Literature DB >> 21581396

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

Davar M Boghaei, Mohammad Mahdi Najafpour, Vickie McKee.

Abstract

In the title compound, the dihedral angles between the 2-amino-5-chloro-pyridyl rings and the pyridine ring are 56.26 (6)° and 78.83 (5)°; the angle between the 2-amino-5-chloro-pyridyl rings is 72.42 (5)°. The solvent water mol-ecules 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 inter-actions are also observed between the 2-amino-5-chloro-pyridyl rings (centroid⋯centroid distance = 3.243 Å).

Entities: Chemical Disease Gene

Year: 2008 PMID： 21581396 PMCID： PMC2960150 DOI： 10.1107/S1600536808035940

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

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 = 364.23 Monoclinic, 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[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 ▶); 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. 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

C₁₆H₁₃Cl₂N₅·H₂O	F₀₀₀ = 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 = 2.4–26.1º
b = 4.4337 (3) Å	µ = 0.41 mm⁻¹
c = 26.236 (2) Å	T = 150 (2) K
β = 124.778 (1)º	Lath, colourless
V = 3288.0 (4) Å³	0.35 × 0.10 × 0.05 mm
Z = 8

Bruker APEXII CCD diffractometer	3778 independent reflections
Radiation source: fine-focus sealed tube	2830 reflections with I > 2σ(I)
Monochromator: graphite	R_int = 0.042
T = 150(2) K	θ_max = 27.5º
φ and ω scans	θ_min = 1.9º
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 on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.101	w = 1/[σ²(F_o²) + (0.0476P)² + 1.3212P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
3778 reflections	Δρ_max = 0.34 e Å⁻³
217 parameters	Δρ_min = −0.25 e Å⁻³
Primary atom site location: structure-invariant direct methods	Extinction correction: none

	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*

	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)

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)

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

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) ; (ii) ; (iii) .

3 in total

1. A short history of SHELX.

Authors: George M Sheldrick
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

2. First row divalent transition metal complexes of aryl-appended tris((pyridyl)methyl)amine ligands: syntheses, structures, electrochemistry, and hydroxamate binding properties.

Authors: Magdalena M Makowska-Grzyska; Ewa Szajna; Crystal Shipley; Atta M Arif; Michael H Mitchell; Jason A Halfen; Lisa M Berreau
Journal: Inorg Chem Date: 2003-11-17 Impact factor: 5.165

3. (Dicyanamido)[tris-(2-pyridylmeth-yl)amine]zinc(II) perchlorate.

Authors: Hong Li; Hong Yan Zhao; Shi Guo Zhang
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2008-02-27

3 in total