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

Abstract

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].

Related literature  

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  

Crystal data  

• C₉H₁₃Cl₂NO₂

• M _r = 238.10

• Monoclinic,

• a = 5.9548 (3) Å

• b = 10.5510 (4) Å

• c = 8.5747 (3) Å

• β = 100.568 (2)°

• V = 529.60 (4) ų

• Z = 2

• Mo Kα radiation

• μ = 0.59 mm⁻¹

• T = 133 K

• 0.07 × 0.05 × 0.02 mm

Data collection  

• Nonius KappaCCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2002 ▸) T _min = 0.616, T _max = 0.746

• 3076 measured reflections

• 2402 independent reflections

• 2085 reflections with I > 2σ(I)

• R _int = 0.030

Refinement  

• R[F ² > 2σ(F ²)] = 0.024

• wR(F ²) = 0.059

• S = 1.09

• 2402 reflections

• 128 parameters

• 1 restraint

• All H-atom parameters refined

• Δρ_max = 0.33 e Å⁻³

• Δρ_min = −0.21 e Å⁻³

• Absolute structure: Flack (1983 ▸), 1115 Friedel pairs

• Absolute structure parameter: 0.08 (4)

Data collection: COLLECT (Nonius, 1998 ▸); cell refinement: DENZO (Otwinowski & Minor, 1997 ▸); data reduction: DENZO; 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.

Supplementary Material

CCDC reference: 1036594

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C1H1AO1i	0.99	2.56	3.413(2)	145
C9H9CO1i	0.98	2.53	3.494(2)	168
C9H9CCl1ii	0.98	2.79	3.770(2)	176

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

S1. Comment

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).

S2. Experimental

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%).

S3. Refinement

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

Figures

Fig. 1.

: Molecular structure of the title compound with thermal ellipsoids drawn at the 50% probability level.

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.

Crystal data

C9H13Cl2NO2	Z = 2
Mr = 238.10	F(000) = 248
Monoclinic, P21	Dx = 1.493 Mg m−3
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 5.9548 (3) Å	µ = 0.59 mm−1
b = 10.5510 (4) Å	T = 133 K
c = 8.5747 (3) Å	Prism, colourless
β = 100.568 (2)°	0.07 × 0.05 × 0.02 mm
V = 529.60 (4) Å3

Data collection

Nonius KappaCCD diffractometer	2402 independent reflections
Radiation source: fine-focus sealed tube	2085 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
phi– + ω–scan	θmax = 27.5°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2002)	h = −5→7
Tmin = 0.616, Tmax = 0.746	k = −13→13
3076 measured reflections	l = −11→11

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.024	All 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 reflections	Δρmax = 0.33 e Å−3
128 parameters	Δρmin = −0.21 e Å−3
1 restraint	Absolute structure: Flack (1983), 1115 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.08 (4)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	1.44673 (6)	0.94886 (3)	0.75108 (4)	0.01711 (9)
Cl2	0.97291 (6)	1.00243 (3)	0.62597 (4)	0.01824 (9)
O1	0.9936 (2)	1.00543 (12)	0.95581 (13)	0.0203 (2)
O2	1.2365 (2)	0.72093 (11)	0.60201 (14)	0.0228 (3)
N1	1.2241 (2)	0.83853 (12)	1.03862 (15)	0.0149 (3)
C1	1.3935 (3)	0.73987 (14)	1.02007 (18)	0.0156 (3)
H1A	1.4037	0.7314	0.9066	0.019*
H1B	1.3440	0.6574	1.0572	0.019*
C2	1.6274 (3)	0.77486 (15)	1.11579 (19)	0.0183 (3)
H2A	1.6857	0.8511	1.0689	0.022*
H2B	1.7358	0.7046	1.1101	0.022*
C3	1.6153 (3)	0.80114 (17)	1.28938 (19)	0.0211 (3)
H3A	1.5787	0.7217	1.3409	0.025*
H3B	1.7656	0.8316	1.3458	0.025*
C4	1.4336 (3)	0.90029 (16)	1.30135 (19)	0.0208 (3)
H4A	1.4784	0.9824	1.2603	0.025*
H4B	1.4203	0.9120	1.4139	0.025*
C5	1.2036 (3)	0.85828 (15)	1.20554 (18)	0.0183 (3)
H5A	1.1546	0.7785	1.2501	0.022*
H5B	1.0867	0.9238	1.2120	0.022*
C6	1.1183 (3)	0.91946 (13)	0.92819 (18)	0.0140 (3)
C7	1.1618 (3)	0.90173 (14)	0.75549 (18)	0.0145 (3)
C8	1.1108 (3)	0.76732 (14)	0.68101 (18)	0.0160 (3)
C9	0.8979 (3)	0.70565 (15)	0.7144 (2)	0.0202 (3)
H9D	0.8409	0.6448	0.6300	0.030*
H9C	0.7814	0.7705	0.7187	0.030*
H9B	0.9321	0.6613	0.8164	0.030*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.01400 (17)	0.01793 (17)	0.02027 (18)	−0.00249 (13)	0.00546 (13)	−0.00093 (14)
Cl2	0.01831 (18)	0.01753 (16)	0.01794 (17)	0.00204 (14)	0.00086 (13)	0.00373 (14)
O1	0.0207 (6)	0.0196 (5)	0.0218 (5)	0.0062 (5)	0.0069 (5)	−0.0008 (5)
O2	0.0234 (6)	0.0232 (6)	0.0229 (6)	−0.0011 (5)	0.0071 (5)	−0.0076 (5)
N1	0.0130 (6)	0.0157 (6)	0.0162 (6)	0.0009 (5)	0.0030 (5)	0.0001 (5)
C1	0.0147 (7)	0.0140 (7)	0.0177 (8)	0.0028 (6)	0.0020 (6)	−0.0007 (5)
C2	0.0133 (7)	0.0199 (7)	0.0212 (8)	0.0014 (6)	0.0019 (6)	0.0002 (6)
C3	0.0184 (8)	0.0259 (8)	0.0178 (8)	−0.0008 (6)	−0.0001 (6)	0.0001 (6)
C4	0.0226 (9)	0.0232 (8)	0.0171 (7)	−0.0012 (7)	0.0050 (6)	−0.0035 (6)
C5	0.0179 (8)	0.0221 (8)	0.0160 (7)	0.0006 (6)	0.0062 (6)	0.0011 (6)
C6	0.0101 (7)	0.0151 (7)	0.0169 (7)	−0.0040 (5)	0.0026 (6)	−0.0014 (5)
C7	0.0115 (7)	0.0153 (7)	0.0172 (7)	−0.0009 (6)	0.0041 (6)	0.0009 (6)
C8	0.0169 (8)	0.0148 (7)	0.0152 (7)	0.0004 (6)	0.0001 (6)	0.0008 (6)
C9	0.0187 (8)	0.0177 (7)	0.0246 (8)	−0.0040 (7)	0.0047 (7)	−0.0016 (6)

Geometric parameters (Å, º)

Cl1—C7	1.7752 (16)	C3—H3A	0.9900
Cl2—C7	1.7802 (15)	C3—H3B	0.9900
O1—C6	1.2226 (19)	C4—C5	1.528 (2)
O2—C8	1.202 (2)	C4—H4A	0.9900
N1—C6	1.3431 (19)	C4—H4B	0.9900
N1—C5	1.4734 (19)	C5—H5A	0.9900
N1—C1	1.4782 (19)	C5—H5B	0.9900
C1—C2	1.527 (2)	C6—C7	1.561 (2)
C1—H1A	0.9900	C7—C8	1.562 (2)
C1—H1B	0.9900	C8—C9	1.499 (2)
C2—C3	1.529 (2)	C9—H9D	0.9800
C2—H2A	0.9900	C9—H9C	0.9800
C2—H2B	0.9900	C9—H9B	0.9800
C3—C4	1.522 (2)
C6—N1—C5	118.90 (12)	H4A—C4—H4B	108.2
C6—N1—C1	127.81 (13)	N1—C5—C4	109.73 (13)
C5—N1—C1	112.57 (12)	N1—C5—H5A	109.7
N1—C1—C2	110.19 (12)	C4—C5—H5A	109.7
N1—C1—H1A	109.6	N1—C5—H5B	109.7
C2—C1—H1A	109.6	C4—C5—H5B	109.7
N1—C1—H1B	109.6	H5A—C5—H5B	108.2
C2—C1—H1B	109.6	O1—C6—N1	123.93 (14)
H1A—C1—H1B	108.1	O1—C6—C7	119.03 (13)
C1—C2—C3	111.45 (13)	N1—C6—C7	117.04 (12)
C1—C2—H2A	109.3	C6—C7—C8	116.30 (12)
C3—C2—H2A	109.3	C6—C7—Cl1	108.20 (10)
C1—C2—H2B	109.3	C8—C7—Cl1	111.13 (11)
C3—C2—H2B	109.3	C6—C7—Cl2	108.94 (10)
H2A—C2—H2B	108.0	C8—C7—Cl2	103.51 (10)
C4—C3—C2	110.58 (13)	Cl1—C7—Cl2	108.45 (8)
C4—C3—H3A	109.5	O2—C8—C9	124.54 (14)
C2—C3—H3A	109.5	O2—C8—C7	120.38 (14)
C4—C3—H3B	109.5	C9—C8—C7	115.07 (13)
C2—C3—H3B	109.5	C8—C9—H9D	109.5
H3A—C3—H3B	108.1	C8—C9—H9C	109.5
C3—C4—C5	110.03 (14)	H9D—C9—H9C	109.5
C3—C4—H4A	109.7	C8—C9—H9B	109.5
C5—C4—H4A	109.7	H9D—C9—H9B	109.5
C3—C4—H4B	109.7	H9C—C9—H9B	109.5
C5—C4—H4B	109.7

Hydrogen-bond geometry (Å, º)

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