Monday, May 29, 2006

Jmol and CML

Jmol is now up and running on For a demonstration of (just some of) Jmol's features, click on the malaria37 demonstration page here. This demo was created using jmol.js, a javascript library which allows jmol to be controlled from your browser via LiveConnect and javascript commands. All in all, a very powerful package.

Jmol can handle molecules in a variety of formats, including, in this case, CML. The individual CML files (e.g., malaria37.066.xml), were generated from an updated version of ConvertFile.xls (strictly speaking, from babel), available as a zip file from (check my 5/12/2006 blog for more information on ConvertFile.xls).

In addition to now generating individual CML files for the entries in a mol or sdf file such as malaria37, ConvertFile.xls will now also generate an xml file for the entire batch when you press the "Save Results" button. This xml file has the structure (I've omitted the actual data):

<?xml version="1.0"?>
<Molecules Source="">
<Molecule Entry="">
<atomArray />
<bondArray />

This schema for this file can easily be used in programming languages such as, for example, .NET, as the basis for a typed dataset, but a more interesting possibility would be to transform it into an RSS feed. This could be done fairly easily with Excel VBA or any other programming language, or an XSLT.

The next step here would seem to be to read the usefulchem-molecules blog, extract the SMILES, and convert to CML in a similar manner. Unfortunately, babel does not yet have the ability to generate molecular coordinates from SMILEs (or InChIs), and while other software can do this (e.g., ChemSketch, JChemPaint), they cannot be automated. The CDK Web Services sports a service to generate coordinates from SMILES, but it is not particularly usable in its current form -- it does, however, show how this can be accomplished with the CDK.

Friday, May 26, 2006

Auto-Oxidation of Catechol

There has been a comment on this blog about the stability of the catechol compounds with respect to the formation of ortho-quinones.

Oxidation of Catechol to o-benzoqiunone is free radical mediated, passing through a semiquinone radical.

"The equilibrium potential for the one-electron transfer between catechol and the semiquinone radical (cat.) is 100 mV at pH 7 (Eberson, 1985). For the second electron transfer between the semiquinone radical and the catechol dianion (cat2-), an equilibrium potential of 530 mV, 139 mV and 43 mV for pH 7, pH 11 and pH 13.5 respectively was reported (Steenken and Neta, 1979). As a consequence, under physiological conditions catechol is not auto-oxidized (IronsandSawahata,1985), except in the presence of heavy metals (e.g. copper). Several enzymes in plants, animals and bacteria are able to catalyze oxidation of catechol to benzoqiunone. "

The passage has been extracted from an aricle " Chemical properties of catechols and their modes of toxic action in cells, from microorrganisms to mammals." Environmental Microbiology (2001)3 (2), 81-91

Sunday, May 21, 2006

Cheminformatics meeting

On Friday I met with my grad student Dave Strumfels to discuss the cheminformatics and automation aspects of UsefulChem.

Dave has made some very nice progress on using VBA in Excel to process information from our UsefulChem-Molecules blog. A click of a button in Excel populates a spreadsheet with the SMILES code for each molecule then puts an image, molecular weight, finds hits in Chmoogle and a bunch other useful stuff.

We discussed the ongoing online chemistry conference CONFCHEM, especially the discussion on the use of jmol. We set a plan to implement the following:
  1. incorporate a jmol view of molecules in the molecules blog
  2. provide a jmol view of the enoyl reductase enzyme and one of the inhibitors sitting in a pocket
  3. use Bioclipse to successfully view an existing CMLRSS feed
  4. using VBA in Excel, generate a CMLRSS feed of the molecules blog and view it in Bioclipse

Saturday, May 20, 2006

UsefulChem Writing Partners

Beth Ritter-Guth and I are writing a proposal for NSF's Cyberinfrastructure program:

Using Cyberinfrastructure in Blogs, Wikis, and other RSS Technology to Promote Open Source Science in Higher Education and Workforce Development

The current draft is maintained on our UsefulChem wiki.

A key part of this project involves facilitating the collaboration between scientists and non-scientists using blogs and wikis. As a first step to demonstrate how this can be done we have started the UsefulChem Writing Partners blog. Students from the Humanities will be following the chemistry posts on the UsefulChem blog trying to relate the concepts there to the larger context.

There is also a section in the wiki detailing assignments.

I encourage all our labrats at Drexel to subscribe to the feeds and comment on the posts.

Thursday, May 18, 2006

Tenderbutton orgo help

Tenderbutton is a smart and interesting organic chemistry blog maintained by Dylan Stiles from the Trost group and I strongly recommend that the labrats in our UsefulChem group subscribe.

I just noticed that there is now an Autotenderizer button to submit your synthetic frustrations. The answers so far have been very thoughtful, similar to the feedback from ChemUnpub.

Tuesday, May 16, 2006

ChemUnpub forum

Thanks to Sciencebase, I have found a new forum dedicated to discussing and posting chemical experiments and results that don't make it to standard publications.

I would invite the UsefulChem group to check it out and post some of your frustrations or unexpected results there.

Update: they gave us some good feedback on our aldehyde problem

Friday, May 12, 2006

Excel VBA Program to Process sdf files

I have developed an Excel VBA program which processes sdf molecule files, or files in other formats, such as malaria37.sdf. The program generates a column of SMILES for the entries in the sdf file, allows you to retrieve molecular weights and supplier info for each entry, and insert an image of each molecule. Note that to insert images, you must have ChemSketch/ChemBasic installed on your computer to generate them; the images are generated by the ChemBasic script ProcessMol.bas. You can also insert the UC numbers, if any, from usefulchem-molecules.

To use the program, download the zip file into an appropriate folder (e.g., c:\ConvertFile), and unzip it. Any sdf files you wish to process should be placed in their own separate folder (e.g., c:\ConvertFile\malaria37), and processed from there. Remember to download and install ChemSketch/ChemBasic if you wish to create images of the molecules.

Sunday, May 07, 2006

Bird Flu chemistry progress

Here is a nice report on E.J. Corey's improved synthesis of shikimic acid , a key intermediate in synthesis of Tamiflu, which is in short supply to prevent an outbreak of bird flu.

This is a good example of chemists focusing their attention on chemical solutions to real immediate problems, which is the spirit of what the UsefulChem project should strive to achieve and maintain.

Thanks to Sundar Babu for the link!

Update: here is a nice discussion of the synthetic strategy from In the Pipeline

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