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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o272.
Published online 2007 December 18. doi:  10.1107/S1600536807065889
PMCID: PMC2915327

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 [triangle]); Case (1965 [triangle]); Thompson et al. (1998 [triangle]); Xu et al. (1997 [triangle], 1998 [triangle], 2000 [triangle], 2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o272-scheme1.jpg

Experimental

Crystal data

  • C10H10N8·2H2O
  • M r = 278.15
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o272-efi1.jpg
  • 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 [triangle]) 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
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.14 e Å−3

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

Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807065889/ng2403Isup2.hkl

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

Acknowledgments

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.

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 Uiso(H) = 1.2Ueq(C or N) for all H atoms.

Figures

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

Crystal data

C10H10N8·2H2OV = 310.41 (19) Å3
Mr = 278.15Z = 1
Triclinic, P1F000 = 146
a = 6.109 (2) ÅDx = 1.489 Mg m3
b = 7.502 (3) ÅMo Kα radiation λ = 0.71073 Å
c = 7.588 (3) ŵ = 0.11 mm1
α = 105.112 (6)ºT = 293 (2) K
β = 106.975 (7)ºPrism, yellow
γ = 99.193 (6)º0.48 × 0.22 × 0.18 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer1036 independent reflections
Radiation source: fine-focus sealed tube778 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.008
T = 293(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 2.9º
Absorption correction: multi-scan(SADABS; Bruker, 2000)h = −7→7
Tmin = 0.949, Tmax = 0.980k = −8→8
1526 measured reflectionsl = −9→8

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H 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 reflectionsΔρmax = 0.15 e Å3
107 parametersΔρmin = −0.14 e Å3
Primary atom site location: structure-invariant direct methodsExtinction 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 (Å2)

xyzUiso*/Ueq
C10.6787 (3)0.9111 (3)1.2198 (3)0.0443 (5)
H1A0.79421.00041.33100.053*
C20.4674 (4)0.8331 (3)1.2312 (3)0.0452 (5)
H2A0.43670.86731.34680.054*
C30.3041 (4)0.7028 (3)1.0649 (3)0.0440 (5)
H3A0.15750.64981.06810.053*
C40.5561 (3)0.7320 (2)0.9025 (2)0.0309 (4)
C50.6110 (3)0.6704 (2)0.7210 (2)0.0307 (4)
N10.7253 (3)0.8640 (2)1.0550 (2)0.0382 (4)
N20.3437 (3)0.6477 (2)0.8988 (2)0.0385 (4)
N30.8159 (3)0.7655 (3)0.7217 (3)0.0469 (5)
H3B0.900 (3)0.857 (3)0.825 (3)0.042 (6)*
H3C0.856 (4)0.732 (3)0.617 (3)0.052 (6)*
N40.4600 (2)0.5260 (2)0.5788 (2)0.0334 (4)
O1W0.0384 (3)0.6771 (2)0.4092 (2)0.0477 (4)
H1WA−0.074 (5)0.593 (4)0.338 (4)0.079 (10)*
H1WB0.153 (5)0.624 (4)0.462 (4)0.088 (10)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0481 (12)0.0404 (11)0.0308 (11)−0.0017 (9)0.0107 (9)0.0008 (9)
C20.0579 (13)0.0404 (11)0.0357 (11)0.0055 (10)0.0225 (10)0.0069 (9)
C30.0444 (11)0.0439 (11)0.0446 (12)0.0037 (9)0.0236 (9)0.0112 (10)
C40.0288 (10)0.0301 (9)0.0312 (10)0.0067 (7)0.0086 (8)0.0085 (8)
C50.0248 (9)0.0309 (9)0.0318 (10)0.0033 (7)0.0087 (8)0.0066 (8)
N10.0375 (9)0.0355 (9)0.0317 (9)0.0005 (7)0.0088 (7)0.0036 (7)
N20.0336 (8)0.0403 (9)0.0355 (9)0.0017 (7)0.0132 (7)0.0055 (7)
N30.0373 (10)0.0480 (11)0.0388 (11)−0.0092 (8)0.0184 (8)−0.0062 (9)
N40.0295 (8)0.0374 (9)0.0285 (8)0.0037 (7)0.0114 (7)0.0043 (7)
O1W0.0387 (9)0.0457 (9)0.0505 (9)0.0026 (8)0.0134 (7)0.0097 (8)

Geometric parameters (Å, °)

C1—N11.335 (2)C4—C51.487 (2)
C1—C21.366 (3)C5—N41.296 (2)
C1—H1A0.9300C5—N31.336 (2)
C2—C31.361 (3)N3—H3B0.85 (2)
C2—H2A0.9300N3—H3C0.89 (2)
C3—N21.325 (3)N4—N4i1.407 (3)
C3—H3A0.9300O1W—H1WA0.79 (3)
C4—N11.328 (2)O1W—H1WB0.91 (3)
C4—N21.339 (2)
N1—C1—C2122.40 (17)N2—C4—C5117.39 (15)
N1—C1—H1A118.8N4—C5—N3125.86 (17)
C2—C1—H1A118.8N4—C5—C4117.26 (15)
C3—C2—C1116.68 (18)N3—C5—C4116.84 (16)
C3—C2—H2A121.7C4—N1—C1116.03 (16)
C1—C2—H2A121.7C3—N2—C4115.50 (16)
N2—C3—C2123.30 (19)C5—N3—H3B116.4 (13)
N2—C3—H3A118.4C5—N3—H3C119.7 (14)
C2—C3—H3A118.4H3B—N3—H3C123.9 (19)
N1—C4—N2126.04 (17)C5—N4—N4i111.67 (16)
N1—C4—C5116.56 (15)H1WA—O1W—H1WB108 (3)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3B···N1ii0.85 (2)2.59 (2)3.276 (2)138.5 (16)
N3—H3C···O1Wiii0.89 (2)2.17 (3)3.043 (3)166.7 (19)
O1W—H1WA···N2iv0.79 (3)2.20 (3)2.979 (2)168 (3)
O1W—H1WB···N40.91 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2403).

References

  • Armstrong, J. A., Barnes, J. C. & Weakley, T. J. R. (1998). Acta Cryst. C54, 1923–1925.
  • Bruker (1998). SMART, SAINT-Plus and SHELXTL Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2000). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Case, F. H. (1965). J. Org. Chem.30, 931–933.
  • Sheldrick, G. M. (1997). SHELXS97 and SHELXL97 University of Göttingen, Germany.
  • 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.
  • 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.
  • Xu, Z. Q., Thompson, L. K. & Miller, D. O. (1997). Inorg. Chem.36, 3985–3995.
  • 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. [PubMed]
  • 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.

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