N (3 Pyridyl)­urea

Acta Cryst.(2001). E57, o719±o720 DOI: 10.1107/S1600536801011424 George and Nangia C₆H₇N₃O

o719

organic papers

Acta Crystallographica Section E Structure Reports Online

ISSN 1600-5368

N

-(3-Pyridyl)urea

Sumod George and Ashwini Nangia*

School of Chemistry, University of Hyderabad, Hyderabad 500 046, India

Correspondence e-mail: [email protected]

Key indicators Single-crystal X-ray study T= 293 K

Mean(C±C) = 0.002 AÊ Rfactor = 0.045 wRfactor = 0.134

Data-to-parameter ratio = 15.4

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2001 International Union of Crystallography Printed in Great Britain ± all rights reserved

The crystal structure of the title compound, C6H7N3O, exhibits

packing typical of amides, with NÐH O hydrogen-bond dimers forming a corrugated tape and NÐH N bonds connecting the tapes.

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 (Georgeet al., 2001), we have determined the crystal structure ofN-(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) N10ÐH8 O9 and (anti) N10ÐH9 O9 hydrogen-bond dimers along the aaxis, with an (anti) N7ÐH7 N4 bond connecting screw-axis-related molecules in theb direction (synandantirefer to ureido H atoms) (Fig. 2). Theaaxis of 4.8558 (10) AÊ in (I) is smaller than the characteristic 5.1 AÊ packing in carboxylic amides because of the zigzag corrugated pattern. A crystal structure assembled by NÐH 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 inN-(2-pyridyl)urea

(Veli-kova et al., 1997) are quite different. This latter structure

contains parallel zigzag ribbons of molecules hydrogen bonded through (syn) NÐH O dimers along the ab diag-onal. The molecule adopts a planar conformation because of an intramolecular (anti) NÐH N interaction. Thus, isomeric 2- and 3-pyridylurea have very different crystal structures.

Experimental

Compound (I) was synthesized by slowly adding NaOCN (130 mg, 2 mmol) dissolved in hot water (1 ml) to a solution of 3-amino-pyridine (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).

Crystal data C6H7N3O

Mr= 137.15

Monoclinic,P21/n

a= 4.8558 (10) AÊ b= 8.1621 (16) AÊ c= 15.919 (3) AÊ

= 92.16 (3)

V= 630.5 (2) AÊ3

Z= 4

Dx= 1.445 Mg mÿ3

MoKradiation Cell parameters from 25

re¯ections

= 9.0±10.6

= 0.10 mmÿ1

T= 293 (2) K Cube, colourless 0.120.110.10 mm Data collection

Enraf±Nonius CAD-4 diffractometer

!scans

2021 measured re¯ections 1835 independent re¯ections 1362 re¯ections withI> 2(I) Rint= 0.010

max= 30.0

h= 0!6 k= 0!11 l=ÿ22!22 3 standard re¯ections

every 150 re¯ections frequency: 90 min intensity decay: none

Re®nement Re®nement onF2

R[F2_{> 2(F}2_{)] = 0.045}

wR(F2_{) = 0.134}

S= 1.08 1835 re¯ections 119 parameters

All H-atom parameters re®ned

w= 1/[2_(F

o2) + (0.0665P)2

+ 0.1436P]

whereP= (Fo2+ 2Fc2)/3

(/)max= 0.019

max= 0.25 e AÊÿ3

min=ÿ0.25 e AÊÿ3

Table 1

Hydrogen-bonding geometry (AÊ,_).

DÐH A DÐH H A D A DÐH A

N7ÐH7 N4i _{0.888 (19) 2.156 (18) 2.984 (2) 155.0 (16)}

N10ÐH8 O9ii _{0.92 (2) 2.05 (2) 2.9657 (19) 173.0 (18)}

N10ÐH9 O9iii _{0.842 (19) 2.193 (19) 2.9734 (19) 154.2 (18)}

C2ÐH2 O9iv _{0.97 (2) 2.67 (2) 3.629 (2) 168.4 (16)}

Symmetry codes: (i) ÿ1

2ÿx;yÿ12;32ÿz; (ii) ÿx;1ÿy;2ÿz; (iii) xÿ1;y;z; (iv) 1ÿx;2ÿy;2ÿz.

Data collection: CAD-4 Software (Enraf±Nonius, 1989); cell re®nement: CAD-4 Software; data reduction: Xtal3.5 (Hall et al., 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to re®ne structure:SHELXL97 (Sheldrick, 1997); molecular graphics: PLUTON-(C) (Spek, 1979±1997); soft-ware used to prepare material for publication:SHELXL97.

The authors thank the DST for funding the X-ray diffractometer facility.

References

Enraf±Nonius (1989).CAD-4Software. Version 5.0. Enraf±Nonius, Delft, The Netherlands.

George, S., Nangia, A. & Lynch, V. M. (2001).Acta Cryst.C57, 777±778. Hall, S. R., Flack, H. D. & Stewart, J. M. (1995). Editors.Xtal3.5Reference

Manual. Universities of Western Australia, Australia, Geneva, Switzerland, and Maryland, USA.

Johnson, C. K. (1976).ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.

Lynch, D. E. & McClenaghan, I. (2001).Acta Cryst.E57, o4-o5.

Palmore, G. T. R. & MacDonald, J. C. (2000).The Amide Linkage: Selected Structural Aspects in Chemistry,Biochemistry and Material Science, edited by A. Greenberg, C. M. Breneman & J. F. Liebman, pp. 291±336. Chichester: John Wiley.

Sheldrick, G. M. (1990).Acta Cryst.A46, 467±473.

Sheldrick, G. M. (1997).SHELXL97. University of GoÈttingen, Germany. Spek, A. L. (1979±1997).PLUTON-(C). Utrecht University, The Netherlands. Velikova, V., Angelova, O. & Kossev, K. (1997).Acta Cryst.C53, 1273±1275. Figure 1

ORTEPII (Johnson, 1976) plot of (I) with 50% probability ellipsoids.

Figure 2

supporting information

sup-1

Acta Cryst. (2001). E57, o719–o720

supporting information

Acta Cryst. (2001). E57, o719–o720 [doi:10.1107/S1600536801011424]

N

-(3-Pyridyl)urea

Sumod George and Ashwini Nangia

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

Figure 1

ORTEPII (Johnson, 1976) plot of (I) with 50% probability ellipsoids.

Figure 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 Mr = 137.15 Monoclinic, P21/n a = 4.8558 (10) Å b = 8.1621 (16) Å c = 15.919 (3) Å β = 92.16 (3)°

Z = 4 F(000) = 288 Dx = 1.445 Mg m−3

supporting information

sup-3

Acta Cryst. (2001). E57, o719–o720 T = 293 K

Cube, colourless

0.12 × 0.11 × 0.10 mm

Data collection

Enraf-Nonius CAD-4 diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

ω scans

2021 measured reflections 1835 independent reflections 1362 reflections with I > 2σ(I)

Rint = 0.010

θmax = 30.0°, θmin = 2.6° h = 0→6

k = 0→11 l = −22→22

3 standard reflections every 150 reflections intensity decay: none

Refinement

Refinement on F2 Least-squares matrix: full R[F2 _{> 2σ(F}2_{)] = 0.045} wR(F2_{) = 0.134} S = 1.08 1835 reflections 119 parameters 0 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

All H-atom parameters refined w = 1/[σ2_(F

o2) + (0.0665P)2 + 0.1436P] where P = (Fo2 + 2Fc2)/3

(Δ/σ)max = 0.019 Δρmax = 0.25 e Å−3 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 F}2_, conventional R-factors R are based on F, with F set to zero for negative F2_{. The threshold expression of F}2 _{> σ(F}2_{) 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₎

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)*

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₎

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)

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

supporting information

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Acta Cryst. (2001). E57, o719–o720

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)}