N-(3-Pyridyl)­urea

The crystal structure of the title compound, C₆H₇N₃O, exhibits packing typical of amides, with N—H...O hydrogen-bond dimers forming a corrugated tape and N—H...N bonds connecting the tapes.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](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

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S1. Comment

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.

S2. Experimental

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).

Computing details

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.

Figures

	Fig. 1. ORTEPII (Johnson, 1976) plot of (I) with 50% probability ellipsoids.
	Fig. 2. The corrugated tape of N—H.·O hydrogen bonds along [100]. For clarity, the N—H···N bond is not shown. Notice the van der Waals packing of pyridyl rings between the hydrogen-bond tapes.

N-(3-Pyridyl)urea

Crystal data

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) Å^3	Cube, colourless
Z = 4	0.12 × 0.11 × 0.10 mm
F(000) = 288

Data collection

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

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)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.134	All H-atom parameters refined
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0665P)^2 + 0.1436P] where P = (Fo^2 + 2Fc^2)/3
1835 reflections	(Δ/σ)max = 0.019
119 parameters	Δρmax = 0.25 e Å^−3
0 restraints	Δρmin = −0.25 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
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 (Ų)

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

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)

D—H···A	D—H	H···A	D···A	D—H···A
N7—H7···N4^i	0.888 (19)	2.156 (18)	2.984 (2)	155.0 (16)
N10—H8···O9^ii	0.92 (2)	2.05 (2)	2.9657 (19)	173.0 (18)
N10—H9···O9^iii	0.842 (19)	2.193 (19)	2.9734 (19)	154.2 (18)
C2—H2···O9^iv	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.