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In the title compound, C4H5N3, the nearly planar 5-amino­pyrimidine mol­ecule has twofold rotation symmetry. The crystal structure is stabilized by a hydrogen bond between the amino group and the ring N atoms, thus forming a two-dimensional network parallel to the ab plane.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805042236/fl6204sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805042236/fl6204Isup2.hkl
Contains datablock I

CCDC reference: 296562

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C)= 0.001 Å
  • R factor = 0.039
  • wR factor = 0.130
  • Data-to-parameter ratio = 17.3

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Comment top

Recently, there has been considerable interest in the use of pyrimidine (pym) as a bridging ligand for the formation of coordination polymers. Strong magnetic couplings can be mediated by µ-bonded pym ligands. One-, two- and three-dimensional structural motifs have been studied. For example, Cu(NO3)2(pym)(H2O)2 behaves as a uniform S = 1/2 antiferromagnetic chain (Feyerherm et al., 2000; Yasui et al., 2001). Structurally, the complex Cu(dca)(NO3)(pym)(H2O) (dca = dicyanamide) is two-dimensional, but magnetically it behaves as a one-dimensional chain, because the magnetic coupling through the 3-atom pym bridges is significantly stronger than that through the 5-atom dca bridges (Manson et al., 2003). Examples of structurally three-dimensional materials include Cu3(dca)6(pym)2·0.75H2O (Manson et al., 2003) and Cu(HCO2)2(pym) (Manson et al., 2005). The former of these has a large exchange coupling constant (J/kB = −69.4 K), while the latter exhibits long-range magnetic ordering below TN = 2.8 K. Spontaneous magnetization is also observed in the three-dimensional complexes M(dca)2(pym) (M = Fe or Co), with ordering temperatures of 3.2 and 1.8 K, respectively (Kusaka et al., 2000).

We are interested in increasing the dimensionality in these systems through the use of pyrimidine derivatives with hydrogen-bonding functionalities. Aminopyrimidines (apym) are one promising family that has this capability. 2-Aminopyrimidine (2-apym) has been used extensively as a ligand in coordination complexes. For example, a novel molecular tube-like structure containing monodentate 2-apym ligands and the relatively rare µ1,3,5 coordination mode for the dca anions has been reported for M(dca)2(2-apym) (M = Co or Ni) (Jensen et al., 2000). Monodentate 2-apym ligands are also found in the complex Cu(dca)2(2-apym)2, which forms one-dimensional dibridged µ1,5-dca chains (van Albada et al., 2000). When 2-apym acts as a bridging ligand, strong exchange coupling contants can be obtained, e.g. in [Cu4(2-apym)6(µ-OCH3)2(µ-F)3(F)2](BF4) (J/kB = −274 K) (van Albada et al., 2003). Another example of bridging 2-apym ligands is found in the zigzag chain structure of Cu2(acetate)4(2-apym) (Smith et al., 1991; Blake et al., 2002). We are aware of no coordination complexes derived from 4-apym or 5-apym. The N atoms of the 2-apym and 4-apym derivatives are more sterically hindered than the 5-apym derivative, thus making 5-apym a promising candiate for a bridging ligand. While the crystal structure of the 4-apym ligand has been published (Van Meervelt & Uytterhoeven, 2003), we report here, for the first time, that of 5-apym, (I).

The 5-apym molecule lies on a twofold axis. The atom-numbering scheme is shown in Fig. 1. The bond lengths and angles are typical of pyrimidines, including pym (Wheatley, 1960; Furberg et al., 1979), 2-apym (Scheinbeim & Schempp, 1976; Furberg et al., 1979) and 4-apym (Van Meervelt & Uytterhoeven, 2003). The ring atoms deviate only slightly from planarity, with atoms N1 and C2 out of the least-squares plane by 0.0022 (6) Å. By symmetry, the amino N atom lies in the plane of the pym ring. The dihedral angle between the plane of the amino group and the least-squares plane of the ring is 9.4 (17)°, signficantly smaller than the 22° angle observed in 2-apym (Scheinbeim & Schempp, 1976).

As illustrated in Fig. 2, the packing of the 5-apym molecules is stabilized by an N2—H3···N1i hydrogen bond (Table 2). The hydrogen-bond network results in the formation of two-dimensional sheets parallel to the ab plane. The pym plane is tilted by 11.50 (6)° with respect to the ab plane. Adjacent sheets are arranged such that uniform slipped stacks of 5-apym molecules form along the a + b diagonal. The 5-apym centroid–centroid distance of 3.723 Å and perpendicular separation of 3.362 Å confirm the presence of ππ interactions (Spek, 2003).

Experimental top

5-Aminopyrimidine was prepared according to the literature procedure of Phillips et al. (1999). Single crystals suitable for X-ray diffraction were grown by recrystallization from benzene.

Refinement top

H atoms on aromatic C atoms were positioned geometrically and refined with a riding model, with C—H = 0.93 Å. [Please check added text] The amino-group H atom was located in a difference map and its position fully refined. For all H atoms, Uiso(H) was constrained to be 1.2 (aromatic) or 1.5 (amino) times Ueq of the carrier atom.

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of 5-aminopyrimidine, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A packing diagram for 5-aminopyrimidine, illustrating the two-dimensional network in the ab plane. Displacement ellipsoids are drawn at the 20% probability level and H atoms are shown as small spheres of arbitrary radii. Hydrogen bonds are depicted as dashed lines.
5-Aminopyrimidine top
Crystal data top
C4H5N3F(000) = 200
Mr = 95.11Dx = 1.374 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1724 reflections
a = 7.5982 (10) Åθ = 3.4–29.5°
b = 10.1226 (13) ŵ = 0.09 mm1
c = 6.8106 (10) ÅT = 298 K
β = 118.596 (5)°Rod, colourless
V = 459.93 (11) Å30.50 × 0.22 × 0.20 mm
Z = 4
Data collection top
Siemens SMART CCD area-detector
diffractometer
641 independent reflections
Radiation source: fine-focus sealed tube584 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
ω scansθmax = 29.5°, θmin = 3.7°
Absorption correction: integration
XPREP in SHELXTL (Sheldrick, 2001)
h = 1010
Tmin = 0.956, Tmax = 0.987k = 1413
2534 measured reflectionsl = 99
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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.12 w = 1/[σ2(Fo2) + (0.0723P)2 + 0.0952P]
where P = (Fo2 + 2Fc2)/3
641 reflections(Δ/σ)max = 0.007
37 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C4H5N3V = 459.93 (11) Å3
Mr = 95.11Z = 4
Monoclinic, C2/cMo Kα radiation
a = 7.5982 (10) ŵ = 0.09 mm1
b = 10.1226 (13) ÅT = 298 K
c = 6.8106 (10) Å0.50 × 0.22 × 0.20 mm
β = 118.596 (5)°
Data collection top
Siemens SMART CCD area-detector
diffractometer
641 independent reflections
Absorption correction: integration
XPREP in SHELXTL (Sheldrick, 2001)
584 reflections with I > 2σ(I)
Tmin = 0.956, Tmax = 0.987Rint = 0.023
2534 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.12Δρmax = 0.31 e Å3
641 reflectionsΔρmin = 0.17 e Å3
37 parameters
Special details top

Experimental. The data collection nominally covered over a hemisphere of reciprocal space, by a combination of four sets of exposures; each set had a different ϕ angle for the crystal and each exposure covered 0.3° in ω. The crystal-to-detector distance was 4.508 cm. Coverage of the unique set was 97.8% complete to at least 29.5° in θ and greater than 99% complete to at least 28.2° in θ. Crystal decay was monitored by repeating the initial 50 frames at the end of data collection and analyzing the duplicate reflections. Decay was found to be less than 1%, and no decay correction was therefore applied.

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
C10.00000.09944 (15)0.25000.0506 (4)
H10.00000.00760.25000.061*
C20.13485 (13)0.29012 (10)0.21038 (17)0.0392 (3)
H20.22780.33440.18240.047*
C30.00000.36475 (12)0.25000.0340 (3)
N10.13606 (12)0.15911 (9)0.21087 (16)0.0469 (3)
N20.00000.49842 (12)0.25000.0491 (4)
H30.101 (3)0.539 (2)0.245 (3)0.074*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0480 (8)0.0327 (7)0.0746 (10)0.0000.0322 (7)0.000
C20.0355 (5)0.0380 (5)0.0500 (6)0.0009 (3)0.0253 (4)0.0007 (3)
C30.0336 (6)0.0328 (6)0.0379 (6)0.0000.0190 (5)0.000
N10.0418 (5)0.0384 (5)0.0653 (6)0.0052 (3)0.0297 (4)0.0017 (4)
N20.0540 (7)0.0311 (6)0.0815 (9)0.0000.0480 (7)0.000
Geometric parameters (Å, º) top
C1—N11.3298 (11)C2—H20.9300
C1—H10.9300C3—N21.3531 (17)
C2—N11.3262 (14)N2—H30.885 (18)
C2—C31.3993 (11)
N1—C1—N1i125.97 (14)C3—C2—H2118.5
N1—C1—H1117.0N2—C3—C2122.68 (6)
N1i—C1—H1117.0C2—C3—C2i114.65 (12)
N1—C2—C3122.97 (9)C2—N1—C1116.72 (9)
N1—C2—H2118.5C3—N2—H3117.7 (12)
N1—C2—C3—N2179.77 (6)C3—C2—N1—C10.43 (12)
N1—C2—C3—C2i0.23 (6)N1i—C1—N1—C20.21 (6)
Symmetry code: (i) x, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H3···N1ii0.885 (18)2.232 (19)3.1078 (11)169.8 (16)
Symmetry code: (ii) x+1/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H5N3
Mr95.11
Crystal system, space groupMonoclinic, C2/c
Temperature (K)298
a, b, c (Å)7.5982 (10), 10.1226 (13), 6.8106 (10)
β (°) 118.596 (5)
V3)459.93 (11)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.50 × 0.22 × 0.20
Data collection
DiffractometerSiemens SMART CCD area-detector
diffractometer
Absorption correctionIntegration
XPREP in SHELXTL (Sheldrick, 2001)
Tmin, Tmax0.956, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections
2534, 641, 584
Rint0.023
(sin θ/λ)max1)0.693
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.130, 1.12
No. of reflections641
No. of parameters37
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.31, 0.17

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 2001), SAINT, SHELXTL (Sheldrick, 2001), SHELXTL and PLATON (Spek, 2003).

Selected geometric parameters (Å, º) top
C1—N11.3298 (11)C2—C31.3993 (11)
C2—N11.3262 (14)C3—N21.3531 (17)
N1—C1—N1i125.97 (14)C2—C3—C2i114.65 (12)
N1—C2—C3122.97 (9)C2—N1—C1116.72 (9)
N2—C3—C2122.68 (6)C3—N2—H3117.7 (12)
N1—C2—C3—N2179.77 (6)C3—C2—N1—C10.43 (12)
N1—C2—C3—C2i0.23 (6)N1i—C1—N1—C20.21 (6)
Symmetry code: (i) x, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H3···N1ii0.885 (18)2.232 (19)3.1078 (11)169.8 (16)
Symmetry code: (ii) x+1/2, y+1/2, z+1/2.
 

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