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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2428.
Published online 2008 November 22. doi:  10.1107/S1600536808035940
PMCID: PMC2960150

2-[Bis(5-chloro-2-pyridylamino)methyl]pyridine monohydrate

Abstract

In the title compound, the dihedral angles between the 2-amino-5-chloro­pyridyl rings and the pyridine ring are 56.26 (6)° and 78.83 (5)°; the angle between the 2-amino-5-chloro­pyridyl rings is 72.42 (5)°. The solvent water mol­ecules are linked to the organic compound by N—H(...)O, O—H(...)O, N—H(...)N and O—H(...)N hydrogen bonds. π(...)π Stacking inter­actions are also observed between the 2-amino-5-chloro­pyridyl rings (centroid(...)centroid distance = 3.243 Å).

Related literature

For related crystallographic studies, see: Makowska-Grzyska et al. (2003 [triangle]); Li et al. (2008 [triangle]); Peori et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o2428-scheme1.jpg

Experimental

Crystal data

  • C16H13Cl2N5·H2O
  • M r = 364.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2428-efi1.jpg
  • a = 34.414 (3) Å
  • b = 4.4337 (3) Å
  • c = 26.236 (2) Å
  • β = 124.778 (1)°
  • V = 3288.0 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.41 mm−1
  • T = 150 (2) K
  • 0.35 × 0.10 × 0.05 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003 [triangle]) T min = 0.870, T max = 0.980
  • 14914 measured reflections
  • 3778 independent reflections
  • 2830 reflections with I > 2σ(I)
  • R int = 0.042

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.101
  • S = 1.04
  • 3778 reflections
  • 217 parameters
  • H-atom parameters constrained
  • Δρmax = 0.34 e Å−3
  • Δρmin = −0.25 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808035940/wn2287sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808035940/wn2287Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We are grateful to the Research Council of Sharif University of Technology, and Loughborough University for their financial support.

supplementary crystallographic information

Comment

Primary amines add to imines to form aminal compounds; these are not stable (Peori et al., 2008). The title compound, C16H13Cl2N5.H2O, was synthesized by the reaction of 2-amino-5-chloropyridine with 2-pyridinecarbaldehyde in ethanol. Tris(pyridyl)amines are very common ligands and many complexes containing such ligands have been reported (Makowska-Grzyska et al., 2003; Li et al., 2008).

In the title compound, intermolecular N—H···O and N—H···N hydrogen bonds involving amine NH and pyridyl groups form a two dimensional network (Table 1 and Fig. 3). π–π stacking interactions are also observed between the 2-amino-5-chloropyridyl rings [centroid···centroid distance = 3.243 Å]. The dihedral angles between the 2-amino-5-chloropyridyl rings and the pyridine ring are 56.26 (6)° and 78.83 (5)°; the angle between the 2-amino-5-chloropyridyl rings is 72.42 (5)°.

Experimental

The title compound was synthesized by adding 2-pyridinecarbaldehyde (1 mmol, 107 mg) to a solution of 2-amino-5-chloropyridine (3 mmol, 386 mg) and manganese acetate (0.02 mmol, 4.90 mg) in ethanol (20 ml). The mixture was refluxed with stirring for 7 h. The resultant yellow solution was filtered. Colourless single crystals of the title compound suitable for X-ray structure determination were recrystallized from a mixture of ethanol / water (5/1) by slow evaporation of the solvents at room temperature over several days.

Refinement

The H atoms bonded to C atoms were positioned geometrically and refined using the riding model with Uiso(H) = 1.2Ueq(parent atom); C—H = 0.95 and 1.00 Å for aromatic and methine C atoms, respectively. The H atoms bonded to N and O atoms were found in the difference Fourier map and refined with the following DFIX restraints: 0.87 (2) Å for N—H and 0.82 (2) Å for O—H. In the final refinement stages the AFIX3 constraint was used for these H atoms.

Figures

Fig. 1.
View of the molecular structure of the title compound, with displacement ellipsoids for non-H atoms drawn at the 50% probability level. The hydrogen atoms are represented by spheres of arbitrary radius. The hydrogen bond is shown as a dashed line.
Fig. 2.
View of the crystal structure packing scheme. The dashed lines indicate hydrogen bonds. H atoms have been omitted.
Fig. 3.
View of the hydrogen bonding (dashed lines) scheme. H atoms have been omitted.

Crystal data

C16H13Cl2N5·H2OF000 = 1504
Mr = 364.23Dx = 1.472 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2781 reflections
a = 34.414 (3) Åθ = 2.4–26.1º
b = 4.4337 (3) ŵ = 0.41 mm1
c = 26.236 (2) ÅT = 150 (2) K
β = 124.778 (1)ºLath, colourless
V = 3288.0 (4) Å30.35 × 0.10 × 0.05 mm
Z = 8

Data collection

Bruker APEXII CCD diffractometer3778 independent reflections
Radiation source: fine-focus sealed tube2830 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.042
T = 150(2) Kθmax = 27.5º
[var phi] and ω scansθmin = 1.9º
Absorption correction: multi-scan(SADABS; Sheldrick, 2003)h = −44→44
Tmin = 0.870, Tmax = 0.980k = −5→5
14914 measured reflectionsl = −34→34

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H-atom parameters constrained
wR(F2) = 0.101  w = 1/[σ2(Fo2) + (0.0476P)2 + 1.3212P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3778 reflectionsΔρmax = 0.34 e Å3
217 parametersΔρmin = −0.25 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
N10.25729 (5)0.5318 (4)0.15040 (7)0.0272 (3)
C10.30054 (7)0.4226 (5)0.17347 (9)0.0308 (4)
H10.32590.48880.21340.037*
C20.31028 (7)0.2185 (4)0.14231 (9)0.0317 (4)
H20.34140.14360.16060.038*
C30.27344 (7)0.1266 (5)0.08383 (9)0.0330 (4)
H30.2789−0.01040.06070.040*
C40.22844 (7)0.2366 (4)0.05934 (9)0.0279 (4)
H40.20260.17590.01920.033*
C50.22143 (6)0.4366 (4)0.09407 (8)0.0232 (4)
C60.17286 (6)0.5693 (4)0.06964 (8)0.0235 (4)
H60.17200.78000.05540.028*
N20.13502 (5)0.4001 (4)0.01720 (6)0.0244 (3)
H2N0.12240.24850.02390.029*
N30.13945 (5)0.6845 (3)−0.05317 (7)0.0254 (3)
C70.12129 (7)0.7555 (4)−0.11245 (9)0.0279 (4)
H70.13680.9051−0.12060.033*
C80.08131 (6)0.6224 (5)−0.16202 (8)0.0286 (4)
Cl10.06183 (2)0.72387 (14)−0.23748 (2)0.04370 (16)
C90.05738 (6)0.4096 (5)−0.15136 (8)0.0296 (4)
H90.02950.3165−0.18500.035*
C100.07470 (6)0.3361 (4)−0.09131 (8)0.0255 (4)
H100.05880.1919−0.08250.031*
C110.11634 (6)0.4768 (4)−0.04267 (8)0.0224 (4)
N40.16586 (5)0.5834 (4)0.11881 (7)0.0273 (4)
H4N0.18390.47380.15180.033*
N50.10283 (5)0.9191 (4)0.06534 (7)0.0267 (3)
C120.06679 (6)1.0659 (4)0.06110 (9)0.0288 (4)
H120.04791.19750.02690.035*
C130.05617 (6)1.0341 (4)0.10388 (9)0.0275 (4)
Cl20.008985 (17)1.23175 (12)0.09516 (3)0.03644 (14)
C140.08384 (7)0.8454 (5)0.15457 (9)0.0298 (4)
H140.07730.82150.18490.036*
C150.12065 (7)0.6949 (4)0.16002 (9)0.0281 (4)
H150.14010.56500.19430.034*
C160.12928 (6)0.7355 (4)0.11388 (8)0.0238 (4)
O10.27352 (5)0.8741 (3)0.24925 (6)0.0359 (3)
H1O0.26440.79740.21570.043*
H2O0.25701.02340.24180.043*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0274 (8)0.0316 (9)0.0225 (8)−0.0008 (7)0.0142 (7)0.0010 (7)
C10.0266 (10)0.0366 (11)0.0260 (10)0.0014 (8)0.0130 (8)0.0040 (8)
C20.0286 (10)0.0339 (11)0.0381 (11)0.0057 (8)0.0224 (9)0.0095 (9)
C30.0399 (11)0.0315 (10)0.0387 (11)0.0032 (9)0.0290 (10)0.0017 (9)
C40.0304 (10)0.0306 (10)0.0253 (9)−0.0008 (8)0.0174 (8)−0.0014 (8)
C50.0267 (9)0.0239 (9)0.0213 (8)−0.0014 (7)0.0150 (7)0.0029 (7)
C60.0246 (9)0.0281 (10)0.0182 (8)−0.0004 (7)0.0125 (7)−0.0008 (7)
N20.0275 (8)0.0275 (8)0.0187 (7)−0.0047 (6)0.0134 (6)0.0003 (6)
N30.0272 (8)0.0288 (8)0.0216 (8)−0.0025 (6)0.0146 (7)−0.0003 (6)
C70.0306 (10)0.0302 (10)0.0272 (9)0.0009 (8)0.0191 (8)0.0033 (8)
C80.0303 (10)0.0363 (11)0.0195 (9)0.0068 (8)0.0144 (8)0.0037 (8)
Cl10.0461 (3)0.0610 (4)0.0212 (2)0.0011 (3)0.0175 (2)0.0074 (2)
C90.0245 (9)0.0343 (11)0.0235 (9)0.0007 (8)0.0099 (8)−0.0018 (8)
C100.0210 (9)0.0279 (10)0.0268 (9)−0.0003 (7)0.0133 (8)0.0004 (8)
C110.0235 (9)0.0237 (9)0.0222 (9)0.0028 (7)0.0144 (7)−0.0010 (7)
N40.0276 (8)0.0366 (9)0.0191 (7)0.0049 (7)0.0142 (7)0.0034 (7)
N50.0260 (8)0.0317 (9)0.0246 (8)−0.0011 (7)0.0157 (7)0.0010 (7)
C120.0254 (9)0.0319 (10)0.0279 (10)−0.0020 (8)0.0145 (8)0.0012 (8)
C130.0241 (9)0.0293 (10)0.0331 (10)−0.0039 (8)0.0186 (8)−0.0062 (8)
Cl20.0296 (3)0.0394 (3)0.0465 (3)−0.0015 (2)0.0254 (2)−0.0073 (2)
C140.0352 (10)0.0333 (10)0.0288 (10)−0.0056 (8)0.0229 (9)−0.0045 (8)
C150.0320 (10)0.0318 (10)0.0222 (9)−0.0009 (8)0.0165 (8)−0.0011 (8)
C160.0258 (9)0.0256 (9)0.0206 (8)−0.0045 (7)0.0137 (7)−0.0049 (7)
O10.0438 (8)0.0344 (8)0.0245 (7)0.0003 (6)0.0165 (6)−0.0050 (6)

Geometric parameters (Å, °)

N1—C11.337 (2)C8—C91.381 (3)
N1—C51.343 (2)C8—Cl11.7484 (18)
C1—C21.383 (3)C9—C101.368 (3)
C1—H10.9500C9—H90.9500
C2—C31.381 (3)C10—C111.409 (2)
C2—H20.9500C10—H100.9500
C3—C41.383 (3)N4—C161.368 (2)
C3—H30.9500N4—H4N0.8698
C4—C51.388 (3)N5—C161.338 (2)
C4—H40.9500N5—C121.348 (2)
C5—C61.526 (2)C12—C131.372 (3)
C6—N41.442 (2)C12—H120.9500
C6—N21.452 (2)C13—C141.389 (3)
C6—H61.0000C13—Cl21.7418 (19)
N2—C111.358 (2)C14—C151.365 (3)
N2—H2N0.8699C14—H140.9500
N3—C71.342 (2)C15—C161.413 (2)
N3—C111.344 (2)C15—H150.9500
C7—C81.375 (3)O1—H1O0.8206
C7—H70.9500O1—H2O0.8206
C1—N1—C5118.11 (16)C9—C8—Cl1121.13 (15)
N1—C1—C2123.50 (18)C10—C9—C8118.51 (17)
N1—C1—H1118.3C10—C9—H9120.7
C2—C1—H1118.3C8—C9—H9120.7
C3—C2—C1118.10 (18)C9—C10—C11119.16 (17)
C3—C2—H2121.0C9—C10—H10120.4
C1—C2—H2121.0C11—C10—H10120.4
C2—C3—C4119.16 (18)N3—C11—N2117.63 (15)
C2—C3—H3120.4N3—C11—C10122.19 (16)
C4—C3—H3120.4N2—C11—C10120.16 (16)
C3—C4—C5119.22 (18)C16—N4—C6123.43 (15)
C3—C4—H4120.4C16—N4—H4N117.7
C5—C4—H4120.4C6—N4—H4N118.5
N1—C5—C4121.90 (16)C16—N5—C12117.83 (15)
N1—C5—C6116.09 (15)N5—C12—C13123.00 (18)
C4—C5—C6121.98 (16)N5—C12—H12118.5
N4—C6—N2110.65 (14)C13—C12—H12118.5
N4—C6—C5110.04 (14)C12—C13—C14119.23 (17)
N2—C6—C5111.98 (15)C12—C13—Cl2120.28 (15)
N4—C6—H6108.0C14—C13—Cl2120.48 (14)
N2—C6—H6108.0C15—C14—C13118.88 (17)
C5—C6—H6108.0C15—C14—H14120.6
C11—N2—C6122.92 (15)C13—C14—H14120.6
C11—N2—H2N117.7C14—C15—C16118.96 (18)
C6—N2—H2N119.3C14—C15—H15120.5
C7—N3—C11117.36 (15)C16—C15—H15120.5
N3—C7—C8123.29 (17)N5—C16—N4118.68 (16)
N3—C7—H7118.4N5—C16—C15122.09 (17)
C8—C7—H7118.4N4—C16—C15119.23 (16)
C7—C8—C9119.47 (17)H1O—O1—H2O106.9
C7—C8—Cl1119.40 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2N···N5i0.872.152.994 (2)165
N4—H4N···O1ii0.872.182.993 (2)156
O1—H1O···N10.821.982.773 (2)164
O1—H2O···O1iii0.821.962.758 (2)163

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: WN2287).

References

  • Bruker (2005). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Li, H., Zhao, H. Y. & Zhang, S. G. (2008). Acta Cryst. E64, m495. [PMC free article] [PubMed]
  • Makowska-Grzyska, M. M., Szajna, E., Shipley, C., Arif, A. M., Mitchell, M. H., Halfen, J. A. & Berreau, L. M. (2003). Inorg. Chem.42, 7472–7488. [PubMed]
  • Peori, M. B., Vaughan, K. & Bertolasi, V. (2008). J. Chem. Crystallogr.38, 61–64.
  • Sheldrick, G. M. (2003). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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