1,2-Bis[amino­(pyrimidin-2-yl)methyl­ene]hydrazine dihydrate

Abstract

The centrosymmetric organic molecule in the title compound, C₁₀H₁₀N₈·2H₂O, is essentially flat and has a trans configuration. The mol­ecules are linked by inter­molecular O—H⋯N, N—H⋯O and N—H⋯N hydrogen bonds to form a linear chain structure.

Related literature

For related structures, see: Armstrong et al. (1998 ▶); Case (1965 ▶); Thompson et al. (1998 ▶); Xu et al. (1997 ▶, 1998 ▶, 2000 ▶, 2001 ▶).

Experimental

Crystal data

• C₁₀H₁₀N₈·2H₂O

• M _r = 278.15

• Triclinic,

• a = 6.109 (2) Å

• b = 7.502 (3) Å

• c = 7.588 (3) Å

• α = 105.112 (6)°

• β = 106.975 (7)°

• γ = 99.193 (6)°

• V = 310.41 (19) ų

• Z = 1

• Mo Kα radiation

• μ = 0.11 mm⁻¹

• T = 293 (2) K

• 0.48 × 0.22 × 0.18 mm

Data collection

• Bruker SMART APEX CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2000 ▶) T _min = 0.949, T _max = 0.980

• 1526 measured reflections

• 1036 independent reflections

• 778 reflections with I > 2σ(I)

• R _int = 0.008

Refinement

• R[F ² > 2σ(F ²)] = 0.036

• wR(F ²) = 0.102

• S = 1.04

• 1036 reflections

• 107 parameters

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

• Δρ_max = 0.15 e Å⁻³

• Δρ_min = −0.14 e Å⁻³

Data collection: SMART (Bruker, 1998 ▶); cell refinement: SMART; data reduction: SAINT-Plus and SHELXTL (Bruker, 1998 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ▶); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3B⋯N1ii	0.85 (2)	2.59 (2)	3.276 (2)	138.5 (16)
N3—H3C⋯O1Wiii	0.89 (2)	2.17 (3)	3.043 (3)	166.7 (19)
O1W—H1WA⋯N2iv	0.79 (3)	2.20 (3)	2.979 (2)	168 (3)
O1W—H1WB⋯N4	0.91 (3)	2.16 (3)	3.055 (2)	172 (2)

Symmetry codes: (ii) ; (iii) ; (iv) .

supplementary crystallographic information

Comment

The title compound, (I) (Fig. 1), can be regarded as a dihydrazidine. It is formed as the major product from mixing 2-cyanopyrimidine and hydrazine in ethanol (Case, 1965) and the minor product is Pyrimidine-2-carboxamide hydrazone, (II)(Scheme. 1). Compound (I) has now been shown to have trans geometry (Fig. 1), with all atoms essentially coplanar. The overall trans configuration is therefore due mainly to steric repulsion effects. The title compound contains a single N—N bond, presents several possible mononucleating and dinucleating coordination modes and, also, the potential for free rotation about the N—N bond. The flexible geometries result from the ability of the systems to rotate freely about the single N—N bond of the diazine fragment of the compound.

Refinement

All H atoms were placed in geometrically positions and constrained to ride on their parent atoms, with N—H distances in the range 0.85—0.89 Å and C—H = 0.93 Å, and with U_iso(H) = 1.2Ueq(C or N) for all H atoms.

Figures

Fig. 1.

The molecular structure of (I), with atom labels.

Crystal data

C10H10N8·2H2O	V = 310.41 (19) Å3
Mr = 278.15	Z = 1
Triclinic, P1	F000 = 146
a = 6.109 (2) Å	Dx = 1.489 Mg m−3
b = 7.502 (3) Å	Mo Kα radiation λ = 0.71073 Å
c = 7.588 (3) Å	µ = 0.11 mm−1
α = 105.112 (6)º	T = 293 (2) K
β = 106.975 (7)º	Prism, yellow
γ = 99.193 (6)º	0.48 × 0.22 × 0.18 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer	1036 independent reflections
Radiation source: fine-focus sealed tube	778 reflections with I > 2σ(I)
Monochromator: graphite	Rint = 0.008
T = 293(2) K	θmax = 25.0º
φ and ω scans	θmin = 2.9º
Absorption correction: multi-scan(SADABS; Bruker, 2000)	h = −7→7
Tmin = 0.949, Tmax = 0.980	k = −8→8
1526 measured reflections	l = −9→8

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.102	w = 1/[σ2(Fo2) + (0.0576P)2 + 0.0469P] where P = (Fo2 + 2Fc2)/3
S = 1.04	(Δ/σ)max < 0.001
1036 reflections	Δρmax = 0.15 e Å−3
107 parameters	Δρmin = −0.14 e Å−3
Primary atom site location: structure-invariant direct methods	Extinction correction: none

Special details

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	0.6787 (3)	0.9111 (3)	1.2198 (3)	0.0443 (5)
H1A	0.7942	1.0004	1.3310	0.053*
C2	0.4674 (4)	0.8331 (3)	1.2312 (3)	0.0452 (5)
H2A	0.4367	0.8673	1.3468	0.054*
C3	0.3041 (4)	0.7028 (3)	1.0649 (3)	0.0440 (5)
H3A	0.1575	0.6498	1.0681	0.053*
C4	0.5561 (3)	0.7320 (2)	0.9025 (2)	0.0309 (4)
C5	0.6110 (3)	0.6704 (2)	0.7210 (2)	0.0307 (4)
N1	0.7253 (3)	0.8640 (2)	1.0550 (2)	0.0382 (4)
N2	0.3437 (3)	0.6477 (2)	0.8988 (2)	0.0385 (4)
N3	0.8159 (3)	0.7655 (3)	0.7217 (3)	0.0469 (5)
H3B	0.900 (3)	0.857 (3)	0.825 (3)	0.042 (6)*
H3C	0.856 (4)	0.732 (3)	0.617 (3)	0.052 (6)*
N4	0.4600 (2)	0.5260 (2)	0.5788 (2)	0.0334 (4)
O1W	0.0384 (3)	0.6771 (2)	0.4092 (2)	0.0477 (4)
H1WA	−0.074 (5)	0.593 (4)	0.338 (4)	0.079 (10)*
H1WB	0.153 (5)	0.624 (4)	0.462 (4)	0.088 (10)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0481 (12)	0.0404 (11)	0.0308 (11)	−0.0017 (9)	0.0107 (9)	0.0008 (9)
C2	0.0579 (13)	0.0404 (11)	0.0357 (11)	0.0055 (10)	0.0225 (10)	0.0069 (9)
C3	0.0444 (11)	0.0439 (11)	0.0446 (12)	0.0037 (9)	0.0236 (9)	0.0112 (10)
C4	0.0288 (10)	0.0301 (9)	0.0312 (10)	0.0067 (7)	0.0086 (8)	0.0085 (8)
C5	0.0248 (9)	0.0309 (9)	0.0318 (10)	0.0033 (7)	0.0087 (8)	0.0066 (8)
N1	0.0375 (9)	0.0355 (9)	0.0317 (9)	0.0005 (7)	0.0088 (7)	0.0036 (7)
N2	0.0336 (8)	0.0403 (9)	0.0355 (9)	0.0017 (7)	0.0132 (7)	0.0055 (7)
N3	0.0373 (10)	0.0480 (11)	0.0388 (11)	−0.0092 (8)	0.0184 (8)	−0.0062 (9)
N4	0.0295 (8)	0.0374 (9)	0.0285 (8)	0.0037 (7)	0.0114 (7)	0.0043 (7)
O1W	0.0387 (9)	0.0457 (9)	0.0505 (9)	0.0026 (8)	0.0134 (7)	0.0097 (8)

Geometric parameters (Å, °)

C1—N1	1.335 (2)	C4—C5	1.487 (2)
C1—C2	1.366 (3)	C5—N4	1.296 (2)
C1—H1A	0.9300	C5—N3	1.336 (2)
C2—C3	1.361 (3)	N3—H3B	0.85 (2)
C2—H2A	0.9300	N3—H3C	0.89 (2)
C3—N2	1.325 (3)	N4—N4i	1.407 (3)
C3—H3A	0.9300	O1W—H1WA	0.79 (3)
C4—N1	1.328 (2)	O1W—H1WB	0.91 (3)
C4—N2	1.339 (2)
N1—C1—C2	122.40 (17)	N2—C4—C5	117.39 (15)
N1—C1—H1A	118.8	N4—C5—N3	125.86 (17)
C2—C1—H1A	118.8	N4—C5—C4	117.26 (15)
C3—C2—C1	116.68 (18)	N3—C5—C4	116.84 (16)
C3—C2—H2A	121.7	C4—N1—C1	116.03 (16)
C1—C2—H2A	121.7	C3—N2—C4	115.50 (16)
N2—C3—C2	123.30 (19)	C5—N3—H3B	116.4 (13)
N2—C3—H3A	118.4	C5—N3—H3C	119.7 (14)
C2—C3—H3A	118.4	H3B—N3—H3C	123.9 (19)
N1—C4—N2	126.04 (17)	C5—N4—N4i	111.67 (16)
N1—C4—C5	116.56 (15)	H1WA—O1W—H1WB	108 (3)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3B···N1ii	0.85 (2)	2.59 (2)	3.276 (2)	138.5 (16)
N3—H3C···O1Wiii	0.89 (2)	2.17 (3)	3.043 (3)	166.7 (19)
O1W—H1WA···N2iv	0.79 (3)	2.20 (3)	2.979 (2)	168 (3)
O1W—H1WB···N4	0.91 (3)	2.16 (3)	3.055 (2)	172 (2)

Symmetry codes: (ii) −x+2, −y+2, −z+2; (iii) x+1, y, z; (iv) −x, −y+1, −z+1.