organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

2-Chloro­pyrimidin-4-amine

aLeiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands, and bDepartment of Chemistry, Faculty of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
*Correspondence e-mail: mghazzali@ksu.edu.sa

(Received 7 December 2011; accepted 27 December 2011; online 7 January 2012)

In the title pyrimidine derivative, C4H4ClN3, the 2-chloro and 4-amino substituents almost lie in the mean plane of the pyrimidine ring, with deviations of 0.003 (1) Å for the Cl atom, and 0.020 (1) Å for the N atom. In the crystal, molecules are linked via pairs of N—H⋯N hydrogen bonds, forming inversion dimers. These dimers are further linked via N—H⋯N hydrogen bonds, forming an undulating two-dimensional network lying parallel to (100).

Related literature

For compounds related to pyrimidin-4-amine, see: Van Albada et al. (1999[Van Albada, G. A., Komaei, S. A., Kooijman, H., Spek, A. L. & Reedijk, J. (1999). Inorg. Chim. Acta, 287, 226-231.], 2003[Van Albada, G. A., Roubeau, O., Mutikainen, I., Turpeinen, U. & Reedijk, J. (2003). New J. Chem. 27, 1693-1697.]); Van Meervelt & Uytterhoeven (2003[Van Meervelt, L. & Uytterhoeven, K. (2003). Z. Kristallogr. New Cryst. Struct. 218, 481-482.]); Kožíšek et al. (2005[Kožíšek, J., Díaz, J. G., Fronc, M. & Svoboda, I. (2005). Acta Cryst. E61, m1150-m1152.]). For the agricultural and pharmaceutical relevance of 2-chloro­pyrimidin-4-amine, see: Zunszain et al. (2005[Zunszain, P. A., Federico, C., Sechi, M., Al-Damluji, S. & Ganellin, C. R. (2005). Bioorg. Med. Chem. 13, 3681-3689.]). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C4H4ClN3

  • Mr = 129.55

  • Monoclinic, P 21 /c

  • a = 3.83162 (19) Å

  • b = 11.8651 (7) Å

  • c = 12.7608 (7) Å

  • β = 100.886 (2)°

  • V = 569.70 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.55 mm−1

  • T = 294 K

  • 0.40 × 0.20 × 0.20 mm

Data collection
  • Rigaku R-AXIS RAPID diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2007[Rigaku (2007). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]) Tmin = 0.840, Tmax = 0.888

  • 9506 measured reflections

  • 1296 independent reflections

  • 962 reflections with I > 2σ(I)

  • Rint = 0.038

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.092

  • S = 1.14

  • 1296 reflections

  • 82 parameters

  • 2 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.27 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2A⋯N3i 0.90 (2) 2.17 (2) 3.069 (2) 174 (2)
N2—H2B⋯N1ii 0.87 (2) 2.16 (2) 3.024 (2) 170 (2)
Symmetry codes: (i) -x, -y+1, -z+1; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: CrystalClear (Rigaku, 2007[Rigaku (2007). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2007[Brandenburg, K. (2007). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

The molecule of 2-chloropyrimidin-4-amine is relevant for agrochemistry as a plant growth regulator and as a pharmaceutical intermediate (Zunszain et al. 2005). It could also be an interesting precursor for chelating ligands after chlorine substitution. Pyrimidin-amines are interesting bridging ligands, as they contain two nitrogen coordination donor atoms, and an amine as a hydrogen bond donor group (Van Albada et al. 1999, 2003). The ligands pyrimidin-4-amine and 2-amine can easily bridge two metal ions (Kožíšek et al. 2005). With the presence of two donor atoms, the title compound might serve as a building block in the formation of coordination polymers. Due to the position of a chloride atom in-between the two donor N atoms of the pyrimidin-4-amine, the bridging would be likely to change. In fact, coordination complexes with the 2-chloropyrimidin-4-amine are yet unreachable. We here present the molecular structure of this compound, (Figure 1).

The 2-chloropyrimidin-4-amine molecule is nearly planar, with r.m.s. deviation of the pyrimidine heterocyclic non-hydrogen atoms is 0.002 (2) Å. In the crystal, molecules are arranged with two N—H···N hydrogen bond motifs, where the amine group serves as a twofold donor of the hydrogen atoms for the two pyrimidine nitrogen atoms. Considering graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptors are R22(8) loops and C(5) chain motifs along the [001] and [010] vectors, respectively. The network can be described as a wobbled two-dimensional network extending in the (100) plane, (Figure 2). It is worth to note that the related pyrimidin-4-amine molecule (Van Meervelt et al. 2003), crystallizes in the orthorhombic Pcab space group and exhibits only the N—H···N hydrogen bond with C(5) chain motif of a one-dimensional zigzag chain.

Related literature top

For compounds related to pyrimidin-4-amine, see: Van Albada et al. (1999, 2003); Van Meervelt & Uytterhoeven (2003); Kožíšek et al. (2005). For the agricultural and pharmaceutical relevance of 2-chloropyrimidin-4-amine, see: Zunszain et al. (2005). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995).

For related literature, see: Kožíšek et al. (2005).

Experimental top

The ligand was used as commercially available. 0.5 mg of the compound was dissolved in 10 ml of methanol. The solution was stand at room temperature in a closed vessel. After two weeks, colourless blocks appeared and separated by filtration.

Refinement top

Carbon-bound H-atoms were placed in ideal calculated positions [aromatic C—H 0.93 Å, Uiso(H) = 1.2Ueq(C)] and refined as riding atoms. The amine H-atoms were constrained into their positions using two distance restraints [N—H 0.91 Å, Uiso(H) = 1.2Ueq(N)].

Computing details top

Data collection: CrystalClear (Rigaku, 2007); cell refinement: CrystalClear (Rigaku, 2007); data reduction: CrystalClear (Rigaku, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2007); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Atomic numbering scheme and thermal ellipsoidal (50% probability level) of the title compound. Hydrogen atoms are presented as spheres of arbitrary radii.
[Figure 2] Fig. 2. bc-plane projection showing the N—H···N hydrogen bonds as dotted line of R22(8) loop (presented in blue color), and C(5) chain (presented in red color). Symmetry codes: (i) -x, -y + 1, -z + 1; (ii) x, -y + 1/2, z + 1/2.
2-Chloropyrimidin-4-amine top
Crystal data top
C4H4ClN3F(000) = 264
Mr = 129.55Dx = 1.510 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ybcCell parameters from 342 reflections
a = 3.83162 (19) Åθ = 3.3–27.5°
b = 11.8651 (7) ŵ = 0.55 mm1
c = 12.7608 (7) ÅT = 294 K
β = 100.886 (2)°Block, colourless
V = 569.70 (5) Å30.40 × 0.20 × 0.20 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
1296 independent reflections
Radiation source: fine-focus sealed tube962 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.038
ω scansθmax = 27.5°, θmin = 3.3°
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2007)
h = 44
Tmin = 0.840, Tmax = 0.888k = 1515
9506 measured reflectionsl = 1616
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092H atoms treated by a mixture of independent and constrained refinement
S = 1.14 w = 1/[σ2(Fo2) + (0.0422P)2 + 0.0697P]
where P = (Fo2 + 2Fc2)/3
1296 reflections(Δ/σ)max < 0.001
82 parametersΔρmax = 0.17 e Å3
2 restraintsΔρmin = 0.27 e Å3
Crystal data top
C4H4ClN3V = 569.70 (5) Å3
Mr = 129.55Z = 4
Monoclinic, P21/cMo Kα radiation
a = 3.83162 (19) ŵ = 0.55 mm1
b = 11.8651 (7) ÅT = 294 K
c = 12.7608 (7) Å0.40 × 0.20 × 0.20 mm
β = 100.886 (2)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
1296 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2007)
962 reflections with I > 2σ(I)
Tmin = 0.840, Tmax = 0.888Rint = 0.038
9506 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0352 restraints
wR(F2) = 0.092H atoms treated by a mixture of independent and constrained refinement
S = 1.14Δρmax = 0.17 e Å3
1296 reflectionsΔρmin = 0.27 e Å3
82 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.05814 (13)0.43867 (4)0.20898 (3)0.0586 (2)
N10.3425 (4)0.25622 (13)0.29987 (11)0.0500 (4)
N20.2112 (5)0.37262 (14)0.59166 (12)0.0522 (4)
H2B0.277 (5)0.3340 (17)0.6504 (14)0.065 (6)*
H2A0.103 (5)0.4395 (14)0.5959 (17)0.061 (6)*
C20.2035 (4)0.35294 (14)0.32044 (13)0.0419 (4)
N30.1530 (4)0.39673 (11)0.41103 (10)0.0407 (3)
C40.2612 (4)0.33227 (13)0.49910 (12)0.0400 (4)
C50.4177 (5)0.22616 (15)0.48826 (14)0.0480 (4)
H50.49610.18060.54730.058*
C60.4495 (5)0.19310 (16)0.38937 (16)0.0531 (5)
H60.55060.12300.38180.064*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0718 (4)0.0665 (4)0.0379 (3)0.0003 (2)0.0113 (2)0.0060 (2)
N10.0570 (9)0.0502 (9)0.0447 (9)0.0005 (7)0.0143 (7)0.0103 (7)
N20.0775 (11)0.0455 (9)0.0345 (8)0.0079 (8)0.0130 (7)0.0007 (7)
C20.0431 (9)0.0456 (9)0.0379 (9)0.0055 (7)0.0101 (7)0.0045 (7)
N30.0496 (8)0.0380 (7)0.0357 (7)0.0010 (6)0.0112 (6)0.0019 (6)
C40.0439 (9)0.0395 (9)0.0372 (8)0.0034 (7)0.0092 (7)0.0013 (7)
C50.0533 (10)0.0429 (10)0.0472 (10)0.0047 (8)0.0075 (8)0.0027 (8)
C60.0550 (11)0.0442 (10)0.0610 (12)0.0047 (8)0.0132 (9)0.0092 (9)
Geometric parameters (Å, º) top
Cl1—C21.7518 (17)C2—N31.315 (2)
N1—C21.312 (2)N3—C41.358 (2)
N1—C61.363 (2)C4—C51.412 (2)
N2—C41.322 (2)C5—C61.349 (2)
N2—H2B0.874 (15)C5—H50.9300
N2—H2A0.902 (16)C6—H60.9300
C2—N1—C6112.47 (15)N2—C4—C5123.11 (16)
C4—N2—H2B120.6 (14)N3—C4—C5119.33 (15)
C4—N2—H2A121.3 (14)C6—C5—C4117.77 (16)
H2B—N2—H2A118 (2)C6—C5—H5121.1
N1—C2—N3130.85 (16)C4—C5—H5121.1
N1—C2—Cl1115.10 (12)C5—C6—N1123.94 (17)
N3—C2—Cl1114.05 (13)C5—C6—H6118.0
C2—N3—C4115.64 (14)N1—C6—H6118.0
N2—C4—N3117.56 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N3i0.90 (2)2.17 (2)3.069 (2)174 (2)
N2—H2B···N1ii0.87 (2)2.16 (2)3.024 (2)170 (2)
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H4ClN3
Mr129.55
Crystal system, space groupMonoclinic, P21/c
Temperature (K)294
a, b, c (Å)3.83162 (19), 11.8651 (7), 12.7608 (7)
β (°) 100.886 (2)
V3)569.70 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.55
Crystal size (mm)0.40 × 0.20 × 0.20
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2007)
Tmin, Tmax0.840, 0.888
No. of measured, independent and
observed [I > 2σ(I)] reflections
9506, 1296, 962
Rint0.038
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.092, 1.14
No. of reflections1296
No. of parameters82
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.17, 0.27

Computer programs: CrystalClear (Rigaku, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2007), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N3i0.902 (16)2.171 (16)3.069 (2)174.0 (19)
N2—H2B···N1ii0.874 (15)2.160 (16)3.024 (2)169.5 (19)
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1/2, z+1/2.
 

Acknowledgements

The authors are indebted to the Deanship of Scientific Research, College of Science Research Center, for supporting this work. The Distinguished Scientist Fellowship Program (DSFP) at King Saud University is gratefully acknowledged.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBrandenburg, K. (2007). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
First citationEtter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationKožíšek, J., Díaz, J. G., Fronc, M. & Svoboda, I. (2005). Acta Cryst. E61, m1150–m1152.  Web of Science CrossRef IUCr Journals Google Scholar
First citationRigaku (2007). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationVan Albada, G. A., Komaei, S. A., Kooijman, H., Spek, A. L. & Reedijk, J. (1999). Inorg. Chim. Acta, 287, 226–231.  Web of Science CSD CrossRef CAS Google Scholar
First citationVan Albada, G. A., Roubeau, O., Mutikainen, I., Turpeinen, U. & Reedijk, J. (2003). New J. Chem. 27, 1693–1697.  CrossRef CAS Google Scholar
First citationVan Meervelt, L. & Uytterhoeven, K. (2003). Z. Kristallogr. New Cryst. Struct. 218, 481–482.  CAS Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZunszain, P. A., Federico, C., Sechi, M., Al-Damluji, S. & Ganellin, C. R. (2005). Bioorg. Med. Chem. 13, 3681–3689.  Web of Science CrossRef PubMed CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds