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14th February 2014 @ 05:33

I did a literature search using SciFinder of the above reaction to see what were the established synthetic routes for the formation of the hydrazone. This search is to add to the Github issue #97 where there has been a discussion regarding the difficulties associated with PIDA cyclisation.

The literature search was carried out using the same method I used here: Literature Search for Carbonylation of Chloropyrazine (Series 4).

Summary of routes using eight different sets of reaciton conditions:

Hydrazone Synthesis.docx


I also did a literature search using the same search method for this reaction:

to see if there were any reaction conditions in the literature for the condensation of a similar hydrazone, other than that use in this paper (DOI: 10.1002/anie.201001999). This search also ties in with the discussion in the Github issue #97.

Summary of routes using three different sets of reaciton conditions:

Hydrazone Condensation.docx
Attached Files
2nd February 2014 @ 23:55

As a continuation of the commercial availability search I conducted for primary amines to be used in the synthesis of series four amides (How To Guide for Commercial Availability Searches: Series Four Amines), I extended the search to include some secondary amines.

I used the same search method as used for the primary amines (as outlined in the How-to guide).

Prices of secondary amines used to conduct the search:

Secondary amines searched.png

Prices of possible new secondary amines to try:

Possible secondary amines to try.png

Just as a reminder, here are the other possible primary amines we could try:

Possible amines to try ACS.png
Attached Files
21st January 2014 @ 22:32

I have conducted a literature search using SciFinder to see if there is an existing straightforward method for the direct carbonylation of chloropyrazine. Finding such a method would be very useful because 6-chloropyrazine-2-carboxylic acid is a key intermediate in the synthesis of series four amides. It will need to be made in large quantities and in such a way that avoids lengthy experimental procedures and the purchase of expensive compounds.

Methods for the synthesis of 6-chloropyrazine-2-carboxylic acid have already been proposed (see Carbonylation Project - Appeal for a collaborator) and are currently being tested.

 The reaction literature search was conducted as follows:

1) I used the ‘Reaction Structure’ search tool in SciFinder.


2) I drew out the carbonylation reaction I wished to investigate.


I then searched using the search type ‘Allow variability only as specified’. As this did not return any results, I then selected ‘Substructure’ instead.


3) This search method was used for the following carbonylation reactions:

Reaction 1.

Reaction 2.

Reaction 3.

All searches for Reactions 1. and 2. returned either no results or unhelpful ones. However, the ‘exact’ and ‘substructure’ searches of Reaction 3. yielded some patented and literature methods which may be of interest:

Possible Methods of Carbonylation from SciFinder Search.docx

In addition, from the answer set result for the ‘exact’ search for Reaction 3., I selected ‘Similar reactions’ and found other experimental procedures of note.


These are summarised here:

Possible Methods of Carbonylation from SciFinder Search_2.docx

Also, I stumbled across another possible reaction pathway in this paper (DOI: 10.1039/C2NJ40791D). The reaction is outlined on p. 400 and is as follows:

This paper, Paladium-catalyzed carbonylation of N-heteroaromatic chloride, may also be of interest.

Linked Posts
Attached Files
20th January 2014 @ 03:54



Today I started what will be a six week Summer Scholarship research project at the University of Sydney with Mat Todd and Alice Williamson. I’ll be working on Series Four, with particular focus on the amide compounds.


I’m just about to start the fifth and final year of my Bachelor of Science (Adv.)/Bachelor of Arts degree. Aside from the courses I’ve taken as part of my chemistry major, I’ve done some other chemistry research projects. These have included work on metal-organic frameworks for use in carbon dioxide capture materials and an investigation into the physical properties of ionic liquids.


Although I do not have a med-chem background, I was drawn to the idea of a project based upon open source research. For me, the idea of a collaborative approach, as opposed to a secretive one in which it is impossible for scientists to share experiences and draw from others’ strengths, was very appealing.


I’m very excited to begin.