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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.

Description

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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Files

File name Size Description
README.txt
MD5md5:4420d7ebe2531570fd578d12381c03a7
2.3 KiB README file detailing the content of all other files in detail.
check_gmol.py
MD5md5:062f1aeae1f005b2cdbb4e98c2afd151
2.3 KiB Python script demonstrating how to use the cell2mol module to import and extract information from the accompanying database.
8-Copper.tar.zip
MD5md5:bb537bfd4ed1f53cfddaea9189033afb
471.4 MiB Database of cell2mol cell objects containing Cu-containing unit cells.
7-Nickel.tar.zip
MD5md5:65a3009dd2086021ceb67f87691b2209
321.7 MiB Database of cell2mol cell objects containing Ni-containing unit cells.
6-Cobalt.tar.zip
MD5md5:91ca67ca07e54358f5f45c21c045dae4
240.3 MiB Database of cell2mol cell objects containing Co-containing unit cells.
5-Chromium.tar.zip
MD5md5:c6ac99b42df49980673e23ca93da713f
54.6 MiB Database of cell2mol cell objects containing Cr-containing unit cells.
4-Rhenium.tar.zip
MD5md5:30523799374c68b5b59d255d400479a2
66.5 MiB Database of cell2mol cell objects containing Re-containing unit cells.
3-Ruthenium.tar.zip
MD5md5:3663da5064d8efe38e3e8220fca3f2f6
180.6 MiB Database of cell2mol cell objects containing Ru-containing unit cells.
2-Manganese.tar.zip
MD5md5:70dd11a0a0bf9ef434ba88d10029737e
96.7 MiB Database of cell2mol cell objects containing Mn-containing unit cells.
1-Iron.tar.zip
MD5md5:ac0717456a8633227e9f1e6c53e02e1d
191.8 MiB Database of cell2mol cell objects containing Fe-containing unit cells.
T-TMCs.tar.zip
MD5md5:958c375933934ab05042f7466cb14646
397.4 MiB Database of cell2mol TM objects containing unique transition metal complexes.
L-Ligands.tar.zip
MD5md5:c72132628a592f17c5007010278f9efd
64.6 MiB Database of cell2mol ligand objects containing unique ligands.
O-Other.tar.zip
MD5md5:8a10a0c191968ae9b96a4c84312c6b5b
5.1 MiB Database of cell2mol molecule objects containing unique species found in unit cells.

License

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)

Keywords

MARVEL Experimental Crystal

Version history:

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