Your SlideShare is downloading. ×
  • Like
20130410 carbohydrates
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×

Now you can save presentations on your phone or tablet

Available for both IPhone and Android

Text the download link to your phone

Standard text messaging rates apply

20130410 carbohydrates

  • 1,118 views
Published

The challenges in dealing with sugar stereochemistry

The challenges in dealing with sugar stereochemistry

Published in Technology , Business
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
1,118
On SlideShare
0
From Embeds
0
Number of Embeds
6

Actions

Shares
Downloads
1
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. Carbohydrate structurerepresentation and public chemistry databases Colin Batchelor, Ken Karapetyan, David Sharpe, Valery Tkachenko and Antony Williams batchelorc@rsc.org ACS New Orleans April 2013
  • 2. OverviewPublic chemistry databases and registrationWhy sugar rings are difficultConsequencesAlgorithmsFuture directions
  • 3. Some public chemistry databases
  • 4. How registration worksStructures are accepted in some machine-readableformat and boiled down to some position-independentcanonical form.Drop exact coordinates and retain only relativecoordinates, disregarding bond length.Canonicalization based on depiction of bonds (wedges orhashes) 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 stereochemistryTake the x-axis as either the line through the toptwo ring atoms or bottom two ring atoms.Substituents with Δy positive are up, Δy negativeare down.Then remap chair to a regular hexagon (tricky).
  • 11. Assigning HaworthstereochemistryThis works for both hexagons andpentagons.Remove any hashes or wedgeswithin 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 tidiedto a regular hexagon grid without too much disruption.The same goes for the Haworth pentagon.
  • 12. Future work: integrate with CVSPStructure validation•Warn on query atoms, pseudo atoms, polymers, etc.•Nonsensical stereoAllows users to put together their own standardization workflow usingmodules provided:•Apply default CVSP or user-defined SMIRKS rules•Layout•Neutralize•Get canonical tautomer using ChemAxon’s algorithms•Get biggest organic fragmenthttp://cv.beta.rsc-us.org/
  • 13. More future workImprove chair tidyingDo not disrupt/flip/invert or move around theaglyconeFused ringsRun over all of ChemSpider
  • 14. Questions?E-mail: batchelorc@rsc.org