Features of IUPAC nomenclature that cannot be represented in Standard InChI will be examined to draw caution to cases where the use of standard InChI (and even in some cases non-standard InChI) may result in a loss of information. These areas include the representation of tautomers and mixtures of stereoisomers.

1. InChI vs IUPAC nomenclature: Aspects to be
aware of when using Standard InChI
Daniel Lowe
Unilever Centre for Molecular Science Informatics
University of Cambridge

3. • InChI is used for checking the correctness of
the results of name to structure
– 172,249 name and InChI pairs used for routine
regression testing
• Failures arising from stereochemistry can be
distinguished from constitutional failures
Plausible interpretations of “alanine”:
InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)
InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1

5. 1H-tetrazole 2H-tetrazole 3H-tetrazole 4H-tetrazole
InChI=1S/CH2N4/c1-2-4-5-3-1/h1H,(H,2,3,4,5)

6. Not all tautomers are equally
important
• Conditions can lead to a particular tautomer being
far more representative of a compound than
another
• Not all tautomers readily interconvert
• A particular tautomer could be the reactive species
A fixed hydrogen layer can always be
removed but cannot be losslessly readded

7. cyclo-tris(tetracarbonylosmium) (3 Os—Os)
InChI=1S/12CO.3Os/c12*1-2;;;
InChI=1/12CO.3Os/c12*1-2;;;/rC12O12Os3/c13-1-25(2-14,3-
15,4-16)26(5-17,6-18,7-19,8-20)27(25,9-21,10-22,11-23)12-24

8. (RS)-2-(4-(2-methylpropyl)phenyl)propanoic acid
InChI=1/C13H18O2/c1-9(2)8-11-4-6-12(7-5-11)10(3)13(14)15/h4-7,9-10H,8H2,1-3H3,(H,14,15)/t10-/s3/f/h14H
/s1 = absolute stereochemistry
/s2 = relative stereochemistry
/s3 = racemic stereochemistry

9. A mixture of relative and absolute stereochemistry, and systems
with multiple groups of relative stereochemistry are not yet
supported
&1
O
&2 &1
O
O
Cl Cl
N
beta-cypermethrin (4 exact structures)

10. Helical stereochemistry
hexahelicene

11. Helical stereochemistry
(M)-hexahelicene (P)-hexahelicene

12. Axial stereochemistry
(Sa)-6,6′-dinitrobiphenyl-2,2′-dicarboxylic acid
(Ra)-6,6′-dinitrobiphenyl-2,2′-dicarboxylic acid

13. Conclusions
• Where useful greater specificity than standard
InChI can be achieved using extra layers
• InChI does not yet support all corner cases of
stereochemistry

14. Any Questions?
Email: daniel@nextmovesoftware.com