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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): o1299.
Published online 2010 May 8. doi:  10.1107/S1600536810016211
PMCID: PMC2979480

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

Abstract

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 R 2 1(7) rings.

Related literature

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

An external file that holds a picture, illustration, etc.
Object name is e-66-o1299-scheme1.jpg

Experimental

Crystal data

  • C11H18N4O3
  • M r = 254.29
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1299-efi1.jpg
  • 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 [triangle]) T min = 0.870, T max = 0.992
  • 7308 measured reflections
  • 2692 independent reflections
  • 2111 reflections with I > 2σ(I)
  • R int = 0.041

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 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

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810016211/lh5033sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810016211/lh5033Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

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).

Experimental

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

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.

Figures

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 ...

Crystal data

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

Bruker APEXII CCD diffractometer2692 independent reflections
Radiation source: fine-focus sealed tube2111 reflections with I > 2σ(I)
graphiteRint = 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 = −17→18
Absorption correction: multi-scan (SADABS; Bruker, 2007)k = −10→13
Tmin = 0.870, Tmax = 0.992l = −10→10
7308 measured reflections

Refinement

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 = 1.03w = 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 = −0.22 e Å3

Special details

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)

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)
N1−0.14125 (10)0.34028 (15)−0.00383 (19)0.0562 (4)
N2−0.08817 (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)
C1−0.02502 (10)0.41229 (14)0.18201 (17)0.0324 (3)
H1−0.0254 (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)

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, °)

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—O1−4.1 (2)C7—N4—C6—C4128.14 (15)
C3—N3—C2—O1−165.84 (14)C5—N4—C6—C4−57.04 (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—O1−3.6 (2)C8—O3—C7—N4−178.51 (11)
N2—C1—C2—N3173.55 (13)C5—N4—C7—O2−177.86 (14)
C2—N3—C3—C5−143.07 (14)C6—N4—C7—O2−3.7 (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—C6−53.89 (17)C7—O3—C8—C1062.39 (16)
C7—N4—C5—C3−128.35 (15)C7—O3—C8—C11−62.62 (16)
C6—N4—C5—C357.18 (17)C7—O3—C8—C9−179.61 (12)
N3—C3—C5—N4−53.86 (17)

Hydrogen-bond geometry (Å, °)

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 codes: (i) −x, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5033).

References

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  • 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. [PubMed]
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