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C. R. Chimie 21 (2018) 987e992Contents lists avaiComptes Rendus Chimie
www.sciencedirect.comPreliminary communication/CommunicationCrystal structure and identification of a pyrimido[6,1-b][1,3]
oxazin-6-one derivative from the reaction of acrolein with 5-
(phenoxymethyl)-2-amino-2-oxazoline
Structure cristalline et identification d’un derive de la pyrimido[6,1-b]
[1,3]oxazin-6-one par reaction de l’acroleine avec la 5-(phenoxymethyl)-
2-amino-2-oxazoline
Jean Guillon a, *, Sandra Rubio a, Solene Savrimoutou a, François Halle a,
Stephane Moreau a, Pascal Sonnet b, Mathieu Marchivie c
a Universite de Bordeaux, UFR des sciences pharmaceutiques, INSERM U1212/UMR CNRS 5320, Laboratoire ARNA, 146, rue Leo-Saignat,
33076 Bordeaux cedex, France
b Universite de Picardie-Jules-Verne, AGIR e Agents infectieux, resistance et chimiotherapie, UFR de pharmacie, 1, rue des Louvels,
80037 Amiens cedex 1, France
c CNRS, University of Bordeaux, ICMCB, UMR 5026, 33600 Pessac, Francea r t i c l e i n f o
Article history:
Received 19 July 2018
Accepted 18 September 2018
Available online 19 October 2018
Keywords:
Pyrimido[6,1-b][1,3]oxazin-6-one
2-Amino-2-oxazoline
Michael reaction
X-ray crystal structure* Corresponding author.
E-mail addresses: jean.guillon@u-bordeaux.f
Savrimoutou), françois.halle@u-bordeaux.fr (F. H
mathieu.marchivie@u-bordeaux.fr (M. Marchivie)
https://doi.org/10.1016/j.crci.2018.09.013
1631-0748/© 2018 Académie des sciences. Publish
creativecommons.org/licenses/by-nc-nd/4.0/).a b s t r a c t
The X-ray crystal structure of 2-(4,5-dihydro-5-phenoxymethyl-1,3-oxazol-2-ylamino)-7-
(2-hydroxy-3-phenoxypropyl)hexahydro-2H,6H-pyrimido[6,1-b][1,3]oxazin-6-one (1), a
structure of adduct formed by the reaction of 5-(phenoxymethyl)-2-amino-2-oxazoline and
acrolein, has been established. The present work deals with the structural identification of
the adduct 1 and presents a plausible mechanism for its formation. It crystallizes in the
monoclinic space group P21/c with cell parameters a ¼ 21.3337 (10) Å, b ¼ 11.3712 (7) Å,
c¼10.4936 (7)Å,b¼103.041 (3),V¼2480.0 (3) Å3, Z¼4. C26H32N4O6,Dc¼1.330g/cm3,m (Cu
Ka) ¼ 1.5418 Å, S ¼ 1.188, F (000) ¼ 1056, R ¼ 0.0501, and wR ¼ 0.1584.
©2018Académiedes sciences. PublishedbyElsevierMasson SAS. This is anopenaccess article
under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Mots-cles:
Pyrimido[6,1-b][1,3]oxazin-6-one
2-Amino-2-oxazoline
Reaction de Michael
Structure cristalline determinee aux rayons Xr e s u m e
La structure complete de la 2-(4,5-dihydro-5-phenoxymethyl-1,3-oxazol-2-ylamino)-7-(2-
hydroxy-3-phenoxypropyl)hexahydro-2H,6H-pyrimido[6,1-b][1,3]oxazin-6-one 1, une
structure d'adduit formee lors de la reaction de la 5-(phenoxymethyl)-2-amino-2-oxazoline
et de l'acroleine, a ete etablie sans equivoque par une analyse cristallographique aux rayons
X. Le present travail porte sur l'identification structurale de l'adduit 1 et presente un
mecanisme plausible pour sa formation. La molecule cristallise dans le systeme
monoclinique, dans le groupe spatial P21/c avec a ¼ 21.3337 (10) Å, b ¼ 11.3712 (7) Å,r (J. Guillon), sandra.rubio@u-bordeaux.fr (S. Rubio), solene.savrimoutou@u-bordeaux.fr (S.
alle), stephane.moreau@u-bordeaux.fr (S. Moreau), pascal.sonnet@sa.u-picardie.fr (P. Sonnet),
.
ed by Elsevier Masson SAS. This is an open access article under the CC BY-NC-ND license (http://
Scheme 1. Synthesis of 2-(4,5-dihydro-5-phenoxyme
6-one (1).
J. Guillon et al. / C. R. Chimie 21 (2018) 987e992988c¼10.4936 (7) Å,b¼103.041 (3),V¼2480.0 (3)Å3, Z¼4. C26H32N4O6,Dc¼1.330g/cm3,m (Cu
Ka) ¼ 1.5418 Å, S ¼ 1.188, F (000) ¼ 1056, R ¼ 0.0501 et wR ¼ 0.1584.
©2018Académiedes sciences. PublishedbyElsevierMasson SAS. This is anopenaccess article
under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).1. Introduction
For the past few decades, we have focused our attention
on the (bio)chemistry and reactivity of 2-amino-2-
oxazolines developed either as synthons or potential
bioactive heterocyclic derivatives. We have previously
described the design and synthesis of biologically active
derivatives based on the reactivity of the amidine group of
2-amino-2-oxazolines with various bis-electrophiles [1e4].
As with other amidines, the 2-amino-2-oxazoline moiety
possesses two competing sites for potential ring annula-
tion, leading to regioselectivity considerations. An empir-
ical observation has emerged from our previous
investigations, which indicates that, in such reactions, the
endocyclic nitrogen is considered generally as the most
nucleophilic and attacks the most electrophilic carbon of
the bis-electrophile. A ring closure between the exocyclic
nitrogen and the second electrophilic function generally
concludes the synthesis [5,6].
As a continuation of our research for pharmaceutical
tools,we herein report the structural characterization of the
2-(4,5-dihydro-5-phenoxymethyl-1,3-oxazol-2-ylamino)-
7-(2-hydroxy-3-phenoxypropyl)hexahydro-2H,6H-pyr-
imido[6,1-b][1,3]oxazin-6-one (1), a serendipity structure
of an adduct formed by a reaction of 5-(phenoxymethyl)-2-
amino-2-oxazoline (2) with acrolein (Scheme 1). Pyrimido
[6,1-b][1,3]oxazine derivatives are heterocyclic building
blocks showing potential biological utilities, such as anti-
human immunodeficiency virus (HIV), antibacterial, anti-
fungal, antiamoebic, and anthelmintic properties [7e9].
2. Results and discussion
As a part of our research program on crystal structure
analysis, the three-dimensional structure of this pyrimido
[6,1-b][1,3]oxazin-6-one 1 has been achieved. Hence, after
crystallization in a mixture of chloroform and methanol
(4/1 v/v) at room temperature, the 2-(4,5-dihydro-5-phen-
oxymethyl-1,3-oxazol-2-ylamino)-7-(2-hydroxy-3-pheno-
xypropyl)hexahydro-2H,6H-pyrimido[6,1-b][1,3]oxazin-6-
one (1) was surprisingly isolated as colorless needles. Title
derivative was then submitted to spectroscopic analysis to
confirm its molecular structure. The structure of 1 is
depicted in Fig. 1. The proposed mechanism to access pyr-
imido[6,1-b][1,3]oxazin-6-one 1 is described in Scheme 2.thyl-1,3-oxazol-2-ylamino)-7Thus, the reaction proceeds via adduct formation first at the
endocyclic nitrogen of 2-amino-2-oxazoline 1 [10,11] via a
Michael reaction leading to intermediate I, and subse-
quently a ring closure takes place at the carbonyl carbon by
the exocyclic nitrogen atom of I to form the ring-fused
monoadduct II through a Dimroth-like rearrangement
(Scheme 2). This first Michael addition is then followed by a
second Michael reaction of acrolein at the exocyclic nitro-
gen atom of the oxazolopyrimidine II to give the interme-
diate III, which is then probably hydrolyzed into the
pyrimidine IV in equilibrium with its tautomeric form V.
We have previously described such hydrolysis in the
opening of the oxazoline ring [4]. Condensation of the
amino function of a second molecule of 2-amino-2-
oxazoline 2 with the carbonyl of V led to the formation of
the imine intermediate VI. Compound 1 is finally obtained
through a second cyclization by addition of the hydroxyl of
the initially formed ring onto the imine group of VI to
complete the reaction sequence. Similar reactivity of a hy-
droxyl function has been previously described by a reaction
of acrolein with adenosine/cytidine and adenine/cytosine,
leading to the formation of diastereoisomers of the adducts,
made up from two fused rings [12,13]. According to the X-
ray data, compound 1 appears only as amixture of 2S*-(4,5-
dihydro-5R*-phenoxymethyl-1,3-oxazol-2-ylamino)-7-(2S*-
hydroxy-3-phenoxypropyl)hexahydro-2H,6H-(9aS*)-pyrimi-
do[6,1-b][1,3]oxazin-6-one and 2S*-(4,5-dihydro-5R*-phe-
noxymethyl-1,3-oxazol-2-ylamino)-7-(2R*-hydroxy-3-
phenoxypropyl)hexahydro-2H,6H-(9aS*)-pyrimido[6,1-b]
[1,3]oxazin-6-one diastereoisomers and their respective
enantiomers. Both diastereoisomers correspond, respec-
tively, to the SRSS and SRRS absolute configurations in the
order of the nomenclature or the corresponding RSRR or
RSSR enantiomers. The only difference between the two
stereoisomers is found for the hydroxyl function at position
2 of the 7-propyl side chain. From these crystallographic
data, the diastereomers were formed in unequal amounts,
that is, 75% and 25%, respectively, but they could not be
separated (see Fig. 2).
Title compound 1 crystallized at 183 K in the mono-
clinic system, space group P21/c with the unit cell pa-
rameters: a ¼ 21.3337 (10) Å, b ¼ 11.3712 (7) Å, c ¼
10.4936 (7) Å, b ¼ 103.041 (3), and V ¼ 2480.0 (3) Å3. Each
asymmetric unit is constituted of one molecule corre-
sponding to the formula C26H32N4O6 with four molecules-(2-hydroxy-3-phenoxypropyl)hexahydro-2H,6H-pyrimido[6,1-b][1,3]oxazin-
Fig. 1. View of the asymmetric unit of 1, with the labeling scheme. The thermal ellipsoids are represented at 50% probability. The disordered OH group on C9 is
not represented for clarity, and only the major diastereoisomer is represented here.
Fig. 2. View of the principal intermolecular interactions in the crystal of pyrimido[6,1-b][1,3]oxazin-6-one 1 that ensure the crystal cohesion in (a) the c direction,
(b) the b direction, and (c) the a direction. Symmetry codes: (i) x, ½  y, ½ þ z; (ii) x, y, 1  z; (iii) 1  x, ½ þ y; 3/2  z.
J. Guillon et al. / C. R. Chimie 21 (2018) 987e992 989in the unit cell (Z ¼ 4) leading to a calculated density (Dc)
of 1.330 g/cm3. The molecular structure of pyrimido[6,1-b]
hydroxy-3-phenoxypropyl[1,3]oxazin-6-one 1 is depicted
in Fig. 1.The double bond C13]O18 of the urea group is found at
1.242(2) Å, whereas the two CeN bonds (C13eN14 ¼ 1.379
(2) Å and C13eN12 ¼ 1.356 (2) Å) of this same function
were in agreement with the C(sp2)eN distance [14]. The
Scheme 2. Hypothetical mechanism for the formation of 2-(4,5-dihydro-5-phenoxymethyl-1,3-oxazol-2-ylamino)-7-(2-hydroxy-3-phenoxypropyl)hexahydro-
2H,6H-pyrimido[6,1-b][1,3]oxazin-6-one (1).
J. Guillon et al. / C. R. Chimie 21 (2018) 987e992990Csp3eO bonds (C15eO22 and C21eO22) of the oxazine ring
were noticed at 1.434 (2) and 1.456 (2) Å, respectively,
whereas the other Csp3eO bonds (C8eO7, C29eO30,
C9eO10, C9eO100, and C26eO25) range from 1.425 (2) to
1.516 (6) Å. The intracyclic double bond C24eN28 of the
oxazoline is measured at 1.282 (2) Å, slightly smaller thanthose observed for C(sp2)]N double bonds [14]. In addi-
tion, the C24eN23 bond of this amidine function is found at
1.349 (2) Å due to the delocalization of the double bond in
the amidine moiety of 2-amino-2-oxazoline. The CeC bond
lengths in the two phenyl rings lie in the range 1.361 (4)e
1.391 (4) Å.
Table 1
Selected bond lengths (Å) and angles ().
Bond lengths
O(7)eC(8) 1.429 (3) C(15)eO(22) 1.434 (2)
C(9)eO(10) 1.434 (3) C(21)eO(22) 1.456 (2)
C(9)eO(100) 1.516 (6) N(23)eC(24) 1.349 (2)
N(12)eC(13) 1.356 (2) C(24)eN(28) 1.282 (2)
C(13)eO(18) 1.242 (2) O(25)eC(26) 1.461 (2)
C(13)eN(14) 1.379 (2) C(29)eO(30) 1.425 (2)
Bond angles
O(22)eC(21)eC(20)eC(19) 51.55 (18) C(1)eO(7)eC(8) 119.7 (2)
O(22)eC(15)eN(14)eC(19) 62.96 (18) C(31)eO(30)eC(29) 117.22 (15)
Table 2
Hydrogen bonds for 1.
DeH/A d(DeH) (Å) d(HeA) (Å) d(DeA) (Å) DeHeA ()
O10eH10/O18i 0.84 1.937 2.714 (3) 153.3
O100eH100/O18i 0.83 2.069 2.748 (4) 139.2
N23eH23/N28ii 0.88 2.064 2.931 (3) 168.1
C4eH4/O7iii 0.95 2.583 3.514 (3) 166.5
Symmetry codes: (i) x,½ y,½þ z; (ii)x,y, 1 z; (iii) 1 x,½þ y; 3/2
 z.
Table 3
Crystallographic data and structure refinement details.
CCDC deposit number 891807
Chemical formula C26H32N4O6
Formula weight 496.56
Temperature (K) 183 (2)
Wavelength (Å) 1.54180
Crystal size (mm) 0.20  0.20  0.15
Crystal system Monoclinic
Space group P21/c
a (Å) 21.3337 (10)
b (Å) 11.3712 (7)
c (Å) 10.4936 (7)
a () 90.00
b () 103.041 (3)
g () 90.00
V (Å3) 2480.0 (3)
Z 4
Dc (g/cm3) 1.330
F (000) 1056
Absorption coefficient (mm1) 0.786
2q range () 4.26e144.62
Index ranges 26  h  26; 13  k  13;
12  l  12
Reflection collected 32,457
Independent reflections 4802 [Rint ¼ 0.0428]
Data/restraints/parameters 4802/2/335
Goodness-of-fit on F2 1.189
R, wR indices [I > 2s(I)] 0.0501, 0.1584
R, wR indices (all data) 0.0569, 0.1878
Largest differential peak
and hole (eÅ3)
0.24, 0.30
J. Guillon et al. / C. R. Chimie 21 (2018) 987e992 991Compound 1 adopts a half-chair conformation for the py-
rimidine ring while oxazine ring is a chair conformation. The
torsion angles of this oxazinemoietyO22eC21eC20eC19and
O22eC15eN14eC19 are 51.55 (18) and 62.96 (18),
respectively. In addition, the C1eO7eC8 and C31eO30eC29
of the phenoxy side chains are found at 119.7 (2) and 117.22
(15) (see Table 1).
The crystal-structure cohesion is essentially ensured by
intermolecular hydrogen bond between the OH group on
C9 and the oxygen O18 from the carbonyl function propa-
gating in the direction c, and between one amino and one
imine group (N23 and N28, respectively) leading to a cyclic
double hydrogen bond propagating in the b direction (Table
2). It is worth noting that both diastereoisomers, which
correspond to two different conformations of the OH group
on C9, lead nevertheless to a very similar H-bond between
the hydroxyl and the carbonyl functions. This can explain
why both diastereoisomers can accommodate in the same
crystal lattice. The slightly weaker H-bond obtained for the
SRRS diastereoisomer may explain why its proportion is
smaller in the crystal leading to the 75/25 M ratio for the
SRSS and SRRS diastereoisomers, respectively (Table 2). A
weaker hydrogen-like interaction between an aromatic
CeH of the phenyl group (C4eH4) with the oxygen O7 of
another symmetrical equivalent O-phenyl group ensures
the crystal cohesion in the c direction.3. Experimental section
3.1. Preparation
The title compound 1 was prepared in moderate yield
(55%) by a direct reaction of 1 equiv of 5-(phenoxymethyl)-
2-amino-2-oxazoline 2 with 1 equiv of acrolein in ethanol
at room temperature for 2 days. The precipitate formed
during the reaction was then filtered and suitable crystals
for X-ray diffraction analysis were obtained from achloroformemethanol (4:1 v/v) solution by slow evapora-
tion of the solvent at þ20 C.3.2. X-ray crystallography
A single crystal of the title compound with dimensions
0.20  0.20  0.15 mm3 was chosen for X-ray diffraction
study. The data were collected using a Rigaku R-axis rapid
diffractometer equippedwithmicro-focus rotating anode Cu
Ka radiation (l¼ 1.5418 Å)mode at 183 (2) K. In the range of
2.13 < q<72.31, a total of 32,457 reflections were collected,
of which 4802 were independent (Rint ¼ 0.0501) and 4497
wereobservedwith I>2s(I). The crystal structurewas solved
by direct methods and successive Fourier difference syn-
theses with the SHELXS program [15]. Refinement of the
crystal structure was performed on F2 by weighted aniso-
tropic full-matrix least-squares methods using the SHELXL
program [15]. An absorption correction was performed by
semiempirical methods using the SADABS program [15]. All
J. Guillon et al. / C. R. Chimie 21 (2018) 987e992992parts of the program were used within the OLEX2 package
[16]. All non-H atoms were refined anisotropically, and the
positions of the H atomswere deduced from the coordinates
of the non-H atoms to which they are linked, confirmed by
Fourier synthesis and treated according to the riding model
during refinement. H atoms were included for structure
factor calculations, but not refined. The final full-matrix
least-squares refinement gave R ¼ 0.0501 and wR ¼ 0.1584
for 4497 reflections with I > 2s(I). The maximum and mini-
mum difference peaks and holes were 0.239 and
0.302 eÅ3, respectively. S ¼ 1.188 and (D/s)max ¼ 0.000.
The crystal data and refinement details are listed in Table 3.
Appendix A. Supplementary data
Supplementary data to this article can be found online
at https://doi.org/10.1016/j.crci.2018.09.013.
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