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

Shi, S.; Yao, T.; Geng, X.; Chen, L.; Ji, L.

doi:10.1107/S1600536807065889

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 64| Part 1| January 2008| Page o272

https://doi.org/10.1107/S1600536807065889

Open

access

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

Shuo Shi,^a ^* Tian-ming Yao,^a Xiao-ting Geng,^a Lin Chen ^b and Liang-nian Ji ^b

^aDepartment of Chemistry, Tongji University, Shanghai, People's Republic of China, and ^bSchool of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, People's Republic of China
^*Correspondence e-mail: shishuo@mail.tongji.edu.cn

(Received 27 November 2007; accepted 6 December 2007; online 18 December 2007)

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, $[P \overline 1]$
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) Å³
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[F² > 2σ(F²)] = 0.036
wR(F²) = 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

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⋯N2^iv	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.

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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536807065889/ng2403sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807065889/ng2403Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

For related structures, see: Armstrong et al. (1998); Case (1964); Thompson et al. (1998); Xu et al. (1997, 1998, 2000, 2001).

Structure description top

For related structures, see: Armstrong et al. (1998); Case (1964); Thompson et al. (1998); Xu et al. (1997, 1998, 2000, 2001).

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SMART (Bruker, 1998); 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 (Bruker, 1998); software used to prepare material for publication: SHELXTL (Bruker, 1998).

Figures top

Fig. 1. The molecular structure of (I), with atom labels.

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

Crystal data top

C₁₀H₁₀N₈·2H₂O	V = 310.41 (19) Å³
M_r = 278.15	Z = 1
Triclinic, P1	F(000) = 146
a = 6.109 (2) Å	D_x = 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)°	T = 293 K
β = 106.975 (7)°	Prism, yellow
γ = 99.193 (6)°	0.48 × 0.22 × 0.18 mm

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	1036 independent reflections
Radiation source: fine-focus sealed tube	778 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.008
φ and ω scans	θ_max = 25.0°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −7→7
T_min = 0.949, T_max = 0.980	k = −8→8
1526 measured reflections	l = −9→8

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.102	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0576P)² + 0.0469P] where P = (F_o² + 2F_c²)/3
1036 reflections	(Δ/σ)_max < 0.001
107 parameters	Δρ_max = 0.15 e Å⁻³
0 restraints	Δρ_min = −0.14 e Å⁻³

Crystal data top

C₁₀H₁₀N₈·2H₂O	γ = 99.193 (6)°
M_r = 278.15	V = 310.41 (19) Å³
Triclinic, P1	Z = 1
a = 6.109 (2) Å	Mo Kα radiation
b = 7.502 (3) Å	µ = 0.11 mm⁻¹
c = 7.588 (3) Å	T = 293 K
α = 105.112 (6)°	0.48 × 0.22 × 0.18 mm
β = 106.975 (7)°

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	1036 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2000)	778 reflections with I > 2σ(I)
T_min = 0.949, T_max = 0.980	R_int = 0.008
1526 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.102	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	Δρ_max = 0.15 e Å⁻³
1036 reflections	Δρ_min = −0.14 e Å⁻³
107 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

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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, º) top

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 code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

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···N2^iv	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.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₀N₈·2H₂O
M_r	278.15
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	6.109 (2), 7.502 (3), 7.588 (3)
α, β, γ (°)	105.112 (6), 106.975 (7), 99.193 (6)
V (Å³)	310.41 (19)
Z	1
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.48 × 0.22 × 0.18

Data collection
Diffractometer	Bruker SMART APEX CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.949, 0.980
No. of measured, independent and observed [I > 2σ(I)] reflections	1526, 1036, 778
R_int	0.008
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.102, 1.04
No. of reflections	1036
No. of parameters	107
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.14

Computer programs: SMART (Bruker, 1998), SAINT-Plus and SHELXTL (Bruker, 1998), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1998).

Selected bond lengths (Å) top

C5—N4	1.296 (2)	N4—N4ⁱ	1.407 (3)
C5—N3	1.336 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

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···N2^iv	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.

Acknowledgements

The authors thank the National Natural Science Foundation of China, the Research Fund for the Doctoral Program of Higher Education, and the Program for Young Excellent Talents in Tongji University for financial support.

References

Armstrong, J. A., Barnes, J. C. & Weakley, T. J. R. (1998). Acta Cryst. C54, 1923–1925. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Bruker (1998). SMART, SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2000). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Case, F. H. (1965). J. Org. Chem. 30, 931–933. CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany. Google Scholar
Thompson, L. K., Xu, Z. Q., Goeta, A. E., Howard, J. A. K., Clase, H. J. & Miller, D. O. (1998). Inorg. Chem. 37, 3217–3229. Web of Science CSD CrossRef CAS Google Scholar
Xu, Z. Q., Thompson, L. K., Black, D. A., Ralph, C., Miller, D. O., Leech, M. A. & Howard, J. A. K. (2001). J. Chem. Soc. Dalton Trans. pp. 2042–2048. Web of Science CSD CrossRef Google Scholar
Xu, Z. Q., Thompson, L. K. & Miller, D. O. (1997). Inorg. Chem. 36, 3985–3995. CSD CrossRef CAS Web of Science Google Scholar
Xu, Z. Q., Thompson, L. K., Miller, D. O., Clase, H. J., Howard, J. A. K. & Goeta, A. E. (1998). Inorg. Chem. 37, 3620–3627. Web of Science CSD CrossRef PubMed CAS Google Scholar
Xu, Z. Q., White, S., Thompson, L. K., Miller, D. O., Ohba, M., Okawa, H., Wilson, C. & Howard, J. A. K. (2000). J. Chem. Soc. Dalton Trans. pp. 1751–1757. Web of Science CSD CrossRef Google Scholar