2-Diazo-1-(1,1-dioxothio­morpholin-4-yl)ethanone

Kaupang, Å.; Görbitz, C.H.; Hansen, T.

doi:10.1107/S1600536811023774

organic compounds

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ISSN: 2056-9890

Volume 67| Part 7| July 2011| Pages o1844-o1845

doi:10.1107/S1600536811023774

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2-Diazo-1-(1,1-dioxothiomorpholin-4-yl)ethanone

Åsmund Kaupang,^a Carl Henrik Görbitz ^a ^* and Tore Hansen ^a

^aDepartment of Chemistry, University of Oslo, PO Box 1033 Blindern, N-0315 Oslo, Norway
^*Correspondence e-mail: c.h.gorbitz@kjemi.uio.no

(Received 7 June 2011; accepted 17 June 2011; online 30 June 2011)

In the molecule of the title compound, C₆H₉N₃O₃S, at 105 K, the six-membered ring is predominantly found in the chair conformation, with 1.89 (14)% in the boat conformation. In the crystal structure, there are five intermolecular C—H⋯O=C and C—H⋯O=S contacts less than 2.6 Å, as well as a weak C—H⋯N=N interaction to the diazo group.

Related literature

For related structures found in the Cambridge Structural Database (Version 5.32 of November 2010; Allen, 2002 ), see: Fenlon et al. (2007 ); Haynes et al. (2006 ); Wang et al. (2006 ); Miller et al. (1991 ); Foces-Foces et al. (1988 ); Ganguly et al. (1980 ); Herdklotz & Sass (1969 ). For details of the synthesis, see: Kaupang (2010 ); Toma et al. (2007 ) and for the synthesis of related diazoacetamides, see: Kaupang et al. (2010 ); Kaupang (2010); Ouihia et al. (1993 ). For quantum chemical calculations involving the acetamide analogue of the title compound, see: Fraenkel et al. (1992 ). For the Chemical Abstracts Service, see: American Chemical Society (2008 ). For hydrogen-bond graph-set notation, see: Etter et al. (1990 ).

Experimental

Crystal data

C₆H₉N₃O₃S
M_r = 203.22
Monoclinic, P 2₁ /n
a = 5.2729 (3) Å
b = 20.1349 (11) Å
c = 7.8683 (4) Å
β = 95.171 (2)°
V = 831.97 (8) Å³
Z = 4
Mo Kα radiation
μ = 0.37 mm⁻¹
T = 105 K
0.80 × 0.30 × 0.20 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2007 ) T_min = 0.849, T_max = 0.929
14742 measured reflections
3951 independent reflections
3029 reflections with I > 2σ(I)
R_int = 0.031

Refinement

R[F² > 2σ(F²)] = 0.056
wR(F²) = 0.165
S = 1.11
3951 reflections
138 parameters
13 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 1.24 e Å⁻³
Δρ_min = −0.71 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯O2ⁱ	0.94 (2)	2.42 (2)	3.326 (2)	163 (2)
C3—H32⋯O1ⁱⁱ	0.99	2.47	3.372 (2)	152
C5—H52⋯O1ⁱⁱⁱ	0.99	2.36	3.022 (2)	123
C5—H51⋯O3^iv	0.99	2.56	3.445 (2)	149
C5—H52⋯N3^v	0.99	2.59	3.417 (3)	141
C6—H61⋯O2^vi	0.99	2.45	3.168 (2)	129
Symmetry codes: (i) x, y, z-1; (ii) x-1, y, z; (iii) -x+1, -y, -z+1; (iv) x+1, y, z; (v) x-1, y, z+1; (vi) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811023774/si2361sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811023774/si2361Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811023774/si2361Isup3.cml

checkCIF report

Comment top

2-Diazo-1-(1,1-dioxido-4-thiomorpholinyl)ethanone (I) was prepared as part of a series of diazoacetamides used in the intramolecular C—H insertion reactions taking place upon thermolysis of their corresponding α-bromodiazoacetamides (Kaupang, 2010). The title compound was synthesized from 2-bromo-1-(1,1-dioxido-4-thiomorpholinyl)ethanone following a procedure reported by Toma et al. (2007), modified to employ 1,1,3,3-tetramethylguanidine as the base instead of 1,8-diazabicyclo[5.4.0]undec-7-ene. No previous reports of this compound were found in the Chemical Abstracts Service (CAS, American Chemical Society, 2008).

In the crystal (I) occurs in the expected chair conformation, with a very minor fraction [occupancy 0.0189 (14)] in a boat conformation as shown in Fig. 1. The unit cell and crystal packing are depicted in Fig. 2, while a list of six C—H···O/N interactions with H···O distance shorter than 2.60 Å are given in Table 1. The two shortest interactions, with C2—H2 and C5—H52 donors, form C(8) chains along the a axis and dimeric R₂²(12) ring motifs, respectively (Etter et al., 1990). H52 is also close to the diazo N3 atom and thus participates in a three-center interaction. The interactions of (I) are different from those observed in our previous, related structure of tert-butyl 4-(2-diazoacetyl)piperazine-1-carboxylate (Kaupang et al., 2010) where the H of the diazoacetyl group was accepted by the O atom of the same group.

Related literature top

For related structures found in the Cambridge Structural Database (Version 5.32 of November 2010; Allen, 2002), see: Fenlon et al. (2007); Haynes et al. (2006); Wang et al. (2006); Miller et al. (1991); Foces-Foces et al. (1988); Ganguly et al. (1980); Herdklotz & Sass (1969). For details of the synthesis, see: Kaupang (2010); Toma et al. (2007) and for the synthesis of related diazoacetamides, see: Kaupang et al. (2010); Kaupang (2010); Ouihia et al. (1993). For quantum chemical calculations involving the acetamide analogue of the title compound, see: Fraenkel et al. (1992). For the Chemical Abstracts Service, see: American Chemical Society (2008). For hydrogen-bond graph-set notation, see: Etter et al. (1990).

Experimental top

A solution of 4.0 mg of the title compound in 500 µL of CH₂Cl₂ was placed in a 2.5 ml vial which was capped and a pinhole (0.5 mm) made in the cap to allow for slow evaporation in darkness at ambient temperature. A single cluster of pale yellow needles appeared after approximately 48 h.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The asymmetric unit of (I) with atomic numbering indicated. Displacement ellipsoids are shown at the 50% probability level with H atoms as spheres of arbitrary size. The wireframe structure represents the minor boat conformation [occupancy 0.189 (14)].
	Fig. 2. The unit cell and crystal packing of (I) viewed approximately along the a axis. A three-dimensional network of weak intermolecular C=O···H, S=O···H and N=N···H contacts with O/N···H < 2.6 Å are shown as dotted lines.

2-Diazo-1-(1,1-dioxothiomorpholin-4-yl)ethanone top

Crystal data top

C₆H₉N₃O₃S	F(000) = 424
M_r = 203.22	D_x = 1.622 Mg m⁻³
Monoclinic, P2₁/n	Melting point = 438–449 K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 5.2729 (3) Å	Cell parameters from 5309 reflections
b = 20.1349 (11) Å	θ = 2.8–36.6°
c = 7.8683 (4) Å	µ = 0.37 mm⁻¹
β = 95.171 (2)°	T = 105 K
V = 831.97 (8) Å³	Needle, yellow
Z = 4	0.80 × 0.30 × 0.20 mm

Data collection top

Bruker APEXII CCD diffractometer	3951 independent reflections
Radiation source: fine-focus sealed tube	3029 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.031
Detector resolution: 8.3 pixels mm^-1	θ_max = 36.8°, θ_min = 2.0°
Sets of exposures each taken over 0.5° ω rotation scans	h = −8→8
Absorption correction: multi-scan (SADABS; Bruker, 2007)	k = −30→32
T_min = 0.849, T_max = 0.929	l = −11→13
14742 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.165	H atoms treated by a mixture of independent and constrained refinement
S = 1.11	w = 1/[σ²(F_o²) + (0.0728P)² + 1.0103P] where P = (F_o² + 2F_c²)/3
3951 reflections	(Δ/σ)_max < 0.001
138 parameters	Δρ_max = 1.24 e Å⁻³
13 restraints	Δρ_min = −0.71 e Å⁻³

Crystal data top

C₆H₉N₃O₃S	V = 831.97 (8) Å³
M_r = 203.22	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 5.2729 (3) Å	µ = 0.37 mm⁻¹
b = 20.1349 (11) Å	T = 105 K
c = 7.8683 (4) Å	0.80 × 0.30 × 0.20 mm
β = 95.171 (2)°

Data collection top

Bruker APEXII CCD diffractometer	3951 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2007)	3029 reflections with I > 2σ(I)
T_min = 0.849, T_max = 0.929	R_int = 0.031
14742 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	13 restraints
wR(F²) = 0.165	H atoms treated by a mixture of independent and constrained refinement
S = 1.11	Δρ_max = 1.24 e Å⁻³
3951 reflections	Δρ_min = −0.71 e Å⁻³
138 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 > 2σ(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	Occ. (<1)
S1	0.12602 (8)	0.17713 (2)	0.58307 (5)	0.01306 (11)	0.9811 (14)
O3	−0.1485 (2)	0.17127 (7)	0.56520 (19)	0.0176 (3)	0.9811 (14)
O2	0.2367 (3)	0.21336 (7)	0.73056 (18)	0.0194 (3)	0.9811 (14)
C5	0.2645 (3)	0.09728 (9)	0.5781 (2)	0.0152 (3)	0.9811 (14)
H51	0.4524	0.1012	0.5913	0.018*	0.9811 (14)
H52	0.2115	0.0703	0.6739	0.018*	0.9811 (14)
C6	0.2280 (3)	0.21174 (9)	0.3937 (2)	0.0156 (3)	0.9811 (14)
H61	0.1529	0.2565	0.3747	0.019*	0.9811 (14)
H62	0.4157	0.2163	0.4051	0.019*	0.9811 (14)
S11	0.385 (3)	0.1792 (3)	0.5843 (11)	0.013*	0.0189 (14)
O12	0.6562 (19)	0.1779 (9)	0.569 (4)	0.018*	0.0189 (14)
O13	0.302 (7)	0.2139 (3)	0.7308 (6)	0.0194 (3)	0.0189 (14)
C15	0.2645 (3)	0.09728 (9)	0.5781 (2)	0.0152 (3)	0.0189 (14)
H151	0.3969	0.0687	0.6379	0.018*	0.0189 (14)
H152	0.1168	0.0968	0.6474	0.018*	0.0189 (14)
C16	0.2280 (3)	0.21174 (9)	0.3937 (2)	0.0156 (3)	0.0189 (14)
H161	0.0734	0.2348	0.4255	0.019*	0.0189 (14)
H162	0.3408	0.2463	0.3519	0.019*	0.0189 (14)
O1	0.5857 (3)	0.02988 (7)	0.23496 (18)	0.0199 (3)
N1	0.2562 (3)	0.10078 (8)	0.26290 (19)	0.0153 (3)
C3	0.1799 (3)	0.06335 (9)	0.4088 (2)	0.0158 (3)
H31	0.2552	0.0183	0.4081	0.019*
H32	−0.0077	0.0585	0.3982	0.019*
C4	0.1452 (4)	0.16671 (9)	0.2410 (2)	0.0175 (3)
H41	−0.042 (3)	0.1625 (15)	0.232 (4)	0.021*
H42	0.197 (5)	0.1864 (13)	0.135 (3)	0.021*
C1	0.4582 (3)	0.07843 (9)	0.1828 (2)	0.0146 (3)
C2	0.5141 (4)	0.11299 (10)	0.0274 (2)	0.0173 (3)
H2	0.410 (5)	0.1428 (12)	−0.039 (3)	0.021*
N2	0.7103 (3)	0.08892 (9)	−0.0445 (2)	0.0200 (3)
N3	0.8809 (4)	0.06859 (12)	−0.1020 (2)	0.0294 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01136 (17)	0.01274 (19)	0.01499 (19)	0.00030 (13)	0.00065 (12)	−0.00052 (13)
O3	0.0102 (5)	0.0198 (6)	0.0230 (6)	0.0005 (4)	0.0021 (4)	0.0000 (5)
O2	0.0209 (6)	0.0185 (6)	0.0182 (6)	−0.0011 (5)	−0.0011 (5)	−0.0042 (5)
C5	0.0151 (7)	0.0143 (7)	0.0163 (7)	0.0017 (5)	0.0013 (5)	0.0016 (5)
C6	0.0160 (7)	0.0132 (7)	0.0175 (7)	0.0001 (5)	0.0010 (5)	0.0017 (5)
O13	0.0209 (6)	0.0185 (6)	0.0182 (6)	−0.0011 (5)	−0.0011 (5)	−0.0042 (5)
C15	0.0151 (7)	0.0143 (7)	0.0163 (7)	0.0017 (5)	0.0013 (5)	0.0016 (5)
C16	0.0160 (7)	0.0132 (7)	0.0175 (7)	0.0001 (5)	0.0010 (5)	0.0017 (5)
O1	0.0195 (6)	0.0180 (6)	0.0224 (6)	0.0039 (5)	0.0026 (5)	0.0040 (5)
N1	0.0182 (6)	0.0130 (6)	0.0151 (6)	0.0021 (5)	0.0032 (5)	0.0019 (5)
C3	0.0177 (7)	0.0132 (7)	0.0168 (7)	−0.0010 (5)	0.0036 (5)	0.0008 (5)
C4	0.0207 (8)	0.0146 (8)	0.0169 (7)	0.0038 (6)	0.0005 (6)	0.0013 (5)
C1	0.0151 (7)	0.0144 (7)	0.0140 (7)	−0.0013 (5)	−0.0003 (5)	−0.0004 (5)
C2	0.0186 (7)	0.0190 (8)	0.0143 (7)	−0.0008 (6)	0.0013 (5)	0.0007 (6)
N2	0.0199 (7)	0.0243 (8)	0.0160 (7)	−0.0043 (6)	0.0022 (5)	0.0005 (5)
N3	0.0240 (8)	0.0410 (11)	0.0245 (9)	0.0015 (8)	0.0087 (7)	0.0003 (7)

Geometric parameters (Å, º) top

S1—O3	1.4463 (13)	O1—C1	1.235 (2)
S1—O2	1.4482 (14)	N1—C1	1.362 (2)
S1—C5	1.7679 (18)	N1—C4	1.455 (2)
S1—C6	1.7718 (18)	N1—C3	1.460 (2)
C5—C3	1.528 (3)	C3—H31	0.9900
C5—H51	0.9900	C3—H32	0.9900
C5—H52	0.9900	C4—H41	0.984 (17)
C6—C4	1.537 (3)	C4—H42	0.983 (16)
C6—H61	0.9900	C1—C2	1.460 (2)
C6—H62	0.9900	C2—N2	1.316 (2)
S11—O12	1.446 (2)	C2—H2	0.940 (17)
S11—O13	1.448 (2)	N2—N3	1.120 (2)

O3—S1—O2	116.52 (9)	C4—N1—C3	115.30 (14)
O3—S1—C5	109.59 (8)	N1—C3—C5	112.05 (14)
O2—S1—C5	109.77 (9)	N1—C3—H31	109.2
O3—S1—C6	109.11 (9)	C5—C3—H31	109.2
O2—S1—C6	110.17 (9)	N1—C3—H32	109.2
C5—S1—C6	100.48 (8)	C5—C3—H32	109.2
C3—C5—S1	109.70 (12)	H31—C3—H32	107.9
C3—C5—H51	109.7	N1—C4—C6	111.28 (15)
S1—C5—H51	109.7	N1—C4—H41	108.6 (17)
C3—C5—H52	109.7	C6—C4—H41	108.7 (17)
S1—C5—H52	109.7	N1—C4—H42	109.1 (17)
H51—C5—H52	108.2	C6—C4—H42	110.1 (17)
C4—C6—S1	109.81 (12)	H41—C4—H42	109 (2)
C4—C6—H61	109.7	O1—C1—N1	122.16 (16)
S1—C6—H61	109.7	O1—C1—C2	120.72 (16)
C4—C6—H62	109.7	N1—C1—C2	117.09 (16)
S1—C6—H62	109.7	N2—C2—C1	114.24 (17)
H61—C6—H62	108.2	N2—C2—H2	116.1 (17)
O12—S11—O13	116.5 (3)	C1—C2—H2	128.1 (18)
C1—N1—C4	124.74 (15)	N3—N2—C2	178.3 (2)
C1—N1—C3	118.42 (15)

O3—S1—C5—C3	59.85 (14)	C3—N1—C4—C6	62.7 (2)
O2—S1—C5—C3	−170.98 (12)	S1—C6—C4—N1	−60.49 (17)
C6—S1—C5—C3	−54.93 (13)	C4—N1—C1—O1	161.34 (18)
O3—S1—C6—C4	−59.84 (14)	C3—N1—C1—O1	−3.9 (3)
O2—S1—C6—C4	171.06 (12)	C4—N1—C1—C2	−20.7 (3)
C5—S1—C6—C4	55.31 (13)	C3—N1—C1—C2	174.07 (15)
C1—N1—C3—C5	103.74 (18)	O1—C1—C2—N2	−1.7 (3)
C4—N1—C3—C5	−62.8 (2)	N1—C1—C2—N2	−179.68 (16)
S1—C5—C3—N1	60.09 (17)	C1—C2—N2—N3	−53 (8)
C1—N1—C4—C6	−102.9 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O2ⁱ	0.94 (2)	2.42 (2)	3.326 (2)	163 (2)
C3—H32···O1ⁱⁱ	0.99	2.47	3.372 (2)	152
C5—H52···O1ⁱⁱⁱ	0.99	2.36	3.022 (2)	123
C5—H51···O3^iv	0.99	2.56	3.445 (2)	149
C5—H52···N3^v	0.99	2.59	3.417 (3)	141
C6—H61···O2^vi	0.99	2.45	3.168 (2)	129

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

Experimental details

Crystal data
Chemical formula	C₆H₉N₃O₃S
M_r	203.22
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	105
a, b, c (Å)	5.2729 (3), 20.1349 (11), 7.8683 (4)
β (°)	95.171 (2)
V (Å³)	831.97 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.37
Crystal size (mm)	0.80 × 0.30 × 0.20

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2007)
T_min, T_max	0.849, 0.929
No. of measured, independent and observed [I > 2σ(I)] reflections	14742, 3951, 3029
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.842

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.165, 1.11
No. of reflections	3951
No. of parameters	138
No. of restraints	13
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	1.24, −0.71

Computer programs: APEX2 (Bruker, 2007), SAINT-Plus (Bruker, 2007), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O2ⁱ	0.940 (17)	2.417 (18)	3.326 (2)	163 (2)
C3—H32···O1ⁱⁱ	0.99	2.47	3.372 (2)	152
C5—H52···O1ⁱⁱⁱ	0.99	2.36	3.022 (2)	123
C5—H51···O3^iv	0.99	2.56	3.445 (2)	149
C5—H52···N3^v	0.99	2.59	3.417 (3)	141
C6—H61···O2^vi	0.99	2.45	3.168 (2)	129

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

References

Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
American Chemical Society (2008). Chemical Abstracts Service, American Chemical Society, Columbus, OH, USA; accessed Apr 27, 2010. Google Scholar
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Volume 67| Part 7| July 2011| Pages o1844-o1845

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