DOI: 10.5281/zenodo.7702311
title: Supramolecular cages benchmark datasets

description: 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