Next Items

Reactions

  1. Measure solubility of all isolated products and starting materials in methanol, ethanol, acetonitrile, toluene and water (see spreadsheet)
  2. Determine precipitate formation at 0.5M in methanol over 16 hours by changing components of EXP099.(see spreadsheet)
  3. Repeat exposure of 5-methylfurfurylamine (A) (EXP073), its acetate (B) and boc-Gly amide (C) to much harsher conditions (refluxing in pure TFA) to confirm that they really do or do not cleave
  4. Expose trifluoromethylfurfuryl Ugi product to 50%TFA/CDCl3
  5. D-EXP014 top results - do reactions and do not pursue those that do not precipitate after sonication after 24 hours.

Cheminformatics

  1. Continue docking libraries to enzymes and systems where we have testing collaborators (falcipain-2 and anti-tumor)
  2. Upload our good spectra of starting materials and characterized products to ChemSpider. (link back to EXP)
  3. Create list of protein targets to inhibit for malaria and other diseases

Miscellaneous

  1. Send rest of isolated Ugi products to Rosenthal group for falcipain-2 inhibition and anti-malarial activity
  2. Bring Master Ugi Product table up to date so we can see patterns in which precipitate
  3. Process Level 1 of Experiment Format starting with most recent experiments
  4. Upload all starting material spectra in ChemSpider

Pending

  1. Order 2-naphthyl isocyanide and make sure we have enough boc-methionine and at least one amine and aldehyde to make at least one of the first 13 Ugi products from the Rajarshi01 list on the CombiUgi page (on hold - waiting to see if larger list of compounds that can ship immediately are better)

Brainstorming

  1. connect spectra peaks with atoms in jmol (see Lancashire aspirin NMR example)
  2. Possibility of Fmoc amino acid protection, acid catalyzed imine formation, for the first step of the Ugi, and base catalyzed cyclization of the Ugi condensation product. This should enable us to use TiCl4 to catalyze the Ugi reaction.
  3. use Googlebase for molecules
  4. ArgusLab to get docking calculation (Sean)
  5. substructure search using Marvin (Dave)
  6. Try Swivel for plotting kinetic runs as described by ElementList but does it do trendlines?
  7. Create a program that can generate possible Ugi products through searching eMolecules for commercially available amines, aldehydes, and amino acids using wildcards in SMARTS.
  8. Remotely automate docking to molecules blog.
  9. use Bioclipse to upload to NMRshiftDB
  10. add tags for InChIs during creation of HTML files from molecules blog as described by Egon
  11. From the molecules html pages, create a link to Google with the InChI as the search string, without the InChI= part
  12. create links to human metabolome project as part of molecule blog processing

Done

  1. combine jcamp spectra into BLOCK file to overlay NMRs - instructions here
  2. understand how to generate SMILES correctly from SDF mol files
  3. Command line is: "babel.exe ---errorlevel 0 -ismi <SDF file>.sdf <SMILES file>.smi"
  4. (---errorlevel 0 and -ismi flags optional)
  5. Don't use CDK Java library, which has bugs!
  6. or use OpenBabel GUI interface (OpenBabelGUI.exe)
  7. provide link for flagging duplicates in UC list Duplicates
  8. (This page should be updated overnight whenever the blog is updated. UC0221 is currently entered twice in the blog.)
  9. combine NMR samples into one CML file and automatically plot integration of one region relative to entire spectrum (details here)
  10. implement substructure searching using OpenBabel on one of our servers and by downloading OpenBabel and txt file (Dave)
  11. Check all compounds listed on the CombiUgi page and make sure they can ship immediately - if not move them down to bottom of page
  12. Add more compounds from each of the 4 groups on the CombiUgi page.
  13. Generate complete SMILES list of Ugi products as a web service based on input from lists of amines, isocyanides, aldehydes and acids. (see complete info on CombiUgi page) Rajarshi has done this.
  14. prepare Ugi product with the demethylated furfurylamine (which should not react easily in TFA) and benzyl isonitrile - according to Hulme, sterically hindered isonitriles lead to Ugi products that do not cyclize easily but benzyl isonitrile Ugi products should cyclize..(Exp108 and EXP110)
  15. create a page with the list of all experiments on the navigation bar - use the Ugi reactions page only for that reaction
  16. Complete representation of a sample (EXP086) Ugi reaction on Second life showing the 2D structure, the physical compounds and in 3D, possible with animations of each step (collaboration with Hiro Sheridan/Andy Lang)