Tag: usefulchem exp098

Posted on

Replication of Usefulchem Exp098 continued

I am continuing this in a new post rather than keeping mucking with the old one.

Currently I am working on reproducing the description of Exp098 from Jean-Claude Bradley’s UsefulChem Wiki within our blog based notebook to identify differences in practise. The reproduction can be found at;

http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/

then click on ‘Usefulchem_exp098’ under the ‘Sandpit Group’ heading on the right hand side and explore from there

18/09/07 15:00 UTC I have added the next two steps of the experiment, the addition of methanol followed by the addition of NaOH to neutralise the solution. In doing this I have possible done something slightly the wrong way around as a reading of the original Exp098 suggests that this step was not originally planned but added later. I still need to add all the NMRs in a sensible fashion. This is it has to be said somewhat tedious but it does keep the relationships between things clear.

I have probably divided this up far more than is necessary in retrospect and the division makes it difficult to read. This probably is a distinction between the way we think about molecular biology and synthetic chemistry. Chemistry does often involve small steps with characterisation along the way on the various materials generated. Each of these steps only require a sentence or more to describe. Most of our molecular biology requires some form of table to detail the inputs and there is usually very little analysis along the way. The differences therefore seem to be: more things in, less in situ analysis.

It might well be more informative to actually do a synthetic chemistry experiment and record that in our system. Because I am doing this replication in bits of spare time I have a bit too much time to think about it as I go along.

Posted on

Replication of UsefulChem Exp098 in the Southampton blog notebook

In a previous post I said I would try to replicate an experiment from the UsefulChem open Wiki notebook within our blog system to see how it might look. This post is to record what I am doing as I do it. Thus this is the lab book I am using to record the process and decisions I have taken in using a lab book. The pages in the notebook can be found at;

http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/

I have chosen to use Exp098 as this involved several different stages and modifications to the wiki page over many weeks. My aim is to try and record this in the way we would. This will involve some changes to the text and the process but I will try to re-use the original text as far as is possible. In the spirit of open notebook science I will make this visible as I go but as this may take me a while (days to a week or two) to finish this page is likely to be unstable and you may wish to come back to it. Ironically I am therefore using this notebook more in the way that Jean-Claude’s group use the Wiki than the way we use the blog.

  1. 13/09 16:58 UTC I have added two initial posts. In the first I have created a product from the previous notional reaction. Exp098 is a study on the stability of a previously generated compound, utilising a specific instance of that compound described in a previous experiment (Exp064). The second post is the initial description of the protocol. This is cut and pasted from the very first version of Exp098 and represents the experimental plan that I would put into the blog before going into the lab.
  2. In Exp098 the process is split into two phases, first a series of reagents are mixed and the reaction is monitored by NMR. After completion the reaction was neutralised and then extracted into organic solvent and dried before further analysis. Because analysis has been carried out on two different ‘samples’ I am therefore going to split the post up in what might appear to be a slightly odd way to an organic chemist. The first stage will generate one product, which will then be subject to analyses (further procedures). The first product will then be subjected to a second procedure (neutralization and drying) to generate a further product (the ‘real’ product) which will be subjected to further analysis.
  3. 13/09 17:20 UTC I have added the first procedure and product post. I now need to make a decision about whether I set up one post with all the NMR analysis from the time course in it or multiple analyses, one for each time point (I can do this with a template) with the data for each in that. Or I could set it up with one procedure post containing all the NMR descriptors but a separate product for each that contains the actual spectrum. I think the latter may be the best. This provides a way of scraping metadata for each of the spectra. It also means that the data can be added slightly later without directly editing the procedure post. I will create a new section for ‘Analysis’ to distinguish it from procedure.
  4. 17/09 13:06 UTC: I have now added all the NMR data for the time course. This was a laborious process obviously but it does meant that it is reasonably clear what goes where. For the separate HOMODEC experiment I didn’t bother putting the data in separately as this is obvious which goes with which. I haven’t as yet put in the NMR data for the starting material 064C which ought really to have been there first.