The crystal structure of the title compound, C
6H
7N
3O, exhibits packing typical of amides, with N—H
O hydrogen-bond dimers forming a corrugated tape and N—H
N bonds connecting the tapes.
Supporting information
CCDC reference: 170903
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.002 Å
- R factor = 0.045
- wR factor = 0.134
- Data-to-parameter ratio = 15.4
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
Compound (I) was synthesized by slowly adding NaOCN (130 mg, 2 mmol) dissolved
in hot water (1 ml) to a solution of 3-aminopyridine (188 mg, 2 mmol) in
glacial AcOH (0.2 ml) with stirring. The aqueous solution was neutralized and
extracted with chloroform to remove the unreacted 3-aminopyridine. Column
chromatography and recrystallization from EtOAc afforded crystals of (I) (m.p.
472–474 K).
Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: Xtal3.5 (Hall et al., 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLUTON-(C) (Spek, 1979-1997); software used to prepare material for publication: SHELXL97.
Crystal data top
C6H7N3O | Dx = 1.445 Mg m−3 |
Mr = 137.15 | Melting point = 472–474 K |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 4.8558 (10) Å | Cell parameters from 25 reflections |
b = 8.1621 (16) Å | θ = 9.0–10.6° |
c = 15.919 (3) Å | µ = 0.10 mm−1 |
β = 92.16 (3)° | T = 293 K |
V = 630.5 (2) Å3 | Cube, colourless |
Z = 4 | 0.12 × 0.11 × 0.10 mm |
F(000) = 288 | |
Data collection top
Enraf-Nonius CAD-4 diffractometer | Rint = 0.010 |
Radiation source: fine-focus sealed tube | θmax = 30.0°, θmin = 2.6° |
Graphite monochromator | h = 0→6 |
ω scans | k = 0→11 |
2021 measured reflections | l = −22→22 |
1835 independent reflections | 3 standard reflections every 150 reflections |
1362 reflections with I > 2σ(I) | intensity decay: none |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.134 | All H-atom parameters refined |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0665P)2 + 0.1436P] where P = (Fo2 + 2Fc2)/3 |
1835 reflections | (Δ/σ)max = 0.019 |
119 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.25 e Å−3 |
Crystal data top
C6H7N3O | V = 630.5 (2) Å3 |
Mr = 137.15 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 4.8558 (10) Å | µ = 0.10 mm−1 |
b = 8.1621 (16) Å | T = 293 K |
c = 15.919 (3) Å | 0.12 × 0.11 × 0.10 mm |
β = 92.16 (3)° | |
Data collection top
Enraf-Nonius CAD-4 diffractometer | Rint = 0.010 |
2021 measured reflections | 3 standard reflections every 150 reflections |
1835 independent reflections | intensity decay: none |
1362 reflections with I > 2σ(I) | |
Refinement top
R[F2 > 2σ(F2)] = 0.045 | 0 restraints |
wR(F2) = 0.134 | All H-atom parameters refined |
S = 1.08 | Δρmax = 0.25 e Å−3 |
1835 reflections | Δρmin = −0.25 e Å−3 |
119 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 | x | y | z | Uiso*/Ueq | |
O9 | 0.1643 (2) | 0.68331 (14) | 0.95030 (7) | 0.0415 (3) | |
N7 | −0.1512 (3) | 0.82764 (15) | 0.86940 (8) | 0.0349 (3) | |
N10 | −0.2605 (3) | 0.57747 (17) | 0.92223 (9) | 0.0378 (3) | |
C6 | −0.0056 (3) | 0.97288 (16) | 0.85816 (8) | 0.0287 (3) | |
N4 | 0.0190 (3) | 1.21723 (17) | 0.77396 (8) | 0.0418 (3) | |
C8 | −0.0680 (3) | 0.69528 (16) | 0.91682 (8) | 0.0302 (3) | |
C5 | −0.0936 (3) | 1.07302 (18) | 0.79136 (9) | 0.0351 (3) | |
C1 | 0.2116 (3) | 1.02820 (19) | 0.90977 (9) | 0.0358 (3) | |
C3 | 0.2266 (4) | 1.2688 (2) | 0.82488 (10) | 0.0441 (4) | |
C2 | 0.3274 (3) | 1.1782 (2) | 0.89246 (10) | 0.0404 (4) | |
H5 | −0.245 (4) | 1.037 (2) | 0.7548 (12) | 0.044 (5)* | |
H1 | 0.282 (4) | 0.962 (2) | 0.9579 (12) | 0.050 (5)* | |
H7 | −0.298 (4) | 0.813 (2) | 0.8353 (11) | 0.042 (5)* | |
H2 | 0.478 (4) | 1.222 (3) | 0.9276 (12) | 0.054 (5)* | |
H3 | 0.299 (4) | 1.374 (2) | 0.8116 (12) | 0.047 (5)* | |
H8 | −0.218 (4) | 0.494 (3) | 0.9593 (13) | 0.057 (6)* | |
H9 | −0.426 (4) | 0.605 (2) | 0.9130 (12) | 0.045 (5)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O9 | 0.0292 (5) | 0.0409 (6) | 0.0535 (7) | 0.0003 (4) | −0.0105 (5) | 0.0149 (5) |
N7 | 0.0337 (6) | 0.0307 (6) | 0.0390 (6) | −0.0028 (5) | −0.0149 (5) | 0.0050 (5) |
N10 | 0.0314 (6) | 0.0349 (7) | 0.0464 (7) | −0.0024 (5) | −0.0083 (5) | 0.0091 (5) |
C6 | 0.0295 (6) | 0.0274 (6) | 0.0289 (6) | 0.0025 (5) | −0.0034 (5) | −0.0005 (5) |
N4 | 0.0480 (8) | 0.0362 (7) | 0.0405 (7) | −0.0017 (6) | −0.0066 (6) | 0.0089 (5) |
C8 | 0.0301 (6) | 0.0289 (6) | 0.0311 (6) | 0.0026 (5) | −0.0035 (5) | 0.0009 (5) |
C5 | 0.0382 (7) | 0.0334 (7) | 0.0329 (6) | 0.0015 (6) | −0.0087 (5) | 0.0024 (5) |
C1 | 0.0361 (7) | 0.0372 (7) | 0.0334 (7) | −0.0026 (6) | −0.0090 (5) | 0.0028 (6) |
C3 | 0.0506 (9) | 0.0359 (8) | 0.0454 (8) | −0.0099 (7) | −0.0039 (7) | 0.0060 (7) |
C2 | 0.0398 (8) | 0.0398 (8) | 0.0409 (8) | −0.0080 (6) | −0.0073 (6) | −0.0021 (6) |
Geometric parameters (Å, º) top
O9—C8 | 1.2331 (17) | N4—C5 | 1.331 (2) |
N7—C8 | 1.3702 (17) | N4—C3 | 1.337 (2) |
N7—C6 | 1.3953 (18) | C5—H5 | 0.97 (2) |
N7—H7 | 0.886 (19) | C1—C2 | 1.379 (2) |
N10—C8 | 1.3459 (19) | C1—H1 | 0.986 (19) |
N10—H8 | 0.92 (2) | C3—C2 | 1.380 (2) |
N10—H9 | 0.84 (2) | C3—H3 | 0.95 (2) |
C6—C1 | 1.3879 (19) | C2—H2 | 0.97 (2) |
C6—C5 | 1.3954 (19) | | |
| | | |
C8—N7—C6 | 126.89 (12) | N4—C5—C6 | 124.05 (14) |
C8—N7—H7 | 116.3 (12) | N4—C5—H5 | 117.0 (12) |
C6—N7—H7 | 115.9 (12) | C6—C5—H5 | 119.0 (12) |
C8—N10—H8 | 115.6 (14) | C2—C1—C6 | 118.48 (13) |
C8—N10—H9 | 117.4 (14) | C2—C1—H1 | 120.3 (12) |
H8—N10—H9 | 120 (2) | C6—C1—H1 | 121.2 (12) |
C1—C6—N7 | 125.31 (12) | N4—C3—C2 | 122.77 (15) |
C1—C6—C5 | 117.69 (13) | N4—C3—H3 | 115.1 (12) |
N7—C6—C5 | 116.95 (12) | C2—C3—H3 | 122.1 (12) |
C5—N4—C3 | 117.27 (13) | C1—C2—C3 | 119.74 (14) |
O9—C8—N10 | 122.81 (13) | C1—C2—H2 | 121.1 (12) |
O9—C8—N7 | 123.13 (13) | C3—C2—H2 | 119.2 (12) |
N10—C8—N7 | 114.05 (13) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H7···N4i | 0.888 (19) | 2.156 (18) | 2.984 (2) | 155.0 (16) |
N10—H8···O9ii | 0.92 (2) | 2.05 (2) | 2.9657 (19) | 173.0 (18) |
N10—H9···O9iii | 0.842 (19) | 2.193 (19) | 2.9734 (19) | 154.2 (18) |
C2—H2···O9iv | 0.97 (2) | 2.67 (2) | 3.629 (2) | 168.4 (16) |
Symmetry codes: (i) −x−1/2, y−1/2, −z+3/2; (ii) −x, −y+1, −z+2; (iii) x−1, y, z; (iv) −x+1, −y+2, −z+2. |
Experimental details
Crystal data |
Chemical formula | C6H7N3O |
Mr | 137.15 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 4.8558 (10), 8.1621 (16), 15.919 (3) |
β (°) | 92.16 (3) |
V (Å3) | 630.5 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.12 × 0.11 × 0.10 |
|
Data collection |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2021, 1835, 1362 |
Rint | 0.010 |
(sin θ/λ)max (Å−1) | 0.703 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.134, 1.08 |
No. of reflections | 1835 |
No. of parameters | 119 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.25, −0.25 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H7···N4i | 0.888 (19) | 2.156 (18) | 2.984 (2) | 155.0 (16) |
N10—H8···O9ii | 0.92 (2) | 2.05 (2) | 2.9657 (19) | 173.0 (18) |
N10—H9···O9iii | 0.842 (19) | 2.193 (19) | 2.9734 (19) | 154.2 (18) |
C2—H2···O9iv | 0.97 (2) | 2.67 (2) | 3.629 (2) | 168.4 (16) |
Symmetry codes: (i) −x−1/2, y−1/2, −z+3/2; (ii) −x, −y+1, −z+2; (iii) x−1, y, z; (iv) −x+1, −y+2, −z+2. |
In a recent monograph on the role of amides in non-covalent syntheses (Palmore & MacDonald, 2000), the urea functional group is considered as part of the amide family. In connection with an ongoing crystallographic study of aromatic ureas (George et al., 2001), we have determined the crystal structure of N-(3-pyridyl) urea, (I).
The pyridyl ring in (I) is tilted to the urea plane by 163.94 (14)° (C8/N7/C6/C5, Fig.1). The crystal structure of (I) contains a corrugated tape of (syn) N10—H8···O9 and (anti) N10—H9···O9 hydrogen-bond dimers along the a axis, with an (anti) N7—H7···N4 bond connecting screw-axis-related molecules in the b direction (syn and anti refer to ureido H atoms) (Fig. 2). The a axis of 4.8558 (10) Å in (I) is smaller than the characteristic 5.1 Å packing in carboxylic amides because of the zigzag corrugated pattern. A crystal structure assembled by N—H···N hydrogen bonding interaction was published recently in this journal (Lynch & McClenaghan, 2001). In contrast to the structure of (I), the molecular conformation and crystal packing in N-(2-pyridyl)urea (Velikova et al., 1997) are quite different. This latter structure contains parallel zigzag ribbons of molecules hydrogen bonded through (syn) N—H···O dimers along the ab diagonal. The molecule adopts a planar conformation because of an intramolecular (anti) N—H···N interaction. Thus, isomeric 2- and 3-pyridylurea have very different crystal structures.