Supplementary material for 'Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes' (doi:10.18419/darus-1752)

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Supplementary material for 'Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes'

doi:10.18419/darus-1752

DaRUS

2021-09-14

1

Kraus, Hamzeh; Hansen, Niels, 2021, "Supplementary material for 'Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes'", https://doi.org/10.18419/darus-1752, DaRUS, V1

Supplementary material for 'Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes'

doi:10.18419/darus-1752

Kraus, Hamzeh (Universität Stuttgart)

Hansen, Niels (Universität Stuttgart)

358283783 - SFB 1333

DaRUS

Kraus, Hamzeh

Hansen, Niels

Kraus, Hamzeh

2021-03-16

https://doi.org/10.18419/darus-1752

Chemistry, Computer and Information Science, Molecular Dynamics Simulation, Molybdenum, Confinement, Olefin Metathesis

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory Mdp) are provided for four simulations - a 2.5 nm pore with one catalyst molecule, a 2.5 nm pore with two catalyst molecules, a 5 nm pore, and a 6 nm pore, all without surface functionalization. The simulation is divided into three steps, an energy-minimization, an NVT equilibration, and an NVT production simulation run. Provided structure files are of an already equilibrated system. Object files are supplied which can be used to load the generated pores into PoreMS for later alteration and analysis. Additionally, short movies can be viewed for the different systems. In the results section, figures from the supporting information are shown.

Input files for molecular dynamics simulations with GROMACS.

Ziegler, Felix; Kraus, Hamzeh; Benedikter, Mathis J.; Wang, Dongren; Bruckner, Johanna R.; Nowakowski, Michal; Weißer, Kilian; Solodenko, Helena; Schmitz, Guido; Bauer, Matthias; Hansen, Niels; Buchmeiser, Michael R. (2021): Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes. In: ACS Catalysis.

10.1021/acscatal.1c03057

Ziegler, Felix; Kraus, Hamzeh; Benedikter, Mathis J.; Wang, Dongren; Bruckner, Johanna R.; Nowakowski, Michal; Weißer, Kilian; Solodenko, Helena; Schmitz, Guido; Bauer, Matthias; Hansen, Niels; Buchmeiser, Michael R. (2021): Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes. In: ACS Catalysis.

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index_2.5nm_1cat.ndx

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Index file of the simulation box of the 2.5nm pore with 1 catalyst molecule in .ndx format.

application/octet-stream

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index_2.5nm_2cat.ndx

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Index file of the simulation box of the 2.5nm pore with 2 catalyst molecules in .ndx format.

application/octet-stream

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index_5nm.ndx

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Index file of the simulation box of the 5nm pore in .ndx format.

application/octet-stream

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index_6nm.ndx

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Index file of the simulation box of the 6nm pore in .ndx format.

application/octet-stream

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min.mdp

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Simulation parameter file of the energy-minimization step in .mdp format.

application/octet-stream

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nvt.mdp

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Simulation parameter file of the equilibration step in .mdp format.

application/octet-stream

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run.mdp

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Simulation parameter file of the production step in .mdp format.

application/octet-stream

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pore_2.5nm_1cat.pms

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PoreMS object file of the 2.5nm pore with 1 catalyst molecule containing all pore properties in pickle format protocol version 3.

application/x-tgif

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pore_2.5nm_2cat.pms

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PoreMS object file of the 2.5nm pore with 2 catalyst molecules containing all pore properties in pickle format protocol version 3.

application/x-tgif

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pore_5nm.pms

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PoreMS object file of the 5nm pore containing all pore properties in pickle format protocol version 3.

application/x-tgif

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pore_6nm.pms

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PoreMS object file of the 6nm pore containing all pore properties in pickle format protocol version 3.

application/x-tgif

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pore_system_2.5nm_1cat.pms

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PoreMS object file of the 2.5nm pore with 1 catalyst molecule containing all pore system properties in pickle format protocol version 3.

application/x-tgif

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pore_system_2.5nm_2cat.pms

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PoreMS object file of the 2.5nm pore with 2 catalyst molecules containing all pore system properties in pickle format protocol version 3.

application/x-tgif

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pore_system_5nm.pms

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PoreMS object file of the 5nm pore containing all pore system properties in pickle format protocol version 3.

application/x-tgif

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pore_system_6nm.pms

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PoreMS object file of the 6nm pore containing all pore system properties in pickle format protocol version 3.

application/x-tgif

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density_2.5.pdf

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Radial number density profiles of the carbonyl oxygen (red) and vinylic carbon (blue) in the substrate (solid lines) and product (dashed lines) as well as of ethene (yellow) in the 2.5 nm pores obtained from a 0.85 μs simulation in a model pore containing one catalyst in the center (a) or two catalysts close to the pore mouth (b). The shaded areas indicate the configurational space accessible by the boron atom (purple) of the anion, the molybdenum atom (blue) of the cation and the silanol oxygen (yellow).

application/pdf

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diffusion.pdf

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Radial dependence of the axial self-diffusion coefficient of substrate (red) and product molecules (green) in the 5 nm pore (solid lines) and the 6 nm pore (dashed lines). The radial distance r from the pore center (where r = 0) is normalized by the effective pore radius, representing the region accessible to the substrate and product molecules. The mean diffusion coefficients are 0.134 / 0.123 and 0.106 / 0.123*10-9 m²/s for the substrate / product molecules in the 5 nm and 6 nm pore, respectively.

application/pdf

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benzene.gro

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Cartesian coordinates of a single benzene molecule in .gro format.

application/octet-stream

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box_2.5nm_1cat.gro

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Cartesian coordinates of the simulation box of the 2.5nm pore with 1 catalyst molecule in .gro format.

application/octet-stream

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box_2.5nm_2cat.gro

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Cartesian coordinates of the simulation box of the 2.5nm pore with 2 catalyst molecules in .gro format.

application/octet-stream

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box_5nm.gro

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Cartesian coordinates of the simulation box of the 5nm pore in .gro format.

application/octet-stream

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box_6nm.gro

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Cartesian coordinates of the simulation box of the 6nm pore in .gro format.

application/octet-stream

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ethene.gro

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Cartesian coordinates of a single ethene molecule in .gro format.

application/octet-stream

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mo3_anion.gro

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Cartesian coordinates of a molybdenum catalyst anion molecule in .gro format. In the manuscript, this structure is referred to as Mo1.

application/octet-stream

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mo3_kation.gro

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Cartesian coordinates of a molybdenum catalyst cation surface molecule in .gro format. In the manuscript, this structure is referred to as Mo1.

application/octet-stream

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product5.gro

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Cartesian coordinates of a single product molecule in .gro format. In the manuscript, this structure is referred to as product 8.

application/octet-stream

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substrate5.gro

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Cartesian coordinates of a single substrate molecule in .gro format. In the manuscript, this structure is referred to as substrate 4.

application/octet-stream

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benzene.itp

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Topology file of a benzene molecule in .itp format.

application/vnd.shana.informed.formtemplate

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ethene.itp

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Topology file of an ethene molecule in .itp format.

application/vnd.shana.informed.formtemplate

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grid.itp

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

application/vnd.shana.informed.formtemplate

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mo3_anion.itp

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Topology file of the molybdenum catalyst anion molecule in .itp format. In the manuscript, this structure is referred to as Mo1.

application/vnd.shana.informed.formtemplate

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mo3_kation.itp

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Topology file of the molybdenum catalyst cation surface molecule in .itp format. In the manuscript, this structure is referred to as Mo1.

application/vnd.shana.informed.formtemplate

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product5.itp

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Topology file of a product molecule in .itp format. In the manuscript, this structure is referred to as product 8.

application/vnd.shana.informed.formtemplate

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slo.itp

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Topology file of a deactivated silanol surface molecule (single and geminal) in .itp format.

application/vnd.shana.informed.formtemplate

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substrate5.itp

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Topology file of a substrate molecule in .itp format. In the manuscript, this structure is referred to as substrate 4.

application/vnd.shana.informed.formtemplate

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tms.itp

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Topology file of a TMS surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

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tmsg.itp

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

application/vnd.shana.informed.formtemplate

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topol_2.5nm_1cat.top

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Main topology file of the simulation box of the 2.5nm pore with 1 catalyst molecule in .top format.

application/octet-stream

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topol_2.5nm_2cat.top

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Main topology file of the simulation box of the 2.5nm pore with 2 catalyst molecules in .top format.

application/octet-stream

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topol_5nm.top

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Main topology file of the simulation box of the 5nm pore in .top format.

application/octet-stream

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topol_6nm.top

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Main topology file of the simulation box of the 6nm pore in .top format.

application/octet-stream

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video_2.5nm_1cat.mp4

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Visualization 2.5nm pore with 1 catalyst molecule of an 850ns long simulation - 1s in the video corresponds to 12 ns simulation time.

video/mp4

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video_2.5nm_2cat.mp4

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Visualization 2.5nm pore with 2 catalyst molecules of an 850ns long simulation - 1s in the video corresponds to 12 ns simulation time.

video/mp4

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video_5nm.mp4

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Visualization 5nm pore of a 1mus long simulation - 1s in the video corresponds to 12 ns simulation time.

video/mp4

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video_6nm.mp4

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Visualization 6nm pore of a 1mus long simulation - 1s in the video corresponds to 12 ns simulation time.

video/mp4