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ISSN: 2056-9890

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

aDepartment of Chemistry, Sharif University of Technology, PO Box 11155-8639, Tehran, Iran, and bDepartment of Chemistry, Loughborough University, Leicestershire LE11 3TU, England
*Correspondence e-mail: dboghaei@sharif.edu

(Received 20 October 2008; accepted 3 November 2008; online 22 November 2008)

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. ππ 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[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.]); Li et al. (2008[Li, H., Zhao, H. Y. & Zhang, S. G. (2008). Acta Cryst. E64, m495.]); Peori et al. (2008[Peori, M. B., Vaughan, K. & Bertolasi, V. (2008). J. Chem. Crystallogr. 38, 61-64.]).

[Scheme 1]

Experimental

Crystal data
  • C16H13Cl2N5·H2O

  • Mr = 364.23

  • Monoclinic, C 2/c

  • 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[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.870, Tmax = 0.980

  • 14914 measured reflections

  • 3778 independent reflections

  • 2830 reflections with I > 2σ(I)

  • Rint = 0.042

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2N⋯N5i 0.87 2.15 2.994 (2) 165
N4—H4N⋯O1ii 0.87 2.18 2.993 (2) 156
O1—H1O⋯N1 0.82 1.98 2.773 (2) 164
O1—H2O⋯O1iii 0.82 1.96 2.758 (2) 163
Symmetry codes: (i) x, y-1, z; (ii) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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). ππ 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)°.

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. View of the crystal structure packing scheme. The dashed lines indicate hydrogen bonds. H atoms have been omitted.
[Figure 3] Fig. 3. View of the hydrogen bonding (dashed lines) scheme. H atoms have been omitted.
2-[Bis(5-chloro-2-pyridylamino)methyl]pyridine monohydrate top
Crystal data top
C16H13Cl2N5·H2OF(000) = 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 = 2.4–26.1°
b = 4.4337 (3) ŵ = 0.41 mm1
c = 26.236 (2) ÅT = 150 K
β = 124.778 (1)°Lath, colourless
V = 3288.0 (4) Å30.35 × 0.10 × 0.05 mm
Z = 8
Data collection top
Bruker APEXII CCD
diffractometer
3778 independent reflections
Radiation source: fine-focus sealed tube2830 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.042
ϕ and ω scansθmax = 27.5°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 4444
Tmin = 0.870, Tmax = 0.980k = 55
14914 measured reflectionsl = 3434
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.101H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0476P)2 + 1.3212P]
where P = (Fo2 + 2Fc2)/3
3778 reflections(Δ/σ)max < 0.001
217 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C16H13Cl2N5·H2OV = 3288.0 (4) Å3
Mr = 364.23Z = 8
Monoclinic, C2/cMo Kα radiation
a = 34.414 (3) ŵ = 0.41 mm1
b = 4.4337 (3) ÅT = 150 K
c = 26.236 (2) Å0.35 × 0.10 × 0.05 mm
β = 124.778 (1)°
Data collection top
Bruker APEXII CCD
diffractometer
3778 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
2830 reflections with I > 2σ(I)
Tmin = 0.870, Tmax = 0.980Rint = 0.042
14914 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.101H-atom parameters constrained
S = 1.04Δρmax = 0.34 e Å3
3778 reflectionsΔρmin = 0.25 e Å3
217 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
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)
H30.27890.01040.06070.040*
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)
H70.13680.90510.12060.033*
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)
H90.02950.31650.18500.035*
C100.07470 (6)0.3361 (4)0.09131 (8)0.0255 (4)
H100.05880.19190.08250.031*
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) top
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, º) top
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, º) top
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, y1, z; (ii) x+1/2, y1/2, z+1/2; (iii) x+1/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC16H13Cl2N5·H2O
Mr364.23
Crystal system, space groupMonoclinic, C2/c
Temperature (K)150
a, b, c (Å)34.414 (3), 4.4337 (3), 26.236 (2)
β (°) 124.778 (1)
V3)3288.0 (4)
Z8
Radiation typeMo Kα
µ (mm1)0.41
Crystal size (mm)0.35 × 0.10 × 0.05
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.870, 0.980
No. of measured, independent and
observed [I > 2σ(I)] reflections
14914, 3778, 2830
Rint0.042
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.101, 1.04
No. of reflections3778
No. of parameters217
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.34, 0.25

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
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, y1, z; (ii) x+1/2, y1/2, z+1/2; (iii) x+1/2, y+1/2, z+1/2.
 

Acknowledgements

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

References

First citationBruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationLi, H., Zhao, H. Y. & Zhang, S. G. (2008). Acta Cryst. E64, m495.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationMakowska-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.  Web of Science CSD CrossRef PubMed CAS Google Scholar
First citationPeori, M. B., Vaughan, K. & Bertolasi, V. (2008). J. Chem. Crystallogr. 38, 61–64.  Google Scholar
First citationSheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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