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Supramolecular cages benchmark datasets

Two benchmark datasets, comprising 22 well-known supramolecular cages, have been selected from the supramolecular chemistry literature to evaluate cavity detection and volume characterization. All supramolecular cage structures were prepared in the following way: the original CIF files were downloaded from the Cambridge Structural Database (CSD) and atoms and molecular fragments, that are not part of the cage-framework, were removed from the structures, using Diamond Crystal and Molecular Structure Visualization software and saved in a PDB format. <ul> <li>Benchmark dataset 1: host-guest pairs</li> </ul> For benchmark dataset 1, the guest structures were obtained, from the corresponding CIF files, by removing the supramolecular cage and other molecular fragments that are not part of the guest.   <table> <tbody> <tr> <td> Supramolecular Cage Identifier  </td> <td> Guest  </td> <td> CSD Identifier  </td> <td> DOI </td> </tr> <tr> <td> B1  </td> <td> Et4N+  </td> <td> 718468  </td> <td> <a href="https://doi.org/10.1021/ic8012848">10.1021/ic8012848</a> </td> </tr> <tr> <td> B2  </td> <td> BnNMe3+  </td> <td> 718469  </td> <td> <a href="https://doi.org/10.1021/ic8012848">10.1021/ic8012848</a> </td> </tr> <tr> <td> B3  </td> <td> (Cp)2Co+  </td> <td> 718470  </td> <td> <a href="https://doi.org/10.1021/ic8012848">10.1021/ic8012848</a> </td> </tr> <tr> <td> B4  </td> <td> (Cp*)2Co+  </td> <td> 718471  </td> <td> <a href="https://doi.org/10.1021/ic8012848">10.1021/ic8012848</a> </td> </tr> <tr> <td> B5  </td> <td> BF4-  </td> <td> 1862753  </td> <td> <a href="https://doi.org/10.1002/asia.201801262">10.1002/asia.201801262</a> </td> </tr> <tr> <td> B6  </td> <td> ClO4-  </td> <td> 1862752  </td> <td> <a href="https://doi.org/10.1002/asia.201801262">10.1002/asia.201801262</a> </td> </tr> <tr> <td> B7  </td> <td> C60  </td> <td> 942782  </td> <td> <a href="https://doi.org/10.1021/ja4110446">10.1021/ja4110446</a> </td> </tr> <tr> <td> B8  </td> <td> C60  </td> <td> 1872778  </td> <td> <a href="https://doi.org/10.1002/chem.201805353">10.1002/chem.201805353</a> </td> </tr> <tr> <td> B9  </td> <td> Adamantane-2,6-dione  </td> <td> 183906  </td> <td> <a href="https://doi.org/10.1002/1521-3757(20021018)114:20<3947::AID-ANGE3947>3.0.CO;2-X">10.1002/1521-3757(20021018)114:20<3947::AID-ANGE3947>3.0.CO;2-X</a> </td> </tr> <tr> <td> B10  </td> <td> Et4N+  </td> <td> 100947  </td> <td> <a href="https://doi.org/10.1002/(SICI)1521-3773(19980803)37:13/14<1840::AID-ANIE1840>3.0.CO;2-D">10.1002/(SICI)1521-3773(19980803)37:13/14<1840::AID-ANIE1840>3.0.CO;2-D</a> </td> </tr> <tr> <td> B11  </td> <td> Corannulene and Cyclohexane  </td> <td> 2068665  </td> <td> <a href="https://doi.org/10.1038/s41467-021-24344-w">10.1038/s41467-021-24344-w</a> </td> </tr> <tr> <td> B12  </td> <td> C60  </td> <td> 2068666  </td> <td> <a href="https://doi.org/10.1038/s41467-021-24344-w">10.1038/s41467-021-24344-w</a> </td> </tr> <tr> <td> B13  </td> <td> C70  </td> <td> 2068667  </td> <td> <a href="https://doi.org/10.1038/s41467-021-24344-w">10.1038/s41467-021-24344-w</a> </td> </tr> </tbody> </table>   Benchmark dataset 2: topologically and morphologically distinct supramolecular cages The single resorcin[4]arene ligand (O2) was prepared from the corresponding resorcin[4]arene-cage (A1) by removing 5 ligands. In the cyclotricatechylene cage (C1), the outward-pointing phenyl groups (that do not affect the cavity calculations) were removed. <table> <tbody> <tr> <td> Supramolecular Cage Identifier  </td> <td> CSD Identifier  </td> <td> DOI </td> </tr> <tr> <td> A1  </td> <td> 1207879  </td> <td> <a href="https://doi.org/10.1038/38985">10.1038/38985</a> </td> </tr> <tr> <td> C1  </td> <td> 1892128  </td> <td> <a href="https://doi.org/10.1039/C9CC02103E">10.1039/C9CC02103E</a> </td> </tr> <tr> <td> F1  </td> <td> 293777  </td> <td> <a href="https://doi.org/10.1126/science.1124985">10.1126/science.1124985</a> </td> </tr> <tr> <td> F2  </td> <td> 1831430  </td> <td> <a href="https://doi.org/10.1038/nature20771">10.1038/nature20771</a> </td> </tr> <tr> <td> H1  </td> <td> 768969  </td> <td> <a href="https://doi.org/10.1039/C0CC00234H">10.1039/C0CC00234H</a> </td> </tr> <tr> <td> N1  </td> <td> 1541839  </td> <td> <a href="https://doi.org/10.1021/jacs.7b05202">10.1021/jacs.7b05202</a> </td> </tr> <tr> <td> O1  </td> <td> 2074472  </td> <td> <a href="https://doi.org/10.1021/acs.joc.1c00794">10.1021/acs.joc.1c00794</a> </td> </tr> <tr> <td> O2  </td> <td> 1207879  </td> <td> <a href="https://doi.org/10.1038/38985">10.1038/38985</a> </td> </tr> <tr> <td> W1  </td> <td> 1416694  </td> <td> <a href="https://doi.org/10.1038/nchem.2452">10.1038/nchem.2452</a> </td> </tr> </tbody> </table>

ShareScore

40/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 16
Reuse readiness: 8
Engagement: 4

Topics

supramolecular cages cavity detection cavity characterization benchmarking