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cell2mol: encoding chemistry to interpret crystallographic data

Sergi Vela1,2*, Ruben Laplaza1,3*, Yuri Cho1,2*, Clemence Corminboeuf1,2,3*

1 Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland

2 National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland

3 National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

* Corresponding authors emails: sergi.vela@ub.edu, ruben.laplazasolanas@epfl.ch, yuri.cho@epfl.ch, clemence.corminboeuf@epfl.ch
DOI10.24435/materialscloud:g5-5r [version v1]

Publication date: Apr 25, 2022

How to cite this record

Sergi Vela, Ruben Laplaza, Yuri Cho, Clemence Corminboeuf, cell2mol: encoding chemistry to interpret crystallographic data, Materials Cloud Archive 2022.55 (2022), doi: 10.24435/materialscloud:g5-5r.


The creation and maintenance of crystallographic data repositories is one of the greatest data-related achievements in chemistry. Platforms such as the Cambridge Structural Database host what is likely the most diverse collection of synthesizable molecules. If properly mined, they could be the basis for the large-scale exploration of new regions of the chemical space using quantum chemistry (QC). However, it is currently challenging to retrieve all the necessary information for QC based exclusively on the available structural data, especially for transition metal complexes. To solve this shortcoming, we present cell2mol, a software that interprets crystallographic data and retrieves the connectivity and total charge of molecules, including the oxidation state (OS) of metal atoms. We prove that cell2mol outperforms other popular methods at assigning the metal OS, while offering a much more comprehensive interpretation of the unit cell, and we make publicly available reliable QC-ready databases totaling 31k transition metal complexes and 13k ligands, encompassing incomparable chemical diversity. This record contains the aforementioned database of crystallographic structures after interpretation using the cell2mol software. The database spans 8 different transition metals (Fe, Mn, Ru, Re, Cr, Co, Ni, Cu; named from 1 to 8) and contains over 31000 different transition metal complexes and 13000 unique ligands, but also contains the interpreted contents of the entire unit cells in terms of discrete chemical species with well-defined charges and connectivities. Details can be found in the README.txt file and an exemplary script is provided for usage. The cell2mol code can be obtained in https://github.com/lcmd-epfl/cell2mol.

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File name Size Description
2.3 KiB README file detailing the content of all other files in detail.
2.3 KiB Python script demonstrating how to use the cell2mol module to import and extract information from the accompanying database.
471.4 MiB Database of cell2mol cell objects containing Cu-containing unit cells.
321.7 MiB Database of cell2mol cell objects containing Ni-containing unit cells.
240.3 MiB Database of cell2mol cell objects containing Co-containing unit cells.
54.6 MiB Database of cell2mol cell objects containing Cr-containing unit cells.
66.5 MiB Database of cell2mol cell objects containing Re-containing unit cells.
180.6 MiB Database of cell2mol cell objects containing Ru-containing unit cells.
96.7 MiB Database of cell2mol cell objects containing Mn-containing unit cells.
191.8 MiB Database of cell2mol cell objects containing Fe-containing unit cells.
397.4 MiB Database of cell2mol TM objects containing unique transition metal complexes.
64.6 MiB Database of cell2mol ligand objects containing unique ligands.
5.1 MiB Database of cell2mol molecule objects containing unique species found in unit cells.


Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Preprint (Manuscript currently in preparation for publication.)
S. Vela, R. Laplaza, Y. Cho, C. Corminboeuf. In Preparation (2022)


MARVEL Experimental Crystal

Version history:

2022.55 (version v1) [This version] Apr 25, 2022 DOI10.24435/materialscloud:g5-5r