Literature DB >> 21754024

2,2',2'',2'''-[Pyridine-2,6-diylbis(methyl-ene-nitrilo)]tetra-ethanol.

Shou-Ying Cao1, Cheng-He Zhou.   

Abstract

In the crystal structure of the title compound C(15)H(27)N(3)O(4), the mol-ecule is located on a twofold axis and the asymmetric unit contains one half-mol-ecule, 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 intra-molecular O-H⋯N and intermolecular O-H⋯N and O-H⋯O hydrogen bonds, thereby forming a closed hydrogen-bonded cage.

Entities:  

Year:  2011        PMID: 21754024      PMCID: PMC3099931          DOI: 10.1107/S1600536811010919

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


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 = 313.40 Orthorhombic, 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[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.098 S = 1.08 1511 reflections 104 parameters 1 restraint H-atom parameters constrained Δρmax = 0.14 e Å−3 Δρmin = −0.17 e Å−3 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. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811010919/rk2270sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811010919/rk2270Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C15H27N3O4F(000) = 340
Mr = 313.40Dx = 1.281 Mg m3
Orthorhombic, P21212Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 2abCell parameters from 2637 reflections
a = 9.145 (6) Åθ = 2.5–27.1°
b = 10.716 (7) ŵ = 0.09 mm1
c = 8.292 (5) ÅT = 298 K
V = 812.6 (9) Å3Block, colourless
Z = 20.45 × 0.45 × 0.45 mm
Bruker SMART APEX diffractometer1441 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.021
graphiteθmax = 25.5°, θmin = 2.5°
φ– and ω–scansh = −11→8
4239 measured reflectionsk = −9→12
1511 independent reflectionsl = −10→8
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.098w = 1/[σ2(Fo2) + (0.0466P)2 + 0.1402P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
1511 reflectionsΔρmax = 0.14 e Å3
104 parametersΔρmin = −0.16 e Å3
1 restraintExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.105 (9)
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.
xyzUiso*/Ueq
C10.00001.00000.8502 (3)0.0603 (7)
H10.00001.00000.96240.072*
C20.0769 (2)0.91187 (18)0.7667 (2)0.0537 (5)
H20.13120.85200.82150.064*
C30.07333 (19)0.91260 (16)0.6004 (2)0.0453 (4)
C40.1444 (2)0.81022 (17)0.5072 (2)0.0564 (5)
H4A0.23460.78730.56100.068*
H4B0.08060.73790.50900.068*
C50.29756 (19)0.93047 (18)0.3315 (3)0.0590 (5)
H5A0.38890.88610.31580.071*
H5B0.30400.97550.43280.071*
C60.2762 (2)1.02106 (18)0.1970 (2)0.0567 (5)
H6A0.36341.07190.18550.068*
H6B0.26180.97570.09700.068*
C70.2098 (2)0.72780 (17)0.2461 (3)0.0617 (5)
H7A0.27380.67470.30930.074*
H7B0.26280.75200.14970.074*
C80.0801 (3)0.65392 (18)0.1972 (3)0.0671 (5)
H8A0.11290.57290.15950.081*
H8B0.01930.64030.29140.081*
N10.00001.00000.5180 (2)0.0460 (5)
N20.17740 (14)0.84064 (12)0.34005 (17)0.0443 (4)
O10.15472 (15)1.09903 (12)0.22517 (18)0.0608 (4)
H1A0.09441.06170.28020.091*
O2−0.0051 (2)0.70862 (16)0.0769 (2)0.0867 (5)
H2A−0.05310.76590.11570.130*
U11U22U33U12U13U23
C10.0685 (17)0.0814 (19)0.0309 (11)−0.0226 (16)0.0000.000
C20.0567 (10)0.0636 (11)0.0408 (9)−0.0147 (9)−0.0090 (8)0.0123 (8)
C30.0449 (9)0.0501 (9)0.0410 (8)−0.0046 (8)−0.0020 (7)0.0090 (7)
C40.0620 (11)0.0540 (10)0.0533 (11)0.0119 (9)−0.0016 (9)0.0147 (8)
C50.0383 (9)0.0654 (11)0.0734 (12)0.0017 (8)−0.0028 (9)0.0111 (10)
C60.0450 (9)0.0621 (11)0.0631 (11)−0.0064 (8)0.0069 (9)0.0084 (10)
C70.0612 (11)0.0542 (10)0.0696 (12)0.0205 (10)0.0148 (10)0.0044 (9)
C80.0867 (14)0.0460 (10)0.0687 (12)0.0053 (10)0.0155 (10)−0.0064 (9)
N10.0536 (11)0.0513 (11)0.0333 (9)0.0073 (10)0.0000.000
N20.0406 (7)0.0433 (7)0.0491 (8)0.0064 (6)0.0038 (6)0.0053 (6)
O10.0550 (8)0.0577 (7)0.0697 (9)0.0026 (6)0.0056 (6)0.0142 (7)
O20.0996 (12)0.0797 (11)0.0807 (10)0.0185 (9)−0.0140 (10)−0.0251 (8)
C1—C2i1.366 (2)C6—O11.410 (2)
C1—C21.366 (2)C6—H6A0.9700
C1—H10.9300C6—H6B0.9700
C2—C31.380 (3)C7—N21.469 (2)
C2—H20.9300C7—C81.482 (3)
C3—N11.339 (2)C7—H7A0.9700
C3—C41.491 (3)C7—H7B0.9700
C4—N21.455 (2)C8—O21.395 (3)
C4—H4A0.9700C8—H8A0.9700
C4—H4B0.9700C8—H8B0.9700
C5—N21.463 (2)N1—C3i1.339 (2)
C5—C61.491 (3)O1—H1A0.8200
C5—H5A0.9700O2—H2A0.8200
C5—H5B0.9700
C2i—C1—C2119.1 (2)C5—C6—H6A109.3
C2i—C1—H1120.5O1—C6—H6B109.3
C2—C1—H1120.5C5—C6—H6B109.3
C1—C2—C3119.4 (2)H6A—C6—H6B108.0
C1—C2—H2120.3N2—C7—C8115.04 (16)
C3—C2—H2120.3N2—C7—H7A108.5
N1—C3—C2121.73 (18)C8—C7—H7A108.5
N1—C3—C4117.91 (15)N2—C7—H7B108.5
C2—C3—C4120.25 (18)C8—C7—H7B108.5
N2—C4—C3114.79 (14)H7A—C7—H7B107.5
N2—C4—H4A108.6O2—C8—C7114.72 (18)
C3—C4—H4A108.6O2—C8—H8A108.6
N2—C4—H4B108.6C7—C8—H8A108.6
C3—C4—H4B108.6O2—C8—H8B108.6
H4A—C4—H4B107.5C7—C8—H8B108.6
N2—C5—C6111.48 (16)H8A—C8—H8B107.6
N2—C5—H5A109.3C3i—N1—C3118.6 (2)
C6—C5—H5A109.3C4—N2—C5110.45 (16)
N2—C5—H5B109.3C4—N2—C7111.27 (14)
C6—C5—H5B109.3C5—N2—C7111.38 (15)
H5A—C5—H5B108.0C6—O1—H1A109.5
O1—C6—C5111.42 (17)C8—O2—H2A109.5
O1—C6—H6A109.3
C2i—C1—C2—C3−1.04 (13)C4—C3—N1—C3i175.19 (18)
C1—C2—C3—N12.2 (3)C3—C4—N2—C570.9 (2)
C1—C2—C3—C4−174.02 (14)C3—C4—N2—C7−164.87 (16)
N1—C3—C4—N223.7 (2)C6—C5—N2—C4−143.71 (17)
C2—C3—C4—N2−160.01 (17)C6—C5—N2—C792.11 (19)
N2—C5—C6—O166.6 (2)C8—C7—N2—C477.8 (2)
N2—C7—C8—O271.9 (2)C8—C7—N2—C5−158.52 (17)
C2—C3—N1—C3i−1.09 (13)
D—H···AD—HH···AD···AD—H···A
O2—H2A···O1i0.821.942.762 (2)175
O1—H1A···N2i0.822.743.248 (2)122
O1—H1A···N20.822.542.935 (2)111
O1—H1A···N10.822.253.004 (2)153
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O2—H2A⋯O1i0.821.942.762 (2)175
O1—H1A⋯N2i0.822.743.248 (2)122
O1—H1A⋯N20.822.542.935 (2)111
O1—H1A⋯N10.822.253.004 (2)153

Symmetry code: (i) .

  3 in total

1.  New pyridine derivatives as potential antimicrobial agents.

Authors:  V Klimesová; M Svoboda; K Waisser; M Pour; J Kaustová
Journal:  Farmaco       Date:  1999-10-30

2.  A short history of SHELX.

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

3.  Synthesis and biological activities of novel amine-derived bis-azoles as potential antibacterial and antifungal agents.

Authors:  Bo Fang; Cheng-He Zhou; Xian-Cai Rao
Journal:  Eur J Med Chem       Date:  2010-06-12       Impact factor: 6.514

  3 in total

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