3-Oxapentane-1,5-diyl dicarbamate

Li, Z.

doi:10.1107/S1600536812011981

organic compounds

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Volume 68| Part 4| April 2012| Page o1171

doi:10.1107/S1600536812011981

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3-Oxapentane-1,5-diyl dicarbamate

Zhi Li ^a ^*

^aDepartment of Chemistry, School of Science, Beijing Jiaotong University, Beijing 100044, People's Republic of China
^*Correspondence e-mail: zhili@bjtu.edu.cn

(Received 19 March 2012; accepted 20 March 2012; online 24 March 2012)

The complete molecule of the title compound, C₆H₁₂N₂O₅, is generated by a rotation about a twofold axis. The conformation along the bond sequence linking the two amino groups is trans-trans-(+)gauche-trans-trans. In the crystal, N—H⋯O hydrogen bonds link the molecules into a three-dimensional supramolecular architecture.

Related literature

For self-assembled mono-layers of alkyl carbamate and alkyl dicarbamate, see: Kim et al. (2003 , 2005a ,b ). For the synthesis of the title compound, see: Sidney et al. (1965 ); Takeuchi & Ninagawa (1971 ); Takeuchi (1974 ). For a closely related structure and background references, see: Xia et al. (2010 , 2011 ).

Experimental

Crystal data

C₆H₁₂N₂O₅
M_r = 192.18
Monoclinic, C 2/c
a = 14.263 (4) Å
b = 5.1412 (15) Å
c = 12.276 (4) Å
β = 99.393 (5)°
V = 888.1 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 294 K
0.30 × 0.20 × 0.14 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.960, T_max = 0.983
2358 measured reflections
904 independent reflections
748 reflections with I > 2σ(I)
R_int = 0.019

Refinement

R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.084
S = 1.06
904 reflections
69 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.14 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.872 (18)	2.046 (18)	2.9086 (17)	169.9 (14)
N1—H1B⋯O2ⁱⁱ	0.852 (17)	2.381 (17)	3.1763 (17)	155.6 (14)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (ii) -x+1, -y+1, -z+1.

Data collection: SMART (Bruker, 2007 ); cell refinement: SAINT (Bruker, 2007); 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 global, I. DOI: 10.1107/S1600536812011981/tk5072sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812011981/tk5072Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812011981/tk5072Isup3.cml

checkCIF report

Comment top

Recently, self-assembled mono-layers of alkyl carbamates and alkyl dicarbamates have been investigated and characterized (Kim et al., 2003, 2005a, 2005b). Further, ligands with two amino moieties demonstrate versatile bonding modes to metal ions and readily form coordination polymers or supramolecular compounds (Xia et al., 2010, 2011). For example, 3,3'-(oxybis(ethane-2,1-diyloxycarbonylimino))dipyridinium functions as a ligand as seen in its copper(II) and zinc(II) complexes (Xia et al., 2011). To further investigate this family of ligands and the self-assembled activity of the dicarbamate linked by an ether chain, the title compound, (I), was synthesized and its structure was confirmed by X-ray diffraction.

The title compound contains one half-molecule as it is disposed about a crystallographic twofold axis with the O3 atom lying on the axis (Fig. 1). The conformation along the bond sequence linking the two amino groups is trans-trans-(+)gauche-trans-trans. The relevant torsion angle are: N1–C1–O2–C2, -178.66 (11)°; C1–O2–C2–C3, -177.18 (10)°; O2–C2–C3–O3, 68.67 (13)°; C2–C3–O3–C3, 170.41 (12)°; C3ⁱ–O3–C3–C2, 170.41 (12)°, symmetry code (i): 1-x, y, 1/2-z]. In the crystal packing, pairs of intermolecular N–H···O hydrogen bonds link the molecules into a three-dimensional supramolecular architecture (Fig. 2 and Table 1).

Related literature top

For self-assembled mono-layers of alkyl carbamate and alkyl dicarbamate, see: Kim et al. (2003, 2005a,b). For the synthesis of the title compound, see: Sidney et al. (1965); Takeuchi & Ninagawa (1971); Takeuchi (1974). For a closely related structure and background references, see: Xia et al. (2010, 2011).

Experimental top

The title compound was synthesized by transesterification of ethyl carbamate with 2,2'-oxydiethanol (Sidney et al., 1965; Takeuchi & Ninagawa 1971; Takeuchi 1974) as follows. A solution of ethyl carbamate (8.9 g, 100 mmol) and 2,2'-oxydiethanol (1.0 g, 10 mmol) in toluene (30 ml) was heated to reflux in the presence of a catalytic amount of ZnCl₂ for 8 h. After cooling to room temperature, the solvent was evaporated under vacuum. The residue was subjected to flash chromatography and the title compound was obtained as colourless crystals (0.97 g; Yield: 50%; M.pt: 428–429 K). Crystals were grown by slow evaporation from its DMF solution.

Structure description top

For self-assembled mono-layers of alkyl carbamate and alkyl dicarbamate, see: Kim et al. (2003, 2005a,b). For the synthesis of the title compound, see: Sidney et al. (1965); Takeuchi & Ninagawa (1971); Takeuchi (1974). For a closely related structure and background references, see: Xia et al. (2010, 2011).

Computing details top

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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, with displacement ellipsoids at the 30% probability level. The molecule has crystallographic twofold symmetry. Unlabelled atoms are related by the symmetry operation 1-x, y, 1/2-z.
	Fig. 2. Crystal packing in the title compound where molecules are linked via N–H···O hydrogen bonds (dashed lines). Except for those involved in hydrogen-bonding interactions, H atoms have been omitted for clarity.

3-Oxapentane-1,5-diyl dicarbamate top

Crystal data top

C₆H₁₂N₂O₅	F(000) = 408
M_r = 192.18	D_x = 1.437 Mg m⁻³
Monoclinic, C2/c	Melting point: 428 K
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 14.263 (4) Å	Cell parameters from 1304 reflections
b = 5.1412 (15) Å	θ = 3.4–26.0°
c = 12.276 (4) Å	µ = 0.13 mm⁻¹
β = 99.393 (5)°	T = 294 K
V = 888.1 (5) Å³	Plate, colourless
Z = 4	0.30 × 0.20 × 0.14 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	904 independent reflections
Radiation source: fine-focus sealed tube	748 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.019
φ and ω scans	θ_max = 26.3°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −16→17
T_min = 0.960, T_max = 0.983	k = −6→6
2358 measured reflections	l = −8→15

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)] = 0.031	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.084	w = 1/[σ²(F_o²) + (0.0407P)² + 0.3363P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max < 0.001
904 reflections	Δρ_max = 0.16 e Å⁻³
69 parameters	Δρ_min = −0.14 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.029 (3)

Crystal data top

C₆H₁₂N₂O₅	V = 888.1 (5) Å³
M_r = 192.18	Z = 4
Monoclinic, C2/c	Mo Kα radiation
a = 14.263 (4) Å	µ = 0.13 mm⁻¹
b = 5.1412 (15) Å	T = 294 K
c = 12.276 (4) Å	0.30 × 0.20 × 0.14 mm
β = 99.393 (5)°

Data collection top

Bruker SMART CCD area-detector diffractometer	904 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	748 reflections with I > 2σ(I)
T_min = 0.960, T_max = 0.983	R_int = 0.019
2358 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.031	0 restraints
wR(F²) = 0.084	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	Δρ_max = 0.16 e Å⁻³
904 reflections	Δρ_min = −0.14 e Å⁻³
69 parameters

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

	x	y	z	U_iso*/U_eq
O1	0.25476 (6)	0.5124 (2)	0.40946 (8)	0.0461 (3)
O2	0.39925 (5)	0.69845 (18)	0.42131 (7)	0.0374 (3)
O3	0.5000	0.8767 (2)	0.2500	0.0358 (3)
N1	0.37706 (8)	0.3841 (3)	0.53985 (10)	0.0451 (3)
H1A	0.3429 (12)	0.260 (3)	0.5619 (13)	0.054 (4)*
H1B	0.4360 (12)	0.398 (3)	0.5657 (13)	0.051 (4)*
C1	0.33731 (8)	0.5279 (2)	0.45456 (10)	0.0333 (3)
C2	0.35837 (8)	0.8634 (3)	0.33006 (11)	0.0392 (3)
H2A	0.3086	0.9708	0.3518	0.047*
H2B	0.3306	0.7572	0.2678	0.047*
C3	0.43501 (9)	1.0321 (3)	0.29804 (11)	0.0379 (3)
H3A	0.4071	1.1628	0.2455	0.045*
H3B	0.4683	1.1206	0.3628	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0300 (5)	0.0575 (6)	0.0477 (6)	−0.0091 (4)	−0.0029 (4)	0.0107 (5)
O2	0.0266 (4)	0.0479 (5)	0.0365 (5)	−0.0039 (4)	0.0020 (4)	0.0091 (4)
O3	0.0363 (6)	0.0328 (6)	0.0403 (7)	0.000	0.0128 (5)	0.000
N1	0.0301 (6)	0.0570 (8)	0.0464 (7)	−0.0046 (5)	0.0007 (5)	0.0168 (6)
C1	0.0277 (6)	0.0402 (7)	0.0321 (6)	−0.0025 (5)	0.0055 (5)	−0.0009 (5)
C2	0.0309 (6)	0.0480 (8)	0.0386 (7)	0.0031 (5)	0.0050 (5)	0.0089 (6)
C3	0.0376 (7)	0.0365 (7)	0.0414 (7)	0.0034 (5)	0.0119 (6)	0.0027 (5)

Geometric parameters (Å, º) top

O1—C1	1.2191 (15)	N1—H1B	0.852 (17)
O2—C1	1.3543 (15)	C2—C3	1.4973 (18)
O2—C2	1.4494 (15)	C2—H2A	0.9700
O3—C3	1.4228 (14)	C2—H2B	0.9700
O3—C3ⁱ	1.4228 (14)	C3—H3A	0.9700
N1—C1	1.3305 (17)	C3—H3B	0.9700
N1—H1A	0.872 (18)

C1—O2—C2	114.33 (9)	C3—C2—H2A	109.9
C3—O3—C3ⁱ	111.63 (13)	O2—C2—H2B	109.9
C1—N1—H1A	117.6 (10)	C3—C2—H2B	109.9
C1—N1—H1B	121.0 (11)	H2A—C2—H2B	108.3
H1A—N1—H1B	120.9 (15)	O3—C3—C2	109.65 (11)
O1—C1—N1	125.25 (12)	O3—C3—H3A	109.7
O1—C1—O2	122.31 (11)	C2—C3—H3A	109.7
N1—C1—O2	112.44 (11)	O3—C3—H3B	109.7
O2—C2—C3	108.85 (10)	C2—C3—H3B	109.7
O2—C2—H2A	109.9	H3A—C3—H3B	108.2

C2—O2—C1—O1	1.42 (17)	C3ⁱ—O3—C3—C2	170.41 (12)
C2—O2—C1—N1	−178.66 (11)	O2—C2—C3—O3	68.67 (13)
C1—O2—C2—C3	−177.18 (10)

Symmetry code: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱⁱ	0.872 (18)	2.046 (18)	2.9086 (17)	169.9 (14)
N1—H1B···O2ⁱⁱⁱ	0.852 (17)	2.381 (17)	3.1763 (17)	155.6 (14)

Symmetry codes: (ii) −x+1/2, −y+1/2, −z+1; (iii) −x+1, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₆H₁₂N₂O₅
M_r	192.18
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	294
a, b, c (Å)	14.263 (4), 5.1412 (15), 12.276 (4)
β (°)	99.393 (5)
V (Å³)	888.1 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.30 × 0.20 × 0.14

Data collection
Diffractometer	Bruker SMART CCD area-detector
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.960, 0.983
No. of measured, independent and observed [I > 2σ(I)] reflections	2358, 904, 748
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.624

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.031, 0.084, 1.06
No. of reflections	904
No. of parameters	69
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.14

Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), 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
N1—H1A···O1ⁱ	0.872 (18)	2.046 (18)	2.9086 (17)	169.9 (14)
N1—H1B···O2ⁱⁱ	0.852 (17)	2.381 (17)	3.1763 (17)	155.6 (14)

Symmetry codes: (i) −x+1/2, −y+1/2, −z+1; (ii) −x+1, −y+1, −z+1.

Acknowledgements

The author thanks Beijing Jiaotong University for financial support. This research was also supported by the Fundamental Research Funds for the Central Universities (2011JBM295).

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