An improved synthesis of 3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline: A key intermediate in the synthesis of photoaffinity probes

Article abstract of DOI:10.1016/j.tetlet.2017.07.031

An improved synthesis of 3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline, achieving an overall yield of 38% over seven steps is reported. Only three chromatographic separations were needed and the preparation of ～0.7?g of the target compound was demon

Full text of DOI:10.1016/j.tetlet.2017.07.031

Accepted Manuscript
An improved synthesis of3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline:
A key intermediate in the synthesis of photoaffinity probes
Torbjörn Wixe, Fredrik Almqvist
PII:
S0040-4039(17)30877-8
DOI:
http://dx.doi.org/10.1016/j.tetlet.2017.07.031
TETL 49113
Reference:
Tetrahedron Letters
To appear in:
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Revised Date:
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1 June 2017
2 July 2017
7 July 2017
Please cite this article as: Wixe, T., Almqvist, F., An improved synthesis of3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-
yl]aniline: A key intermediate in the synthesis of photoaffinity probes, Tetrahedron Letters (2017), doi: http://
dx.doi.org/10.1016/j.tetlet.2017.07.031
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Tetrahedron Letters
An improved synthesis of 3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline: A key
intermediate in the synthesis of photoaffinity probes
Torbjörn Wixea , Fredrik Almqvista, 
a Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
An improved synthesis of 3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline, achieving an
overall yield of 38% over seven steps is reported. Only three chromatographic separations were
needed and the preparation of ~0.7 g of the target compound was demonstrated. The stability of
the diazirine in solution at room temperature while exposed to ambient light was studied. No
significant degradation of the compound was observed over the course of five weeks in a 130
mM sample and only minor degradation was observed in weaker samples (10, 5, and 2.5 mM),
as demonstrated by 1H and 19F NMR.
Available online
Keywords:
Diazirine
Preparative synthesis
Photolysis
Stability
2009 Elsevier Ltd. All rights reserved.
 Fredrik Almqvist. Tel.: +46-707 397 9097; e-mail: fredrik.almqvist@umu.se

2
Introduction
The use of aryl diazirines for labeling biological macromolecules
was first proposed by Smith and Knowles in the early 1970’s.1
Since then diazirines have been used to identify the active sites of
hemeproteins,2 the binding site of barbiturate in the GABAA
receptors,3 and the binding sites of SIRT2 inhibitors,4 to mention
only a few examples. Excellent reviews on the subject have also
6
been published.5, As part of our research on ring fused 2-
pyridones,7 we were in need of aniline 1 (Fig. 1) with the
intention of developing probes for activity-based protein
profiling (ABPP). While diazirines containing benzyl amine (2),
benzyl alcohol (3) and benzoic acid (4) substituents are
commercially available and well studied,8-11 diazirine 1 is not as
easily acquired.
Scheme 1. Overview of published syntheses of diazirine 1.
In the light of the issues we had reproducing available
procedures, herein we report a detailed protocol for the reliable,
efficient, and high yielding synthesis of diazirine 1. The stability
of 1 in solution when exposed to the ambient light was also
studied.
Figure 1. Aromatic diazirines used for labeling biological
macromolecules. Diazirines 2-4 are commercially available.
Over the past decades, several synthetic procedures towards 1
have been published. The compound was first described by
Dolder and co-workers, but unfortunately synthetic details or
analytical data was not provided.12 Starting from 2,2,2-
trifluoroacetophenone (5), Darrow and co-workers schematically
described their synthesis of 1 (Scheme 1, route A),13 but limited
experimental details made it challenging to repeat this procedure.
Instead, we turned our attention to the work of Biasotti and co-
workers who started their synthesis from 6 (Scheme 1, route B).14
The final step was a sodium dithionite reduction of 7, yielding 1
in 47% yield and a reported overall yield of 26%.15 The reduction
has recently been improved to 58% yield, but the overall reported
yield of 1 was still low (18%).16 It is known that Na2S2O4
reductions are highly dependent on the quality of the reagent,17
and the final step did not work satisfactorily in our hands.
Results and Discussion
Starting from compound 6, attempted reduction of the nitro group
using Pd/C/H2(g),18 exclusively gave alcohol 8. Using formic
acid, Et3N and Pd/C2, 19 resulted in a ~2:1 mixture of alcohol 8
and aniline 9. Instead iron and hydrochloric acid was used to
reduce compound 6 to aniline 9. The crude product was used
without purification to furnish compound 10 in 62% yield over
two steps. Tosyloxime 11 was synthesized from 10 in 87% yield
over two steps, as described by Wang and co-workers.20
Scheme 2. Synthesis of tosyloxime 11.
Compound 11 was then heated in NH3 (l), contained in a sealed
pressure tube, in an attempt to obtain diazirine 12. However, only
the corresponding diaziridine (13) was obtained, despite an
extended reaction time (Scheme 3).20 Diaziridine 13 was oxidised
using iodine to give diazirine 12, which was directly used

3
without further purification to furnish diazirine 1 in 71% yield
over three steps, after purification. This corresponds to an overall
yield of 38% over seven steps. Diazirine 1 has been reported as a
solid,14, 16 but in our hands it was always an oil, despite prolonged
heating under vacuum or co-evaporation from CHCl3, Et2O or
EtOAc. However, all spectroscopic data (ESI) were in full
agreement with previous reports.14, 16
Foundation. Dr. Andrew Gerard Cairns is acknowledged for
valuable input to the manuscript.
Supplementary data
Supplementary data: Experimental procedures and NMR spectra.
References
1
Smith, R. A. G.; Knowles, J. R. J Am Chem Soc 1973,
95, 5072.
2
Tschirret-Guth, R. A.; Medzihradszky, K. F.; de
Montellano, P. R. O. J Am Chem Soc 1999, 121, 4731.
Savechenkov, P. Y.; Zhang, X.; Chiara, D. C.; Stewart,
3
D. S.; Ge, R. L.; Zhou, X. J.; Raines, D. E.; Cohen, J. B.; Forman, S.
A.; Miller, K. W.; Bruzik, K. S. J Med Chem 2012, 55, 6554.
4
Seifert, T.; Malo, M.; Lengqvist, J.; Sihlbom, C.; Jarho,
E. M.; Luthman, K. J Med Chem 2016, 59, 10794.
Dubinsky, L.; Krom, B. P.; Meijler, M. M. Bioorgan
Med Chem 2012, 20, 554.
5
6
Ziegler, S.; Pries, V.; Hedberg, C.; Waldmann, H.
Scheme 3. Final steps in the synthesis of diazirine 1.
Angew Chem Int Edit 2013, 52, 2744.
7
Good, J. A. D.; Silver, J.; Nunez-Otero, C.; Bahnan, W.;
Diazirines are typically synthesized and handled in the dark. This
is an obvious and simple precaution to take since light is used to
trigger photolysis. However, knowing that UV light (~365 nm) is
required for photolysis, compounds such as 1 should be stable in
the ambient light from the fluorescent bulbs that illuminate most
laboratories. Thus, photolysis should be of no practical concern
when using diazirine 1 in synthesis. To verify this, a sample of 1
was dissolved in MeOH-d4 and constantly exposed to ambient
light at room temperature. The concentration of 1 was 130 mM,
in the range of a typical reaction mixture. Also, the sample was
not placed close to a light source but was instead allowed to sit in
Krishnan, K. S.; Salin, O.; Engstrom, P.; Svensson, R.;
Artursson, P.; Gylfe, A.; Bergstrom, S.; Almqvist, F. J Med Chem
2016, 59, 2094.
8
Ambroise, Y.; Pillon, F.; Mioskowski, C.; Valleix, A.;
Rousseau, B. Eur J Org Chem 2001, 3961.
Bender, T.; Huss, M.; Wieezorek, H.; Grond, S.; von
Zezschwitz, P. Eur J Org Chem 2007, 3870.
10 Kumar, A. B.; Tipton, J. D.; Manetsch, R. Chem
Commun 2016, 52, 2729.
9
11
3084.
12
1990, 9, 407.
13
Weber, T.; Brunner, J. J Am Chem Soc 1995, 117,
the NMR tube in a lit room to mimic normal handing. 1H and 19
F
NMR spectra were regularly recorded over five weeks. No
Dolder, M.; Michel, H.; Sigrist, H. J Protein Chem
1
degradation was detected by H NMR, but a small change could
be observed as upfield 19F resonances, as expected for MeOH-d4
incorporation (see Fig. S1 and S2, ESI).
Darrow, J. W.; Hadac, E. M.; Miller, L. J.; Sugg, E. E.
Bioorg Med Chem Lett 1998, 8, 3127.
In order to see if the photolysis varied with
concentration, 10, 5 and 2.5 mM samples in MeOH-d4 were
handled in the same way and NMR spectra recorded over three
weeks (Fig. S3-S8). Minor MeOH-d4 incorporation was detected,
and appeared to be more pronounced in the weaker samples.
The low rate of photolysis observed over this long time
frame suggests this should not be a concern for the normal
handling and use of this compound.
14
Biasotti, B.; Dallavalle, S.; Merlini, L.; Farina, C.;
Gagliardi, S.; Parini, C.; Belfiore, P. Bioorgan Med Chem 2003,
11, 2247.
15
163% yield, and is therefore excluded when the yield is
estimated.
16
The first step in their synthesis appears to have a
O'Neill, L. C., R.; Cooper, M.; Robertson, A; Schroder,
K;, WO 2016/131098, 2016
17
29, 8.
18
Redemann, C. T.; Redemann, C. E. Org Synth 1949,
Conclusion
A robust and high yielding (38% over seven steps) synthesis of
diazirine 1 from commercially available starting materials is
reported. With only three chromatographic purifications it is a
quick and efficient synthetic procedure. The stability of 1 in
solution when exposed to ambient light was also studied. No
relevant photolysis was detected over the course of five weeks in
a sample at a concentration comparable to a reaction mixture.
Photolysis was easier to detect in samples of weaker
concentration. Given the time scale, there seems to be no reason
to take any precautions regarding light during synthesis or
purification when using compound 1.
Bae, I. H. S., J.B.; Han, S.M.; Kwak, E.J.; Kim, H.S.; Song,
J.Y.; Byun, E.Y.; Jun, S.A.; Ahn, Y.G., WO 2013/100632, 2013
19
20
K.; Sakihama, Y.; Hashidoko, Y.; Hatanaka, Y.; Hashimoto, M.
Org Lett 2015, 17, 616.
Terpko, M. O.; Heck, R. F. J Org Chem 1980, 45, 4992.
Wang, L.; Murai, Y.; Yoshida, T.; Ishida, A.; Masuda,
Acknowledgement
We acknowledge funding from the Swedish Foundation for
Strategic Research, the Swedish Research Council the Knut and
Alice Wallenberg Foundation and the Göran Gustafsson

4
Highlights




A quick and robust synthetic method of
an important diazirine was developed
Chromatographic purifications were kept
at a minimum
The overall yield was improved
compared with known procedures
Limited photolysis of the diazirine under
ambient conditions was observed

5
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An improved synthesis of 3-[3-(trifluoromethyl)-3H-1,2-diazirin-3-yl]aniline: A key intermediate
in the synthesis of photoaffinity probes
Torbjörn Wixe and Fredrik Almqvist