2-Methyl­pyridine–urea (1/1)

Ashurov, J.; Ibragimov, B.; Talipov, S.

doi:10.1107/S1600536812002164

organic compounds

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ISSN: 2056-9890

Volume 68| Part 2| February 2012| Page o504

doi:10.1107/S1600536812002164

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2-Methylpyridine–urea (1/1)

Jamshid Ashurov,^a ^* Bakhtiyar Ibragimov ^a and Samat Talipov ^a

^aInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, H. Abdullaev Str. 83, Tashkent 100125, Uzbekistan
^*Correspondence e-mail: atom.uz@mail.ru

(Received 30 December 2011; accepted 18 January 2012; online 21 January 2012)

In the crystal structure of the title compound, C₆H₇N·CH₄N₂O, the 2-methylpyridine and urea molecules are linked via N—H⋯O and N—H⋯N hydrogen bonds, forming ribbons extending along the a axis. The dihedral angle between the 2-methylpyridine and urea mean planes is 89.09 (9)°. The methyl group shows rotational disorder wherein the H atoms are located over two sets of sites with equal occupancies.

Related literature

For crystal structures of urea inclusion compounds, see: Izotova et al. (2008 ); Chadwick et al. (2009 ).

Experimental

Crystal data

C₆H₇N·CH₄N₂O
M_r = 153.19
Orthorhombic, P b c a
a = 7.471 (5) Å
b = 14.916 (5) Å
c = 15.338 (5) Å
V = 1709.2 (14) Å³
Z = 8
Cu Kα radiation
μ = 0.68 mm⁻¹
T = 293 K
0.36 × 0.30 × 0.22 mm

Data collection

Oxford Diffraction Xcalibur Ruby diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007 $[Oxford Diffraction (2007). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.]$ ) T_min = 0.337, T_max = 1.000
5969 measured reflections
1756 independent reflections
1011 reflections with I > 2σ(I)
R_int = 0.049

Refinement

R[F² > 2σ(F²)] = 0.056
wR(F²) = 0.167
S = 0.97
1756 reflections
112 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2B⋯N1	0.91 (2)	2.26 (2)	3.131 (3)	160 (2)
N2—H2A⋯O1ⁱ	0.84 (2)	2.11 (2)	2.953 (3)	179 (2)
N3—H3B⋯N1	0.88 (2)	2.30 (2)	3.137 (3)	161 (2)
N3—H3A⋯O1ⁱⁱ	0.91 (2)	2.03 (2)	2.938 (3)	177 (2)
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Data collection: CrysAlis PRO (Oxford Diffraction, 2007 $[Oxford Diffraction (2007). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.]$ ); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812002164/pv2503sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812002164/pv2503Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812002164/pv2503Isup3.cml

checkCIF report

Comment top

The crystal structure of the title compound (Fig. 1) consists of a 2-methylpyridine and a urea molecules. The urea molecules are mutually bonded by pair of N—H···O hydrogen bonds and form infinite chains along the a-axis (Fig. 2). The molecules of 2-methylpyridine are connected by its N1-atom to the urea molecules via both amino groups resulting in N—H···N type hydrogen bonds. The mean-planes angle between the planes of 2-methylpyridine and urea is 89.09 (9)°. The methyl group of 2-methylpyridine showed rotational disorder with each H-atom located over two positions with occupation factors of 0.50 and 0.50.

The crystal structures of urea inclusion compounds closely related to the title structure have been recently reported (Izotova et al., (2008); Chadwick et al., 2009).

Related literature top

For crystal structures of urea inclusion compounds, see: Izotova et al. (2008); Chadwick et al. (2009).

Experimental top

The compound was purchased from Sigma-Aldrich and used as supplied. A single-crystal sample of the 1/1 clathrate was recrystallized from a saturated solution of urea in 2-methylpyridine by isothermal solvent evaporation at room temperature (298 K).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2007); cell refinement: CrysAlis PRO (Oxford Diffraction, 2007); data reduction: CrysAlis PRO (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as small spheres of arbitrary radius.
	Fig. 2. A view of the N—-H···O and N—H···N hydrogen bonds (dotted lines) in the crystal structure of the title compound. H atoms non-participating in hydrogen-bonding were omitted for clarity.

2-Methylpyridine–urea (1/1) top

Crystal data top

C₆H₇N·CH₄N₂O	F(000) = 656
M_r = 153.19	D_x = 1.191 Mg m⁻³
Orthorhombic, Pbca	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1430 reflections
a = 7.471 (5) Å	θ = 4.1–75.6°
b = 14.916 (5) Å	µ = 0.68 mm⁻¹
c = 15.338 (5) Å	T = 293 K
V = 1709.2 (14) Å³	Block, colourless
Z = 8	0.36 × 0.30 × 0.22 mm

Data collection top

Oxford Diffraction Xcalibur Ruby diffractometer	1756 independent reflections
Radiation source: fine-focus sealed tube	1011 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.049
Detector resolution: 10.2576 pixels mm^-1	θ_max = 76.0°, θ_min = 5.8°
ω scans	h = −5→9
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007)	k = −18→17
T_min = 0.337, T_max = 1.000	l = −18→19
5969 measured reflections

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)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.167	H atoms treated by a mixture of independent and constrained refinement
S = 0.97	w = 1/[σ²(F_o²) + (0.0982P)²] where P = (F_o² + 2F_c²)/3
1756 reflections	(Δ/σ)_max < 0.001
112 parameters	Δρ_max = 0.16 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₆H₇N·CH₄N₂O	V = 1709.2 (14) Å³
M_r = 153.19	Z = 8
Orthorhombic, Pbca	Cu Kα radiation
a = 7.471 (5) Å	µ = 0.68 mm⁻¹
b = 14.916 (5) Å	T = 293 K
c = 15.338 (5) Å	0.36 × 0.30 × 0.22 mm

Data collection top

Oxford Diffraction Xcalibur Ruby diffractometer	1756 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007)	1011 reflections with I > 2σ(I)
T_min = 0.337, T_max = 1.000	R_int = 0.049
5969 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	0 restraints
wR(F²) = 0.167	H atoms treated by a mixture of independent and constrained refinement
S = 0.97	Δρ_max = 0.16 e Å⁻³
1756 reflections	Δρ_min = −0.20 e Å⁻³
112 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	U_iso*/U_eq	Occ. (<1)
N1	0.1107 (2)	0.45154 (12)	0.27525 (10)	0.0620 (5)
C1	0.1128 (3)	0.42217 (15)	0.19345 (13)	0.0672 (6)
H1	0.1138	0.3605	0.1843	0.081*
C2	0.1137 (3)	0.47652 (19)	0.12219 (13)	0.0763 (7)
H2	0.1153	0.4528	0.0661	0.092*
C3	0.1121 (3)	0.5668 (2)	0.13573 (17)	0.0910 (8)
H3	0.1129	0.6061	0.0887	0.109*
C4	0.1093 (3)	0.59912 (18)	0.21957 (18)	0.0860 (8)
H4	0.1076	0.6606	0.2297	0.103*
C5	0.1089 (3)	0.53974 (15)	0.28912 (13)	0.0645 (6)
C6	0.1069 (3)	0.5697 (2)	0.38257 (15)	0.0963 (9)
H6A	0.0145	0.5382	0.4135	0.144*	0.50
H6B	0.0841	0.6329	0.3851	0.144*	0.50
H6C	0.2207	0.5570	0.4089	0.144*	0.50
H6D	0.1984	0.6139	0.3915	0.144*	0.50
H6E	0.1287	0.5191	0.4198	0.144*	0.50
H6F	−0.0078	0.5951	0.3961	0.144*	0.50
O1	0.11116 (17)	0.23145 (9)	0.50993 (9)	0.0637 (4)
N2	−0.0400 (3)	0.31459 (13)	0.41139 (12)	0.0653 (5)
H2A	−0.140 (3)	0.3013 (17)	0.4331 (16)	0.078*
H2B	−0.025 (3)	0.3550 (15)	0.3672 (14)	0.078*
N3	0.2633 (3)	0.31788 (13)	0.41459 (13)	0.0713 (6)
H3A	0.370 (3)	0.3003 (18)	0.4372 (16)	0.086*
H3B	0.248 (3)	0.3551 (16)	0.3712 (14)	0.086*
C7	0.1115 (3)	0.28588 (12)	0.44860 (12)	0.0526 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0673 (11)	0.0681 (10)	0.0505 (9)	−0.0007 (8)	−0.0018 (8)	0.0054 (7)
C1	0.0662 (14)	0.0735 (13)	0.0619 (12)	−0.0010 (11)	−0.0006 (10)	−0.0058 (10)
C2	0.0743 (15)	0.1072 (19)	0.0475 (11)	0.0073 (14)	0.0015 (10)	0.0011 (11)
C3	0.098 (2)	0.108 (2)	0.0674 (14)	0.0061 (16)	0.0033 (14)	0.0344 (14)
C4	0.100 (2)	0.0643 (13)	0.0932 (18)	0.0032 (12)	0.0015 (15)	0.0087 (12)
C5	0.0656 (14)	0.0698 (12)	0.0580 (11)	−0.0027 (11)	0.0015 (10)	−0.0036 (9)
C6	0.107 (2)	0.112 (2)	0.0696 (16)	−0.0082 (16)	0.0021 (14)	−0.0273 (15)
O1	0.0554 (9)	0.0729 (9)	0.0628 (8)	0.0026 (7)	0.0010 (6)	0.0233 (7)
N2	0.0512 (10)	0.0796 (12)	0.0652 (11)	0.0020 (9)	−0.0005 (9)	0.0235 (9)
N3	0.0557 (11)	0.0851 (13)	0.0730 (12)	−0.0003 (10)	0.0030 (9)	0.0315 (10)
C7	0.0527 (11)	0.0552 (9)	0.0498 (9)	0.0006 (9)	0.0006 (9)	0.0040 (8)

Geometric parameters (Å, º) top

N1—C1	1.329 (3)	C6—H6B	0.9600
N1—C5	1.333 (3)	C6—H6C	0.9600
C1—C2	1.361 (3)	C6—H6D	0.9600
C1—H1	0.9300	C6—H6E	0.9600
C2—C3	1.362 (4)	C6—H6F	0.9600
C2—H2	0.9300	O1—C7	1.243 (2)
C3—C4	1.374 (4)	N2—C7	1.338 (3)
C3—H3	0.9300	N2—H2A	0.84 (2)
C4—C5	1.387 (3)	N2—H2B	0.91 (2)
C4—H4	0.9300	N3—C7	1.337 (3)
C5—C6	1.501 (3)	N3—H3A	0.91 (2)
C6—H6A	0.9600	N3—H3B	0.88 (2)

C1—N1—C5	118.43 (18)	H6A—C6—H6D	141.1
N1—C1—C2	124.2 (2)	H6B—C6—H6D	56.3
N1—C1—H1	117.9	H6C—C6—H6D	56.3
C2—C1—H1	117.9	C5—C6—H6E	109.5
C1—C2—C3	117.8 (2)	H6A—C6—H6E	56.3
C1—C2—H2	121.1	H6B—C6—H6E	141.1
C3—C2—H2	121.1	H6C—C6—H6E	56.3
C2—C3—C4	119.3 (2)	H6D—C6—H6E	109.5
C2—C3—H3	120.3	C5—C6—H6F	109.5
C4—C3—H3	120.3	H6A—C6—H6F	56.3
C3—C4—C5	119.7 (2)	H6B—C6—H6F	56.3
C3—C4—H4	120.1	H6C—C6—H6F	141.1
C5—C4—H4	120.1	H6D—C6—H6F	109.5
N1—C5—C4	120.5 (2)	H6E—C6—H6F	109.5
N1—C5—C6	116.5 (2)	C7—N2—H2A	120.5 (17)
C4—C5—C6	123.0 (2)	C7—N2—H2B	115.0 (15)
C5—C6—H6A	109.5	H2A—N2—H2B	124 (2)
C5—C6—H6B	109.5	C7—N3—H3A	119.6 (16)
H6A—C6—H6B	109.5	C7—N3—H3B	114.2 (16)
C5—C6—H6C	109.5	H3A—N3—H3B	126 (2)
H6A—C6—H6C	109.5	O1—C7—N3	122.04 (18)
H6B—C6—H6C	109.5	O1—C7—N2	122.02 (19)
C5—C6—H6D	109.5	N3—C7—N2	115.93 (18)

C5—N1—C1—C2	0.1 (3)	C1—N1—C5—C4	0.0 (3)
N1—C1—C2—C3	−0.1 (4)	C1—N1—C5—C6	−179.89 (19)
C1—C2—C3—C4	−0.2 (4)	C3—C4—C5—N1	−0.2 (3)
C2—C3—C4—C5	0.3 (4)	C3—C4—C5—C6	179.7 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2B···N1	0.91 (2)	2.26 (2)	3.131 (3)	160 (2)
N2—H2A···O1ⁱ	0.84 (2)	2.11 (2)	2.953 (3)	179 (2)
N3—H3B···N1	0.88 (2)	2.30 (2)	3.137 (3)	161 (2)
N3—H3A···O1ⁱⁱ	0.91 (2)	2.03 (2)	2.938 (3)	177 (2)

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

Experimental details

Crystal data
Chemical formula	C₆H₇N·CH₄N₂O
M_r	153.19
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	7.471 (5), 14.916 (5), 15.338 (5)
V (Å³)	1709.2 (14)
Z	8
Radiation type	Cu Kα
µ (mm⁻¹)	0.68
Crystal size (mm)	0.36 × 0.30 × 0.22

Data collection
Diffractometer	Oxford Diffraction Xcalibur Ruby diffractometer
Absorption correction	Multi-scan (CrysAlis PRO; Oxford Diffraction, 2007)
T_min, T_max	0.337, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	5969, 1756, 1011
R_int	0.049
(sin θ/λ)_max (Å⁻¹)	0.629

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.167, 0.97
No. of reflections	1756
No. of parameters	112
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.20

Computer programs: CrysAlis PRO (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2B···N1	0.91 (2)	2.26 (2)	3.131 (3)	160 (2)
N2—H2A···O1ⁱ	0.84 (2)	2.11 (2)	2.953 (3)	179 (2)
N3—H3B···N1	0.88 (2)	2.30 (2)	3.137 (3)	161 (2)
N3—H3A···O1ⁱⁱ	0.91 (2)	2.03 (2)	2.938 (3)	177 (2)

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

Acknowledgements

This work was supported by a Grant for Fundamental Research from the Center of Science and Technology, Uzbekistan (No. FA—F3—T-141).

References

Chadwick, K., Davey, R., Sadiq, G., Cross, W. & Pritchard, R. (2009). CrystEngComm, 11, 412–414. Web of Science CSD CrossRef CAS Google Scholar
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Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar