Friday, June 30, 2006

RSS Feeds from Excel VBA

RSS 1.0 feeds are now available for UsefulChem Molecules ( and malaria37 ( To view these feeds, you can use an on-line reader such as Bloglines, or a desktop aggregator such as RSS Bandit. A typical entry for these feeds is:


InChI: InChI=1/C4H11NO3/c5-1-3(7)4(8)2-6/h3-4,6-8H,1-2,5H2
Canonical MW: 121.135056
Natural MW: 121.13649


Note that clicking on the image loads an HTML page with the molecule displayed in the Jmol
applet. The development of these feeds is part of the on-going work with Microsoft Excel to process cheminformatic data with Visual Basic for Applications (VBA), in combination with Open Source software such as Babel, the Chemistry Development Kit (CDK) , and Jmol. The current versions of this software can be downloaded from here and here. To use this software, you must download and install the Chemistry Development Kit (the installation directory should be C:\cdk; if you select a different directory, you must modify the .ini files appropriately).

Tuesday, June 27, 2006

New members

Here is a summary of our lab meeting yesterday:

1) We welcomed two new members: Lin is with us for the summer under a Maryanoff undergraduate scholarship and Dave B (our second Dave) has started as a graduate student.

2) Now that we're having more luck with getting NMRs from our 300MHz machine things should move more quickly. Well, at least we are getting good proton spectra. Carbon is still problematic. We would like to publish these spectra using JSpecView, as described by Lancashire in his recent CONFCHEM paper.

3) We are going to be recording the experiments in the UsefulChem wiki before copying them over to the experiments blog when finalized. That way, we can track who did what and when. This comes with a third party timestamp to indicate when experiments were done and conclusions reached. James has started to move over his EXP015.

4) Dave B will get started on using the THINK software to see if methylating the catechol moiety in our first anti-malarial target will prevent binding to enoyl reductase.

5) James is about to find out if any aldehyde was obtained from the decomposition of adrenaline in phosphoric acid. That should be very obvious from the NMR of the ether extract.

6) Khalid is about to run another Chromatotron on his attempted Ugi reaction. The cyclized product should be in one of the fast moving spots so he'll look at those first.

Tuesday, June 20, 2006

Access Chemistry News

The latest issue of the Reactive Reports chemistry news site is now live. In it, I discuss various advances in the chemical sciences and also interview Will Griffiths. Griffiths is a chemist by training but, like me, opted out of the laboratory world with the aim of applying his chemical knowledge through a different medium. He is now investing his time and energy in developing the website, which offers chemists every quick and open access to the free full-text chemistry literature.

Tuesday, June 13, 2006

Open Source Chemistry Article

Mat Todd and friends have just published an article on open source chemistry in the Australian Journal of Chemistry.

Monday, June 12, 2006

Processing usefulchem-molecules with Excel and the CDK

I have modified MoleculeBlogInfo.xls to generate mol and cml files from the entries in usefulchem-molecules. To use this software, you must first download and unzip the Chemical
Development Kit (CDK)
(both the CDK and its source code can also be found at It is suggested you place the CDK in the folder C:\cdk; if you choose a different folder, you must edit MoleculeBogInfo.ini, modifying the line
ConversionProgram=java -cp .;C:\cdk ProcessSMILES
accordingly. It may also be necessary to install the latest version (5.0) of the Java JRE.

The CDK is a powerful Java library of chemical conversion and manipulation routines, and is used in a number of open source programs such as Jmol and JChemPaint. With it, you can easily write programs to generate molecular coordinates from SMILES, calculate molecular weights, compare fingerprints, and many, many other functions. The CDK Web
and "Java Snippet" page by Rajarshi Guha are excellent examples (and source code source) of CDK usage.

Like FileConvert.xls, MoleculeBlogInfo.xls now creates cml files, which can be viewed with Jmol at the demonstration page. In addition to generating individual cml files, MoleculeBlogInfo.xls will also generate an xml file for the entire usefulchem-molecules site when you press the "Save Results" button. This xml file has the structure (I've omitted the actual data):

<?xml version="1.0" encoding="ISO-8859-1"?>
<molecules source="" xmlns="">
<molecule id="UC####">
A version of FileConvert.xls which also uses the CDK, is also available.

Friday, June 09, 2006

DOPAL NMR and phosphoric acid

Following up on our need for DOPAL in the malaria project, here is a good review of DOPAL syntheses, noting that the full characterization (including H NMR) was first made by Li et al in 1998. Unfortunately it is not a trivial synthesis and involves a very low yielding final step of deprotecting the methylenedioxy-protected catechol group, as Brett has noted previously.

They also link to a 1966 synthesis from adrenaline using phosphoric acid. This might be worth trying, since we still have some adrenaline, using chromatography to purify instead of the bisulfite adduct used in the paper.

Thursday, June 08, 2006


Here is a report in New Scientist Tech about a program that facilitates representing experimental data into an ontology. It is really hard to understand exactly what it does from the article, especially since the last part says that there is long manual process. How is this different from manually parsing an experimental description into XML? Anybody from UsefulChem want to play with it to find out what it can do in chemistry? The article says the source code is available.

Thanks to Sundar for the link.

Monday, June 05, 2006

Interview with Wendy Warr

If Usefulchem'ers ever need an expert opinion on chemical informatics, then Wendy Warr is the expert you need. I interviewed her for the latest issue of the chemistry webzine Reactive Reports and she offered some insights into the cheminformatics world.

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