Wednesday, March 01, 2017
I guess it is old news but it only caught my eye today at the BBC website. Apparently Nature did a survey last summer (2016) were scientist were asked if they had "failed to reproduce another scientist's experiments"? What really surprised me was that only 70% on average said yes to that question. Obviously, scientists from all disciplines participated in the survey and chemistry did better in reproducibility than biology and medicine (when judged by themselves) but it looks pretty bleak overall. In synthetic organic chemistry, I would estimate that >95% of chemists have been unable to reproduce a published synthesis (as in get any of the desired molecule and not necessarily just the same high yield). Personally, I have had methods across the impact factor landscape fail in my hands, from Synlett to Nature Methods. On more than one occasion everything has just decomposed and gone black. Unless it is published in Organic Syntheses it's a bit of a lottery. Anyway, both articles are quite interesting and worth reading (although they are somewhat depressing). D!
Monday, February 20, 2017
I have on several occasions been asked to make a DCVC video tutorial and quite liked the idea of doing so. Thus, I have started my acting career as you can see in the video below. I think the video will be a useful guide for first time DCVCers. For more info you should consult this and this blog post on DCVC. Many thanks to the University of Copenhagen's Communication Department, in particular Jacob Lejbach Sørensen, for investing some time in making this possible. D!
Friday, September 05, 2014
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
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
Monday, August 12, 2013
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 email@example.com 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
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: http://internal.eps.hw.ac.uk/services/analytical/chn-league.htm
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: http://pubs.acs.org/doi/abs/10.1021/om4000067
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
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
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)
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
(10) South Korea
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.
|Silver catalysed Wolff rearragement in a sonicator. Left t = 0 hr; Right t = 2 hr.|
|Diazoinsane clear seal distillation kit purchased from Sigma-Aldrich.|
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
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 firstname.lastname@example.org
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!