This document discusses carbohydrate structure representation in public chemistry databases. It begins with an overview of public chemistry databases and challenges in representing sugar rings. It then discusses algorithms for canonicalizing chair and Haworth representations of hexagons and pentagons in sugars. Future work proposed includes integrating these algorithms with chemical validation tools and improving representation of more complex carbohydrate structures.

1. Carbohydrate structure
representation and public
chemistry databases
Colin Batchelor, Ken Karapetyan, David Sharpe,
Valery Tkachenko and Antony Williams
batchelorc@rsc.org
ACS New Orleans April 2013

2. Overview
Public chemistry databases and registration
Why sugar rings are difficult
Consequences
Algorithms
Future directions

3. Some public chemistry databases

4. How registration works
Structures are accepted in some machine-readable
format and boiled down to some position-independent
canonical form.
Drop exact coordinates and retain only relative
coordinates, disregarding bond length.
Canonicalization based on depiction of bonds (wedges or
hashes) rather than 3D positions around atoms.

5. Why sugars are difficult

6. Why sugar rings are difficult

7. Consequences

8. Algorithm for hexagons
• Identify the perspective conformation (boat,
chair, regular hexagon, and so on)
• Determine perspective stereo
• Assign wedge or hash to the bonds
accordingly
• (tricky) Reconstruct the sugar ring so as to
minimize disruption of the rest of the
molecule

9. Hexagons in the plane

10. Assigning chair stereochemistry
Take the x-axis as either the line through the top
two ring atoms or bottom two ring atoms.
Substituents with Δy positive are up, Δy negative
are down.
Then remap chair to a regular hexagon (tricky).

11. Assigning Haworth
stereochemistry
This works for both hexagons and
pentagons.
Remove any hashes or wedges
within the ring.
Take the x-axis as a line through one of the ring C–O bonds.
Substituents with Δy positive are up, Δy negative are down.
The Haworth LLLLLL/RRRRRR hexagon is unappealing, but can be tidied
to a regular hexagon grid without too much disruption.
The same goes for the Haworth pentagon.

12. Future work: integrate with CVSP
Structure validation
•Warn on query atoms, pseudo atoms, polymers, etc.
•Nonsensical stereo
Allows users to put together their own standardization workflow using
modules provided:
•Apply default CVSP or user-defined SMIRKS rules
•Layout
•Neutralize
•Get canonical tautomer using ChemAxon’s algorithms
•Get biggest organic fragment
http://cv.beta.rsc-us.org/

13. More future work
Improve chair tidying
Do not disrupt/flip/invert or move around the
aglycone
Fused rings
Run over all of ChemSpider

14. Questions?
E-mail: batchelorc@rsc.org