Friday, September 05, 2014

Total Recall - Synthetic organic chemistry is kinda slow and complicated!

To everyone's surprise I spent a day in the lab the other day doing some actual real life research. I forgot how hard, slow and complicated that stuff is. It would probably not be a bad idea for supervisors to leave the office and spend a day doing some lab work occasionally. I certainly appreciate what the guys are doing more after that ordeal. During my brief lab exposure I was reminded of the common messy lab balance problem. It is almost more common to find the balance littered with chemicals, dirty spatulas etc. than in a clean and tidy state. Anyway, the guys in my lab have sorted this out. A panda seems to do the trick. D!

Friday, December 27, 2013

Curly Arrow - Established 18th October 2006

It really is becoming the rule rather than the exception that I forget Curly Arrow's birthday. Its been running for 7 years now and as always here are some stats on the year that has passed. As you can see the lack of new posts really isn't deterring people from using all the info posted here over the years (Although visitor numbers are in decline for the first time). Hopefully I can squeeze a few post out in between everything else in 2014. D! 

From 18th October 2012 to 18th October 2013:
Absolute unique visitors: 36,032
Total visits: 42,428 ( 116 visits/day)
Page views: 68,627
Average time on site: 2:24 min
Top 10 most frequent visitors identifiable:
(1) University of California San Diego
(2) Oxford University
(3) Universite de Liege
(4) Johannes Gutenberg-Iniversitaet Mainz
(5) The Scripps Research Institute
(6) University of Cambridge
(7) University of California Irvine
(8) Stanford University
(9) ETH Zürich
(10) Columbia University
Top 10 countries that visit the blog:
(1) United States
(2) United Kingdom
(3) India
(4) Germany
(5) Canada
(6) Australia
(7) Japan
(8) Denmark
(9) France
(10) Netherlands

Monday, August 12, 2013

Free Ligands - The Calcilytic Agent NPS2143, a Calcium-Sensing Receptor Modulator

We recently synthesised a significant quantity of the calcilytic ligand NPS2143 for our research programme on G protein-coupled receptors. NPS2143 is a negative allosteric modulator of the human calcium-sensing receptor and as such an important pharmacological tool compound. Recently, we developed and published a synthesis of optically pure NPS2143 in Beilstein Journal of Organic Chemistry (Open access journal that you should check out).
Anyway, now we have come to realise that we have a lot of this compound on the shelf that we are highly unlikely to ever use. So the idea to simply give the compound away to anyone that needs some free high quality NPS2143 popped up. So here we go! If you would like 5 mg of optically pure NPS2143 and you can fulfil the requirements below we will ship it to you:
  • You are an employee at an academic institution (Associate or Full Professor)
  • You will only use the compound for non-profit academic research purposes. Please provide a brief description (will be treated confidentially)
  • You can pay the shipment costs by courier (alternatively we will ship it by regular mail)
  • You will be kind enough to cite our paper "Synthesis of the calcilytic compound NPS 2143" if you ever publish a paper were you have used it

Please email Associate Professor Daniel Sejer Pedersen at if you are interested.

NPS2143 is by no means the only interesting compound we have sitting on the shelf and if this turns out to be a success we will definitely offer more free compounds. Let's see what happens. D!

Friday, August 09, 2013

Faking it - Elemental Analysis!

Earlier this year I was refereeing a rather good paper and had I not taken the time to inspect the experimental section I would have accepted it with minor corrections. However, whoever wrote the experimental had clearly never run an elemental analysis before and was hopeless at making them up. The numbers were simply to good and although everything else looked great I had to reject the paper due to serious misconduct/fraud. This made me think that there must be thousands of papers out there with made up elemental and HRMS analyses  as these are really simple to make up. Have a look at this web page for inspiration for realistic elemental data:
After this incident I always read the experimental section first and check the spectra and I really wish that my refereeing colleagues would do the same. The crap you find in the experimental section of all journals including the most prestigious ones is simply unbelievable. Even when the experimental stuff looks great it is remarkable how many procedures we are completely unable to reproduce in our lab.
Anyway, not all hustlers are equally talented as a good friend of mine pointed out yesterday when he sent me this interesting paper by Reto Dorta and co-workers:
My friend simply wrote check out supplementary information page 12. And so I did and this is what I found (click on image to enlarge):

Many thanks to Reto Dorta and co-workers for this excellent example of what I guess must be classified as attempted fraud since the fake elemental analysis was never added. D!  

Monday, January 07, 2013

Anti-GMO activist sees the light!

I picked this up at one of my favourite blogs (in the pipeline) and simply have to share it. A former fanatical anti-GMO campaigner read some scientific papers and realised his wrong doings. What a fantastic start to the New Year. It makes me think that there still may be hope for humanity when someone like Mark Lynas can come around and realise his mistakes and openly admit it. As a minimum you should watch the first 6 minutes of his presentation at the Oxford Farming Conference. D!

Tuesday, December 11, 2012

Curly Arrow - Established 18th October 2006

So I missed my blog birthday again this year! As usual the stats for the past year at Curly Arrow follows below. Thanks to all the blog followers and everyone else who is using the blog. I wish I had more time to post stuff here but running my university research is very time consuming. When I finally get home I really need to do something that isn't chemistry to avoid going insane.
However, the many posts from over the years and the many very valuable comments by the visitors makes this a great resource and forum for exchange of knowledge for students and more experienced chemists. It really is amazing how may people make it here every day in the search for tips and tricks. Merry Christmas and Happy New Year to those of you that are into that stuff, D!

From 18th October 2011 to 18th October 2012:
Absolute unique visitors: 40,669
Total visits: 57,222 (157 visits/day)
Pageviews: 84,446
Average time on site: 2:27 min
The 10 most frequent visitors identifiable:
(1) Oxford University
(2) Princeton University
(3) Universite de Liege
(4) University of California San Diego
(5) University of Cambridge
(6) Imperial College London
(7) Universidade de Sao Paulo
(8) University of Wisconsin Madison
(9) Stanford University
(10) University of Hull
Top 10 countries that visit the blog:
(1) United States
(2) United Kingdom
(3) Germany
(4) India
(5) Canada
(6) Australia
(7) Denmark
(8) Japan
(9) France
(10) South Korea

Diazomethane and the Arndt-Eistert Homologation

For the past year we have been starting peptidomimetic chemistry up as a new research area in our group. Many chemists believe that peptide chemistry is easy and that peptide chemists aren't "real chemists". However, let me tell you from personal experience that there is absolutely nothing trivial about peptide chemistry. Even short sequences with normal alpha amino acids can be a nightmare to make, troubleshooting is complicated, purification can be a major pain and yields that a small molecule chemist would consider a total fail is generally acceptable in this area of research. Some years ago I was working with a Post Doc that came from Dieter Seebach's lab at ETH. He introduced me to beta amino acids and ever since I have been fascinated by the use of these building blocks in peptidomimetic research. Inspired by the work of Samuel Gellman we are focusing on the use of beta-3 amino acids in combination with alpha amino acids. Consequently, we synthesise beta-3 amino acids to incorporate these in our peptides.
There is a number of ways to make beta-3 amino acids but from personal experience one method stands out as the best route to these molecules: the Arndt-Eistert homologation. In this classic approach an alpha amino acid is converted to a diazoketone followed by the Wolff rearrangement to provide beta-3 amino acids. The Arndt-Eistert homologation basically homologates a carboxylic acid with one methylene group as shown in the scheme below.
The last step, the Wolff rearrangement, is carried out by sonicating the diazoketone in the presence of a silver catalyst (in the dark). Because nitrogen is evolved during the course of the reaction we normally have an empty balloon fitted on the flask to avoid pressure build up. I rather like the feature that the balloon slowly gets inflated during the course of the reaction as shown in the picture below.
Silver catalysed Wolff rearragement in a sonicator. Left t = 0 hr; Right t = 2 hr.
However, as you may have noticed there is a down side to the Arndt-Eistert homologation: diazomethane! The reagent has a fearsome reputation and I have heard of a couple of guys who have managed to blow themselves up and gone deaf in the process. Allegedly, one chemist at our department even managed to set fire to himself! This was a long time a go when less attention was being paid to laboratory safety and the accidents were due to sloppiness and improper handling of diazomethane. If you are careful and use the correct glassware (with clear seal joints) there is (almost) nothing to worry about. We have purchased the setup shown on the picture below. This is a very nice diazomethane still consisting of only three pieces that will produce up to 40 mmol of diazomethane in approximately one hour. We only use hot water as the heating source and keep everything behind a blast shield just in case. Diazomethan is generated from Diazald  as shown in the scheme below and used immediately. The procedure it quite simple. In the separatory funnel you place a solution of Diazald in ether this is added dropwise to a heated mixture of aqueous potassium hydroxide, ether and a high boiling alcohol [commonly 2-(2-ethoxy-ethoxy)ethanol]. Diazald reacts with the base to produce diazomethane that is distilled with ether to the receiving flask.
Notice that diazomethane is always handled in solution. The neat stuff is known to explode unpredictably so don't even think about doing that. Because of the way that diazomethane is produced it is hard to add an exact number of equivalents to a reaction. For the synthesis of diazoketones we simply go for an excess of diazomethane (approximately 2-3 equivalents based on a 70% yield of diazomethane). We commonly distill the diazomethan directly into the reaction flask to minimise handling. For the synthesis of beta-3 amino acids the alpha amino acid is first transformed into a mixed anhydride which is exposed directly to an excess of diazomethane.
Diazoinsane clear seal distillation kit purchased from Sigma-Aldrich.
Unlike diazomethane, Diazald is reasonably stable and easy to handle yellow solid. Unfortunately, Diazald has obtained a rather bad reputation despite being relatively safe to deal with as long as you don't eat it, set fire to it, beat it with a hammer or something similarly stupid. Consequently, it can be rather hard to get hold of. When I worked in Australia it was particularly problematic as it can only be shipped by road and isn't produced in the country! Here in Denmark we get it from Germany but it does take a while because they don't send it with the regular shipments so you have to plan a bit ahead.
If you think that playing around with beta-3 amino acids could be fun I can recommend the company Anand Chem based in Slovakia. They produce almost all beta-3 amino acids with the proteinogenic side chains of excellent quality at a highly competitive price. Depending on what they have in stock you may have to wait a couple of weeks for the stuff but it is worth the wait considering the quality and the price. D!

Sunday, November 18, 2012

Diazotransfer - Synthesising Azides from Amines

In our group we work a lot with diazotransfer reagents and diazomethane so I thought it might be a good idea to share some of our knowledge. These reaction involve reagents that are very dangerous and azide products can also be explosive so you shouldn't do any of this chemistry without being 100% sure you know what you are doing. However, if experiments are performed thoughtfully and with care the chemistry is predictable and well behaved. We are doing diazotransfer all the time these days to convert amino acids into azide derivatives. There are many reagents available for the diazotransfer reaction with the most common depicted in the figure below.

We recently, published a review that gives a detailed description of the various diazotransfer reagents when used on amino acids but I believe it would be of interest to anyone attempting the conversion of an amine to an azide. Check it out here for the full story. The conclusion is that we favour reagents 4 that was developed by Goddard-Borger and Stick and first reported here. Later a safety update was published here followed by a comprehensive stability study that was published here. The problem is that the HCl salt of 4 is hygroscopic and when it becomes wet is starts to decompose forming hydrazoic acid (HN3) which is very nasty and totally unpredictable. Fortunately, it is easy to see when the decomposition has kicked in because the product turns into a black tar. The tetrafluoroborate and hydrogensulfate salts of 4 were found to be much better with respect to shelf life. In the future we will use the hydrogensulfate salt of 4, however, we have a big pile of the HCl salt we have to get through first. Fortunately, we discovered that rigorous drying of the HCl salt of 4 followed by storage at -20 oC makes it stable for >1 year. Anyway, if you are new to this stuff you should definitely go for the hydrogensulfate salt. Using the HCl salt of 4 we regularly synthesise amino acids with terminal azides in the side chain (see below). 

This is easily achieved from the corresponding amine (in this example lysine). The pH of the reaction has to be adjusted to approx. 8 to get it going. We normally insert a pH meter to keep an eye on things and simply adjust pH by adding sat. aq. NaHCO3 when required. The fantastic thing about this reaction is that the crude product is of such high purity that we never perform any chromatography but simply dry it and use it as it is. The synthesis of this particular azide has been reported many times in the literature. For a recent detailed procedure check out our SYNLETT paper on the synthesis of Fmoc-L-Lys(N3)-OH and a number of other azide and alkyne derivatised amino acids.
Note that we are synthesising high molecular weight azides so these guys are not explosive. However, if you consider synthesising smaller azides please be aware that it isn't considered safe to handle azides with less than 6 heavy atoms per azido group (see our recent review for details).
Some of you are probably thinking what is the mechanism for this reaction? Well I'll leave that to someone else to have a go at. I don't think the actual mechanism has been conclusively established and the suggested arrow pushing is rather exotic. Suffice to say that it works and that nitrogen gets transferred from reagent to product without too much fuss. Have fun diazotransferring. D!
If you don't have access to our papers reprints can be requested from
On a non-chemistry note I have started the blog Molt Bé, No? about Barcelona (and Catalonia). I spend a lot of time in Barcelona since my better half lives there and now I have started writing about our favourite spots. I find that guide books, news papers etc. are a disaster regarding their recommended restaurants, bars etc. so I thought I would do my bit to help visitors to Barcelona have a nice and authentic experience when visiting the Catalan capital (and the surrounding area). Check it out here if you are heading in that direction. D!

Thursday, March 08, 2012

Total Synthsis?

We had our weekly journal club this morning. Interesting paper from a Korean group but maybe the ACS editorial office should wake up. D!

Tuesday, December 27, 2011

Curly Arrow - Established 18th October 2006

Merry Christmas and Happy New Year! I Hope that everyone is getting some well-deserved time off. I used to do a yearly post on visitor stats around the blogs birthday but forgot this year!. Since it was the 5th birthday on 18th October 2011 I have decided to have a look back at how things developed in the past year.
From 18th October 2010 to 18th October 2011:
Absolute unique visitors: 34,488
Total visits: 61,799 (169 Visits/Day)
Average time on site: 1:25 minute
The 10 most frequent visitors identifiable:
(1) ETH Zürich
(2) University of Hull
(3) Queens University Belfast
(4) Universite de Liege
(5) Princeton University
(6) The Scripps Research Institute
(7) Oxford University
(8) University of Ghent
(9) The University of Nottingham
(10) Johann Wolfgang Goethe Universitaet Frankfurt 
Top 10 countries that visit the blog:
(1) United States (18,348 visits)
(2) United Kingdom (8,642 visits)
(3) Germany (3,707 visits)
(4) India (3,016 visits)
(5) Australia (2,549 visits)
(6) Canada (2,490 visits)
(7) Switzerland (1,895 visits)
(8) Denmark (1,603 visits)
(9) Japan (1,497 visits)
(10) Belgium (1,366 visits)