3-Pyridyl­methyl urea dihydrate

The geometrical parameters of the title compound, C₁₃H₁₄N₄O·2H₂O, are normal. The carbonyl group occupies a twofold symmetry axis to generate the complete 3-pyridyl­methyl urea mol­ecule. The crystal packing is defined by hydrogen bonding involving the water mol­ecule, as well as π...π stacking and weak C—H...π interactions.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.030
• wR factor = 0.090
• Data-to-parameter ratio = 12.0

checkCIF results

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S1. Comment

The geometrical parameters of the title compound, (I) (Fig. 1), are normal and comparable to those reported for the silver complex of the same ligand by Schauer et al. (1997). In (I), the carbonyl group occupies a twofold symmetry axis to generate the complete molecule. The same situation occurs in several of the related ureylenedicarboxylic acid phases (Zhao et al., 1993) which are of intetest for their supramolecular packing motifs.

The crystal packing for (I) (Fig. 2) is defined by hydrogen bonding involving the water molecule as well as π···π stacking involving pairs of aromatic moieties and weak C—H···π interactions. The hydrogen-bonding motif (Fig. 3) involves stacks of 3-pyridylmethyl urea and water molecules propagating in the [010] direction. The water molecule serves to bridge adjacent 3-pyridylmethyl urea molecules by acting as both an N1—H1···O2 acceptor and an O2—H3···O1 donor (Table 2). Crystal symmetry dictates that adjacent 3-pyridylmethyl urea molecules are linked by a pair of water molecules (Fig. 3) related by the twofold symmetry axis. Additionally, an O2—H2···N2 hydrogen bond to a pyridyl-N atom acceptor serves as a crosslink to an adjacent 3-pyridylmethyl urea/water stack.

Crystal symmetry generates a distinctive motif (Fig. 4) of C5—H51···π···π···H51—C5 interactions. Thus each pyridyl moiety interacts with a similar species by π···π stacking on one ring face, and accepts a weak C—H···π interaction on the other. The separation of adjacent pyridyl ring centroids is 3.698 Å, with the ring centroid given by the coordinates 0.2581 0.4220 0.3877 (Spek, 1990). These interactions are orientated in the (011) plane.

S2. Experimental

The title compound was recrystallized from hot water.

S3. Refinement

The positions and U_iso for the N—H and O—H H atoms were freely refined; C—H H atoms refined by riding, with U_iso constrained to be 1.2 × that of U_eq for the attached C atom.

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SMART; data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. Molecular structure of (I); 50% displacement ellipsoids, circles of arbitrary radius for H atoms. Symmetry code: (i) -x, y, -z + 1/2.
	Fig. 2. Packing diagram for (I) with C—H hydrogen atoms omitted for clarity. Atom colours as in Fig. 1; 50% displacement ellipsoids.
	Fig. 3. Detail showing the hydrogen-bonding scheme in (I) with H bonds indicated by dotted lines. Atom colours as in Fig. 1; 50% displacement ellipsoids. Symmetry codes: (i) x - 1/2, 1/2 - y,z - 1/2; (ii) -x, y - 1, 1/2 - z.
	Fig. 4. Detail showing C—H···π and π-π interactions in (I). Atom colours as in Fig. 1; 50% displacement ellipsoids.

(I)

Crystal data

C13N4OH14·2H2O	F(000) = 592
Mr = 278.31	Dx = 1.294 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.5784 (11) Å	Cell parameters from 2260 reflections
b = 7.1077 (5) Å	θ = 2.5–25.0°
c = 12.1751 (8) Å	µ = 0.09 mm^−1
β = 95.475 (2)°	T = 298 K
V = 1428.10 (17) Å^3	Lump, colourless
Z = 4	0.48 × 0.24 × 0.24 mm

Data collection

Bruker SMART1000 CCD diffractometer	1260 independent reflections
Radiation source: fine-focus sealed tube	1047 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
ω scans	θmax = 25.0°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 1999)	h = −14→19
Tmin = 0.803, Tmax = 0.928	k = −8→8
4018 measured reflections	l = −14→14

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)] = 0.030	H-atom treatment, see text
wR(F^2) = 0.090	w = 1/[σ^2(Fo^2) + (0.0503P)^2 + 0.2493P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max < 0.001
1260 reflections	Δρmax = 0.11 e Å^−3
105 parameters	Δρmin = −0.11 e Å^−3
0 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0129 (16)

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	0.0000	0.23678 (16)	0.2500	0.0588 (4)
O2	−0.05686 (7)	−0.09244 (14)	0.12998 (10)	0.0656 (3)
H2	−0.0985 (12)	−0.071 (3)	0.0759 (16)	0.092 (6)*
H3	−0.0441 (10)	0.013 (3)	0.1631 (15)	0.091 (6)*
N1	0.03712 (6)	0.51349 (15)	0.33376 (10)	0.0532 (3)
H1	0.0367 (8)	0.635 (2)	0.3282 (12)	0.064 (4)*
N2	0.31436 (6)	0.50382 (16)	0.46439 (10)	0.0609 (4)
C1	0.0000	0.4118 (2)	0.2500	0.0457 (4)
C2	0.08796 (7)	0.43039 (18)	0.42404 (10)	0.0502 (3)
H21	0.0693	0.3034	0.4362	0.060*
H22	0.0823	0.5022	0.4906	0.060*
C3	0.17641 (7)	0.42391 (16)	0.40382 (9)	0.0432 (3)
C4	0.20244 (8)	0.34010 (19)	0.31077 (11)	0.0554 (4)
H41	0.1652	0.2845	0.2587	0.066*
C5	0.28325 (8)	0.3393 (2)	0.29560 (12)	0.0619 (4)
H51	0.3014	0.2836	0.2334	0.074*
C6	0.33701 (8)	0.4222 (2)	0.37403 (13)	0.0620 (4)
H61	0.3918	0.4211	0.3633	0.074*
C7	0.23506 (7)	0.50289 (17)	0.47739 (10)	0.0504 (3)
H71	0.2185	0.5594	0.5404	0.060*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0602 (8)	0.0390 (7)	0.0722 (8)	0.000	−0.0191 (6)	0.000
O2	0.0662 (7)	0.0480 (6)	0.0775 (7)	0.0036 (5)	−0.0202 (5)	0.0040 (5)
N1	0.0464 (6)	0.0414 (6)	0.0686 (7)	0.0029 (4)	−0.0111 (5)	−0.0060 (5)
N2	0.0459 (7)	0.0640 (8)	0.0697 (8)	−0.0070 (5)	−0.0101 (5)	0.0047 (6)
C1	0.0334 (8)	0.0415 (9)	0.0609 (10)	0.000	−0.0021 (7)	0.000
C2	0.0430 (7)	0.0538 (7)	0.0525 (7)	−0.0008 (5)	−0.0020 (5)	−0.0048 (6)
C3	0.0433 (7)	0.0379 (6)	0.0471 (6)	0.0002 (5)	−0.0027 (5)	0.0019 (5)
C4	0.0520 (8)	0.0575 (8)	0.0553 (7)	−0.0006 (6)	−0.0018 (6)	−0.0088 (6)
C5	0.0575 (9)	0.0676 (9)	0.0614 (8)	0.0070 (7)	0.0108 (7)	−0.0008 (7)
C6	0.0433 (7)	0.0663 (9)	0.0767 (9)	0.0023 (6)	0.0076 (6)	0.0161 (8)
C7	0.0487 (7)	0.0510 (7)	0.0499 (7)	−0.0015 (5)	−0.0044 (5)	−0.0016 (5)

Geometric parameters (Å, º)

O1—C1	1.244 (2)	C2—H21	0.9700
O2—H2	0.92 (2)	C2—H22	0.9700
O2—H3	0.87 (2)	C3—C7	1.3772 (16)
N1—C1	1.3495 (13)	C3—C4	1.3848 (17)
N1—C2	1.4459 (17)	C4—C5	1.3697 (19)
N1—H1	0.866 (16)	C4—H41	0.9300
N2—C6	1.3294 (19)	C5—C6	1.375 (2)
N2—C7	1.3391 (16)	C5—H51	0.9300
C1—N1^i	1.3495 (13)	C6—H61	0.9300
C2—C3	1.5105 (17)	C7—H71	0.9300
H2—O2—H3	108.8 (15)	C7—C3—C2	121.17 (11)
C1—N1—C2	123.12 (11)	C4—C3—C2	121.98 (11)
C1—N1—H1	118.4 (10)	C5—C4—C3	119.83 (12)
C2—N1—H1	117.8 (10)	C5—C4—H41	120.1
C6—N2—C7	116.98 (11)	C3—C4—H41	120.1
O1—C1—N1	122.38 (7)	C4—C5—C6	118.81 (13)
O1—C1—N1^i	122.38 (7)	C4—C5—H51	120.6
N1—C1—N1^i	115.25 (15)	C6—C5—H51	120.6
N1—C2—C3	113.15 (10)	N2—C6—C5	123.11 (13)
N1—C2—H21	108.9	N2—C6—H61	118.4
C3—C2—H21	108.9	C5—C6—H61	118.4
N1—C2—H22	108.9	N2—C7—C3	124.43 (12)
C3—C2—H22	108.9	N2—C7—H71	117.8
H21—C2—H22	107.8	C3—C7—H71	117.8
C7—C3—C4	116.84 (11)
C2—N1—C1—N1^i	−172.41 (10)	C2—N1—C1—O1	7.59 (12)
C1—N1—C2—C3	91.90 (12)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2^ii	0.92 (2)	1.95 (2)	2.8633 (15)	175.3 (17)
O2—H3···O1	0.87 (2)	2.01 (2)	2.8699 (15)	171.5 (17)
N1—H1···O2^iii	0.866 (16)	2.023 (16)	2.8495 (14)	159.3 (13)
C5—H51···π^iv	0.93	3.08	3.735	129

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