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Unit Cell to Molecule Interpretation

About

cell2mol interprets crystallographic data and retrieves the connectivity, total charge, and spin of molecular complexes and their components including the oxidation state (OS) of metal atoms and the charge of ligands. This interface interprets any .cif or .info file (created with cif2cell), and generates an output file containing the charge, spin, and the xyz coordinates of any molecular component isolated to make it ready for quantum chemical computations.

Instructions

  • Upload the input file, select its corresponding file format, and press Calculate my structure .

  • If the input file was imported and interpreted successfully, you will be able to view basic structure information under the Structure information tab. Press Run cell2mol and wait. The waiting time depends on the structure size and complexity.

  • If the structure was analyzed successfully, you will be able to view its analysis under the Structure analysis tab. You can download the cell object in .gmol format by pressing Download cell (.gmol) . Press View structure to view, interact and download specific molecules or complexes.

  • By double-clicking on the 3d structure you will be able to zoom in, zoom out, and rotate the model. On the left column, you can select which molecular components (ligands, molecules, or metals) are displayed. Below the 3d structure, you will find a toggle button to select if you want to view the cell or one mol (molecule or complex). When mol is selected, you can use the dropdown menu to choose one to visualize. The xyz file of the selected mol containing charge, spin, and cartesian coordinates (ready for quantum chemical calculations), can be downloaded by clicking Download selected mol (.xyz) .

If one of the steps fail, please verify your input file or try to use a different cif2cell version if using info file as input.

Acknowledgements

This tool is based on the cell2mol package by LCMD at EPFL.

You can find a full list of contributors in the README of the GitHub repository.

We acknowledge financial support by the MARVEL NCCR, the swissuniversities P-5 project "Materials Cloud" for the implementation of this tool.

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How to cite

Vela, S.; Laplaza, R.; Cho, Y.; Corminboeuf, C. cell2mol: encoding chemistry to interpret crystallographic data. Npj Comput. Mater. 2022. 8. 188; doi: 10.1038/s41524-022-00874-9

Note: if you want to use the code on your computer, you can download the cell2mol python library from the cell2mol GitHub repository . You can also find pre-built Docker images for this web app on GitHub .