Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions' (ICPSR doi:10.18419/darus-1170)

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Part 2: Study Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions'

Identification Number:

doi:10.18419/darus-1170

Distributor:

DaRUS

Date of Distribution:

2021-02-10

Version:

1

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

Study Description

Citation

Title:

Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions'

Identification Number:

doi:10.18419/darus-1170

Authoring Entity:

Kraus, Hamzeh (Universität Stuttgart)

Grant Number:

358283783 - SFB 1333

Distributor:

DaRUS

Access Authority:

Kraus, Hamzeh

Access Authority:

Hansen, Niels

Depositor:

Kraus, Hamzeh

Date of Deposit:

2020-12-08

Study Scope

Keywords:

Chemistry, Computer and Information Science

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.

Kind of Data:

Supporting python scripts for generating pore structures for simulation.

Methodology and Processing

Sources Statement

Data Access

Notes:

CC BY Waiver

Other Study Description Materials

Related Publications

Citation

Identification Number:

10.1080/08927022.2020.1871478

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.

Citation

Identification Number:

10.5281/zenodo.3984865

Bibliographic Citation:

Kraus, Hamzeh; Hansen, Niels (2020). PoreMS: 0.2.0 (Version v0.2.0). In: Zenodo.

Other Study-Related Materials

Label:

c18.gro

Text:

C18 chain structure in gro format placed on the RPLC mesopore model.

Notes:

application/octet-stream

Other Study-Related Materials

Label:

catabm.gro

Text:

Ruthenium catalyst structure in gro format placed on the catalytic mesopore model.

Notes:

application/octet-stream

Other Study-Related Materials

Label:

cata.ipynb

Text:

Jupyter Notebook for generating a cylindrical catalytic mesopore model.

Notes:

application/x-ipynb+json

Other Study-Related Materials

Label:

fig_1.pdf

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.

Notes:

application/pdf

Other Study-Related Materials

Label:

fig_2.pdf

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.

Notes:

application/pdf

Other Study-Related Materials

Label:

fig_3.pdf

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.

Notes:

application/pdf

Other Study-Related Materials

Label:

fig_4.pdf

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.

Notes:

application/pdf

Other Study-Related Materials

Label:

rplc.ipynb

Text:

Jupyter Notebook for generating a cylindrical RPLC mesopore model.

Notes:

application/x-ipynb+json