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

Boghaei, D.M.; Najafpour, M.M.; McKee, V.

doi:10.1107/S1600536808035940

organic compounds

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Volume 64| Part 12| December 2008| Page o2428

doi:10.1107/S1600536808035940

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

Davar M. Boghaei,^a ^* Mohammad Mahdi Najafpour ^a and Vickie McKee ^b

^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. 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 ); Li et al. (2008 ); Peori et al. (2008 ).

Experimental

Crystal data

C₁₆H₁₃Cl₂N₅·H₂O
M_r = 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 ) 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[F² > 2σ(F²)] = 0.039
wR(F²) = 0.101
S = 1.04
3778 reflections
217 parameters
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; 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.

Supporting information

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

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

checkCIF report

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). 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)°.

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.

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

	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.

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

Crystal data top

C₁₆H₁₃Cl₂N₅·H₂O	F(000) = 1504
M_r = 364.23	D_x = 1.472 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2781 reflections
a = 34.414 (3) Å	θ = 2.4–26.1°
b = 4.4337 (3) Å	µ = 0.41 mm⁻¹
c = 26.236 (2) Å	T = 150 K
β = 124.778 (1)°	Lath, colourless
V = 3288.0 (4) Å³	0.35 × 0.10 × 0.05 mm
Z = 8

Data collection top

Bruker APEXII CCD diffractometer	3778 independent reflections
Radiation source: fine-focus sealed tube	2830 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.042
ϕ and ω scans	θ_max = 27.5°, θ_min = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −44→44
T_min = 0.870, T_max = 0.980	k = −5→5
14914 measured reflections	l = −34→34

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.101	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0476P)² + 1.3212P] where P = (F_o² + 2F_c²)/3
3778 reflections	(Δ/σ)_max < 0.001
217 parameters	Δρ_max = 0.34 e Å⁻³
0 restraints	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₁₆H₁₃Cl₂N₅·H₂O	V = 3288.0 (4) Å³
M_r = 364.23	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 34.414 (3) Å	µ = 0.41 mm⁻¹
b = 4.4337 (3) Å	T = 150 K
c = 26.236 (2) Å	0.35 × 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)
T_min = 0.870, T_max = 0.980	R_int = 0.042
14914 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.101	H-atom parameters constrained
S = 1.04	Δρ_max = 0.34 e Å⁻³
3778 reflections	Δρ_min = −0.25 e Å⁻³
217 parameters

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

	x	y	z	U_iso*/U_eq
N1	0.25729 (5)	0.5318 (4)	0.15040 (7)	0.0272 (3)
C1	0.30054 (7)	0.4226 (5)	0.17347 (9)	0.0308 (4)
H1	0.3259	0.4888	0.2134	0.037*
C2	0.31028 (7)	0.2185 (4)	0.14231 (9)	0.0317 (4)
H2	0.3414	0.1436	0.1606	0.038*
C3	0.27344 (7)	0.1266 (5)	0.08383 (9)	0.0330 (4)
H3	0.2789	−0.0104	0.0607	0.040*
C4	0.22844 (7)	0.2366 (4)	0.05934 (9)	0.0279 (4)
H4	0.2026	0.1759	0.0192	0.033*
C5	0.22143 (6)	0.4366 (4)	0.09407 (8)	0.0232 (4)
C6	0.17286 (6)	0.5693 (4)	0.06964 (8)	0.0235 (4)
H6	0.1720	0.7800	0.0554	0.028*
N2	0.13502 (5)	0.4001 (4)	0.01720 (6)	0.0244 (3)
H2N	0.1224	0.2485	0.0239	0.029*
N3	0.13945 (5)	0.6845 (3)	−0.05317 (7)	0.0254 (3)
C7	0.12129 (7)	0.7555 (4)	−0.11245 (9)	0.0279 (4)
H7	0.1368	0.9051	−0.1206	0.033*
C8	0.08131 (6)	0.6224 (5)	−0.16202 (8)	0.0286 (4)
Cl1	0.06183 (2)	0.72387 (14)	−0.23748 (2)	0.04370 (16)
C9	0.05738 (6)	0.4096 (5)	−0.15136 (8)	0.0296 (4)
H9	0.0295	0.3165	−0.1850	0.035*
C10	0.07470 (6)	0.3361 (4)	−0.09131 (8)	0.0255 (4)
H10	0.0588	0.1919	−0.0825	0.031*
C11	0.11634 (6)	0.4768 (4)	−0.04267 (8)	0.0224 (4)
N4	0.16586 (5)	0.5834 (4)	0.11881 (7)	0.0273 (4)
H4N	0.1839	0.4738	0.1518	0.033*
N5	0.10283 (5)	0.9191 (4)	0.06534 (7)	0.0267 (3)
C12	0.06679 (6)	1.0659 (4)	0.06110 (9)	0.0288 (4)
H12	0.0479	1.1975	0.0269	0.035*
C13	0.05617 (6)	1.0341 (4)	0.10388 (9)	0.0275 (4)
Cl2	0.008985 (17)	1.23175 (12)	0.09516 (3)	0.03644 (14)
C14	0.08384 (7)	0.8454 (5)	0.15457 (9)	0.0298 (4)
H14	0.0773	0.8215	0.1849	0.036*
C15	0.12065 (7)	0.6949 (4)	0.16002 (9)	0.0281 (4)
H15	0.1401	0.5650	0.1943	0.034*
C16	0.12928 (6)	0.7355 (4)	0.11388 (8)	0.0238 (4)
O1	0.27352 (5)	0.8741 (3)	0.24925 (6)	0.0359 (3)
H1O	0.2644	0.7974	0.2157	0.043*
H2O	0.2570	1.0234	0.2418	0.043*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0274 (8)	0.0316 (9)	0.0225 (8)	−0.0008 (7)	0.0142 (7)	0.0010 (7)
C1	0.0266 (10)	0.0366 (11)	0.0260 (10)	0.0014 (8)	0.0130 (8)	0.0040 (8)
C2	0.0286 (10)	0.0339 (11)	0.0381 (11)	0.0057 (8)	0.0224 (9)	0.0095 (9)
C3	0.0399 (11)	0.0315 (10)	0.0387 (11)	0.0032 (9)	0.0290 (10)	0.0017 (9)
C4	0.0304 (10)	0.0306 (10)	0.0253 (9)	−0.0008 (8)	0.0174 (8)	−0.0014 (8)
C5	0.0267 (9)	0.0239 (9)	0.0213 (8)	−0.0014 (7)	0.0150 (7)	0.0029 (7)
C6	0.0246 (9)	0.0281 (10)	0.0182 (8)	−0.0004 (7)	0.0125 (7)	−0.0008 (7)
N2	0.0275 (8)	0.0275 (8)	0.0187 (7)	−0.0047 (6)	0.0134 (6)	0.0003 (6)
N3	0.0272 (8)	0.0288 (8)	0.0216 (8)	−0.0025 (6)	0.0146 (7)	−0.0003 (6)
C7	0.0306 (10)	0.0302 (10)	0.0272 (9)	0.0009 (8)	0.0191 (8)	0.0033 (8)
C8	0.0303 (10)	0.0363 (11)	0.0195 (9)	0.0068 (8)	0.0144 (8)	0.0037 (8)
Cl1	0.0461 (3)	0.0610 (4)	0.0212 (2)	0.0011 (3)	0.0175 (2)	0.0074 (2)
C9	0.0245 (9)	0.0343 (11)	0.0235 (9)	0.0007 (8)	0.0099 (8)	−0.0018 (8)
C10	0.0210 (9)	0.0279 (10)	0.0268 (9)	−0.0003 (7)	0.0133 (8)	0.0004 (8)
C11	0.0235 (9)	0.0237 (9)	0.0222 (9)	0.0028 (7)	0.0144 (7)	−0.0010 (7)
N4	0.0276 (8)	0.0366 (9)	0.0191 (7)	0.0049 (7)	0.0142 (7)	0.0034 (7)
N5	0.0260 (8)	0.0317 (9)	0.0246 (8)	−0.0011 (7)	0.0157 (7)	0.0010 (7)
C12	0.0254 (9)	0.0319 (10)	0.0279 (10)	−0.0020 (8)	0.0145 (8)	0.0012 (8)
C13	0.0241 (9)	0.0293 (10)	0.0331 (10)	−0.0039 (8)	0.0186 (8)	−0.0062 (8)
Cl2	0.0296 (3)	0.0394 (3)	0.0465 (3)	−0.0015 (2)	0.0254 (2)	−0.0073 (2)
C14	0.0352 (10)	0.0333 (10)	0.0288 (10)	−0.0056 (8)	0.0229 (9)	−0.0045 (8)
C15	0.0320 (10)	0.0318 (10)	0.0222 (9)	−0.0009 (8)	0.0165 (8)	−0.0011 (8)
C16	0.0258 (9)	0.0256 (9)	0.0206 (8)	−0.0045 (7)	0.0137 (7)	−0.0049 (7)
O1	0.0438 (8)	0.0344 (8)	0.0245 (7)	0.0003 (6)	0.0165 (6)	−0.0050 (6)

Geometric parameters (Å, º) top

N1—C1	1.337 (2)	C8—C9	1.381 (3)
N1—C5	1.343 (2)	C8—Cl1	1.7484 (18)
C1—C2	1.383 (3)	C9—C10	1.368 (3)
C1—H1	0.9500	C9—H9	0.9500
C2—C3	1.381 (3)	C10—C11	1.409 (2)
C2—H2	0.9500	C10—H10	0.9500
C3—C4	1.383 (3)	N4—C16	1.368 (2)
C3—H3	0.9500	N4—H4N	0.8698
C4—C5	1.388 (3)	N5—C16	1.338 (2)
C4—H4	0.9500	N5—C12	1.348 (2)
C5—C6	1.526 (2)	C12—C13	1.372 (3)
C6—N4	1.442 (2)	C12—H12	0.9500
C6—N2	1.452 (2)	C13—C14	1.389 (3)
C6—H6	1.0000	C13—Cl2	1.7418 (19)
N2—C11	1.358 (2)	C14—C15	1.365 (3)
N2—H2N	0.8699	C14—H14	0.9500
N3—C7	1.342 (2)	C15—C16	1.413 (2)
N3—C11	1.344 (2)	C15—H15	0.9500
C7—C8	1.375 (3)	O1—H1O	0.8206
C7—H7	0.9500	O1—H2O	0.8206

C1—N1—C5	118.11 (16)	C9—C8—Cl1	121.13 (15)
N1—C1—C2	123.50 (18)	C10—C9—C8	118.51 (17)
N1—C1—H1	118.3	C10—C9—H9	120.7
C2—C1—H1	118.3	C8—C9—H9	120.7
C3—C2—C1	118.10 (18)	C9—C10—C11	119.16 (17)
C3—C2—H2	121.0	C9—C10—H10	120.4
C1—C2—H2	121.0	C11—C10—H10	120.4
C2—C3—C4	119.16 (18)	N3—C11—N2	117.63 (15)
C2—C3—H3	120.4	N3—C11—C10	122.19 (16)
C4—C3—H3	120.4	N2—C11—C10	120.16 (16)
C3—C4—C5	119.22 (18)	C16—N4—C6	123.43 (15)
C3—C4—H4	120.4	C16—N4—H4N	117.7
C5—C4—H4	120.4	C6—N4—H4N	118.5
N1—C5—C4	121.90 (16)	C16—N5—C12	117.83 (15)
N1—C5—C6	116.09 (15)	N5—C12—C13	123.00 (18)
C4—C5—C6	121.98 (16)	N5—C12—H12	118.5
N4—C6—N2	110.65 (14)	C13—C12—H12	118.5
N4—C6—C5	110.04 (14)	C12—C13—C14	119.23 (17)
N2—C6—C5	111.98 (15)	C12—C13—Cl2	120.28 (15)
N4—C6—H6	108.0	C14—C13—Cl2	120.48 (14)
N2—C6—H6	108.0	C15—C14—C13	118.88 (17)
C5—C6—H6	108.0	C15—C14—H14	120.6
C11—N2—C6	122.92 (15)	C13—C14—H14	120.6
C11—N2—H2N	117.7	C14—C15—C16	118.96 (18)
C6—N2—H2N	119.3	C14—C15—H15	120.5
C7—N3—C11	117.36 (15)	C16—C15—H15	120.5
N3—C7—C8	123.29 (17)	N5—C16—N4	118.68 (16)
N3—C7—H7	118.4	N5—C16—C15	122.09 (17)
C8—C7—H7	118.4	N4—C16—C15	119.23 (16)
C7—C8—C9	119.47 (17)	H1O—O1—H2O	106.9
C7—C8—Cl1	119.40 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, y−1/2, −z+1/2; (iii) −x+1/2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₃Cl₂N₅·H₂O
M_r	364.23
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	150
a, b, c (Å)	34.414 (3), 4.4337 (3), 26.236 (2)
β (°)	124.778 (1)
V (Å³)	3288.0 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.41
Crystal size (mm)	0.35 × 0.10 × 0.05

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.870, 0.980
No. of measured, independent and observed [I > 2σ(I)] reflections	14914, 3778, 2830
R_int	0.042
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.101, 1.04
No. of reflections	3778
No. of parameters	217
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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+1/2, y−1/2, −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

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