This dataset contains the computational files supporting the study Single atom iron catalyses CS hydrogenation on amorphous silica. The data document the reaction mechanism for sequential CS hydrogenation by H₂ on a single Fe⁰ site supported on amorphous silica, investigated using periodic density functional theory, climbing-image nudged elastic band calculations, vibrational analysis, binding-energy calculations, and kinetic modelling. The study shows that CS binds strongly to the supported Fe centre, that the Fe–silica interface assists H₂ activation, and that hydrogenation to surface-bound H₂CS is kinetically accessible at low temperature, whereas further hydrogenation toward CH₃SH is strongly hindered by a much higher barrier. The supplementary calculations include relative energies for intermediates and transition states, together with Arrhenius plots for the elementary reaction steps. These files are provided to enable transparency, reproducibility, and reuse of the computational results reported in the associated article and supplementary information.
METHODOLOGICAL INFORMATION
- Description of methods used for collection-generation of data:
The dataset was generated through periodic electronic-structure calculations on a single-atom Fe0 site supported on amorphous silica (Fe0@SiO2). Geometry optimizations, reaction-path calculations, and vibrational analyses were performed mainly with CP2K under periodic boundary conditions. Transition states were investigated using climbing-image nudged elastic band (CI-NEB) calculations. Energetic refinement and part of the binding-energy analysis were carried out with CRYSTAL17. The deposited files correspond to optimized stationary points, reaction paths, vibrational calculations, single-point calculations, and adsorption/binding-energy workflows associated with the hydrogenation sequence CS -> HCS -> H2CS -> CH3S -> CH3SH.
Relevant methodological references:
Kuhne, T. D., Iannuzzi, M., Del Ben, M., Rybkin, V. V., et al. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J. Chem. Phys. 2020, 152, 194103.
VandeVondele, J., Krack, M., Mohamed, F., Parrinello, M., et al. Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Comput. Phys. Commun. 2005, 167, 103-128.
Goedecker, S., Teter, M. Separable dual-space Gaussian pseudopotentials. Phys. Rev. B 1996, 54, 1703-1710.
Lippert, G., Hutter, J., Parrinello, M. A hybrid Gaussian and plane wave density functional scheme. Mol. Phys. 1997, 92, 477-488.
Zarkevich, N. A., Johnson, D. D. Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes. J. Chem. Phys. 2015, 142, 24106.
Marcus, R. A. Unimolecular dissociations and free radical recombination reactions. J. Chem. Phys. 1952, 20, 359-364.
Eckart, C. The penetration of a potential barrier by electrons. Phys. Rev. 1930, 35, 1303-1309.
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Methods for processing the data:
The repository is deposited largely in its original research-working form. It preserves the original folder hierarchy and file names used during the project. Processed scientific results reported in the manuscript, such as relative energies, zero-point-energy-corrected values, and Arrhenius plots, were obtained by analysing these raw calculation files and are summarized in the associated manuscript and supporting information.
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Instrument- or software-specific information needed to interpret the data:
Main software used:
- CP2K: periodic DFT geometry optimizations, CI-NEB calculations, and vibrational calculations.
- CRYSTAL17: higher-level single-point refinements and part of the binding-energy/counterpoise analysis.
Additional scripts:
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Slurm submission scripts (.sh, .slm) used in the original HPC environment.
Interpretation of the dataset therefore requires familiarity with computational chemistry outputs from CP2K and CRYSTAL17, as well as general HPC job-submission workflows.
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Instruments, calibration and standards information:
Not applicable in the conventional experimental sense. The dataset was produced computationally. Electronic-structure methods, basis sets, dispersion corrections, and catalyst-model details are described in the associated manuscript and supplementary information.
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Environmental or experimental conditions:
The calculations were carried out in a Linux-based high-performance computing environment using batch submission through Slurm. Several files preserve original scheduler directives, absolute paths, and environment-specific information from the original HPC systems. These files are retained for provenance and transparency, but they may require modification before reuse on a different computing system.
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Quality-assurance procedures performed on the data:
Quality assurance was carried out through standard computational-chemistry validation procedures, including convergence of geometry optimizations, characterization of stationary points by vibrational analysis, identification of first-order saddle points for transition states, and energetic consistency checks between optimized structures, NEB calculations, and post-processed summaries. The associated manuscript and supplementary information contain the validated energetic and kinetic summaries derived from these files.
