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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 1| January 2008| Page o272
https://doi.org/10.1107/S1600536807065889

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

Shuo Shi,a* Tian-ming Yao,a Xiao-ting Geng,a Lin Chenb and Liang-nian Jib

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[Armstrong, J. A., Barnes, J. C. & Weakley, T. J. R. (1998). Acta Cryst. C54, 1923-1925.]); Case (1965[Case, F. H. (1965). J. Org. Chem. 30, 931-933.]); Thompson et al. (1998[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 et al. (1997[Xu, Z. Q., Thompson, L. K. & Miller, D. O. (1997). Inorg. Chem. 36, 3985-3995.], 1998[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.], 2000[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.], 2001[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.]).

[Scheme 1]

Experimental

Crystal data

  • C10H10N8·2H2O

  • Mr = 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[Bruker (2000). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.949, Tmax = 0.980

  • 1526 measured reflections

  • 1036 independent reflections

  • 778 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.15 e Å−3

  • Δρmin = −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⋯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.

Data collection: SMART (Bruker, 1998[Bruker (1998). SMART, SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SMART; data reduction: SAINT-Plus and SHELXTL (Bruker, 1998[Bruker (1998). SMART, SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); 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).

Refinement top

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.

Structure description 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.

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
[Figure 1] Fig. 1. The molecular structure of (I), with atom labels.
1,2-Bis[amino(pyrimidin-2-yl)methylene]hydrazine dihydrate top
Crystal data top
C10H10N8·2H2OV = 310.41 (19) Å3
Mr = 278.15Z = 1
Triclinic, P1F(000) = 146
a = 6.109 (2) ÅDx = 1.489 Mg m−3
b = 7.502 (3) ÅMo Kα radiation, λ = 0.71073 Å
c = 7.588 (3) ŵ = 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 tube778 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.008
φ and ω scansθmax = 25.0°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −7→7
Tmin = 0.949, Tmax = 0.980k = −8→8
1526 measured reflectionsl = −9→8
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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0576P)2 + 0.0469P]
where P = (Fo2 + 2Fc2)/3
1036 reflections(Δ/σ)max < 0.001
107 parametersΔρmax = 0.15 e Å−3
0 restraintsΔρmin = −0.14 e Å−3
Crystal data top
C10H10N8·2H2Oγ = 99.193 (6)°
Mr = 278.15V = 310.41 (19) Å3
Triclinic, P1Z = 1
a = 6.109 (2) ÅMo Kα radiation
b = 7.502 (3) ŵ = 0.11 mm−1
c = 7.588 (3) ÅT = 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)
Tmin = 0.949, Tmax = 0.980Rint = 0.008
1526 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.15 e Å−3
1036 reflectionsΔρmin = −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
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) top
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, º) top
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 code: (i) −x+1, −y+1, −z+1.
Hydrogen-bond geometry (Å, º) top
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.

Experimental details

Crystal data
Chemical formulaC10H10N8·2H2O
Mr278.15
Crystal system, space groupTriclinic, 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)
Z1
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.48 × 0.22 × 0.18
Data collection
DiffractometerBruker SMART APEX CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.949, 0.980
No. of measured, independent and
observed [I > 2σ(I)] reflections		1526, 1036, 778
Rint0.008
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.102, 1.04
No. of reflections1036
No. of parameters107
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (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—N41.296 (2)N4—N4i1.407 (3)
C5—N31.336 (2)
Symmetry code: (i) −x+1, −y+1, −z+1.
Hydrogen-bond geometry (Å, º) top
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.
 

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

First citationArmstrong, 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
 First citationBruker (1998). SMART, SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBruker (2000). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationCase, F. H. (1965). J. Org. Chem. 30, 931–933.  CrossRef CAS Web of Science Google Scholar
 First citationSheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.  Google Scholar
 First citationThompson, 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
 First citationXu, 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
 First citationXu, Z. Q., Thompson, L. K. & Miller, D. O. (1997). Inorg. Chem. 36, 3985–3995.  CSD CrossRef CAS Web of Science Google Scholar
 First citationXu, 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
 First citationXu, 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

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 1| January 2008| Page o272
https://doi.org/10.1107/S1600536807065889
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