2,2′,2′′,2′′′-[Pyridine-2,6-diylbis(methyl­ene­nitrilo)]tetra­ethanol

Cao, S.-Y.; Zhou, C.-H.

doi:10.1107/S1600536811010919

organic compounds

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doi:10.1107/S1600536811010919

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2,2′,2′′,2′′′-[Pyridine-2,6-diylbis(methylenenitrilo)]tetraethanol

Shou-Ying Cao ^a and Cheng-He Zhou ^a ^*

^aSchool of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, People's Republic of China
^*Correspondence e-mail: zhouch@swu.edu.cn

(Received 10 March 2011; accepted 23 March 2011; online 31 March 2011)

In the crystal structure of the title compound C₁₅H₂₇N₃O₄, the molecule is located on a twofold axis and the asymmetric unit contains one half-molecule, with one N and one C atom lying on the rotation axis. The pyridine ring is the hydrogen-bond acceptor, while two hydroxyl O atoms act as hydrogen-bond donors in intramolecular O—H⋯N and intermolecular O—H⋯N and O—H⋯O hydrogen bonds, thereby forming a closed hydrogen-bonded cage.

Related literature

For general background to pyridine, see: Klimesova et al. (1990 ); Rabasseda et al. (1999 ) . For the synthesis, see: Fang et al. (2010 ).

Experimental

Crystal data

C₁₅H₂₇N₃O₄
M_r = 313.40
Orthorhombic, P 2₁ 2₁ 2
a = 9.145 (6) Å
b = 10.716 (7) Å
c = 8.292 (5) Å
V = 812.6 (9) Å³
Z = 2
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 298 K
0.45 × 0.45 × 0.45 mm

Data collection

Bruker SMART APEX diffractometer
4239 measured reflections
1511 independent reflections
1441 reflections with I > 2σ(I)
R_int = 0.021

Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.098
S = 1.08
1511 reflections
104 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.14 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2A⋯O1ⁱ	0.82	1.94	2.762 (2)	175
O1—H1A⋯N2ⁱ	0.82	2.74	3.248 (2)	122
O1—H1A⋯N2	0.82	2.54	2.935 (2)	111
O1—H1A⋯N1	0.82	2.25	3.004 (2)	153
Symmetry code: (i) -x, -y+2, z.

Data collection: SMART (Bruker, 2000 ); cell refinement: SAINT (Bruker, 2000); 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/S1600536811010919/rk2270sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811010919/rk2270Isup2.hkl

checkCIF report

Comment top

Pyridine is an important type of nitrogen–containing aromatic heterocycle which is widely used as building block for preparing a variety of drugs, insecticides and herbicides in the pharmaceutical industry (Klimesova et al., 1999; Rabasseda et al., 1999). Recently, our researches have been focused on the development of aromatic ring–derived nitrogen mustards as potential antitumor agents. As part of our work, herein we report the molecular and crystal structures of the title compound as an intermediate for the pyridine–derived nitrogen mustards.

The molecular structure of the title compound is shown in Fig. 1. In the crystal structure of the title compound, C₁₅H₂₇N₃O₄, reveals that the molecule placed on two–fold axis (C1, H1 and N1 atoms placed on twofold axis) and asymmetric unit contains a half molecule. In the molecule, pyridine ring is the hydrogen–bond acceptor, and two hydroxyls which move closer to the pyridine ring via O—H···N intramolecular hydrogen bond perform as hydrogen–bond donor, thus the closed hydrogen bond cage has been formed.

Related literature top

For general background to pyridine, see: Klimesova et al. (1999); Rabasseda et al. (1999). For the synthesis, see: Fang et al. (2010).

Experimental top

The title compound was prepared according to the procedure of Fang et al. (2010). Single crystals were grown by slow evaporation of a solution of the title compound in the mixture of dichloromethane and n–hexane at room temperature.

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); 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. The molecular structure of the title compound, showing the atom–numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as a small spheres of arbitrary radius.

2,2',2'',2'''-[Pyridine-2,6-diylbis(methylenenitrilo)]tetraethanol top

Crystal data top

C₁₅H₂₇N₃O₄	F(000) = 340
M_r = 313.40	D_x = 1.281 Mg m⁻³
Orthorhombic, P2₁2₁2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 2ab	Cell parameters from 2637 reflections
a = 9.145 (6) Å	θ = 2.5–27.1°
b = 10.716 (7) Å	µ = 0.09 mm⁻¹
c = 8.292 (5) Å	T = 298 K
V = 812.6 (9) Å³	Block, colourless
Z = 2	0.45 × 0.45 × 0.45 mm

Data collection top

Bruker SMART APEX diffractometer	1441 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.021
Graphite monochromator	θ_max = 25.5°, θ_min = 2.5°
ϕ– and ω–scans	h = −11→8
4239 measured reflections	k = −9→12
1511 independent reflections	l = −10→8

Refinement top

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)] = 0.036	H-atom parameters constrained
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0466P)² + 0.1402P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
1511 reflections	Δρ_max = 0.14 e Å⁻³
104 parameters	Δρ_min = −0.17 e Å⁻³
1 restraint	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.105 (9)

Crystal data top

C₁₅H₂₇N₃O₄	V = 812.6 (9) Å³
M_r = 313.40	Z = 2
Orthorhombic, P2₁2₁2	Mo Kα radiation
a = 9.145 (6) Å	µ = 0.09 mm⁻¹
b = 10.716 (7) Å	T = 298 K
c = 8.292 (5) Å	0.45 × 0.45 × 0.45 mm

Data collection top

Bruker SMART APEX diffractometer	1441 reflections with I > 2σ(I)
4239 measured reflections	R_int = 0.021
1511 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	1 restraint
wR(F²) = 0.098	H-atom parameters constrained
S = 1.08	Δρ_max = 0.14 e Å⁻³
1511 reflections	Δρ_min = −0.17 e Å⁻³
104 parameters

Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 F², conventional R–factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) 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) top

	x	y	z	U_iso*/U_eq
C1	0.0000	1.0000	0.8502 (3)	0.0603 (7)
H1	0.0000	1.0000	0.9624	0.072*
C2	0.0769 (2)	0.91187 (18)	0.7667 (2)	0.0537 (5)
H2	0.1312	0.8520	0.8215	0.064*
C3	0.07333 (19)	0.91260 (16)	0.6004 (2)	0.0453 (4)
C4	0.1444 (2)	0.81022 (17)	0.5072 (2)	0.0564 (5)
H4A	0.2346	0.7873	0.5610	0.068*
H4B	0.0806	0.7379	0.5090	0.068*
C5	0.29756 (19)	0.93047 (18)	0.3315 (3)	0.0590 (5)
H5A	0.3889	0.8861	0.3158	0.071*
H5B	0.3040	0.9755	0.4328	0.071*
C6	0.2762 (2)	1.02106 (18)	0.1970 (2)	0.0567 (5)
H6A	0.3634	1.0719	0.1855	0.068*
H6B	0.2618	0.9757	0.0970	0.068*
C7	0.2098 (2)	0.72780 (17)	0.2461 (3)	0.0617 (5)
H7A	0.2738	0.6747	0.3093	0.074*
H7B	0.2628	0.7520	0.1497	0.074*
C8	0.0801 (3)	0.65392 (18)	0.1972 (3)	0.0671 (5)
H8A	0.1129	0.5729	0.1595	0.081*
H8B	0.0193	0.6403	0.2914	0.081*
N1	0.0000	1.0000	0.5180 (2)	0.0460 (5)
N2	0.17740 (14)	0.84064 (12)	0.34005 (17)	0.0443 (4)
O1	0.15472 (15)	1.09903 (12)	0.22517 (18)	0.0608 (4)
H1A	0.0944	1.0617	0.2802	0.091*
O2	−0.0051 (2)	0.70862 (16)	0.0769 (2)	0.0867 (5)
H2A	−0.0531	0.7659	0.1157	0.130*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0685 (17)	0.0814 (19)	0.0309 (11)	−0.0226 (16)	0.000	0.000
C2	0.0567 (10)	0.0636 (11)	0.0408 (9)	−0.0147 (9)	−0.0090 (8)	0.0123 (8)
C3	0.0449 (9)	0.0501 (9)	0.0410 (8)	−0.0046 (8)	−0.0020 (7)	0.0090 (7)
C4	0.0620 (11)	0.0540 (10)	0.0533 (11)	0.0119 (9)	−0.0016 (9)	0.0147 (8)
C5	0.0383 (9)	0.0654 (11)	0.0734 (12)	0.0017 (8)	−0.0028 (9)	0.0111 (10)
C6	0.0450 (9)	0.0621 (11)	0.0631 (11)	−0.0064 (8)	0.0069 (9)	0.0084 (10)
C7	0.0612 (11)	0.0542 (10)	0.0696 (12)	0.0205 (10)	0.0148 (10)	0.0044 (9)
C8	0.0867 (14)	0.0460 (10)	0.0687 (12)	0.0053 (10)	0.0155 (10)	−0.0064 (9)
N1	0.0536 (11)	0.0513 (11)	0.0333 (9)	0.0073 (10)	0.000	0.000
N2	0.0406 (7)	0.0433 (7)	0.0491 (8)	0.0064 (6)	0.0038 (6)	0.0053 (6)
O1	0.0550 (8)	0.0577 (7)	0.0697 (9)	0.0026 (6)	0.0056 (6)	0.0142 (7)
O2	0.0996 (12)	0.0797 (11)	0.0807 (10)	0.0185 (9)	−0.0140 (10)	−0.0251 (8)

Geometric parameters (Å, º) top

C1—C2ⁱ	1.366 (2)	C6—O1	1.410 (2)
C1—C2	1.366 (2)	C6—H6A	0.9700
C1—H1	0.9300	C6—H6B	0.9700
C2—C3	1.380 (3)	C7—N2	1.469 (2)
C2—H2	0.9300	C7—C8	1.482 (3)
C3—N1	1.339 (2)	C7—H7A	0.9700
C3—C4	1.491 (3)	C7—H7B	0.9700
C4—N2	1.455 (2)	C8—O2	1.395 (3)
C4—H4A	0.9700	C8—H8A	0.9700
C4—H4B	0.9700	C8—H8B	0.9700
C5—N2	1.463 (2)	N1—C3ⁱ	1.339 (2)
C5—C6	1.491 (3)	O1—H1A	0.8200
C5—H5A	0.9700	O2—H2A	0.8200
C5—H5B	0.9700

C2ⁱ—C1—C2	119.1 (2)	C5—C6—H6A	109.3
C2ⁱ—C1—H1	120.5	O1—C6—H6B	109.3
C2—C1—H1	120.5	C5—C6—H6B	109.3
C1—C2—C3	119.4 (2)	H6A—C6—H6B	108.0
C1—C2—H2	120.3	N2—C7—C8	115.04 (16)
C3—C2—H2	120.3	N2—C7—H7A	108.5
N1—C3—C2	121.73 (18)	C8—C7—H7A	108.5
N1—C3—C4	117.91 (15)	N2—C7—H7B	108.5
C2—C3—C4	120.25 (18)	C8—C7—H7B	108.5
N2—C4—C3	114.79 (14)	H7A—C7—H7B	107.5
N2—C4—H4A	108.6	O2—C8—C7	114.72 (18)
C3—C4—H4A	108.6	O2—C8—H8A	108.6
N2—C4—H4B	108.6	C7—C8—H8A	108.6
C3—C4—H4B	108.6	O2—C8—H8B	108.6
H4A—C4—H4B	107.5	C7—C8—H8B	108.6
N2—C5—C6	111.48 (16)	H8A—C8—H8B	107.6
N2—C5—H5A	109.3	C3ⁱ—N1—C3	118.6 (2)
C6—C5—H5A	109.3	C4—N2—C5	110.45 (16)
N2—C5—H5B	109.3	C4—N2—C7	111.27 (14)
C6—C5—H5B	109.3	C5—N2—C7	111.38 (15)
H5A—C5—H5B	108.0	C6—O1—H1A	109.5
O1—C6—C5	111.42 (17)	C8—O2—H2A	109.5
O1—C6—H6A	109.3

C2ⁱ—C1—C2—C3	−1.04 (13)	C4—C3—N1—C3ⁱ	175.19 (18)
C1—C2—C3—N1	2.2 (3)	C3—C4—N2—C5	70.9 (2)
C1—C2—C3—C4	−174.02 (14)	C3—C4—N2—C7	−164.87 (16)
N1—C3—C4—N2	23.7 (2)	C6—C5—N2—C4	−143.71 (17)
C2—C3—C4—N2	−160.01 (17)	C6—C5—N2—C7	92.11 (19)
N2—C5—C6—O1	66.6 (2)	C8—C7—N2—C4	77.8 (2)
N2—C7—C8—O2	71.9 (2)	C8—C7—N2—C5	−158.52 (17)
C2—C3—N1—C3ⁱ	−1.09 (13)

Symmetry code: (i) −x, −y+2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···O1ⁱ	0.82	1.94	2.762 (2)	175
O1—H1A···N2ⁱ	0.82	2.74	3.248 (2)	122
O1—H1A···N2	0.82	2.54	2.935 (2)	111
O1—H1A···N1	0.82	2.25	3.004 (2)	153

Symmetry code: (i) −x, −y+2, z.

Experimental details

Crystal data
Chemical formula	C₁₅H₂₇N₃O₄
M_r	313.40
Crystal system, space group	Orthorhombic, P2₁2₁2
Temperature (K)	298
a, b, c (Å)	9.145 (6), 10.716 (7), 8.292 (5)
V (Å³)	812.6 (9)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.45 × 0.45 × 0.45

Data collection
Diffractometer	Bruker SMART APEX diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	4239, 1511, 1441
R_int	0.021
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.098, 1.08
No. of reflections	1511
No. of parameters	104
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.17

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), 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
O2—H2A···O1ⁱ	0.82	1.94	2.762 (2)	175
O1—H1A···N2ⁱ	0.82	2.74	3.248 (2)	122
O1—H1A···N2	0.82	2.54	2.935 (2)	111
O1—H1A···N1	0.82	2.25	3.004 (2)	153

Symmetry code: (i) −x, −y+2, z.

Acknowledgements

The authors thank Southwest University (SWUB2006018, XSGX0602 and SWUF2007023) and the Natural Science Foundation of Chongqing (2007BB5369) for financial support.

References

Bruker (2000). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Fang, B., Zhou, C. H. & Rao, X. C. (2010). Eur. J. Med. Chem. 45, 4388–4398. Web of Science CrossRef CAS PubMed Google Scholar
Klimesova, V., Svoboda, M., Waisser, K., Pour, M. & Kaustova, J. (1999). Farmaco, 54, 666–672. Web of Science PubMed CAS Google Scholar
Rabasseda, X., Silverstre, J. & Castaner, J. (1999). Drug Future, 24, 375–380. CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 67| Part 4| April 2011| Page o1003

doi:10.1107/S1600536811010919

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