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Part 1: Document Description
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Citation |
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Title: |
Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions' |
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Identification Number: |
doi:10.18419/darus-1170 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2021-02-10 |
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Version: |
1 |
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Bibliographic Citation: |
Kraus, Hamzeh, 2021, "Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions'", https://doi.org/10.18419/darus-1170, DaRUS, V1 |
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Citation |
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Title: |
Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions' |
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Identification Number: |
doi:10.18419/darus-1170 |
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Authoring Entity: |
Kraus, Hamzeh (Universität Stuttgart) |
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Grant Number: |
358283783 - SFB 1333 |
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Distributor: |
DaRUS |
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Access Authority: |
Kraus, Hamzeh |
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Access Authority: |
Hansen, Niels |
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Depositor: |
Kraus, Hamzeh |
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Date of Deposit: |
2020-12-08 |
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Holdings Information: |
https://doi.org/10.18419/darus-1170 |
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Study Scope |
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Keywords: |
Chemistry, Computer and Information Science |
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Abstract: |
This dataset contains Jupiter Notebooks and the necessary structure files needed for generating the pore systems discussed in the related publication. Additionally, high-resolution figures discussed in the paper are added. |
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Kind of Data: |
Supporting python scripts for generating pore structures for simulation. |
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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: |
Kraus, Hamzeh; Rybka, Julia; Alexandra, Höltzel; Trebel, Nicole; Tallarek, Ulrich; Hansen, Niels (2021): PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions. In: Molecular Simulation. |
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Identification Number: |
10.1080/08927022.2020.1871478 |
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Bibliographic Citation: |
Kraus, Hamzeh; Rybka, Julia; Alexandra, Höltzel; Trebel, Nicole; Tallarek, Ulrich; Hansen, Niels (2021): PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions. In: Molecular Simulation. |
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Citation |
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Title: |
Kraus, Hamzeh; Hansen, Niels (2020). PoreMS: 0.2.0 (Version v0.2.0). In: Zenodo. |
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Identification Number: |
10.5281/zenodo.3984865 |
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Bibliographic Citation: |
Kraus, Hamzeh; Hansen, Niels (2020). PoreMS: 0.2.0 (Version v0.2.0). In: Zenodo. |
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Label: |
fig_1.pdf |
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Text: |
Building block of beta-cristobalite viewed (a) from the xy-plane, (b) from the zy-plane and (c) from the xz-plane. Si and O atoms are coloured yellow and red, respectively. |
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Notes: |
application/pdf |
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Label: |
fig_2.pdf |
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Text: |
Cylindrical RPLC mesopore model generated with PoreMS. (a) Side view of the simulation box indicating the length of the central silica block and the solvent reservoirs. (b) and (c) Front and side view, respectively, of the pierced silica block containing the 9nm diameter pore. The chemistry of the exterior surface is based on the (111) face of beta-cristobalite silica. Exterior planar and interior curved surface are covered with the bonded phase consisting of C18 chains as the main ligand and TMS groups for endcapping. Bonded-phase groups are randomly distributed on the silica surface. Ligand and endcapping densities, residual surface hydroxylation. Colour code: Si, yellow lines; O, red lines; C18 chains, blue; TMS groups, magenta; residual surface silanol groups, yellow. |
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Notes: |
application/pdf |
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Label: |
fig_3.pdf |
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Text: |
Functionalization at the interior (a,b) and exterior surface (c) of the generated cylindrical silica pore model for heterogeneous catalysis. (a) Ruthenium catalyst, (b) dimethoxydimethylsilyl (DMDMS) group, (c) trimethylsilyl (TMS) group. |
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Notes: |
application/pdf |
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Label: |
fig_4.pdf |
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Text: |
Cylindrical catalytic mesopore model generated with PoreMS. (a) Side view of the simulation box indicating the length of the central silica block and the solvent reservoirs. (b) and (c) Front and side view, respectively, of the pierced silica block containing the 4.8nm pore. The chemistry of the exterior surface is based on the (111) face of beta-cristobalite silica. The exterior planar and interior curved surfaces are covered with randomly distributed TMS and DMDMS groups, respectively. Two organometallic catalyst groups are attached to the interior surface in point symmetry with respect to the pore centre. Colour code: Si atoms, yellow line; O atoms, red line; DMDMS groups, blue; TMS groups, magenta; catalyst, purple; residual surface silanol groups, yellow. |
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Notes: |
application/pdf |
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Label: |
cata.ipynb |
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Text: |
Jupyter Notebook for generating a cylindrical catalytic mesopore model. |
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Notes: |
application/x-ipynb+json |
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Label: |
rplc.ipynb |
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Text: |
Jupyter Notebook for generating a cylindrical RPLC mesopore model. |
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Notes: |
application/x-ipynb+json |
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Label: |
c18.gro |
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Text: |
C18 chain structure in gro format placed on the RPLC mesopore model. |
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Notes: |
application/octet-stream |
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Label: |
catabm.gro |
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Text: |
Ruthenium catalyst structure in gro format placed on the catalytic mesopore model. |
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Notes: |
application/octet-stream |