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Journal ArticleDOI

4-Amino-2-chloro-5-nitro-6-(propylamino)pyrimidine

01 Jul 2004-Acta Crystallographica Section E-structure Reports Online (Munksgaard International Publishers)-Vol. 60, Iss: 7, pp 1260-1262

AbstractThe title compound, C7H10ClN5O2, was synthesized as part of a study to demonstrate the reactivity of 4-amino-2,6-di­chloro-5-nitro­pyrimidine with respect to various amine substitutions. The structure determination allowed unambiguous assignment of the regioselectivity of the substitution of the propyl­amine group at the 6-position. Intra- and intermolecular N—H⋯O and N—H⋯N hydrogen bonding yields polymeric chains of coplanar mol­ecules. There are two independent molecules in the asymmetric unit.

Topics: Regioselectivity (50%)

Summary (1 min read)

Jump to: [Comment] and [Experimental]

Comment

  • The title compound, (I), was synthesized by substitution of one chloro substituent of 4-amino-2,6-dichloro-5-nitro- pyrimidine with propylamine.
  • The determination of the crystal structure has allowed the assignment of the regioselectivity of the substi- tution at the 6-position.
  • Relevant bond lengths and angles are listed in Table 1.
  • Two intermolecular hydrogen-bonding interactions are also observed between the two independent molecules.

Experimental

  • Propylamine (32 ml, 0.38 mmol), which had been distilled before use, was added and the reaction left to stir.
  • After 4 h, thin-layer chromatography and gas chromato- graphy±mass spectroscopy analysis indicated the reaction was complete.
  • Puri®cation on a column (silica gel, CHCl3) followed by slow evaporation of the solvent gave a pale-yellow crystalline solid 465 K).

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4-amino-2-chloro-5-nitro-6-(propylamino)pyrimidine
Author
McKeveney, D, Quinn, RJ, Janssen, CO, Healy, PC
Published
2004
Journal Title
ACTA Crystallographica Section E - Structure Reports Online
DOI
https://doi.org/10.1107/S1600536804015028
Copyright Statement
© The Author(s) 2004. For information about this journal please refer to the journal's website.
All articles published in Acta Crystallographica Section E are open access and distributed
under the Creative Commons Attribution License, which permits unrestricted use, distribution,
and reproduction in any medium, provided the original work is properly cited. See http://
creativecommons.org/licenses/by/2.0/uk/legalcode
Downloaded from
http://hdl.handle.net/10072/5770
Link to published version
http://journals.iucr.org/e/journalhomepage.html
Griffith Research Online
https://research-repository.griffith.edu.au

organic papers
o1260 Declan McKeveney et al.
C
7
H
10
ClN
5
O
2
DOI: 10.1107/S1600536804015028 Acta Cryst. (2004). E60, o1260±o1262
Acta Crystallographica Section E
Structure Reports
Online
ISSN 1600-5368
4-Amino-2-chloro-5-nitro-6-(propylamino)pyrimidine
Declan McKeveney,
a
Ronald J.
Quinn,
a
Christian O. Janssen
a
and Peter C. Healy
b
*
a
Natural Product Discovery, Eskitis Institute,
Griffith University, Nathan, Brisbane 4111,
Australia, and
b
School of Science, Griffith
University, Nathan, Brisbane 4111, Australia
Correspondence e-mail: p.healy@griffith.edu.au
Key indicators
Single-crystal X-ray study
T = 295 K
Mean (C±C) = 0.007 A
Ê
R factor = 0.050
wR factor = 0.158
Data-to-parameter ratio = 13.1
For details of how these key indicators were
automatically derived from the article, see
http://journals.iucr.org/e.
# 2004 International Union of Crystallography
Printed in Great Britain ± all rights reserved
The title compound, C
7
H
10
ClN
5
O
2
, was synthesized as part of
a study to demonstrate the reactivity of 4-amino-2,6-dichloro-
5-nitropyrimidine with respect to various amine substitutions.
The structure determination allowed unambiguous assignment
of the regioselectivity of the substitution of the propylamine
group at the 6-position. Intra- and intermolecular NÐHO
and NÐHN hydrogen bonding yields polymeric chains of
coplanar molecules. There are two independent molecules in
the asymmetric unit.
Comment
The title compound, (I), was synthesized by substitution of
one chloro substituent of 4-amino-2,6-dichloro-5-nitro-
pyrimidine with propylamine. While it was clear from the
spectroscopic data that monosubstitution had been achieved,
the question remained as to whether the chloro group at the 2-
or 6-position had been substituted. NMR experiments could
not answer this question satisfactorily and so crystals of (I)
were grown. The determination of the crystal structure has
allowed the assignment of the regioselectivity of the substi-
tution at the 6-position.
The crystal structure of (I) contains two independent mol-
ecules in the asymmetric unit disposed across a pseudo-centre
of symmetry (Fig. 1). Relevant bond lengths and angles are
listed in Table 1. With the exception of the peripheral
propylamine substituents, both molecules are essentially
coplanar.
Each molecule exhibits two intramolecular S(6) (Bernstein
et al., 1995) NÐHO hydrogen-bonding interactions. The
®rst of these is between the ortho amine and the nitro groups
on C4 and C5 (cf. McKeveney et al., 2004; Glidewell et al.,
2003), and the second is between the ortho propylamine and
the nitro groups on C6 and C5 (Table 2 and Fig. 2).
Two intermolecular hydrogen-bonding interactions are also
observed between the two independent molecules. The ®rst is
an R
2
2
(8) NÐHN interaction between the ortho amino
group and the ring N3 atom (cf. Glidewell et al., 2003; Lynch &
McClenaghan, 2004). The second is an R
2
2
(12) NÐHO
Received 15 June 2004
Accepted 21 June 2004
Online 26 June 2004

interaction between the ortho propylamine and the nitro
groups (Table 2, Fig. 2). This complex hydrogen-bonding
pattern results in the formation of polymeric chains of
coplanar molecules, which lie approximately parallel to the bc
plane and along the direction of the crystallographic c axis.
Experimental
4-Amino-2,6-dichloro-5-nitropyrimidine (40 mg, 0.19 mmol) was
taken up in CHCl
3
(4 ml) at 273 K. Propylamine (32 ml, 0.38 mmol),
which had been distilled before use, was added and the reaction left
to stir. After 4 h, thin-layer chromatography and gas chromato-
graphy±mass spectroscopy analysis indicated the reaction was
complete. Puri®cation on a column (silica gel, CHCl
3
) followed by
slow evaporation of the solvent gave a pale-yellow crystalline solid
suitable for X-ray diffraction studies (32 mg, 72.7% yield; m.p. 463±
465 K). Spectroscopic analysis:
1
H NMR (d
6
-DMSO, , p.p.m.): 9.48
(brs, NH), 8.84 (brs,NH
2
), 3.43 (CH
2
), 1.58 (CH
2
), 0.89 (t,CH
3
);
13
C NMR (d
6
-DMSO, , p.p.m.): 160.76, 159.61, 157.32, 110.69, 42.82,
21.79, 11.11.
Crystal data
C
7
H
10
ClN
5
O
2
M
r
= 231.65
Triclinic, P
1
a = 7.406 (3) A
Ê
b = 11.074 (3) A
Ê
c = 13.886 (5) A
Ê
= 112.54 (2)
= 94.82 (3)
= 101.69 (3)
V = 1013.4 (7) A
Ê
3
Z =4
D
x
= 1.518 Mg m
ÿ3
Mo K radiation
Cell parameters from 25
re¯ections
= 12.7±17.4
= 0.37 mm
ÿ1
T = 295 K
Prism, pale yello
0.30 0.15 0.10 mm
Data collection
Rigaku AFC-7R diffractometer
!/2 scans
Absorption correction: none
3994 measured re¯ections
3565 independent re¯ections
1948 re¯ections with I >2(I)
R
int
= 0.025
max
= 25.0
h = ÿ8 ! 8
k = ÿ12 ! 13
l = ÿ16 ! 7
3 standard re¯ections
every 150 re¯ections
intensity decay: 2.9%
Re®nement
Re®nement on F
2
R[F
2
>2(F
2
)] = 0.050
wR(F
2
) = 0.158
S = 1.02
3565 re¯ections
272 parameters
H-atom parameters constrained
w = 1/[
2
(F
o
2
) + (0.0687P)
2
+ 0.5417P]
where P =(F
o
2
+2F
c
2
)/3
(/)
max
< 0.001
max
= 0.41 e A
Ê
ÿ3
min
= ÿ0.32 e A
Ê
ÿ3
Table 1
Selected geometric parameters (A
Ê
,
).
Cl2AÐC2A 1.738 (4)
Cl2BÐC2B 1.732 (4)
O51AÐN5A 1.228 (5)
O52AÐN5A 1.233 (4)
O51BÐN5B 1.235 (5)
O52BÐN5B 1.239 (4)
N1AÐC2A 1.306 (5)
N1AÐC6A 1.352 (5)
N3AÐC4A 1.360 (5)
N3AÐC2A 1.314 (6)
N4AÐC4A 1.319 (5)
N5AÐC5A 1.406 (5)
N6AÐC6A 1.327 (6)
N6AÐC7A 1.453 (7)
N1BÐC2B 1.316 (5)
N1BÐC6B 1.355 (5)
N3BÐC2B 1.316 (6)
N3BÐC4B 1.356 (5)
N4BÐC4B 1.324 (5)
N5BÐC5B 1.410 (5)
N6BÐC6B 1.323 (6)
N6BÐC7B 1.469 (7)
C4AÐC5A 1.430 (5)
C5AÐC6A 1.430 (6)
C4BÐC5B 1.422 (5)
C5BÐC6B 1.439 (6)
C2AÐN1AÐC6A 115.7 (4)
C2AÐN3AÐC4A 115.6 (3)
O51AÐN5AÐO52A 120.0 (3)
O51AÐN5AÐC5A 121.1 (3)
O52AÐN5AÐC5A 118.9 (3)
C6AÐN6AÐC7A 124.9 (4)
C2BÐN1BÐC6B 115.9 (4)
C2BÐN3BÐC4B 115.7 (3)
O51BÐN5BÐO52B 119.8 (3)
O52BÐN5BÐC5B 119.6 (3)
O51BÐN5BÐC5B 120.6 (3)
C6BÐN6BÐC7B 124.5 (4)
Cl2AÐC2AÐN1A 114.5 (3)
Cl2AÐC2AÐN3A 114.2 (3)
N1AÐC2AÐN3A 131.2 (4)
N3AÐC4AÐC5A 119.7 (3)
N3AÐC4AÐN4A 115.1 (3)
N4AÐC4AÐC5A 125.2 (3)
N5AÐC5AÐC4A 120.2 (3)
C4AÐC5AÐC6A 117.7 (3)
N5AÐC5AÐC6A 122.1 (3)
N6AÐC6AÐC5A 123.9 (4)
N1AÐC6AÐN6A 115.9 (4)
N1AÐC6AÐC5A 120.1 (4)
N6AÐC7AÐC8A 116.2 (5)
Cl2BÐC2BÐN1B 114.7 (3)
Cl2BÐC2BÐN3B 114.4 (3)
N1BÐC2BÐN3B 130.9 (4)
N4BÐC4BÐC5B 125.3 (3)
N3BÐC4BÐC5B 119.9 (3)
N3BÐC4BÐN4B 114.8 (3)
N5BÐC5BÐC4B 120.5 (3)
C4BÐC5BÐC6B 118.1 (3)
N5BÐC5BÐC6B 121.5 (3)
N1BÐC6BÐN6B 116.9 (4)
N6BÐC6BÐC5B 123.8 (4)
N1BÐC6BÐC5B 119.3 (4)
N6BÐC7BÐC8B 111.4 (5)
organic papers
Acta Cryst. (2004). E60, o1260±o1262 Declan McKeveney et al.
C
7
H
10
ClN
5
O
2
o1261
Figure 2
The hydrogen-bonding interactions in (I), shown as dashed lines.
Figure 1
The two independent molecules of (I), showing the atomic numbering
scheme. Displacement ellipsoids are drawn at the 30% probability level
and H atoms are shown as small spheres of arbitrary radii.

Table 2
Hydrogen-bonding geometry (A
Ê
,
).
DÐHADÐH HADADÐHA
N6AÐH6AO52A 0.95 1.91 2.601 (5) 128
N6AÐH6AO52B 0.95 2.24 3.076 (5) 147
N6BÐH6BO52A 0.95 2.22 3.052 (5) 146
N6BÐH6BO52B 0.95 1.89 2.599 (5) 129
N4AÐH41AO51A 0.95 1.94 2.607 (4) 125
N4BÐH41BO51B 0.95 1.94 2.607 (4) 125
N4AÐH42AN3B
i
0.95 2.07 3.024 (4) 177
N4BÐH42BN3A
ii
0.95 2.06 3.003 (4) 176
Symmetry codes: (i) x; y; z ÿ 1; (ii) x; y; 1 z.
H atoms were constrained in the riding-model approximation,
®xed to their parent C or N atoms, with CÐH and NÐH distances of
0.95 A
Ê
and with U
iso
(H) = 1.2U
eq
(C,N).
Data collection: MSC/AFC-7 Diffractometer Control for Windows
(Molecular Structure Corporation, 1999); cell re®nement: MSC/AFC-
7 Diffractometer Control for Windows; data reduction: TEXSAN for
Windows (Molecular Structure Corporation, 1997±2001); program(s)
used to solve structure: TEXSAN for Windows; program(s) used to
re®ne structure: TEXSAN for Windows and SHELXL97 (Sheldrick,
1997); molecular graphics: PLATON for Windows (Spek, 2001) and
ORTEP-3 (Farrugia, 1997); software used to prepare material for
publication: TEXSAN for Windows and PLATON for Windows.
The authors thank the Australian Research Council and
Grif®th University for ®nancial support.
References
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555±1573.
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.
Glidewell, C., Low, J. N., Melguizo, M. & Quesada, A. (2003). Acta Cryst. C59,
o14±o18.
Lynch, D. E. & McClenaghan, I. (2004). Cryst. Eng. 6, 1±14.
McKeveney, D., Quinn, R. J., Janssen, C. O. & Healy, P. C. (2004). Acta Cryst.
E60, o241±o243.
Molecular Structure Corporation (1999). MSC/AFC-7 Diffractometer Control
for Windows. Version 1.02. MSC, 9009 New Trails Drive, The Woodlands,
TX 77381-5209, USA.
Molecular Structure Corporation (1997±2001). TEXSAN for Windows.
Version 1.06. MSC, 9009 New Trails Drive, The Woodlands, TX 77381-
5209, USA.
Sheldrick, G. M. (1997). SHELXL97. University of Go
È
ttingen, Germany.
Spek, A. L. (2001). PLATON for Windows. Version 121201. University of
Utrecht, The Netherlands.
organic papers
o1262 Declan McKeveney et al.
C
7
H
10
ClN
5
O
2
Acta Cryst. (2004). E60, o1260±o1262
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Copyright Statement © The Author ( s ) 2004. All articles published in Acta Crystallographica Section E are open access and distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.