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

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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.036
• wR factor = 0.102
• Data-to-parameter ratio = 9.7

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.95

Alert level C
REFLT03_ALERT_3_C  Reflection count < 95% complete
           From the CIF: _diffrn_reflns_theta_max           25.02
           From the CIF: _diffrn_reflns_theta_full          25.02
           From the CIF: _reflns_number_total               1036
           TEST2: Reflns within _diffrn_reflns_theta_max
           Count of symmetry unique reflns         1092
           Completeness (_total/calc)             94.87%
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ....       0.95
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............       0.50 Ratio
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT088_ALERT_3_C Poor Data / Parameter Ratio ....................       9.68
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT150_ALERT_1_C Volume as Calculated Differs from that Given ...     310.41 Ang-3
PLAT194_ALERT_1_C Missing _cell_measurement_reflns_used datum ....          ?
PLAT195_ALERT_1_C Missing _cell_measurement_theta_max   datum ....          ?
PLAT196_ALERT_1_C Missing _cell_measurement_theta_min   datum ....          ?
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          2

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
  13 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

  10 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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.

Related literature

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

S2. 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.

Computing details

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

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

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

Crystal data

C10H10N8·2H2O	V = 310.41 (19) Å^3
Mr = 278.15	Z = 1
Triclinic, P1	F(000) = 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)°	T = 293 K
β = 106.975 (7)°	Prism, yellow
γ = 99.193 (6)°	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)
Graphite monochromator	Rint = 0.008
φ and ω scans	θmax = 25.0°, θmin = 2.9°
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 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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.102	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0576P)^2 + 0.0469P] where P = (Fo^2 + 2Fc^2)/3
1036 reflections	(Δ/σ)max < 0.001
107 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.14 e Å^−3

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)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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—N4^i	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—N4^i	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)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3B···N1^ii	0.85 (2)	2.59 (2)	3.276 (2)	138.5 (16)
N3—H3C···O1W^iii	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.