Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807047526/hk2332sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807047526/hk2332Isup2.hkl |
CCDC reference: 1259447
Key indicators
- Single-crystal X-ray study
- T = 273 K
- Mean (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
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).
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.
H5A and H5B (for H2O) were located in difference syntheses and refined isotropically [O—H = 0.894 (18) and 0.855 (18) Å, Uiso(H) = 0.107 (18) and 0.085 (12) Å2]. 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 Uiso(H) = 1.2Ueq(C,N).
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.
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).
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).
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) Å3 | 0.64 × 0.13 × 0.09 mm |
Z = 4 |
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 on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.058 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.178 | w = 1/[σ2(Fo2) + (0.1781P)2 + 0.01P] where P = (Fo2 + 2Fc2)/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+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.10 (4) |
C6H9N4O·H2O | V = 726.4 (4) Å3 |
Mr = 171.19 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 12.8769 (14) Å | µ = 0.12 mm−1 |
b = 4.002 (2) Å | T = 273 K |
c = 15.4412 (17) Å | 0.64 × 0.13 × 0.09 mm |
β = 114.084 (3)° |
Bruker SMART CCD area-detector diffractometer | 1400 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 871 reflections with I > 2σ(I) |
Tmin = 0.927, Tmax = 0.989 | Rint = 0.053 |
4336 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 3 restraints |
wR(F2) = 0.178 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.53 e Å−3 |
1400 reflections | Δρmin = −0.44 e Å−3 |
118 parameters |
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. |
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)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
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···O2i | 0.86 | 2.39 | 3.248 (4) | 174 |
N3—H3A···O2i | 0.86 | 2.15 | 2.941 (4) | 153 |
N4—H4A···O1ii | 0.86 | 2.06 | 2.920 (4) | 179 |
N4—H4B···O2i | 0.86 | 2.05 | 2.860 (5) | 156 |
O2—H5A···N2iii | 0.85 (2) | 2.26 (3) | 3.018 (4) | 149 (4) |
O2—H5A···N2iv | 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. |
Experimental details
Crystal data | |
Chemical formula | C6H9N4O·H2O |
Mr | 171.19 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 273 |
a, b, c (Å) | 12.8769 (14), 4.002 (2), 15.4412 (17) |
β (°) | 114.084 (3) |
V (Å3) | 726.4 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.64 × 0.13 × 0.09 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.927, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4336, 1400, 871 |
Rint | 0.053 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.178, 1.07 |
No. of reflections | 1400 |
No. of parameters | 118 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.53, −0.44 |
Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Siemens, 1996).
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···O2i | 0.86 | 2.39 | 3.248 (4) | 174 |
N3—H3A···O2i | 0.86 | 2.15 | 2.941 (4) | 153 |
N4—H4A···O1ii | 0.86 | 2.06 | 2.920 (4) | 179 |
N4—H4B···O2i | 0.86 | 2.05 | 2.860 (5) | 156 |
O2—H5A···N2iii | 0.848 (19) | 2.26 (3) | 3.018 (4) | 149 (4) |
O2—H5A···N2iv | 0.848 (19) | 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. |
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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.