20130410 carbohydrates
DESCRIPTION
The challenges in dealing with sugar stereochemistryTRANSCRIPT
Carbohydrate structure representation and public
chemistry databasesColin Batchelor, Ken Karapetyan, David Sharpe,
Valery Tkachenko and Antony [email protected]
ACS New Orleans April 2013
Overview
Public chemistry databases and registrationWhy sugar rings are difficultConsequencesAlgorithmsFuture directions
Some public chemistry databases
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.
Why sugars are difficult
Why sugar rings are difficult
Consequences
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
Hexagons in the plane
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).
Assigning HaworthstereochemistryThis 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.
Future work: integrate with CVSPStructure validation•Warn on query atoms, pseudo atoms, polymers, etc.•Nonsensical stereoAllows 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/
More future work
Improve chair tidyingDo not disrupt/flip/invert or move around the aglyconeFused ringsRun over all of ChemSpider
