Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Nanomaterials - Tập 10 Số 12 - Trang 2493
Iseult Lynch1, Antreas Afantitis2, Thomas Exner3, Martin Himly4, Vladimir Lobaskin5, Philip Doganis6, Dieter Maier7, Natasha Sanabria8, Anastasios G. Papadiamantis2,1, Anna Rybińska‐Fryca9, Maciej Gromelski9, Tomasz Puzyn9, Egon Willighagen10, Blair D. Johnston11, Mary Gulumian12,8, Marianne Matzke13, Amaia Green Etxabe13, Nathan Bossa14, Angela Serra15, Irene Liampa6, Stacey L. Harper16, Kaido Tämm17, Alexander CØ Jensen18, Pekka Kohonen19, Luke T. Slater20, Andreas Tsoumanis2, Dario Greco15, David A. Winkler21,22,23,24, Haralambos Sarimveis6, Georgia Melagraki2
1School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
2Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus
3Edelweiss Connect GmbH, Hochbergerstrasse 60C, 4057 Basel, Switzerland
4Department Biosciences, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
5School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
6School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
7Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
8National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa
9QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland
10Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
11Department Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
12Haematology and Molecular Medicine, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg 2000, South Africa
13UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB, UK
14LEITAT Technological Center, Circular Economy Business Unit, C/ de La Innovació 2, 08225, Terrassa, Barcelona, Spain
15Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
16School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall 105 SW 26th St., Corvallis, OR 97331, USA
17Institute of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
18The National Research Center for the Work Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark
19Misvik Biology OY, Karjakatu 35 B, 20520 Turku, Finland
20Institute of Cancer and Genomics, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
21CSIRO Data61, Pullenvale 4069, Australia
22Institute of Molecular Sciences, La Trobe University, Kingsbury Drive, Bundoora 3086, Australia
23Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
24School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK

Tóm tắt

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.

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