Retracted: N-(2-Amino-3-pyrid­yl)urea monohydrate

In the crystal structure of the title compound, C₆H₉N₄O·H₂O, inter­molecular O—H...N and N—H...O hydrogen bonds result in the formation of a supra­molecular network structure; intra­molecular O—H...N hydrogen bonds are also present.

Key indicators

• Single-crystal X-ray study
• T = 273 K
• Mean [sigma](C-C) = 0.006 Å
• H-atom completeness 91%
• R factor = 0.058
• wR factor = 0.177
• Data-to-parameter ratio = 11.9

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    N1     -   C1      ..      13.69 su
PLAT230_ALERT_2_B Hirshfeld Test Diff for    N1     -   C2      ..       9.73 su
PLAT241_ALERT_2_B Check High      Ueq as Compared to Neighbors for         N1
PLAT416_ALERT_2_B Short Intra D-H..H-D       H2A    ..  H3A     ..       1.52 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H2A    ..  H5A     ..       2.09 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H2B    ..  H5A     ..       1.96 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H2B    ..  H5B     ..       1.33 Ang.

Alert level C
PLAT031_ALERT_4_C Refined Extinction Parameter within Range ......       2.50 Sigma
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.64 mm
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C1     -   C5      ..       5.03 su
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C1
PLAT245_ALERT_2_C U(iso) H5B     Smaller than U(eq) O2      by ...       0.02 AngSq
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          6
PLAT480_ALERT_4_C Long H...A H-Bond Reported H5B    ..  N1      ..       2.78 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H5A    ..  N2      ..       2.68 Ang.

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C6 H11 N4 O2
            Atom count from the _atom_site data:  C6 H10 N4 O2
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    4
           From the CIF: _chemical_formula_sum  C6 H11 N4 O2
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         24.00     24.00    0.00
           H         44.00     40.00    4.00
           N         16.00     16.00    0.00
           O          8.00      8.00    0.00
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          3

   0 ALERT level A = In general: serious problem
   7 ALERT level B = Potentially serious problem
  12 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

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

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S1. Comment

In the synthesis of crystal structures by design, the assembly of molecular units in predefined arrangements is a key goal (Desiraju, 1995, 1997; Braga et al., 1998). Due to hydrogen-bonding interactions are of critical importance in biological systems, organic materials and coordination chemistry, hydrogen-bonding is currently the best tool in achieving this goal (Zaworotko, 1997; Braga & Grepioni, 2000). Supramolecular architectures are of considerable contemporary interest by virtue of their potential applications in various fields (Moulton & Zaworotko, 2001; Pan et al., 2001; Ma et al., 2001; Prior & Rosseinsky, 2001). We originally attempted to synthesize complexes featuring La metal chains by reaction of the lanthanum(III) ion with N-(1-amino-2-pyridyl)-carbamide ligand. Unfortunately, we obtained only the title compound, (I), and report herein its crystal structure.

In the molecule of (I) (Fig. 1), the ligand bond lengths and angles are within normal ranges (Allen et al., 1987). It contains one N-(2-amino-3-pyridyl)urea molecule and one H₂O molecule.

In the crystal structure, intermolecular O—H···N and N—H···O hydrogen bonds (Table 1 and Fig. 2) result in the formation of a supramolecular network structure; intramolecular O—H···N hydrogen bonds are also present.

Related literature

For general background, see: Braga et al. (1998); Braga & Grepioni (2000); Desiraju (1995); Desiraju (1997); Ma et al. (2001); Moulton & Zaworotko (2001); Pan et al. (2001); Prior & Rosseinsky (2001); Zaworotko (1997). For bond-length data, see: Allen et al. (1987).

S2. Experimental

Crystals of the title compound were synthesized using hydrothermal method in a 23 ml Teflon-lined Parr bomb. Lanthanum (III) nitrate hexahydrate (216.4 mg, 0.5 mmol), N-(1-amino-2-pyridyl)carbamide (163.2 mg, 1 mmol) and distilled water (5 g) were placed into the bomb and sealed. The bomb was then heated under autogenous pressure up to 453 K over the course of 7 d and allowed to cool at room temperature for 24 h. Upon opening the bomb, a clear colorless solution was decanted from small colorless crystals. These crystals were washed with distilled water followed by ethanol, and allowed to air-dry at room temperature.

S3. Refinement

H5A and H5B (for H₂O) were located in difference syntheses and refined isotropically [O—H = 0.894 (18) and 0.855 (18) Å, U_iso(H) = 0.107 (18) and 0.085 (12) Ų]. The remaining H atoms were positioned geometrically, with N—H = 0.86 Å (for NH and NH₂) and C—H = 0.93 Å for aromatic H, and constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C,N).

Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Siemens, 1996); software used to prepare material for publication: SHELXTL (Siemens, 1996).

Figures

	Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A packing diagram for (I). Hydrogen bonds are shown as dashed lines.

N-(2-Amino-3-pyridyl)urea monohydrate

Crystal data

C6H9N4O·H2O	F(000) = 364
Mr = 171.19	Dx = 1.565 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1898 reflections
a = 12.8769 (14) Å	θ = 2.6–27.9°
b = 4.002 (2) Å	µ = 0.12 mm^−1
c = 15.4412 (17) Å	T = 273 K
β = 114.084 (3)°	Prism, colorless
V = 726.4 (4) Å^3	0.64 × 0.13 × 0.09 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer	1400 independent reflections
Radiation source: fine-focus sealed tube	871 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.053
φ and ω scans	θmax = 26.0°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −15→15
Tmin = 0.927, Tmax = 0.989	k = −4→4
4336 measured reflections	l = −19→19

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.058	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.178	w = 1/[σ^2(Fo^2) + (0.1781P)^2 + 0.01P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max < 0.001
1400 reflections	Δρmax = 0.53 e Å^−3
118 parameters	Δρmin = −0.44 e Å^−3
3 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.10 (4)

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
O1	0.8205 (2)	1.1190 (8)	−0.13722 (18)	0.0666 (10)
O2	0.5041 (3)	0.5300 (9)	0.1084 (2)	0.0721 (10)
C1	0.7325 (3)	0.8489 (8)	0.0830 (2)	0.0412 (9)
N2	0.6334 (2)	0.9690 (8)	0.0666 (2)	0.0584 (10)
H2A	0.5989	1.0920	0.0175	0.070*
H2B	0.6016	0.9260	0.1047	0.070*
N3	0.7135 (3)	1.1140 (8)	−0.0520 (2)	0.0520 (9)
H3A	0.6512	1.1879	−0.0512	0.062*
N4	0.6563 (3)	1.3945 (9)	−0.1916 (2)	0.0644 (11)
H4A	0.6634	1.4634	−0.2417	0.077*
H4B	0.5972	1.4486	−0.1820	0.077*
N1	0.7876 (4)	0.6668 (11)	0.1628 (3)	0.0887 (14)
C2	0.8910 (3)	0.5406 (11)	0.1824 (3)	0.0642 (11)
H2	0.9287	0.4131	0.2366	0.077*
C3	0.9400 (3)	0.6060 (10)	0.1192 (3)	0.0626 (12)
H3	1.0118	0.5217	0.1310	0.075*
C4	0.8848 (3)	0.7896 (10)	0.0414 (3)	0.0571 (11)
H4	0.9186	0.8293	−0.0006	0.069*
C5	0.7800 (3)	0.9194 (9)	0.0226 (3)	0.0506 (10)
C6	0.7367 (3)	1.2042 (10)	−0.1291 (2)	0.0515 (10)
H5A	0.515 (4)	0.341 (6)	0.089 (4)	0.07 (2)*
H5B	0.552 (3)	0.629 (8)	0.092 (3)	0.053 (11)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0620 (17)	0.091 (2)	0.0634 (18)	−0.0063 (14)	0.0423 (15)	−0.0087 (14)
O2	0.084 (2)	0.075 (2)	0.075 (2)	0.0057 (17)	0.0501 (17)	0.0045 (17)
C1	0.0478 (18)	0.0396 (18)	0.0463 (17)	0.0045 (13)	0.0294 (15)	0.0072 (14)
N2	0.0616 (18)	0.065 (2)	0.074 (2)	0.0238 (15)	0.0526 (16)	0.0318 (16)
N3	0.0535 (17)	0.059 (2)	0.0526 (18)	−0.0043 (14)	0.0314 (15)	0.0008 (14)
N4	0.068 (2)	0.079 (2)	0.058 (2)	−0.0069 (18)	0.0375 (18)	0.0049 (17)
N1	0.109 (3)	0.082 (3)	0.089 (3)	0.004 (2)	0.055 (3)	0.004 (2)
C2	0.065 (2)	0.063 (3)	0.066 (2)	0.005 (2)	0.028 (2)	0.003 (2)
C3	0.052 (2)	0.067 (3)	0.068 (3)	−0.0031 (18)	0.024 (2)	−0.007 (2)
C4	0.051 (2)	0.063 (2)	0.068 (2)	−0.0097 (17)	0.0342 (19)	−0.006 (2)
C5	0.056 (2)	0.049 (2)	0.055 (2)	−0.0137 (16)	0.0305 (17)	−0.0113 (17)
C6	0.055 (2)	0.060 (2)	0.0471 (19)	−0.0189 (17)	0.0289 (17)	−0.0116 (17)

Geometric parameters (Å, º)

O1—C6	1.187 (4)	N4—C6	1.330 (5)
O2—H5A	0.848 (19)	N4—H4A	0.8600
O2—H5B	0.85 (4)	N4—H4B	0.8600
C1—N2	1.288 (4)	N1—C2	1.338 (6)
C1—C5	1.337 (4)	C2—C3	1.386 (6)
C1—N1	1.356 (5)	C2—H2	0.9300
N2—H2A	0.8600	C3—C4	1.339 (6)
N2—H2B	0.8600	C3—H3	0.9300
N3—C5	1.364 (5)	C4—C5	1.363 (5)
N3—C6	1.387 (4)	C4—H4	0.9300
N3—H3A	0.8600
H5A—O2—H5B	94 (2)	N1—C2—H2	121.1
N2—C1—C5	118.8 (3)	C3—C2—H2	121.1
N2—C1—N1	119.2 (3)	C4—C3—C2	120.6 (4)
C5—C1—N1	121.9 (3)	C4—C3—H3	119.7
C1—N2—H2A	120.0	C2—C3—H3	119.7
C1—N2—H2B	120.0	C3—C4—C5	121.1 (4)
H2A—N2—H2B	120.0	C3—C4—H4	119.4
C5—N3—C6	126.4 (3)	C5—C4—H4	119.4
C5—N3—H3A	116.8	C1—C5—C4	117.8 (4)
C6—N3—H3A	116.8	C1—C5—N3	113.7 (3)
C6—N4—H4A	120.0	C4—C5—N3	128.5 (3)
C6—N4—H4B	120.0	O1—C6—N4	124.0 (3)
H4A—N4—H4B	120.0	O1—C6—N3	122.6 (4)
C2—N1—C1	120.7 (4)	N4—C6—N3	113.3 (3)
N1—C2—C3	117.8 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H5B···N2	0.85 (4)	1.85 (2)	2.674 (5)	160 (4)
O2—H5B···N1	0.85 (4)	2.78 (3)	3.439 (6)	135 (3)
N2—H2A···O2^i	0.86	2.39	3.248 (4)	174
N3—H3A···O2^i	0.86	2.15	2.941 (4)	153
N4—H4A···O1^ii	0.86	2.06	2.920 (4)	179
N4—H4B···O2^i	0.86	2.05	2.860 (5)	156
O2—H5A···N2^iii	0.85 (2)	2.26 (3)	3.018 (4)	149 (4)
O2—H5A···N2^iv	0.85 (2)	2.68 (5)	3.242 (5)	125 (5)

Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+3/2, y+1/2, −z−1/2; (iii) x, y−1, z; (iv) −x+1, −y+1, −z.