The Dimroth rearrangement as a probable cause for structural misassignments in imidazo[1,2-a]pyrimidines: A 15N-labelling study and an easy method for the determination of regiochemistry

Article abstract of DOI:10.1016/j.tet.2018.06.033

Structural misassignments are often seen for complex natural products, but this can also be an issue with seemingly simpler structures. In this paper, we describe how, using a ¹⁵N-labelled analogue, we established that the Dimroth rearrangement

Full text of DOI:10.1016/j.tet.2018.06.033

Accepted Manuscript
The Dimroth rearrangement as a probable cause for structural misassignments
15
in imidazo[1,2-a]pyrimidines: A N-labelling study and an easy method for the
determination of regiochemistry
Maria Chatzopoulou, R. Fernando Martínez, Nicky J. Willis, Timothy D.W. Claridge,
Francis X. Wilson, Graham M. Wynne, Stephen G. Davies, Angela J. Russell
PII:
S0040-4020(18)30734-8
10.1016/j.tet.2018.06.033
TET 29629
DOI:
Reference:
To appear in: Tetrahedron
Received Date: 15 March 2018
Revised Date: 13 June 2018
Accepted Date: 14 June 2018
Please cite this article as: Chatzopoulou M, Martínez RF, Willis NJ, Claridge TDW, Wilson FX,
Wynne GM, Davies SG, Russell AJ, The Dimroth rearrangement as a probable cause for structural
15
misassignments in imidazo[1,2-a]pyrimidines: A N-labelling study and an easy method for the
determination of regiochemistry, Tetrahedron (2018), doi: 10.1016/j.tet.2018.06.033.
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The Dimroth rearrangement as a probable
cause for structure misassignments in
imidazo[1,2-a]pyrimidines: A 15N-labelling
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determination of regio-chemistry
Maria Chatzopouloua, R. Fernando Martíneza, Nicky J. Willisa, Timothy D. W. Claridgea, Francis X. Wilsonb,
Graham M. Wynnea, Stephen G. Daviesa, Angela J. Russella,c*
a Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford,
OX1 3TA, UK; b Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14
4SB, UK;c Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK

1
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Tetrahedron
journal homepage: www.elsevier.com
The Dimroth rearrangement as a probable cause for structural misassignments in
imidazo[1,2-a]pyrimidines: A 15N-labelling study and an easy method for the
determination of regiochemistry
Maria Chatzopouloua, R. Fernando Martíneza, Nicky J. Willisa, Timothy D. W. Claridgea, Francis X.
Wilsonb, Graham M. Wynnea, Stephen G. Daviesa, Angela J Russella,c,*
a Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
b Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, UK
c Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
Structural misassignments are often seen for complex natural products, but this can also be an
issue with seemingly simpler structures. In this paper, we describe how, using a 15N-labelled
analogue, we established that the Dimroth rearrangement can occur in imidazo[1,2-
a]pyrimidines and result in an incorrect regiochemical assignment of such compounds. These
studies supported a rearrangement mechanism involving addition of hydroxide ion followed by
ring opening. It was also observed that C(2) and C(3) substituted regioisomers could be readily
distinguished using 1H NMR spectroscopy.
Available online
Keywords:
Dimroth rearrangement
Imidazo[1,2-a]pyrimidine
Azaheterocycle
2009 Elsevier Ltd. All rights reserved
.
Polyazaindolizine
Misassignment
1. Introduction
of a Dimroth-type ring opening in the literature dates back to
1888,18 it is not uncommon for incomplete data to be provided for
new analogues and regiochemical assignments made by
comparison (often erroneously) with existing literature data, as
the use of more complicated and time-consuming X-ray studies
to unequivocally assign the regiochemistry is frequently not
carried out.
The imidazo[1,2-a]pyrimidine scaffold is an emerging
heterobicyclic scaffold of significant interest in the contemporary
medicinal chemistry literature. In recent years there have been an
increasing number of reports of activity of this class of
compound against various different targets (mGlu2, mGlu5, D1,
Lp-PLA2, TNF, PI3K, SUV39H2,IAP-BIR and DPP-4)1-9 and in
multiple therapeutic areas (AIDS, antiparasitic, antiproliferative,
autotaxine associated disease, Peyronie’s disease, spinal
muscular atrophy),10-15 as well as their use as blue fluorescent
light emitters.16 A more comprehensive list on the potential
therapeutic areas can be found in a recent review on synthetic
approaches for this scaffold.17 Furthermore, imidazo[1,2-
a]pyrimidines are found in a number of commercially available
compound libraries, probably due to their privileged
physicochemical properties and their resemblance to natural
substrates such as purines.
Figure 1. Postulated mechanism of the Dimroth rearrangement under
basic conditions in the imidazo[1,2-a]pyrimidine ring.
A
feature of aza heterocycles such as imidazo[1,2-
Many factors influence the propensity of aza-heterocycles to
undergo the Dimroth rearrangement. In general, decreasing the π
electron density of the fused 6-ring increases the rate of
rearrangement. Thus, aza-substitution in the imidazo[1,2-
a]pyridine system to give the corresponding imidazo[1,2-
a]pyrimidine leads to more facile nucleophilic attack at position 5
(Figure 1), and the same is observed with electron withdrawing
a]pyrimidines is that they can undergo the Dimroth
rearrangement when subjected to appropriate reaction conditions.
This transformation is described as a translocation of two
heteroatoms in a heterocyclic system with or without changes in
the ring structure, and it is an often undesired side reaction that
occurs, usually in basic media and as a result can lead to structure
misassignments for the products. Even though the first mention

2
Tetrahedron
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Scheme 1. Synthetic routes towards carboxylic acid derivatives of imidazo[1,2-a]pyrimidines. a. 1) ethyl bromopyruvate, THF, rt,
2h, 2) EtOH, 95 oC, 1h b. ethyl bromopyruvate, EtOH, 95 oC, 6h, 52% over two steps c. arylboronic acid, Pd(OAc)2, P(o-Tol)3, CsF,
DME, 90 oC, 20h, 22-75% d. CaCl2, amine, MeOH, 70 oC, 1 h, 10-34% e. NaOH, EtOH, THF, H2O, 60 oC, 3h, f. amine, HBTU, TEA,
MeCN, rt, 2h, 17-64% for 3a-e, 37-45% over two steps for 5a-e, g. arylboronic acid, Pd(dppf)Cl2, K2CO3, dioxane/H2O, rt, 15 min, 73-
93% h. bromopyruvic acid, DMF, rt, 4d, 67-74%.
groups. As a result 2-phenylimidazo[1,2-a]pyridine does not
undergo the rearrangement under alkaline conditions, however,
the same ring system will undergo a rearrangement in the
presence of electron withdrawing substituents such as a nitro
group at C6 or C8.19 The rate of rearrangement is dependent on
pH, with the product distribution usually dependent on the
substituents.20,21 Of the rearrangements that have been described
for the imidazo[1,2-a]pyrimidine core,20,22-25 the most common
occurrence was with the use of hydrolytic23,25 or haloformic
conditions,22,24 as outlined above. The Dimroth rearrangement
can also take place in acidic conditions or with photo-activation
in other aza-heterocycles and especially triazolo species,
although such transformations have not been observed with the
imidazo[1,2-a]pyrimidine system.
Table 1. Amides 3a-e and 5a-e produced via Routes A and B
in Scheme 1
Cpd
3a
R1
3-OMe
R2
R3
Route
A
Yield
33%
N-morpholino
C
64%
3b
3c
3d
3-Cl,4-Cl
3-CF3
3-OMe
Me
Me
Me
Et
Et
Et
C
C
A
40%
17%
10%
C
49%
3e
5a
5b
5c
5d
5e
3-OMe
3-OMe
3-Cl,4-Cl
3-CF3
3-OMe
3-OMe
N-pyrrolydinyl
N-morpholino
A
B
B
B
B
B
63%
37% (from 2a)
39% (from 2a)
39% (from 2a)
41% (from 2a)
45% (from 2a)
Me
Me
Me
Et
Et
Et
Mechanistic aspects of the rearrangement have been
described, including some important kinetic and computational
calculations, which have been provided by Guerret et al.20
identifying the minimal characteristics of aza-heterocycles to
undergo the Dimroth rearrangement. In this study the authors
recognise the possibilities of water addition by other mechanisms
such as 1,4-addition or tautomerism, but conclude their data best
supports a mechanism involving nucleophilic attack at C5/ring
opening (as depicted in Figure 1).
N-pyrrolydinyl
2. Results and Discussion
We became interested in these ring systems whilst
investigating access to a range of imidazo[1,2-a]pyrimidine
analogues substituted at C2 and C6. We initially followed a route
wherein the bicyclic core was formed by reaction of 2-amino-5-
iodopyrimidine with ethyl bromopyruvate. A Suzuki reaction was
then followed by a direct conversion of esters 2 to the
corresponding amides 3 (Scheme 1, Route A). A small series of
amide analogues was prepared using this method (compounds 3a,
3d, 3e Table 1). However, when an alternative route was
employed involving initial hydrolysis of esters 2 followed by
amide coupling of the resultant carboxylic acids 4 (Scheme 1,
Route B, compounds 5a-e, Table 1) we noted that there was a
discrepancy in the analytical data of the products formed. For
example, the products 3a and 5a were of the same mass, but their
NMR spectra and TLC retention factors differed significantly.
We suspected this may have been caused by a Dimroth
rearrangement of ester intermediate 2a. However, we needed to
Interestingly, in surveying the literature data on this class of
heterocycle, we noted that there was surprisingly little supporting
evidence for the assigned structures, particularly in the patent
literature where often more limited data are provided. In most
cases the authors assigned either of the two regioisomers based
on previous observations. Moreover, there were frequently
discrepancies in the spectroscopic data even where the same
regioisomer was claimed. Given the emergence of the scaffold in
multiple commercially available compound libraries, and the
increasing frequency with which these compounds are mentioned
in the literature, it is crucial to be able to distinguish between the
two possible regioisomeric products, as well as to characterize
the conditions that induce the rearrangement.

3
unambiguously determine the regiochemistry within products 3a
and 5a.
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The reaction of 2-aminopyrimidines with α-halocarbonyl
species to afford the C2 regioisomer as the kinetic product is very
well precedented, and mixtures of isomers can usually be
obtained in different ratios by subsequent rearrangement under
aqueous basic conditions.20,25,26 Given that intermediates 1 and 2
and products 3 were all obtained as a single regioisomer, and that
each transformation in route A was conducted under anhydrous
conditions, we initially tentatively assigned the structures as the
C2-substituted regioisomers. Regioisomer 3 could also be
accessed via a different route avoiding a basic saponification step
wherein the imidazo[1,2-a]pyrimidine-2-carboxylic acids 7a-c
were synthesized directly from reaction of 2-aminopyrimidines
6a-c with bromopyruvic acid. Amide coupling of carboxylic
acids 7a-c gave products 3a-e each as a single regioisomer
(Scheme 1, Route C, Table 1).
Scheme 2. Synthetic routes for both the 15N-labelled and 14N-
imidazo[1,2-a]pyrimidines. a. PhB(OH)2, Pd(OAc)2, K3PO4,
EG, 80 oC, 2h, 90% b. ethyl bromopyruvate or bromopyruvic
acid, DMF, rt, 4d, 18-41% c. NH4Cl, 1M NaOH, 150 oC,
MW, 30 min, 61% d. PhB(OH)2, Pd(OAc)2, Na2CO3,
H2O/EtOH, 45 oC, 0.5 h, 80% e. 15NH4Cl, 1M NaOH, 150 oC,
MW, 30 min, 81%.
In Route B we reasoned that the isomerization must have
occurred either at the hydrolysis or the amide formation steps,
most plausibly at the ester hydrolysis step as this proceeded
under aqueous basic conditions. We therefore tentatively
assigned 4a and 5a as the C3 substituted regioisomers. However,
Thus, samples of 14N-C2-substituted ethyl ester and the
corresponding carboxylic acid were prepared following a two-
step protocol from 2-amino-5-iodopyrimidine. A Suzuki cross-
coupling with phenylboronic acid afforded 2-aminopyrimidine
intermediate 6 and subsequent cyclisation with either ethyl
bromopyruvate or bromopyruvic acid gave the desired 2-
substituted imidazo[1,2-a]pyrimidines 8a and 8b respectively.
The 15N-labelled counterparts 8c and 8d were accessed via a
three-step procedure from 5-bromo-2-chloropyrimidine involving
Suzuki cross-coupling, substitution at C2 using 15NH4Cl under
mildly basic conditions and cyclisation with either ethyl
bromopyruvate or bromopyruvic acid. To ensure that no
rearrangement had occurred under these latter reaction
conditions, samples of 6, 8a and 8b were also prepared by this
route: analytical data was shown to be identical (Scheme 2).
Formation of 3-carboxylic acid 11a as a single regioisomer was
achieved by subjecting ethyl ester 8a to the basic saponification
conditions described above (Scheme 3).
1
on comparing the H NMR data for 3a, 4a and 5a with very
similar compounds in the literature assigned as C2 regioisomers
we noticed a discrepancy (Supplementary Information, Table 2,
Entries 1 and 3).27 These compounds had been prepared using
basic hydrolysis conditions from the corresponding ethyl ester,
but no supporting evidence for the regiochemical assignment was
provided. However, their data was not in agreement with several
other literature sources reporting spectroscopic data for the C2
regioisomer where a significant deshielding effect in the shift of
H-5 is observed with electron withdrawing substituents at C3.22-24
As these data were contradictory and there are no unambiguous
assignments for both regioisomers made possible through
correlation with techniques such as X-ray crystallography, we
decided to prepare a small array of unlabelled and 15N-labelled
analogues both to use as mechanistic probes and to attempt to
assign unambiguously the regiochemistry of each C2 and C3
isomer (Scheme 2).
Figure 2. 2D NOESY spectra showing nOe correlations in compounds 8b and 11a.

4
Tetrahedron
(C-7: 150-152 ppm, C-5: 130-134 ppm, C-3: 115-120 ppm and
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C-2: 139-144 ppm). This strongly supports that the NMR shift of
H-5 can be used to provide an initial indication of which
regioisomer is produced, with further supporting evidence being
derived from more detailed NMR analysis, such as HSQC
correlations. A final confirmation with NOESY or HMBC would
be required for unambiguous characterisation, but at least in this
manner one would have a quick indication of which isomer to
expect.
Although others have performed kinetic and computational
analyses to yield insights into the rearrangement mechanism, to
our knowledge, no isotopic labelling studies of imidazo[1,2-
a]pyrimidines have been performed to support the proposed
mechanism of the rearrangement. In order to establish whether
the transformation observed was a result of the Dimroth
rearrangement, we investigated the reaction of 15N-labelled
aminopyrimidines 8c under basic conditions.
Scheme 3. Products obtained from the ester derivatives 8a or
8c under different conditions. a. 5% NaOH, MeOH, H2O, 70
oC, 18h, 0% b. NaOH, EtOH, THF, H2O, 60 oC, 6h, 51-55% c.
EtONa, EtOH, 95 oC, 20h, 26-29%.
The regiochemistry within 11a was confirmed by full
assignment and NOESY correlations (Supporting Information).
As expected, there are NOE correlations between the two protons
of the pyrimidine ring and the phenyl ortho protons (11a), while
in the case of 8a there is a further correlation between H-5 and H-
3 (Figure 2). This was further corroborated by 15N NMR, as
described below. It is also apparent that there is deshielding of H-
5 in 3-regioisomers and this was observed in all the analogues
synthesized (Supplementary Table 1). Interestingly this effect
was more pronounced when CDCl3 was used as a solvent (rather
than MeOH-d4, MeCN-d3 or DMSO-d6) where the corresponding
increase in chemical shift was greater than 1 ppm, possibly due to
the presence of acid in CDCl3. No major differences were
observed in the shifts of the other two protons of interest, H-7
and H-2 or H-3. Assignment of the pyrimidine protons could be
readily achieved from their coupling constant (2-3 Hz) and it was
also observed that the 13C chemical shifts were also diagnostic
The ester 8c was first subjected to the previously reported
Dimroth conditions ([a] 5% NaOH aqueous methanolic solution,
Scheme 3). Interestingly, we observed only limited conversion to
the other isomer, some hydrolysis in the case of the ester, but
mainly decomposition. The use of THF as a co-solvent has been
described as facilitating the rearrangement and minimizing
decomposition in other substrates.28 Treatment of esters 8a and
8c under these conditions gave the corresponding carboxylic
acids 11a and 11b in good yields (Scheme 3, [b]). The
rearrangement was also observed upon treatment of 8a with
EtONa in EtOH allowing access to the respective 3-substituted
esters (12a-b). We further wanted to investigate if
a
rearrangement takes place in this ring system in the presence of
acid or by photoactivation. No conversion was observed in the
presence of formic acid after 24 h or after irradiation at 365 nm
(100 W) for 30 min for either 2- and 3-regioisomeric esters 8a or
11a.
1
Figure 3. H-15N HMBC correlations in compounds 8c and 12b (spectra optimised to JNH = 2 Hz for 8c and 5 Hz for 12b)

5
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Figure 4. Schematic representation of the literature findings. A. Imidazo[1,2-a]pyrimidines and sub-classes occurrence in the
literature and respective spectral data B. Pie chart showing the regioisomeric subclasses of interest. C: Pie chart illustrating the
availability of structural characterization data in 2,6- and 3,6-disubstituted imidazo[1,2-a]pyrimidines D. Pie chart illustrating the
availability of 1H-NMR data in carboxylic acid derivatives of 2,6- and 3,6-imidazo[1,2-a]pyrimidines and incidences of correct or
incorrect regiochemical assignments.
Extensive NMR characterization verified the regiochemistry
of all the 15N-labelled compounds and showed that indeed the 15
structures in the literature. We conducted a literature search in
Reaxys (December 2017, Figure 4): 9302 substances were found
containing the imidazo[1,2-a]pyrimidine core in 1426 research
papers and 936 patents. It was thus confirmed that this is indeed a
ubiquitous scaffold. The quantity and quality of the data used to
assign structure for these examples was analysed in detail, as it
was this that was of particular interest. We then narrowed our
search down to 2,6- and 3,6-disubstituted analogues, because
these were the scaffolds of direct relevance to the studies we had
conducted. 1354 2,6-disubstituted imidazo[1,2-a]pyrimidines
derivatives were reported in 138 research papers and 116 patents.
Out of the 1354 compounds only 284 were reported with 1H
NMR data (in 44 out of 138 research papers and 29 out of 116
patents). Similar observations were noted for 3,6-disubstituted
imidazo[1,2-a]pyrimidines (355 reported compounds in 55
research papers and 47 patents), where again only 73 out of 355
N
atom initially occupying position 1 in analogue 8c was in
position 4 in analogues 11b and 12b after the rearrangement had
taken place. A decrease in chemical shift was observed for 15N
from 239.9 and 241.1 ppm for 8c and 8d respectively, to 188.5
and 187.7 ppm for 11b and 12b respectively, when the 15N was
positioned at the ring junction within the bicyclic system in the
two latter analogues, and consistent with the change from sp2 to
1
sp3 environments. Further confirmation came from the H-15N
n
HMBC correlations for 8c and 12b (Figure 3). For 8c all JNH
couplings constants of the labelled nitrogen were very small (< 1
1
1
Hz), being unresolved in the H and the H-coupled 15N spectra.
As such, the 15N HMBC correlation intensities for 8c were very
sensitive to the JNH value chosen for the HMBC acquisition (5 or
2 Hz). This also meant correlations to unlabeled nitrogen centres
were of comparable intensity to those of the labelled nitrogen in
the 5 Hz optimised HMBC in particular (NMR Supplementary
Material ). For 12b, the JNH couplings of H2 and H5 were clearly
1
compounds had H-NMR data reported (25 research papers and
19 patents). Of particular note was that the vast majority of these
documents did not unambiguously verify the structure using
further crystallographic or 2D-NMR data. Most tellingly, we
1
resolved in the H spectrum (3.0 and 1.3 Hz respectively) and
1
gave rise to the dominant correlations in the 5 Hz-optimised
HMBC.. Finally, the multiplicities of protons and carbons
neighboring 15N also changed accordingly (NMR Supplementary
Material).
were able to find a matched pair of H NMR and X-ray data in
only in one patent and a single research paper. Rassapali et al.29
confirmed their structure with X-ray in the total synthesis of
oroidin and related alkaloids. However, in this case the authors
were interested only in one of the two regioisomers and
spectroscopic data for the regioisomer was not provided. Also, in
the patent application WO200607175230 the authors confirmed
the structure of their 2-substituted carboxylic acid/ester
Having investigated the spectroscopic properties of these
compounds, we next used this information to assess whether
there were any other apparent misassignments of such compound

6
Tetrahedron
derivatives using X-ray crystallography, but again 1H NMR
internally calibrated with polyalanine, or a Micromass GCT
ACCEPTED MANUSCRIPT
data is provided only for the 2-regioisomer.
instrument fitted with a Scientific Glass Instruments BPX5
column (15 m × 0.25 mm) using amyl acetate as a lock mass. For
the UV irradiation experiments a UVP High-Intensity UV
Inspection Lamp Model B-100AP was used.
As the only available crystal structures were on carboxylic
acid derivatives, and our synthetic efforts were targeting such
scaffolds, we focused our search on this type of compound. It
was very concerning that out of 106 reported compounds in
4.2. Ethyl 6-iodoimidazo[1,2-a]pyrimidine-2-carboxylate (1)
1
Reaxys only 21 had associated NMR data. The H NMR data
Ethyl bromopyruvate (1.51 mL, 10.86 mmol) was added
dropwise to a solution of 2-amino-4-iodopyrimidine (0.80 g, 3.62
mmol) in dry THF (40 mL). The mixture was stirred at rt for 2 h
after which it was filtered. This solid was then dissolved in
ethanol (20 mL) and refluxed for 1 h. The reaction mixture was
cooled down, concentrated in vacuo and partitioned between
CH2Cl2 (20 mL) and saturated aqueous NaHCO3 (20 mL). The
organic layer was dried (MgSO4), filtered and concentrated in
vacuo. Purification by flash column chromatography (eluent
30−40 °C petrol/EtOAc, 3:1 to 1:6) afforded 1 as a white solid
(0.59 g, 52%): mp 209-211 °C; νmax (cm–1) 1721 (C=O); 1H NMR
(400 MHz, CDCl3) 8.77 (d, J = 2.0 Hz, 1H), 8.69 (d, J = 2.0 Hz,
1H), 8.10 (s,1H), 4.45 (q, J = 7.0 Hz, 2H), 1.42 (t, J = 7.0 Hz,
3H); 13C NMR (100 MHz, CDCl3) 162.6, 157.0, 146.1, 138.3,
114.8, 75.6, 61.7, 14.5; HRMS (ESI+) C9H9O2N3127I+ [M+H]+
requires 317.9734; found 317.9725.
available is reported in Supplementary Table 2 (Supplementary
Information). There we looked for the characteristic H-5 shifts to
assess the regiochemistry of the compounds. Even in this small
sample, we observed that 12 (>50%) compounds have potentially
misassigned structures across 7 documents. This finding confirms
that this is a very important issue that needs to be brought to the
attention of the scientific community.
3. Conclusion
In order to explore further an unexpected Dimroth
rearrangement observed whilst synthesizing some imidazo[1,2-
a]pyrimidine derivatives, we synthesized unlabelled and 15N-
labelled analogues in order to unambiguously assign the
regiochemistry of the 2- and 3-substituted isomers and elucidate
the reaction mechanism. These studies supported a rearrangement
mechanism involving addition of hydroxide ion followed by ring
opening. Confirmation of structure with X-ray is the usual way to
determine regioisomerism for most derivatives, but for mono-
substituted imidazo[1,2-a]pyrimidines on the imidazole ring, the
structure can be determined with a NOESY or an HMBC
experiment. In fact, the chemical shifts of the pyrimidine ring
protons in conjunction with an HSQC can also serve as a first
indication, since the H-5 proton appears to be significantly
deshielded in 3-substituted derivatives, due to the presence of the
carbonyl substituent. However, final confirmation with either two
2D-NMR experiments or X-ray crystallography would allow
more confidence in the regiochemical assignment. This has
potentially far reaching consequences both in terms of similar
effects with related ring systems, but also provides a cautionary
tale against relying directly on published data for structural
assignments.
4.3. General Method A. Synthesis of ethyl 6-arylimidazo[1,2-
a]pyrimidine-2-carboxylate
Ethyl 6-iodoimidazo[1,2-a]pyrimidine-2-carboxylate 1 (1 eq),
caesium fluoride (2.5 eq), arylphenylboronic acid (2 eq), tri(o-
tolyl)phosphine (0.1 eq) and palladium acetate (0.05 eq) were
dissolved in 1,2-dimethoxyethane (0.1 M) and the mixture was
evacuated and degassed. The reaction mixture was stirred at 90
°C for 20 h, after which it was diluted with CH2Cl2 and washed
with H2O. The organic layer was dried (MgSO4), filtered and
concentrated in vacuo. The residue was purified by flash column
chromatography (eluent 30−40 °C petrol/EtOAc, 10:1 to 1:5).
Representative spectra for cpd 2a are given below.
4.3.1. Ethyl 6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidine-2-carboxylate (2a)
1
Yield: 75%. mp 207-208 °C; νmax (cm–1) 1722 (C=O); H
NMR (400 MHz, CDCl3) 8.90 (d, J = 2.5 Hz, 1H), 8.57 (d, J =
2.5 Hz, 1H), 8.18 (s, 1H), 7.44 (t, J = 8.0 Hz, 1H), 7.14 (d, J =
8.0 Hz, 1H), 7.08 (s, 1H), 7.01 (dd, J = 8.0, 1.8 Hz, 1H), 4.47 (q,
J = 7.0 Hz, 2H), 3.88 (s, 3H), 1.45 (t, J = 7.0 Hz, 3H); 13C NMR
(100 MHz, CDCl3) 163.0, 160.6, 152.8, 147.6, 138.6, 134.9,
130.8, 130.5, 124.6, 119.5, 115.5, 114.4, 113.2, 61.6, 55.6, 14.5;
4. Experimental
4.1. General
+
HRMS (ESI+) C16H16O3N3 [M+H]+ requires 298.1186; found
All reactions involving moisture-sensitive reagents were
carried out under a nitrogen or argon atmosphere using standard
vacuum line techniques and glassware that was flame dried and
cooled under nitrogen before use. Water was purified by an
Elix® UV-10 system. All other reagents were used as supplied
(analytical or HPLC grade) without prior purification. Thin layer
chromatography was performed on aluminium plates coated with
60 F254 silica. Flash column chromatography was performed
either on Kieselgel 60 silica on a glass column, or on a Biotage
SP4 automated flash column chromatography platform. Melting
points were recorded on a EZ-Melt Automated Melting Point
Apparatus (EZ Melt) and are uncorrected. IR spectra were
recorded on a Bruker Tensor 27 FT-IR spectrometer. Selected
characteristic peaks are reported in cm–1. NMR spectra were
recorded on Bruker Avance III spectrometers (at 400, 500 or 600
MHz) using the deuterated solvent stated and at rt unless
otherwise stated. The field was locked by external referencing to
298.1183.
4.4. General Method B. Synthesis of amides via Route A
To a suspension of 2a (1 eq) in anhydrous MeOH (0.1 M),
CaCl2 (1 eq) and the appropriate amine (1 eq) were added and
refluxed for 1 h. The solvent was then removed in vacuo and 3a-e
were isolated after flash column chromatography (eluent
30−40 °C petrol/EtOAc, 4:1 to 1:1).
4.4.1. (6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidin-2-yl)(morpholino)methanone (3a)
o
1
Yield: 33%. mp 273-275 C; H NMR (500 MHz, CDCl3) δ
8.86 (d, J = 2.5 Hz, 1H, H-7), 8.58 (d, J = 2.5 Hz, 1H, H-5), 8.18
(s, 1H, H-3), 7.50 – 7.40 (m, 1H, H-5’), 7.15 (ddd, J = 7.7, 1.8,
0.9 Hz, 1H, H-6’), 7.09 (t, J = 2.1 Hz, 1H, H-2’), 7.01 (ddd, J =
8.3, 2.6, 0.9 Hz, 1H, H-4’), 4.52 (t, J = 4.8 Hz, 2H, H-2”), 3.89
(s, 3H, OCH3), 3.86 – 3.77 (m, 6H, H-2” and H-3”); 13C NMR
(125.5 MHz, CDCl3) δ 162.3 (C=O), 160.6 (C-3’), 152.0 (C-7),
146.4 (C-9), 142.6 (C-2), 134.9 (C-1’), 130.8 (C-5’), 130.4 (C-5),
1
the relevant deuteron resonance. The JNH value for the H-15N
HMBC acquisition was 5 Hz unless otherwise stated. Accurate
mass measurements were run on either a Bruker MicroTOF

7
124.4 (C-6), 119.5 (C-6’), 115.8 (C-3), 114.3 (C-4’), 113.2 (C-
2’), 67.6 (C-3”), 67.1 (C-3”), 55.6 (OCH3), 47.5 (C-2”), 43.4 (C-
rotamer 1), 1.26 (t, J = 7.1 Hz, 1.3H, CH2CH3, rotamer 2); 13C
ACCEPTED MANUSCRIPT
2”); HRMS (ESI+) C18H19N4O3 ([M+H]+) requires 339.14572;
NMR (125.5 MHz, CDCl3) δ 163.4-163.0 (C=O), 150.9-150.8
(C-7), 146.4-146.3 (C-9), 144.0-143.7 (C-2), 134.7 (C-1’), 132.2
(q, J = 32.6 Hz, C-3’), 130.8 (s, C-5), 130.5 (C-6’), 130.3 (C-5’),
125.8 (q, J = 4.0 Hz, C-2’), 124.0 (q, J = 3.9 Hz, C-4’), 123.9 (q,
J = 272.6 Hz, CF3), 123.0 (d, J = 3.1 Hz, C-6), 115.3-115.2 (C-
3), 45.7-43.8 (CH2CH3), 36.5-34.1 (NCH3), 14.3-12.2 (CH2CH3);
HRMS (ESI+) C17H16F3N4O+ ([M+H]+) requires 349.12762;
found 349.12645.
+
found 339.14506.
4.4.2. N-ethyl-6-(3-methoxyphenyl)-N-
methylimidazo[1,2-a]pyrimidine-2-carboxamide
(3d).
o
Yield: 10%. mp 178-180 C; 1H NMR (500 MHz, CDCl3) δ
8.84 (t, J = 2.9 Hz, 1H, H-7), 8.58 (d, J = 2.5 Hz, 1H, H-5), 8.13
(s, 1H, H-3), 7.44 (app t, J = 8.0 Hz, H-5’), 7.15 (ddd, J = 7.6,
1.8, 0.9 Hz, 1H, H-6’), 7.08 (t, J = 2.1 Hz, 1H, H-2’), 7.00 (ddd,
J = 8.3, 2.6, 0.9 Hz, 1H, H-4’), 4.15 (q, J = 7.1 Hz, 1.1 H,
CH2CH3 rotamer 1), 3.88 (s, 3H, OCH3), 3.62 (q, J = 7.2 Hz, 0.9
H, CH2CH3 rotamer 2), 3.59 (s, 1.3H, NCH3 rotamer 1), 3.13 (s,
1.7H, NCH3 rotamer 2), 1.31 (t, J = 7.1 Hz, 1.7H, CH2CH3,
rotamer 1), 1.26 (t, J = 7.2 Hz, 1.3H, CH2CH3, rotamer 2); 13C
NMR (125.5 MHz, CDCl3) δ 163.6-163.2 (C=O), 160.5 (C-3’),
151.6-151.5 (C-7), 146.5-146.4 (C-9), 143.5-143.3 (C-2), 135.1
(C-1’), 130.8 (C-5’), 130.4 (C-5), 124.2 (C-6), 119.5 (C-6’),
115.1 (C-3), 114.2 (C-4’), 113.1 (C-2’), 55.6 (OCH3), 45.7-43.8
(CH2CH3), 36.5-34.1 (NCH3), 14.3-12.2 (CH2CH3); HRMS
4.5.4. N-ethyl-6-(3-methoxyphenyl)-N-
methylimidazo[1,2-a]pyrimidine-2-carboxamide
(3d).
Yield: 49%. Same as the product obtained from Route A
4.5.5. (6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidin-2-yl)(pyrrolidin-1-yl)methanone (3e).
o
Yield: 63%. mp 214-216 C; 1H NMR (500 MHz, CDCl3) δ
8.84 (d, J = 2.5 Hz, 1H, H-7), 8.58 (d, J = 2.5 Hz, 1H, H-5), 8.20
(s, 1H, H-3), 7.43 (app t, J = 8.0 Hz, 1H, H-5’), 7.15 (ddd, J =
7.6, 1.8, 0.9 Hz, 1H, H-6’), 7.08 (t, J = 2.1 Hz, 1H, H-2’), 7.00
(ddd, J = 8.3, 2.5, 0.9 Hz, 1H, H-4’), 4.25 (t, J = 6.8 Hz, 2H, H-
2”), 3.88 (s, 3H, OCH3), 3.71 (t, J = 6.9 Hz, 2H, H-2”), 2.00 (pd,
J = 6.6, 1.1 Hz, 2H H-3”), 1.93 (pd, J = 6.7, 1.2 Hz, 2H H-3”);
13C NMR (125.5 MHz, CDCl3) δ 161.8 (C=O), 160.5 (C-3’),
151.5 (C-7), 146.7 (C-9), 143.6 (C-2), 135.1 (C-1’), 130.8 (C-5’),
130.4 (C-5), 124.2 (C-6), 119.5 (C-6’), 114.9 (C-3), 114.2 (C-4’),
113.1 (C-2’), 55.6 (OCH3), 49.2 (C-2”), 47.3 (C-2”), 26.8 (C-3”),
+
(ESI+) C17H19N4O2 ([M+H]+) requires 311.15080; found
311.14994.
4.5. General Method C. Synthesis of amides via Route C
A solution of 7a-c (1 eq), HBTU (2.0 eq) and triethylamine
(1.5 eq) in acetonitrile (0.1 M) was stirred at rt for 15 min. Then
the amine (1.5 eq) was added and the resulting mixture was
stirred at rt for further 2 h. The solvent was evaporated in vacuo,
and the residue was dissolved in EtOAc and extracted with water.
The organic layer was washed with brine, dried over Na2SO4 and
concentrated in vacuo. Purification via flash column
chromatography (eluent 30−40 °C petrol/EtOAc, 3:1 to 1:3) gave
3a-e (Yields:17-64%)
23.9 (C-3”); HRMS (ESI+) C18H19N4O2 ([M+H]+) requires
+
323.15080; found 323.14988.
4.6. General method D. Synthesis of amides via Route B.
To a refluxing solution of 2a-c (1 eq) in THF/EtOH (1:1, 0.15
M), 1M NaOH in H2O (3 eq, 1:1) was added and the reaction
refluxed for 3 h. It was then cooled to rt, pH was adjusted to 8
(NaHCO3) and extracted with EtOAc. Then, the aqueous phase
was further acidified to pH 3 (1N HCl), and the white precipitate
formed was collected, washed with Et2O to obtain crude 4a-c.
The latter were converted to the respective amides following the
procedure described in General Method C.
4.5.1. (6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidin-2-yl)(morpholino)methanone (3a)
Yield: 64%. Same as the product obtained from Route A
4.5.2. N-ethyl-6-(3,4-dichlororophenyl)-N-
methylimidazo[1,2-a]pyrimidine-2-carboxamide
(3b).
4.6.1. (6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidin-3-yl)(morpholino)methanone (5a).
o
Yield: 40%. mp 201-202 C; 1H NMR (500 MHz, CDCl3) δ
o
1
Yield from 2a: 37%. mp 204-205 C; H NMR (500 MHz,
CDCl3) δ 9.51 (d, J = 2.6 Hz, 1H, H-5), 8.93 (d, J = 2.5 Hz, 1H,
H-7), 8.05 (s, 1H, H-2), 7.46 – 7.39 (m, 1H, H-5’), 7.19 (ddd, J =
7.7, 1.8, 0.9 Hz, 1H, H-6’), 7.13 (dd, J = 2.5, 1.8 Hz, 1H, H-2’),
6.99 (ddd, J = 8.2, 2.5, 0.9 Hz, 1H, H-4’), 3.93 – 3.89 (m, 4H, H-
8.79 (t, J = 2.9 Hz, 1H, H-7), 8.60 (d, J = 2.5 Hz, 1H, H-5), 8.16
(s, 1H, H-3), 7.69 (d, J = 2.1 Hz, 1H, H-2’), 7.61 (d, J = 8.3 Hz,
1H, H-5’), 7.43 (dd, J = 8.3, 2.2 Hz, 1H, H-6’), 4.14 (q, J = 7.0
Hz, 1.1H, CH2CH3), 3.63 (q, J = 7.2 Hz, 0.9H, CH2CH3), 3.59 (s,
1.4H, NCH3), 3.14 (s, 1.6H, NCH3), 1.32 (t, J = 7.0 Hz, 1.6H,
CH2CH3), 1.26 (t, J = 7.1 Hz, 1.4H, CH2CH3); 13C NMR (125.5
MHz, CDCl3) δ 163.3-163.0 (C=O), 150.6 (C-7), 146.3 (C-9),
144.0-143.8 (C-2), 134.1 (C-1’), 133.8 (C-2’), 131.7 (C-5’),
130.6-130.5 (C-5’), 129.0 (C-2’), 126.4 (C-6’), 122.2-122.1 (C-
6), 115.3-115.2 (C-3), 45.7-43.83 (CH2CH3), 36.5-34.1 (NCH3),
14.3-12.2 (CH2CH3); HRMS (ESI+) C16H15Cl2N4O+ ([M+H]+)
requires 349.06229; found 349.06152.
2”), 3.88 (s, 3H, OCH3), 3.80 (dd, J = 5.7, 4.0 Hz, 4H, H-3”); 13
C
NMR (125.5 MHz, CDCl3) δ 160.5 (C-3’), 160.3 (C=O), 152.3
(C-7), 149.8 (C-9), 139.0 (C-2), 135.2 (C-1’), 133.1 (C-5), 130.7
(C-5’), 124.5 (C-6), 119.7 (C-6’), 116.0 (C-3), 114.2 (C-4’),
113.2 (C-2’), 67.0 (C-3”), 55.6 (OCH3), 44.4 (C-2”); HRMS
+
(ESI+) C18H19N4O3 ([M+H]+) requires 339.14572; found
339.14502.
4.6.2. N-ethyl-6-(3,4-dichlororophenyl)-N-
methylimidazo[1,2-a]pyrimidine-3-carboxamide
(5b).
4.5.3. N-ethyl-6-(3-trifluorophenyl)-N-
methylimidazo[1,2-a]pyrimidine-2-carboxamide
(3c).
o
1
Yield from 2b: 39%. mp 105-106 C; H NMR (500 MHz,
CDCl3) δ 9.74 (s, 1H, H-5), 8.87 (d, J = 2.6 Hz, 1H, H-5), 8.16
(s, 1H, H-2), 7.72 (d, J = 2.2 Hz, 1H, H-2’), 7.59 (d, J = 8.3 Hz,
1H, H-5’), 7.47 (dd, J = 8.3, 2.2 Hz, 1H, H-6’), 3.71 (q, J = 7.2
o
Yield: 17%. mp 200 C; 1H NMR (500 MHz, CDCl3) δ 8.85
(dd, J = 3.7, 2.5 Hz, 1H, H-7), 8.66 (d, J = 2.6 Hz, 1H, H-5), 8.18
(s, 1H, H-3), 7.83 (s, 1H, H-4’), 7.78 (d, J = 7.7 Hz, 1H, H-6’),
7.76-7.72 (m, 1H, H-2’), 7.68 (app t, J = 7.7 Hz, 1H, H-5’), 4.14
(q, J = 7.1 Hz, 1.1 H, CH2CH3 rotamer 1), 3.62 (q, J = 7.2 Hz,
0.9 H, CH2CH3 rotamer 2), 3.59 (s, 1.3H, NCH3 rotamer 1), 3.14
(s, 1.7H, NCH3 rotamer 2), 1.32 (t, J = 7.1 Hz, 1.7H, CH2CH3,
Hz, 2H, CH2CH3), 3.29 (s, 3H, NCH3), 1.34 (s, 3H, CH2CH3); 13
C
NMR (125.5 MHz, CDCl3) δ 160.9 (C=O), 151.2 (C-7), 149.5
(C-9), 139.4 (C-2), 134.0 (C-3’), 133.9 (C-4’), 133.7 (C-5), 133.4
(C-1’), 131.5 (C-5’), 129.1 (C-2’), 126.5 (C-6’), 122.1 (C-6),

8
Tetrahedron
4.7.2. Method 2.
117.0 (C-3), 44.3 (CH2CH3), 35.8 (NCH3), 13.1 (CH2CH3);
ACCEPTED MANUSCRIPT
HRMS (ESI+) C16H15Cl2N4O+ ([M+H]+) requires 349.06229;
found 349.06178.
A
solution of 1M aq NaOH (5.0 mL), 2-chloro-5-
phenylpyrimidine 6 (100 mg, 0.53 mmol) and NH4Cl (253 mg,
4.72 mmol) were added to a 10-20 mL vial, sealed with a crimp
cap and placed in a CEM Discover Lab Mate reactor microwave
cavity. After irradiation at 150 oC for 30 min, the reaction
mixture was cooled to rt and the precipitate was filtered, and
washed with water to provide a white crystalline solid (55 mg,
4.6.3. N-ethyl-6-(3-trifluorophenyl)-N-
methylimidazo[1,2-a]pyrimidine-3-carboxamide
(5c).
o
1
Yield from 2c: 39%. mp 132-133 C; H NMR (500 MHz,
CDCl3) δ 9.77 (s, 1H, H-5), 8.98 (d, J = 2.6 Hz, 1H, H-7), 8.17
(s, 1H, H-2), 7.86 (d, J = 1.8 Hz, 1H, H-4’), 7.81 (dt, J = 7.8, 1.4
Hz, 1H, H-6’), 7.72 (dd, J = 7.5, 1.6 Hz, 1H, H-2’), 7.65 (app t, J
= 7.8 Hz, 1H, H-5’), 3.71 (q, J = 7.2 Hz, 2H, CH2CH3), 3.29 (s,
3H, NCH3), 1.35 (t, J = 7.4 Hz, 3H, CH2CH3); 13C NMR (125.5
MHz, CDCl3) δ 161.0 (C=O), 151.5 (C-7), 149.5 (C-9), 139.3 (C-
2), 135.0 (C-1’), 133.9 (s, C-5), 132.1 (q, J = 32.5 Hz, C-3’),
130.8 (C-6’), 130.1 (C-5’), 125.6 (q, J = 3.8 Hz, C-2’), 124.2 (q,
J = 3.8 Hz, C-4’), 124.1 (q, J = 272.6 Hz, CF3), 123.0 (C-6),
117.0 (C-3), 44.4 (CH2CH3), 35.5 (NCH3), 13.1 (CH2CH3);
HRMS (ESI+) C17H16F3N4O+ ([M+H]+) requires 349.12762;
found 349.12651.
61%). mp 162-163 oC (lit. 158-159 oC35), H NMR (400 MHz,
1
MeOH-d4) δ 8.53 (s, 2H), 7.28-7.56 (m, 5H).
4.8. 2-chloro-5-phenylpyrimidine (9).
Based on a literature method31 5-bromo-2-chloropyrimidine
(1.00 mg, 5.17 mmol), phenylboronic acid (1.26 g, 10.34 mmol),
Pd(OAc)2 (58 mg, 0.26 mmol) and Na2CO3 (1.10 g, 10.34 mmol)
o
in H2O/EtOH (4:1, 50 mL) were heated at 45 C for 30 min. The
reaction was then allowed to cool at rt, and it was added to brine,
extracted with DCM (3x50 mL), dried over Na2SO4 and
concentrated in vacuo. Purification via flash column
chromatography (eluent CH2Cl2) gave 8 as a white solid (1.57 g,
80%). mp 132 oC (lit. 132 oC32; 131-133 oC33), 1H NMR
(400 MHz, CDCl3) δ 8.82 (s, 2H), 7.44-7.62 (m, 5H).
4.6.4. N-ethyl-6-(3-methoxyphenyl)-N-
methylimidazo[1,2-a]pyrimidine-3-carboxamide
(5d).
Yield from 2a: 41%. mp 96-97 oC; H NMR (500 MHz,
1
CDCl3) δ 9.68 (s, 1H, H-5), 8.90 (d, J = 2.6 Hz, 1H, H-7), 8.15
(s, 1H, H-2), 7.40 (app t, J = 8.0 Hz, H-5’), 7.18 (ddd, J = 7.6,
1.9, 0.9 Hz, 1H, H-6’), 7.12 (t, J = 2.1 Hz, 1H, H-2’), 6.96 (ddd,
J = 8.2, 2.6, 0.9 Hz, 1H, H-4’), 3.86 (s, 3H, OCH3), 3.68 (p, J =
7.3, 6.5 Hz, 2H, CH2CH3), 3.26 (s, 3H, NCH3), 1.32 (t, J = 7.1
Hz, 3H, CH2CH3); 13C NMR (125.5 MHz, CDCl3) δ 161.0
(C=O), 160.4 (C-3’), 152.0 (C-7), 149.6 (C-9), 139.0 (C-2),
135.3 (C-1’), 133.5 (C-5), 130.6 (C-5’), 124.2 (C-6), 119.7 (C-
6’), 116.8 (C-3), 114.1 (C-4’), 113.1 (C-2’), 55.6 (OCH3), 44.1
(CH2CH3), 35.3 (NCH3), 13.1 (CH2CH3); HRMS (ESI+)
C17H19N4O2+ ([M+H]+) requires 311.15080; found 311.15001.
4.9. General Method E. Synthesis of 2-substituted 6-
arylimidazo[1,2-a]pyrimidines.
To a solution of 6, 6a-c or 10 (1 eq) in DMF (0.1 M) the
appropriate bromo pyruvate reagent (2 eq) was added and the
reaction mixture was stirred under Ar at r.t. for 4 days. For the
ethyl ester derivatives, the reaction mixture was then poured into
saturated NaHCO3, extracted with CH2Cl2, washed with water,
and brine, dried over anhydrous MgSO4 and concentrated in
vacuo. The esters were purified with flash column
chromatography (eluent 30−40 °C petrol/EtOAc, 3:1 to 1:1),
followed by recrystallization from EtOH. For the acid
derivatives, the reaction mixture was poured into saturated
NaHCO3, adjusted to pH 8 and extracted with CH2Cl2. Then, the
aqueous phase was adjusted to pH 3 with conc. HCl and
extracted with iPrOH/CHCl3 (1:3 v/v), dried over Na2SO4 and
concentrated in vacuo. The final products were obtained after
recrystallization with EtOH. Representative spectra for cpds 8a-d
follow.
4.6.5. (6-(3-methoxyphenyl)imidazo[1,2-
a]pyrimidin-3-yl)(pyrrolidin-1-yl)methanone (5e).
o
1
Yield from 2a: 45%. mp 138-139 C; H NMR (500 MHz,
CDCl3) δ 10.06 (d, J = 2.6 Hz, 1H, H-5), 8.94 (d, J = 2.6 Hz, 1H,
H-7), 8.24 (s, 1H, H-2), 7.41 (app t, J = 8.0 Hz, 1H, H-5’), 7.21
(ddd, J = 7.6, 1.8, 0.9 Hz, 1H, H-6’), 7.14 (t, J = 2.1 Hz, 1H, H-
2’), 6.98 (ddd, J = 8.3, 2.6, 0.9 Hz, 1H, H-4’), 3.88 (s, 3H,
OCH3), 3.87-3.83 (m, 2H, H-2”), 3.78-3.70 (m, 2H, H-2”), 2.16-
1.96 (m, 4H, H-3”); 13C NMR (125.5 MHz, CDCl3) δ 160.5 (C-
3’), 159.8 (C=O), 152.2 (C-7), 149.5 (C-9), 139.6 (C-2), 135.4
(C-1’), 133.9 (C-5), 130.6 (C-5’), 124.3 (C-6), 119.8 (C-6’),
117.7 (C-3), 114.2 (C-4’), 113.1 (C-2’), 55.6 (OCH3), 48.7 (C-
2”), 47.1 (C-2”), 26.8 (C-3”), 24.1 (C-3”); HRMS (ESI+)
C18H19N4O2+ ([M+H]+) requires 323.15080; found 323.15025.
4.9.1. ethyl 6-phenylimidazo[1,2-a]pyrimidine-2-
carboxylate (8a)
Yield: 47%. mp 234-235 oC, vmax 1724 (CO) cm-1, H NMR
1
(500 MHz, DMSO-d6) δ 9.30 (d, J = 2.7 Hz, 1H), 9.06 (d, J =
2.6 Hz, 1H), 8.46 (s, 1H), 7.81 – 7.77 (m, 2H), 7.60 – 7.54 (m,
2H), 7.51 – 7.46 (m, 1H), 4.35 (q, J = 7.1 Hz, 2H), 1.34 (t, J =
7.1 Hz, 3H), 13C NMR (125.5 MHz, DMSO-d6) δ 13C NMR (126
MHz, DMSO) δ 162.4, 152.7, 146.9, 136.4, 133.4, 132.6, 129.4,
128.6, 126.8, 122.6, 116.8, 60.5, 14.2. HRMS (ESI+)
C15H14N3O2+ ([M+H]+) requires 268.10805; found 268.10777.
4.7. 2-amino-5-phenylpyrimidine (6)
4.7.1. Method 1.
Based on a literature method34 2-amino-5-iodopyrimidine
(2.00 g, 9.05 mmol), phenylboronic acid (1.66 mg, 13.57 mmol),
Pd(OAc)2 (20 mg, 0.09 mmol) and K3PO4.7H2O (3.84 mg, 18.1
4.9.2. 6-phenylimidazo[1,2-a]pyrimidine-2-
carboxylic acid (8b)
o
Yield 20%. mp 232-233 oC, vmax 3147 (OH), 1687 (CO) cm-1,
1H NMR (500 MHz, DMSO-d6) δ 13.01 (bs, 1H), 9.31 (d, J =
2.6 Hz, 1H), 9.04 (d, J = 2.6 Hz, 1H), 8.40 (s, 1H), 7.82 – 7.77
(m, 2H), 7.60 – 7.54 (m, 2H), 7.51 – 7.46 (m, 1H), 13C NMR
(125.5 MHz, DMSO-d6) δ 163.8, 152.4, 146.8, 137.4, 133.5,
132.6, 129.3, 128.6, 126.8, 122.5, 116.5. HRMS (ESI+)
C13H10N3O2+ ([M+H]+) requires 240.07675; found 240.07682.
mmol) in ethylene glycol (36 mL) were heated at 80 C for 120
min. The reaction was then allowed to cool to rt, and it was
added to brine, extracted with Et2O (3x50 mL), dried over
Na2SO4 and concentrated in vacuo. Then NaOH (3.6 g) was
added and stirred for 2 h. The mixture was added to brine and
extracted with Et2O (3x100 mL) to give 6 as a light yellow solid
(1.40 g, 90%). mp 161-163 oC (lit. 158-159 oC35), 1H NMR
(400 MHz, MeOH-d4) δ 8.53 (s, 2H), 7.56-7.49 (m, 2H), 7.47-
7.39 (m, 2H), 7.37-7.30 (m, 1H).
4.9.3. 1 5 N-ethyl 6-phenylimidazo[1,2-a]pyrimidine-
2-carboxylate (8c)

9
1
+
Yield: 41%. mp 234-235 oC, vmax 1712 (CO) cm-1, H NMR
188.5. HRMS (ESI+) C13H10N215NO2
241.07379; found 241.07368.
([M+H]+) requires
ACCEPTED MANUSCRIPT
(500 MHz, DMSO-d6) δ 9.30 (d, J = 2.7 Hz, 1H), 9.06 (d, J =
2.6 Hz, 1H), 8.46 (s, 1H), 7.81 – 7.76 (m, 2H), 7.59 – 7.53 (m,
2H), 7.50 – 7.46 (m, 1H), 4.35 (q, J = 7.1 Hz, 2H), 1.35 (t, J =
7.1 Hz, 3H), 13C NMR (125.5 MHz, DMSO-d6) δ 162.9 (d, J =
7.7 Hz), 153.2 (d, J = 3.8 Hz), 147.3 (d, J = 6.6 Hz), 136.9,
133.9, 133.1, 129.8, 129.1, 127.3, 123.1, 117.2, 61.0, 14.7,
4.13. ethyl 6-phenylimidazo[1,2-a]pyrimidine-3-carboxylate
(12a).
A degassed suspension of 8a (52 mg, 0.195 mmol) and EtONa
(132 mg, 1.95 mmol) in EtOH (2.0 mL) was heated at reflux for
18 h. It was then cooled to rt, added to NaHCO3 (10 mL),
extracted with CH2Cl2 (10 mL × 4), washed with water (10 mL),
and brine (10 mL), dried over MgSO4, and concentrated in vacuo.
Purification via flash column chromatography (eluent 30−40 °C
petrol/EtOAc, 2:1→1:1), gave 12a as a white crystalline solid
(15 mg, 29%). mp 127-129 oC, vmax (film) 1694 (CO) cm-1,
1H NMR (500 MHz, DMSO-d6) δ 9.59 (d, J = 2.6 Hz, 1H), 9.14
(d, J = 2.6 Hz, 1H), 8.46 (s, 1H), 7.83 – 7.76 (m, 2H), 7.60 –
7.54 (m, 2H), 7.52 – 7.46 (m, 1H), 4.39 (q, J = 7.1 Hz, 2H), 1.36
(t, J = 7.1 Hz, 3H), 13C NMR (125.5 MHz, DMSO-d6) δ 159.6,
152.3, 149.8, 142.3, 133.3, 132.2, 129.4, 128.7, 127.1, 123.7,
15N NMR (60 MHz, DMSO-d6)
δ
239.9. HRMS (ESI+)
C15H14N215NO2+ ([M+H]+) requires 269.10509; found 269.10504.
4.9.4. 1 5 N-6-phenylimidazo[1,2-a]pyrimidine-2-
carboxylic acid (8d)
Yield: 18%. mp 229-231 oC, vmax (film) 3147 (OH), 1687
(CO) cm-1, H NMR (500 MHz, DMSO-d6) δ 13.02 (bs, 1H),
1
9.31 (d, J = 2.7 Hz, 1H), 9.04 (d, J = 2.6 Hz, 1H), 8.40 (s, 1H),
7.81 – 7.76 (m, 2H), 7.59 – 7.53 (m, 2H), 7.51 – 7.46 (m, 1H),
13C NMR (125.5 MHz, DMSO-d6) δ 163.8 (d, J = 7.7 Hz), 152.4
(d, J = 4.3 Hz), 146.8 (d, J = 6.1 Hz), 137.3, 133.5, 132.6, 129.3,
128.6, 126.8, 122.5, 116.5, 15N NMR (60 MHz, DMSO-d6) δ
114.3, 60.6, 14.3. HRMS (ESI+) C15H14N3O2 ([M+H]+) requires
+
241.1. HRMS (ESI+) C13H10N215NO2
241.07379; found 241.07370.
([M+H]+) requires
+
268.10805; found 268.10834.
4.14. 15N-ethyl 6-phenylimidazo[1,2-a]pyrimidine-3-carboxylate
4.10. 2-15N-amino-5-phenylpyrimidine (10)
(12b).
A
solution of 1M aq NaOH (5.0 mL), 2-chloro-5-
Following a similar procedure to that for the preparation of
12a, a degassed suspension of 8c (62 mg, 0.231 mmol) and
EtONa (158 mg, 2.31mmol) in EtOH (2.0 mL) was heated at
reflux for 18 h. It was then cooled to rt, added to NaHCO3
(10 mL), extracted with CH2Cl2 (10 mL × 4), washed with water
(10 mL), and brine (10 mL), dried over MgSO4, and concentrated
in vacuo. Purification via flash column chromatography (eluent
30−40 °C petrol/EtOAc, 2:1→1:1), gave 12b as a white
crystalline solid (16 mg, 26%). mp 129-131 oC, vmax (film) 1693
phenylpyrimidine 6 (100 mg, 0.53 mmol) and 15NH4Cl (257 mg,
4.72 mmol) were added to a 10-20 mL vial, sealed with a crimp
cap and placed in a CEM Discover Lab Mate reactor microwave
cavity. After irradiation at 150 oC for 30 min, the reaction
mixture was cooled to rt and the precipitate was filtered, and
washed with water to provide a white crystalline solid (74 mg,
81%). mp 161-163 oC, vmax 3146 (NH2) cm-1, 1H NMR
(400 MHz, MeOH-d4, 9:1 mixture δ 8.43 (s, 2H), 7.50-7.45 (m,
2H), 7.42-7.37 (m, 2H), 7.30-7.23 (m, 1H); 8.53 (s, 2H), 7.57-
7.52 (m, 2H), 7.45-7.42 (m, 2H), 7.37-7.32 (m, 1H). HRMS
(ESI+) C10H10N215N+ ([M+H]+) requires 173.08396; found
173.08406.
1
(CO) cm-1, H NMR (500 MHz, DMSO-d6) δ 9.61 (dd, J = 2.6,
1.4 Hz, 1H), 9.15 (dd, J = 2.6, 0.9 Hz, 1H), 8.47 (d, J = 2.8 Hz,
1H), 7.84 – 7.77 (m, 2H), 7.62 – 7.55 (m, 2H), 7.53 – 7.47 (m,
1H), 4.40 (q, J = 7.1 Hz, 2H), 1.37 (t, J = 7.1 Hz, 3H), 13C NMR
(125.5 MHz, DMSO-d6) δ 160.1 (d, J = 2.9 Hz), 152.8 (d, J =
4.5 Hz), 150.28 (d, J = 8.5 Hz), 142.8 (d, J = 5.1 Hz), 133.8,
132.7 (d, J = 12.7 Hz), 129.9, 129.2, 127.6, 124.2, 114.7 (d, J =
17.3 Hz), 61.1, 14.7, 15N NMR (60 MHz, DMSO-d6) δ 187.7.
4.11. 6-phenylimidazo[1,2-a]pyrimidine-3-carboxylic acid (11a).
Following a similar procedure to the first step of General
Method D, to a refluxing solution of 8a (100 mg) in THF/EtOH
(1/1 mL), 1M NaOH in H2O (1.12 mL in 1.5 mL) was added and
the reaction refluxed for 3 h. It was then cooled to rt, pH was
adjusted to 8 (NaHCO3) and extracted with EtOAc. Then, the
aqueous phase was further acidified to pH 3 (1N HCl), and the
white precipitate formed was collected, washed with Et2O to
obtain 11a (49 mg, 55%). mp 225-227 oC, vmax (film) 3286 (OH),
+
HRMS (ESI+) C15H14N215NO2 ([M+H]+) requires 269.10509;
found 269.10472.
Acknowledgements
1692 (CO) cm-1, H NMR (500 MHz, DMSO-d6) δ 13.56 (bs,
1
The authors wish to thank Summit Therapeutics plc and
Duchenne UK for financial support.
1H), 9.68 (d, J = 2.5 Hz, 1H), 9.17 (d, J = 2.6 Hz, 1H), 8.50 (s,
1H), 7.86 – 7.77 (m, 2H), 7.62 – 7.55 (m, 2H), 7.56 – 7.48 (m,
1H), 13C NMR (125.5 MHz, DMSO-d6) δ 161.1, 152.6, 149.1,
141.1, 133.3, 132.4, 129.5, 128.8, 127.2, 123.9, 115.1. HRMS
Supplementary data
Supplementary data associated with this article
(supplementary tables, copies of NMR spectra) are available and
can be found at XXXX.
(ESI+) C13H10N3O2 ([M+H]+) requires 240.07675; found
+
240.07669.
4.12. 15N 6-phenylimidazo[1,2-a]pyrimidine-3-carboxylic acid
(11b).
5. References and Notes
Following a similar procedure to that for the preparation of
11a, from 8c. Yield: 51%. mp 230-232 oC, vmax (film) 3286 (OH),
1.
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