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Crystal structure of 2,2-di­chloro-1-(piperidin-1-yl)butane-1,3-dione

aUniversity Koblenz-Landau, Institute for Natural Sciences, Universitätsstrasse 1, 56070 Koblenz, Germany, and bFriedrich-Schiller-University Jena, Institute of Inorganic and Analytical Chemistry, Humboldtstrasse 8, 07743 Jena, Germany
*Correspondence e-mail: imhof@uni-koblenz.de

Edited by P. C. Healy, Griffith University, Australia (Received 19 November 2014; accepted 28 November 2014; online 1 January 2015)

In the title compound, C9H13Cl2NO2, the piperidine ring shows a chair conformation and the O—C—C—O torsion angle between the carbonyl groups is 183.6 (4)°. In the crystal, mol­ecules are linked into an infinite layer along the ab plane by a bifurcated C—H⋯O hydrogen bond between the carbonyl O atom adjacent to the methyl group and one of the methyl­ene groups next to nitro­gen and an additional hydrogen bond of the C—H⋯Cl type. These layers are connected into a three-dimensional supra­molecular arrangement by O⋯Cl contacts [2.8979 (12) and 3.1300 (12) Å].

1. Related literature

For the synthetic procedure, see: Schank (1967[Schank, K. (1967). Chem. Ber. 100, 2292-2295.]). For a survey concerning weak hydrogen bonds, see: Desiraju & Steiner (1999[Desiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond. Oxford University Press.]). For a description of the nature of inter­molecular inter­actions between chlorine and oxygen, see: Lommerse et al. (1996[Lommerse, J. P. M., Stone, A. J., Taylor, R. & Allen, F. H. (1996). J. Am. Chem. Soc. 118, 3108-3116.]). For the X-ray structure of the starting compound, see: Schwierz et al. (2014[Schwierz, M., Görls, H. & Imhof, W. (2014). Acta Cryst. E70, o1297.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C9H13Cl2NO2

  • Mr = 238.10

  • Monoclinic, P 21

  • a = 5.9548 (3) Å

  • b = 10.5510 (4) Å

  • c = 8.5747 (3) Å

  • β = 100.568 (2)°

  • V = 529.60 (4) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.59 mm−1

  • T = 133 K

  • 0.07 × 0.05 × 0.02 mm

2.2. Data collection

  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2002[Bruker (2002). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.616, Tmax = 0.746

  • 3076 measured reflections

  • 2402 independent reflections

  • 2085 reflections with I > 2σ(I)

  • Rint = 0.030

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 0.059

  • S = 1.09

  • 2402 reflections

  • 128 parameters

  • 1 restraint

  • All H-atom parameters refined

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.21 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1115 Friedel pairs

  • Absolute structure parameter: 0.08 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1A⋯O1i 0.99 2.56 3.413 (2) 145
C9—H9C⋯O1i 0.98 2.53 3.494 (2) 168
C9—H9C⋯Cl1ii 0.98 2.79 3.770 (2) 176
Symmetry codes: (i) [-x+2, y-{\script{1\over 2}}, -z+2]; (ii) x-1, y, z.

Data collection: COLLECT (Nonius, 1998[Nonius (1998). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO; 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: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

The title compound is an intermediate in the synthesis of 2,2-dimethoxy-1-(pyridin-2-yl)ethanone and has been synthesized from 1-(piperidin-1-yl)butane-1,3-dione (Schwierz et al., 2014) following a modified procedure (Schank, 1967). As it is expected the piperidine ring shows a chair conformation and the amide substructure is planar (Figure 1). The dihedral angle O1—C6—C8—O2 between the carbonyl groups measures to 183.6 (4)°. The C—O bond of the amide carbonyl group is slightly elongated with respect to the other carbonyl group due to delocalization of the nitrogen lone pair (C6—O1 1.221 (3) Å versus. C8—O2 1.205 (3) Å). In the crystal structure, molecules are linked to infinite layers along the ab plane by a bifurcated hydrogen bond between one of the carbonyl oxygen atoms (O1) towards the methyl group and one of the methylene groups next to nitrogen and an additional hydrogen bond of the C—H···Cl type (Desiraju & Steiner, 1999). In addition, these layers are connected to a 3D supramolecular arrangement by oxygen chlorine contacts (Lommerse et al., 1996).

Related literature top

For the synthetic procedure, see: Schank (1967). For a survey concerning weak hydrogen bonds, see: Desiraju & Steiner (1999). For a description of the nature of intermolecular interactions between chlorine and oxygen, see: Lommerse et al. (1996). For the X-ray structure of the starting compound, see: Schwierz et al. (2014).

Experimental top

25.4 g (0.15 mol) 1-(piperidin-1-yl)butane-1,3-dione were dissolved in 70 ml dichloromethane. To this solution, 24.3 ml (40.6 g, 0.3 mol) sulfuryl dichloride was added dropwise and the resulting mixture refluxed for 5 h. After cooling to room temperature 30 ml diethylether were added and the solution washed with brine (3 ×20 ml), dried over CaCl2, filtered and evaporated to dryness. The resulting highly viscous product was distilled in vacuo (0.2 mbar). Condensation of the distillate into a Schlenk tube cooled with liquid nitrogen yielded crystalline material suitable for X-ray diffraction (Combined yield of all fractions: 32.5 g, 91%).

Refinement top

Hydrogen atoms have been calculated into idealized positions with C–H = 0.98 - 0.99 Å . Methylene and methyl hydrogen atoms were refined with Uiso = 1.2 Ueq(C) and 1.5 Ueq(C) respectively.

Structure description top

The title compound is an intermediate in the synthesis of 2,2-dimethoxy-1-(pyridin-2-yl)ethanone and has been synthesized from 1-(piperidin-1-yl)butane-1,3-dione (Schwierz et al., 2014) following a modified procedure (Schank, 1967). As it is expected the piperidine ring shows a chair conformation and the amide substructure is planar (Figure 1). The dihedral angle O1—C6—C8—O2 between the carbonyl groups measures to 183.6 (4)°. The C—O bond of the amide carbonyl group is slightly elongated with respect to the other carbonyl group due to delocalization of the nitrogen lone pair (C6—O1 1.221 (3) Å versus. C8—O2 1.205 (3) Å). In the crystal structure, molecules are linked to infinite layers along the ab plane by a bifurcated hydrogen bond between one of the carbonyl oxygen atoms (O1) towards the methyl group and one of the methylene groups next to nitrogen and an additional hydrogen bond of the C—H···Cl type (Desiraju & Steiner, 1999). In addition, these layers are connected to a 3D supramolecular arrangement by oxygen chlorine contacts (Lommerse et al., 1996).

For the synthetic procedure, see: Schank (1967). For a survey concerning weak hydrogen bonds, see: Desiraju & Steiner (1999). For a description of the nature of intermolecular interactions between chlorine and oxygen, see: Lommerse et al. (1996). For the X-ray structure of the starting compound, see: Schwierz et al. (2014).

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. : Molecular structure of the title compound with thermal ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. : Crystal structure of the title compound showing a 3D supramolecular network built up by C–H···O and C–H···Cl hydrogen bonds and chlorine oxygen contacts. Hydrogen atoms at piperidine residues that are not involved in hydrogen bonding are omitted for the sake of clarity.
2,2-Dichloro-1-(piperidin-1-yl)butane-1,3-dione top
Crystal data top
C9H13Cl2NO2Z = 2
Mr = 238.10F(000) = 248
Monoclinic, P21Dx = 1.493 Mg m3
Hall symbol: P 2ybMo Kα radiation, λ = 0.71073 Å
a = 5.9548 (3) ŵ = 0.59 mm1
b = 10.5510 (4) ÅT = 133 K
c = 8.5747 (3) ÅPrism, colourless
β = 100.568 (2)°0.07 × 0.05 × 0.02 mm
V = 529.60 (4) Å3
Data collection top
Nonius KappaCCD
diffractometer
2402 independent reflections
Radiation source: fine-focus sealed tube2085 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
phi– + ω–scanθmax = 27.5°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
h = 57
Tmin = 0.616, Tmax = 0.746k = 1313
3076 measured reflectionsl = 1111
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.024All H-atom parameters refined
wR(F2) = 0.059 w = 1/[σ2(Fo2) + (0.0215P)2 + 0.1164P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
2402 reflectionsΔρmax = 0.33 e Å3
128 parametersΔρmin = 0.21 e Å3
1 restraintAbsolute structure: Flack (1983), 1115 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.08 (4)
Crystal data top
C9H13Cl2NO2V = 529.60 (4) Å3
Mr = 238.10Z = 2
Monoclinic, P21Mo Kα radiation
a = 5.9548 (3) ŵ = 0.59 mm1
b = 10.5510 (4) ÅT = 133 K
c = 8.5747 (3) Å0.07 × 0.05 × 0.02 mm
β = 100.568 (2)°
Data collection top
Nonius KappaCCD
diffractometer
2402 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
2085 reflections with I > 2σ(I)
Tmin = 0.616, Tmax = 0.746Rint = 0.030
3076 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.024All H-atom parameters refined
wR(F2) = 0.059Δρmax = 0.33 e Å3
S = 1.09Δρmin = 0.21 e Å3
2402 reflectionsAbsolute structure: Flack (1983), 1115 Friedel pairs
128 parametersAbsolute structure parameter: 0.08 (4)
1 restraint
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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
xyzUiso*/Ueq
Cl11.44673 (6)0.94886 (3)0.75108 (4)0.01711 (9)
Cl20.97291 (6)1.00243 (3)0.62597 (4)0.01824 (9)
O10.9936 (2)1.00543 (12)0.95581 (13)0.0203 (2)
O21.2365 (2)0.72093 (11)0.60201 (14)0.0228 (3)
N11.2241 (2)0.83853 (12)1.03862 (15)0.0149 (3)
C11.3935 (3)0.73987 (14)1.02007 (18)0.0156 (3)
H1A1.40370.73140.90660.019*
H1B1.34400.65741.05720.019*
C21.6274 (3)0.77486 (15)1.11579 (19)0.0183 (3)
H2A1.68570.85111.06890.022*
H2B1.73580.70461.11010.022*
C31.6153 (3)0.80114 (17)1.28938 (19)0.0211 (3)
H3A1.57870.72171.34090.025*
H3B1.76560.83161.34580.025*
C41.4336 (3)0.90029 (16)1.30135 (19)0.0208 (3)
H4A1.47840.98241.26030.025*
H4B1.42030.91201.41390.025*
C51.2036 (3)0.85828 (15)1.20554 (18)0.0183 (3)
H5A1.15460.77851.25010.022*
H5B1.08670.92381.21200.022*
C61.1183 (3)0.91946 (13)0.92819 (18)0.0140 (3)
C71.1618 (3)0.90173 (14)0.75549 (18)0.0145 (3)
C81.1108 (3)0.76732 (14)0.68101 (18)0.0160 (3)
C90.8979 (3)0.70565 (15)0.7144 (2)0.0202 (3)
H9D0.84090.64480.63000.030*
H9C0.78140.77050.71870.030*
H9B0.93210.66130.81640.030*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01400 (17)0.01793 (17)0.02027 (18)0.00249 (13)0.00546 (13)0.00093 (14)
Cl20.01831 (18)0.01753 (16)0.01794 (17)0.00204 (14)0.00086 (13)0.00373 (14)
O10.0207 (6)0.0196 (5)0.0218 (5)0.0062 (5)0.0069 (5)0.0008 (5)
O20.0234 (6)0.0232 (6)0.0229 (6)0.0011 (5)0.0071 (5)0.0076 (5)
N10.0130 (6)0.0157 (6)0.0162 (6)0.0009 (5)0.0030 (5)0.0001 (5)
C10.0147 (7)0.0140 (7)0.0177 (8)0.0028 (6)0.0020 (6)0.0007 (5)
C20.0133 (7)0.0199 (7)0.0212 (8)0.0014 (6)0.0019 (6)0.0002 (6)
C30.0184 (8)0.0259 (8)0.0178 (8)0.0008 (6)0.0001 (6)0.0001 (6)
C40.0226 (9)0.0232 (8)0.0171 (7)0.0012 (7)0.0050 (6)0.0035 (6)
C50.0179 (8)0.0221 (8)0.0160 (7)0.0006 (6)0.0062 (6)0.0011 (6)
C60.0101 (7)0.0151 (7)0.0169 (7)0.0040 (5)0.0026 (6)0.0014 (5)
C70.0115 (7)0.0153 (7)0.0172 (7)0.0009 (6)0.0041 (6)0.0009 (6)
C80.0169 (8)0.0148 (7)0.0152 (7)0.0004 (6)0.0001 (6)0.0008 (6)
C90.0187 (8)0.0177 (7)0.0246 (8)0.0040 (7)0.0047 (7)0.0016 (6)
Geometric parameters (Å, º) top
Cl1—C71.7752 (16)C3—H3A0.9900
Cl2—C71.7802 (15)C3—H3B0.9900
O1—C61.2226 (19)C4—C51.528 (2)
O2—C81.202 (2)C4—H4A0.9900
N1—C61.3431 (19)C4—H4B0.9900
N1—C51.4734 (19)C5—H5A0.9900
N1—C11.4782 (19)C5—H5B0.9900
C1—C21.527 (2)C6—C71.561 (2)
C1—H1A0.9900C7—C81.562 (2)
C1—H1B0.9900C8—C91.499 (2)
C2—C31.529 (2)C9—H9D0.9800
C2—H2A0.9900C9—H9C0.9800
C2—H2B0.9900C9—H9B0.9800
C3—C41.522 (2)
C6—N1—C5118.90 (12)H4A—C4—H4B108.2
C6—N1—C1127.81 (13)N1—C5—C4109.73 (13)
C5—N1—C1112.57 (12)N1—C5—H5A109.7
N1—C1—C2110.19 (12)C4—C5—H5A109.7
N1—C1—H1A109.6N1—C5—H5B109.7
C2—C1—H1A109.6C4—C5—H5B109.7
N1—C1—H1B109.6H5A—C5—H5B108.2
C2—C1—H1B109.6O1—C6—N1123.93 (14)
H1A—C1—H1B108.1O1—C6—C7119.03 (13)
C1—C2—C3111.45 (13)N1—C6—C7117.04 (12)
C1—C2—H2A109.3C6—C7—C8116.30 (12)
C3—C2—H2A109.3C6—C7—Cl1108.20 (10)
C1—C2—H2B109.3C8—C7—Cl1111.13 (11)
C3—C2—H2B109.3C6—C7—Cl2108.94 (10)
H2A—C2—H2B108.0C8—C7—Cl2103.51 (10)
C4—C3—C2110.58 (13)Cl1—C7—Cl2108.45 (8)
C4—C3—H3A109.5O2—C8—C9124.54 (14)
C2—C3—H3A109.5O2—C8—C7120.38 (14)
C4—C3—H3B109.5C9—C8—C7115.07 (13)
C2—C3—H3B109.5C8—C9—H9D109.5
H3A—C3—H3B108.1C8—C9—H9C109.5
C3—C4—C5110.03 (14)H9D—C9—H9C109.5
C3—C4—H4A109.7C8—C9—H9B109.5
C5—C4—H4A109.7H9D—C9—H9B109.5
C3—C4—H4B109.7H9C—C9—H9B109.5
C5—C4—H4B109.7
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.992.563.413 (2)145
C9—H9C···O1i0.982.533.494 (2)168
C9—H9C···Cl1ii0.982.793.770 (2)176
Symmetry codes: (i) x+2, y1/2, z+2; (ii) x1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.992.5583.413 (2)145
C9—H9C···O1i0.982.5293.494 (2)168
C9—H9C···Cl1ii0.982.793.770 (2)176
Symmetry codes: (i) x+2, y1/2, z+2; (ii) x1, y, z.
 

Acknowledgements

MS gratefully acknowledges a PhD grant from the Deutsche Bundesstiftung Umwelt.

References

First citationBruker (2002). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationDesiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond. Oxford University Press.  Google Scholar
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