organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

tert-Butyl 4-(2-diazo­acet­yl)piperazine-1-carboxyl­ate

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

(Received 22 April 2010; accepted 3 May 2010; online 8 May 2010)

The title crystal structure, C11H18N4O3, is the first diazo­acetamide in which the diazo­acetyl group is attached to an N atom. The piperazine ring is in a chair form and hence the mol­ecule has an extended conformation. Both ring N atoms are bonded in an essentially planar configuration with the sum of the C—N—C angles being 359.8 (2) and 357.7 (2)°. In the crystal structure, the O atom of the diazo­acetyl group accepts two H atoms from C—H donors, thus generating chains of weak hydrogen-bonded R21(7) rings.

Related literature

For the only other reported synthesis of a diazo­acetamide in the Chemical Abstracts Service (CAS, American Chemical Society, 2008[American Chemical Society (2008). Chemical Abstracts Service, American Chemical Society, Columbus, OH, USA; accessed Apr 27, 2010.]) with a 1,4-diaza six-membered ring, see: Mickelson et al. (1996[Mickelson, J. W., Jacobsen, E. J., Carter, D. B., Im, H. K., Im, W. B., Schreur, P. J. K. D., Sethy, V. H., Tang, A. H., McGee, J. E. & Petke, J. D. (1996). J. Med. Chem. 39, 4654—4666.]). For other diazo­acetamides, see: Ouihia et al. (1993[Ouihia, A., Rene, L., Guilhem, J., Pascard, C. & Badet, B. (1993). J. Org. Chem. 58, 1641-1642.]). For related structures, see: Fenlon et al. (2007[Fenlon, T. W., Schwaebisch, D., Mayweg, A. V. W., Lee, V., Adlington, R. M. & Baldwin, J. E. (2007). Synlett, pp. 2679-2682.]); Wang et al. (2006[Wang, J., Zeng, T., Li, M.-L., Duan, E.-H. & Li, J.-S. (2006). Acta Cryst. E62, o2912-o2913.]); Miller et al. (1991[Miller, R. D., Theis, W., Heilig, G. & Kirchmeyer, S. (1991). J. Org. Chem. 56, 1453-1463.]). For synthetic details, see: Kaupang (2010[Kaupang, Å. (2010). Masters thesis, University of Oslo, Norway. Available at http://www.duo.uio.no/ .]); Toma et al. (2007[Toma, T., Shimokawa, J. & Fukuyama, T. (2007). Org. Lett. 9, 3195-3197.]). For hydrogen-bond graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For a description of the Cambridge Structural Database, see: Allen (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]).

[Scheme 1]

Experimental

Crystal data
  • C11H18N4O3

  • Mr = 254.29

  • Monoclinic, P 21 /c

  • a = 14.654 (10) Å

  • b = 10.548 (7) Å

  • c = 8.553 (6) Å

  • β = 91.122 (6)°

  • V = 1321.8 (15) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 105 K

  • 0.55 × 0.42 × 0.08 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2007[Bruker (2007). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.870, Tmax = 0.992

  • 7308 measured reflections

  • 2692 independent reflections

  • 2111 reflections with I > 2σ(I)

  • Rint = 0.041

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.103

  • S = 1.03

  • 2692 reflections

  • 169 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1⋯O1i 0.946 (17) 2.313 (18) 3.250 (3) 170.6 (14)
C3—H32⋯O1i 0.99 2.36 3.327 (3) 164
Symmetry code: (i) [-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2007[Bruker (2007). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The tert-butyl 4-(2-diazoacetyl)piperazine-1-carboxylate (I) was prepared as part of a series of diazoacetamides, to be used in intramolecular C—H insertion reactions (Kaupang, 2010). It was synthesized from tert-butyl 4-(2-bromoacetyl)piperazine-1-carboxylate by a slight modification of the procedure reported by Toma et al. (2007), employing 1,1,3,3-tetramethylguanidine as the base instead of 1,8-diazabicyclo[5.4.0]undec-7-ene.

Diffraction data were first collected at ambient temperature, yielding a structure with a massively disordered six-membered ring. At 105 K the ring is completely ordered in a well defined chair conformation, Fig. 1.

The diazoacetyl moiety is not an uncommon functional group in organic molecules, however only 15 occurrences were found in the Cambridge Structural Database (Version 5.31 of November 2009; Allen, 2002), and none where, as here, the group is attached to a N atom. In only two structures the group sits on a non-aromatic ring (Miller et al., 1991; Fenlon et al., 2007).

In a model molecule like trimethylamine the N atom is located about 0.45 Å above the plane defined by the three C atoms. In the structure of (I) N3 is 0.125 (2) Å above the plane defined by C2, C3 and C4, while N4 is only 0.039 (2) Å above the plane defined by C5, C6 and C7, which essentially shows a planar configuration (sum of C—N—C angles 359.8 (2) °). This is due to the double bond character of the amidic N3—C2 and N4—C7 bonds measuring 1.3515 (18) and 1.3483 (18) Å, respectively. An example of a related structure is 1,4-di(chloroacetyl)piperazine (Wang et al., 2006).

In the crystal structure, the O atom of the diazoacetyl group accepts two H atoms from C—H donors, thus generating chains of hydrogen-bonded R12(7) rings (Bernstein et al., 1995).

Related literature top

For the only other reported synthesis of a diazoacetamide in CAS with a 1,4-diaza six-membered ring, see: American Chemical Society (2008); Mickelson et al. (1996). For other diazoacetamides, see: Ouihia et al. (1993). For related structures, see: Fenlon et al. (2007); Wang et al. (2006); Miller et al. (1991). For synthetic details, see: Kaupang (2010); Toma et al. (2007). For hydrogen-bond graph-set notation, see: Bernstein et al. (1995). For a description of the Cambridge Structural Database, see: Allen (2002).

Experimental top

A 2.5 ml vial containing tert-butyl 4-(2-diazoacetyl)piperazine-1-carboxylate (10.8 mg) and dichloromethane (1000 ml) was capped and a pinhole (0.5 mm) was made in the cap to allow for vapour diffusion of solvents. This vial was placed inside a 25 ml vial containing n-pentane (8 ml) that was subsequently capped and stored in the dark at ambient temperature for approximately 48 hours, affording bright yellow plate-shaped crystals.

Refinement top

Coordinates were refined for H1 (bonded to C1), which is involved in the shortest intermolcular interaction. Other H atoms were positioned with idealized geometry and fixed C–H distances set to 0.98 Å (methyl) or 0.99 Å (methylene). Free rotation was permitted for the methyl groups. Uiso values were 1.2Ueq of the carrier atom or 1.5Ueq for methyl groups.

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
[Figure 1] Fig. 1. The asymmetric unit of (I), with atomic numbering indicated, together with selected atoms of neighbouring molecules connected by weak hydrogen bonds shown as dotted lines (see Table 1, symmetry operations are -x,1/2+y,1/2-z for O', -x,-1/2+y,1/2-z for H1" and H32"). Displacement ellipsoids are shown at the 50% probability level with H atoms as spheres of arbitrary size.
tert-Butyl 4-(2-diazoacetyl)piperazine-1-carboxylate top
Crystal data top
C11H18N4O3F(000) = 544
Mr = 254.29Dx = 1.278 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 14.654 (10) ÅCell parameters from 2404 reflections
b = 10.548 (7) Åθ = 2.4–26.4°
c = 8.553 (6) ŵ = 0.10 mm1
β = 91.122 (6)°T = 105 K
V = 1321.8 (15) Å3Plate, yellow
Z = 40.55 × 0.42 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer
2692 independent reflections
Radiation source: fine-focus sealed tube2111 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
Detector resolution: 8.3 pixels mm-1θmax = 26.4°, θmin = 2.4°
Three sets of frames each taken over 0.3° ω rotation with 20 s exposure time. Detector set at 2θ = 26°, crystal–to–detector distance 6.00 cm. scansh = 1718
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
k = 1013
Tmin = 0.870, Tmax = 0.992l = 1010
7308 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0463P)2 + 0.1671P]
where P = (Fo2 + 2Fc2)/3
2692 reflections(Δ/σ)max = 0.001
169 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C11H18N4O3V = 1321.8 (15) Å3
Mr = 254.29Z = 4
Monoclinic, P21/cMo Kα radiation
a = 14.654 (10) ŵ = 0.10 mm1
b = 10.548 (7) ÅT = 105 K
c = 8.553 (6) Å0.55 × 0.42 × 0.08 mm
β = 91.122 (6)°
Data collection top
Bruker APEXII CCD
diffractometer
2692 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2007)
2111 reflections with I > 2σ(I)
Tmin = 0.870, Tmax = 0.992Rint = 0.041
7308 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.17 e Å3
2692 reflectionsΔρmin = 0.23 e Å3
169 parameters
Special details top

Experimental. Crystallized from dichloromethane and n-pentane.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.02567 (7)0.20344 (9)0.19361 (12)0.0353 (3)
O20.38950 (6)0.35633 (9)0.62995 (11)0.0296 (2)
O30.33388 (6)0.55670 (8)0.64091 (11)0.0294 (2)
N10.14125 (10)0.34028 (15)0.00383 (19)0.0562 (4)
N20.08817 (8)0.37402 (12)0.08229 (16)0.0377 (3)
N30.10933 (7)0.34931 (10)0.32642 (14)0.0293 (3)
N40.27460 (8)0.42179 (11)0.46913 (15)0.0350 (3)
C10.02502 (10)0.41229 (14)0.18201 (17)0.0324 (3)
H10.0254 (10)0.4999 (17)0.2058 (19)0.039*
C20.03721 (9)0.31392 (13)0.23569 (16)0.0276 (3)
C30.11676 (9)0.47080 (12)0.40835 (18)0.0301 (3)
H310.09710.46040.51770.036*
H320.07600.53370.35680.036*
C40.17261 (10)0.25284 (13)0.38538 (18)0.0317 (3)
H410.16810.17630.31880.038*
H420.15610.22870.49310.038*
C50.21342 (9)0.51824 (13)0.40729 (18)0.0322 (3)
H510.23040.53970.29900.039*
H520.21880.59600.47170.039*
C60.26896 (10)0.30251 (13)0.38538 (19)0.0349 (4)
H610.31040.23990.43570.042*
H620.28860.31500.27630.042*
C70.33775 (9)0.43825 (12)0.58409 (16)0.0259 (3)
C80.39795 (9)0.59837 (13)0.76528 (15)0.0275 (3)
C90.36780 (11)0.73381 (14)0.79087 (18)0.0387 (4)
H910.37210.78110.69270.058*
H920.40730.77340.87070.058*
H930.30450.73460.82580.058*
C100.49473 (10)0.59327 (15)0.70952 (17)0.0354 (4)
H1010.49890.63860.60990.053*
H1020.51290.50470.69510.053*
H1030.53540.63330.78730.053*
C110.38403 (10)0.52052 (14)0.91124 (17)0.0351 (4)
H1110.31900.51900.93580.053*
H1120.41860.55830.99870.053*
H1130.40550.43370.89390.053*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0331 (6)0.0239 (5)0.0487 (6)0.0044 (4)0.0025 (5)0.0072 (5)
O20.0298 (5)0.0242 (5)0.0348 (5)0.0047 (4)0.0017 (4)0.0004 (4)
O30.0326 (5)0.0217 (5)0.0336 (5)0.0019 (4)0.0074 (4)0.0042 (4)
N10.0446 (8)0.0565 (10)0.0665 (10)0.0058 (7)0.0207 (8)0.0054 (8)
N20.0320 (7)0.0341 (7)0.0469 (8)0.0010 (5)0.0060 (6)0.0007 (6)
N30.0279 (6)0.0200 (6)0.0398 (7)0.0018 (5)0.0042 (5)0.0041 (5)
N40.0304 (6)0.0239 (6)0.0503 (8)0.0057 (5)0.0125 (6)0.0096 (5)
C10.0297 (8)0.0281 (8)0.0390 (8)0.0023 (6)0.0063 (6)0.0020 (6)
C20.0257 (7)0.0241 (7)0.0332 (7)0.0038 (5)0.0042 (6)0.0018 (6)
C30.0324 (8)0.0204 (7)0.0373 (8)0.0039 (6)0.0050 (6)0.0041 (6)
C40.0342 (8)0.0202 (7)0.0406 (8)0.0031 (6)0.0035 (6)0.0040 (6)
C50.0341 (8)0.0224 (7)0.0396 (8)0.0002 (6)0.0089 (6)0.0014 (6)
C60.0325 (8)0.0264 (7)0.0455 (9)0.0053 (6)0.0054 (7)0.0121 (6)
C70.0241 (7)0.0237 (7)0.0300 (7)0.0013 (5)0.0030 (5)0.0008 (6)
C80.0314 (7)0.0259 (7)0.0249 (7)0.0041 (6)0.0037 (6)0.0013 (5)
C90.0523 (10)0.0268 (8)0.0367 (8)0.0006 (7)0.0048 (7)0.0049 (6)
C100.0346 (8)0.0390 (8)0.0325 (8)0.0078 (7)0.0006 (6)0.0005 (6)
C110.0398 (8)0.0354 (8)0.0302 (8)0.0032 (7)0.0025 (6)0.0019 (6)
Geometric parameters (Å, º) top
O1—C21.2303 (17)C4—H410.9900
O2—C71.2099 (16)C4—H420.9900
O3—C71.3422 (17)C5—H510.9900
O3—C81.4722 (16)C5—H520.9900
N1—N21.1189 (18)C6—H610.9900
N2—C11.3099 (19)C6—H620.9900
N3—C21.3515 (18)C8—C101.506 (2)
N3—C41.4600 (18)C8—C111.511 (2)
N3—C31.4635 (18)C8—C91.513 (2)
N4—C71.3483 (18)C9—H910.9800
N4—C51.4490 (18)C9—H920.9800
N4—C61.4494 (19)C9—H930.9800
C1—C21.450 (2)C10—H1010.9800
C1—H10.946 (17)C10—H1020.9800
C3—C51.503 (2)C10—H1030.9800
C3—H310.9900C11—H1110.9800
C3—H320.9900C11—H1120.9800
C4—C61.506 (2)C11—H1130.9800
C7—O3—C8120.57 (10)N4—C6—H61109.6
N1—N2—C1179.04 (18)C4—C6—H61109.6
C2—N3—C4119.35 (12)N4—C6—H62109.6
C2—N3—C3124.53 (11)C4—C6—H62109.6
C4—N3—C3113.83 (11)H61—C6—H62108.1
C7—N4—C5125.93 (12)O2—C7—O3125.31 (12)
C7—N4—C6120.26 (11)O2—C7—N4124.15 (13)
C5—N4—C6113.59 (12)O3—C7—N4110.52 (11)
N2—C1—C2114.68 (13)O3—C8—C10110.59 (12)
N2—C1—H1115.7 (9)O3—C8—C11109.89 (11)
C2—C1—H1129.6 (9)C10—C8—C11112.67 (12)
O1—C2—N3122.08 (12)O3—C8—C9101.68 (11)
O1—C2—C1120.21 (13)C10—C8—C9111.04 (12)
N3—C2—C1117.64 (12)C11—C8—C9110.43 (13)
N3—C3—C5110.49 (12)C8—C9—H91109.5
N3—C3—H31109.6C8—C9—H92109.5
C5—C3—H31109.6H91—C9—H92109.5
N3—C3—H32109.6C8—C9—H93109.5
C5—C3—H32109.6H91—C9—H93109.5
H31—C3—H32108.1H92—C9—H93109.5
N3—C4—C6110.29 (12)C8—C10—H101109.5
N3—C4—H41109.6C8—C10—H102109.5
C6—C4—H41109.6H101—C10—H102109.5
N3—C4—H42109.6C8—C10—H103109.5
C6—C4—H42109.6H101—C10—H103109.5
H41—C4—H42108.1H102—C10—H103109.5
N4—C5—C3109.92 (12)C8—C11—H111109.5
N4—C5—H51109.7C8—C11—H112109.5
C3—C5—H51109.7H111—C11—H112109.5
N4—C5—H52109.7C8—C11—H113109.5
C3—C5—H52109.7H111—C11—H113109.5
H51—C5—H52108.2H112—C11—H113109.5
N4—C6—C4110.27 (12)
C4—N3—C2—O14.1 (2)C7—N4—C6—C4128.14 (15)
C3—N3—C2—O1165.84 (14)C5—N4—C6—C457.04 (17)
C4—N3—C2—C1178.83 (13)N3—C4—C6—N453.39 (17)
C3—N3—C2—C117.1 (2)C8—O3—C7—O22.4 (2)
N2—C1—C2—O13.6 (2)C8—O3—C7—N4178.51 (11)
N2—C1—C2—N3173.55 (13)C5—N4—C7—O2177.86 (14)
C2—N3—C3—C5143.07 (14)C6—N4—C7—O23.7 (2)
C4—N3—C3—C554.32 (16)C5—N4—C7—O33.0 (2)
C2—N3—C4—C6142.52 (13)C6—N4—C7—O3177.17 (13)
C3—N3—C4—C653.89 (17)C7—O3—C8—C1062.39 (16)
C7—N4—C5—C3128.35 (15)C7—O3—C8—C1162.62 (16)
C6—N4—C5—C357.18 (17)C7—O3—C8—C9179.61 (12)
N3—C3—C5—N453.86 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···O1i0.946 (17)2.313 (18)3.250 (3)170.6 (14)
C3—H32···O1i0.992.363.327 (3)164
Symmetry code: (i) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H18N4O3
Mr254.29
Crystal system, space groupMonoclinic, P21/c
Temperature (K)105
a, b, c (Å)14.654 (10), 10.548 (7), 8.553 (6)
β (°) 91.122 (6)
V3)1321.8 (15)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.55 × 0.42 × 0.08
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2007)
Tmin, Tmax0.870, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections
7308, 2692, 2111
Rint0.041
(sin θ/λ)max1)0.625
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.103, 1.03
No. of reflections2692
No. of parameters169
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.17, 0.23

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···O1i0.946 (17)2.313 (18)3.250 (3)170.6 (14)
C3—H32···O1i0.9902.3633.327 (3)164.0
Symmetry code: (i) x, y+1/2, z+1/2.
 

References

First citationAllen, F. H. (2002). Acta Cryst. B58, 380–388.  Web of Science CrossRef CAS IUCr Journals
First citationAmerican Chemical Society (2008). Chemical Abstracts Service, American Chemical Society, Columbus, OH, USA; accessed Apr 27, 2010.
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science
First citationBruker (2007). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationFenlon, T. W., Schwaebisch, D., Mayweg, A. V. W., Lee, V., Adlington, R. M. & Baldwin, J. E. (2007). Synlett, pp. 2679–2682.
First citationKaupang, Å. (2010). Masters thesis, University of Oslo, Norway. Available at http://www.duo.uio.no/ .
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