Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions'doi:10.18419/darus-1170DaRUS2021-02-101Kraus, 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, V1Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions'doi:10.18419/darus-1170Kraus, Hamzeh358283783 - SFB 1333DaRUSKraus, HamzehHansen, NielsKraus, Hamzeh2020-12-08ChemistryComputer and Information ScienceThis 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.Supporting python scripts for generating pore structures for simulation.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.10.1080/08927022.2020.1871478Kraus, 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.Kraus, Hamzeh; Hansen, Niels (2020). PoreMS: 0.2.0 (Version v0.2.0). In: Zenodo.10.5281/zenodo.3984865Kraus, Hamzeh; Hansen, Niels (2020). PoreMS: 0.2.0 (Version v0.2.0). In: Zenodo.fig_1.pdfBuilding 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.application/pdffig_2.pdfCylindrical 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.application/pdffig_3.pdfFunctionalization 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.application/pdffig_4.pdfCylindrical 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.application/pdfcata.ipynbJupyter Notebook for generating a cylindrical catalytic mesopore model.application/x-ipynb+jsonrplc.ipynbJupyter Notebook for generating a cylindrical RPLC mesopore model.application/x-ipynb+jsonc18.groC18 chain structure in gro format placed on the RPLC mesopore model.application/octet-streamcatabm.groRuthenium catalyst structure in gro format placed on the catalytic mesopore model.application/octet-stream