Diazonamide A and Chats with TotallySynthetic.Com

23 Sep

As discussed in an earlier blog I spent some time chatting with Paul Doherty and Peter Murray Rust this weekend…specifically around InChIs and InChIKeys. I’d originally suggested to Paul that he put InChIs on the site so that I could use them to check for presence of the structures he draws in the ChemSpider database. Well, now he’s started to include them on his postings I get to check them.

I started with a search on the term Diazonamide A in Pubchem. Two hits….shown below.

Diazonamide A on PubChem 

Diazonamide A is a complex structure. Those structure representations drawn above are NASTY and do need cleaning for sure. Unfortunately Chempider has the same issues for these two structures (see below) since we did not CLEAN the PubChem dataset. Cleaning these structures in not an easy task. We are working on improving this as discussed previously.

The two shown on PubChem have different Isomeric SMILES and different InChIs. Why? ONE stereocenter difference…see the highlighted difference below (in red) and the arrow to the one stereocenter difference.

Stereo Differences

 It is appropriate to have two structures in PubChem..they are unique. But now we don’t know which one is Diazonamide A. Shucks.

And so, let’s check eMolecules. I didn’t find any hits. eMolecules did take a lot of PubChem into their dataset. the reason for not finding it might be “it’s not there” because of eMolecules focus on commercial suppliers OR because “I queried incorrectly”. Don’t know.

So, to ChemSpider. A search on Diazonamide A gave SIX hits. Two of these are the exact ones from PubChem. The four others are shown below…

Marinlit Diazonamide A

Of these four two of them have an “additional oxygen and two hydrogen atoms” in the molecular formula.

Is that right or wrong? TotallySynthetic has the formula as C40H34Cl2N6O6 so we’ll trust Paul and curate these two records as IN ERROR as shown below (A primary advantage of ChemSpider is we are allowing curating!). I’ll also let Marinlit know…


 Curate Out

 The differences between Diazonamide A and the “incorrect structure” are shown below just for information. SIGNIFICANTLY different.

Differences in Marinlit

Let’s take a look at the different InChIs for all structures we are considering – 2 PubChem, 2 ChemSpider (from Marinlit) and 1 from TotallySynthetic. They are ALL different and all differ in the sterochemistry layer.

PubChem CID: 395475

PubChem CID: 5492609
InChI=1/C40H34Cl2N6O6/c1-15(2)27-37-46-29-32(54-37)40-20-9-5-8-19(18-7-6-10-22-25(18)26(33(41)43-22)31-34(42)48-38(29)53-31)28(20)47-39(40)52-24-12-11-17(13-21(24)40)14-23(35(50)45-27)44-36(51)30(49)16(3)4/h5-13,15-16,23,27,30,39,43,47,49H,14H2,1-4H3,(H,44,51)(H,45,50)/t23-,27-,30-,39-,40u /m0/s1/f/h44-45H

ChemSpider CID: 10478902 


ChemSpider CID: 17212293 

InChI=1/C40H34Cl2N6O6/c1-15(2)27-37-46-29-32(54-37)40-20-9-5-8-19(18-7-6-10-22-25(18)26(33(41)43-22)31-34(42)48-38(29)53-31)28(20)47-39(40)52-24-12-11-17(13-21(24)40)14-23(35(50)45-27)44-36(51)30(49)1 6(3)4/h5-13,15-16,23,27,30,39,43,47,49H,14H2,1-4H3,(H,44,51)(H,45,50)/t23-,27+,30+,39-,40+/m1/s1 

Totally Synthetic



The TotallySynthetic structure has the stereo layer t23-,27-,30-,39?,40-. In real terms this relates to five stereo centers. At this point I have to question whether the structure as drawn is correct or not..what we have is five structures with the SAME connectivities but with different stereochemistries. This is similar to the issue I blogged about previously in regards to Taxol.


I’m not sure that we have the right structure of Diazonamide A yet..but I’m sure we’ll get there very quickly with this question out there in the open. I HOPE SO!


About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database ( Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (, a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service ( and the RSC lead for the PharmaSea project ( attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on September 23, 2007 in ChemSpider Chemistry


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