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.

Benchmark dataset 1: host-guest pairs

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.  

Supramolecular Cage Identifier 

Guest 

CSD Identifier 

DOI

B1 

Et4N+ 

718468 

10.1021/ic8012848

B2 

BnNMe3+ 

718469 

10.1021/ic8012848

B3 

(Cp)2Co+ 

718470 

10.1021/ic8012848

B4 

(Cp*)2Co+ 

718471 

10.1021/ic8012848

B5 

BF4- 

1862753 

10.1002/asia.201801262

B6 

ClO4- 

1862752 

10.1002/asia.201801262

B7 

C60 

942782 

10.1021/ja4110446

B8 

C60 

1872778 

10.1002/chem.201805353

B9 

Adamantane-2,6-dione 

183906 

10.1002/1521-3757(20021018)114:20<3947::AID-ANGE3947>3.0.CO;2-X

B10 

Et4N+ 

100947 

10.1002/(SICI)1521-3773(19980803)37:13/14<1840::AID-ANIE1840>3.0.CO;2-D

B11 

Corannulene and Cyclohexane 

2068665 

10.1038/s41467-021-24344-w

B12 

C60 

2068666 

10.1038/s41467-021-24344-w

B13 

C70 

2068667 

10.1038/s41467-021-24344-w

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.

Supramolecular Cage Identifier 

CSD Identifier 

DOI

A1 

1207879 

10.1038/38985

C1 

1892128 

10.1039/C9CC02103E

F1 

293777 

10.1126/science.1124985

F2 

1831430 

10.1038/nature20771

H1 

768969 

10.1039/C0CC00234H

N1 

1541839 

10.1021/jacs.7b05202

O1 

2074472 

10.1021/acs.joc.1c00794

O2 

1207879 

10.1038/38985

W1 

1416694 

10.1038/nchem.2452