: |
Simulation parameter file of the equilibration step in .mdp format |
Notes: |
application/octet-stream |
Label: |
productmmc.gro |
Text: |
Cartesian coordinates of a single product molecule in .gro format |
Notes: |
application/octet-stream |
Label: |
productmmc.itp |
Text: |
Topology file of a Product molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
run.mdp |
Text: |
Simulation parameter file of the production step in .mdp format |
Notes: |
application/octet-stream |
Label: |
silyl.gro |
Text: |
Cartesian coordinates of a TMS surface molecule in .gro format |
Notes: |
application/octet-stream |
Label: |
silyl.itp |
Text: |
Topology file of a TMS surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
silylg.itp |
Text: |
Topology file of a geminal TMS surface molecule in .itp format |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
topol_modified.top |
Text: |
Main topology file of the simulation box of the modified pore in .top format |
Notes: |
application/octet-stream |
Label: |
topol_unmodified.top |
Text: |
Main topology file of the simulation box of the unmodified pore in .top format |
Notes: |
application/octet-stream |