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UC on ChemSpider
Alicia's Masters Thesis
Open Web Drug Dev.
To Do List
Ugi NMR Analysis
Measure solubility of all
and starting materials in methanol, ethanol, acetonitrile, toluene and water (see
Determine precipitate formation
at 0.5M in methanol over 16 hours by changing components of
Repeat exposure of 5-methylfurfurylamine (A) (
), 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
Expose trifluoromethylfurfuryl Ugi product to 50%TFA/CDCl3
top results - do reactions and do not pursue those that do not precipitate after sonication after 24 hours.
to enzymes and systems where we have testing collaborators (falcipain-2 and anti-tumor)
Upload our good spectra of starting materials and characterized products to
. (link back to EXP)
list of protein targets
to inhibit for malaria and other diseases
Send rest of
isolated Ugi products
to Rosenthal group for falcipain-2 inhibition and anti-malarial activity
Master Ugi Product table
up to date so we can see patterns in which precipitate
Process Level 1 of
starting with most recent experiments
Upload all starting material spectra in ChemSpider
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
on hold - waiting to see if larger list of compounds that can ship immediately are better
connect spectra peaks with atoms in jmol (see
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
to get docking calculation (Sean)
substructure search using Marvin (Dave)
for plotting kinetic runs as described by
but does it do trendlines?
Create a program that can generate possible Ugi products through searching eMolecules for commercially available amines, aldehydes, and amino acids using wildcards in SMARTS.
Remotely automate docking to molecules blog.
use Bioclipse to upload to NMRshiftDB
add tags for InChIs during creation of HTML files from molecules blog as
described by Egon
From the molecules html pages, create a link to Google with the InChI as the search string, without the InChI= part
create links to
human metabolome project
as part of molecule blog processing
combine jcamp spectra into BLOCK file to overlay NMRs -
understand how to generate SMILES correctly from SDF mol files
Command line is: "babel.exe ---errorlevel 0 -ismi <SDF file>.sdf <SMILES file>.smi"
(---errorlevel 0 and -ismi flags optional)
use CDK Java library, which has bugs!
or use OpenBabel GUI interface (OpenBabelGUI.exe)
provide link for flagging duplicates in UC list
(This page should be updated overnight whenever the blog is updated. UC0221 is currently entered twice in the blog.)
combine NMR samples into one CML file and automatically plot integration of one region relative to entire spectrum (
implement substructure searching using OpenBabel on one of our servers and by downloading OpenBabel and txt file (Dave)
Check all compounds listed on the
page and make sure they can ship immediately - if not move them down to bottom of page
Add more compounds from each of the 4 groups on the
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
page) Rajarshi has done this.
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..(
create a page with the list of all experiments on the navigation bar - use the Ugi reactions page only for that reaction
Complete representation of a sample (
) 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)
help on how to format text
Turn off "Getting Started"