5-Amino­pyrimidine

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.

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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S1. Comment

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/k_B = −69.4 K), while the latter exhibits long-range magnetic ordering below T_N = 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 µ_1,3,5 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 µ_1,5-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/k_B = −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 π–π interactions (Spek, 2003).

S2. Experimental

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.

S3. Refinement

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, U_iso(H) was constrained to be 1.2 (aromatic) or 1.5 (amino) times U_eq of the carrier atom.

Computing details

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

	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.
	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

Crystal data

C4H5N3	F(000) = 200
Mr = 95.11	Dx = 1.374 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1724 reflections
a = 7.5982 (10) Å	θ = 3.4–29.5°
b = 10.1226 (13) Å	µ = 0.09 mm^−1
c = 6.8106 (10) Å	T = 298 K
β = 118.596 (5)°	Rod, colourless
V = 459.93 (11) Å^3	0.50 × 0.22 × 0.20 mm
Z = 4

Data collection

Siemens SMART CCD area-detector diffractometer	641 independent reflections
Radiation source: fine-focus sealed tube	584 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
ω scans	θmax = 29.5°, θmin = 3.7°
Absorption correction: integration XPREP in SHELXTL (Sheldrick, 2001)	h = −10→10
Tmin = 0.956, Tmax = 0.987	k = −14→13
2534 measured reflections	l = −9→9

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.12	w = 1/[σ^2(Fo^2) + (0.0723P)^2 + 0.0952P] where P = (Fo^2 + 2Fc^2)/3
641 reflections	(Δ/σ)max = 0.007
37 parameters	Δρmax = 0.31 e Å^−3
0 restraints	Δρmin = −0.17 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.0000	0.09944 (15)	0.2500	0.0506 (4)
H1	0.0000	0.0076	0.2500	0.061*
C2	0.13485 (13)	0.29012 (10)	0.21038 (17)	0.0392 (3)
H2	0.2278	0.3344	0.1824	0.047*
C3	0.0000	0.36475 (12)	0.2500	0.0340 (3)
N1	0.13606 (12)	0.15911 (9)	0.21087 (16)	0.0469 (3)
N2	0.0000	0.49842 (12)	0.2500	0.0491 (4)
H3	0.101 (3)	0.539 (2)	0.245 (3)	0.074*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0480 (8)	0.0327 (7)	0.0746 (10)	0.000	0.0322 (7)	0.000
C2	0.0355 (5)	0.0380 (5)	0.0500 (6)	0.0009 (3)	0.0253 (4)	0.0007 (3)
C3	0.0336 (6)	0.0328 (6)	0.0379 (6)	0.000	0.0190 (5)	0.000
N1	0.0418 (5)	0.0384 (5)	0.0653 (6)	0.0052 (3)	0.0297 (4)	−0.0017 (4)
N2	0.0540 (7)	0.0311 (6)	0.0815 (9)	0.000	0.0480 (7)	0.000

Geometric parameters (Å, º)

C1—N1	1.3298 (11)	C2—H2	0.9300
C1—H1	0.9300	C3—N2	1.3531 (17)
C2—N1	1.3262 (14)	N2—H3	0.885 (18)
C2—C3	1.3993 (11)
N1—C1—N1^i	125.97 (14)	C3—C2—H2	118.5
N1—C1—H1	117.0	N2—C3—C2	122.68 (6)
N1^i—C1—H1	117.0	C2—C3—C2^i	114.65 (12)
N1—C2—C3	122.97 (9)	C2—N1—C1	116.72 (9)
N1—C2—H2	118.5	C3—N2—H3	117.7 (12)
N1—C2—C3—N2	179.77 (6)	C3—C2—N1—C1	0.43 (12)
N1—C2—C3—C2^i	−0.23 (6)	N1^i—C1—N1—C2	−0.21 (6)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H3···N1^ii	0.885 (18)	2.232 (19)	3.1078 (11)	169.8 (16)

Symmetry code: (ii) −x+1/2, y+1/2, −z+1/2.