(IUCr) Crystallography Journals Online

Abstract top

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.

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).

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

Crystal data top

C₁₁H₁₈N₄O₃	F(000) = 544
M_r = 254.29	D_x = 1.278 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 14.654 (10) Å	Cell parameters from 2404 reflections
b = 10.548 (7) Å	θ = 2.4–26.4°
c = 8.553 (6) Å	µ = 0.10 mm⁻¹
β = 91.122 (6)°	T = 105 K
V = 1321.8 (15) Å³	Plate, yellow
Z = 4	0.55 × 0.42 × 0.08 mm

Data collection top

Bruker APEXII CCD diffractometer	2692 independent reflections
Radiation source: fine-focus sealed tube	2111 reflections with I > 2σ(I)
graphite	R_int = 0.041
Detector resolution: 8.3 pixels mm^-1	θ_max = 26.4°, θ_min = 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. scans	h = −17→18
Absorption correction: multi-scan (SADABS; Bruker, 2007)	k = −10→13
T_min = 0.870, T_max = 0.992	l = −10→10
7308 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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0463P)² + 0.1671P] where P = (F_o² + 2F_c²)/3
2692 reflections	(Δ/σ)_max = 0.001
169 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.22 e Å⁻³

Crystal data top

C₁₁H₁₈N₄O₃	V = 1321.8 (15) Å³
M_r = 254.29	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 14.654 (10) Å	µ = 0.10 mm⁻¹
b = 10.548 (7) Å	T = 105 K
c = 8.553 (6) Å	0.55 × 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)
T_min = 0.870, T_max = 0.992	R_int = 0.041
7308 measured reflections	θ_max = 26.4°

Refinement top

R[F² > 2σ(F²)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.103	Δρ_max = 0.17 e Å⁻³
S = 1.03	Δρ_min = −0.22 e Å⁻³
2692 reflections	Absolute structure: ?
169 parameters	Flack parameter: ?
0 restraints	Rogers parameter: ?

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.

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

	x	y	z	U_iso*/U_eq
O1	0.02567 (7)	0.20344 (9)	0.19361 (12)	0.0353 (3)
O2	0.38950 (6)	0.35633 (9)	0.62995 (11)	0.0296 (2)
O3	0.33388 (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)
N3	0.10933 (7)	0.34931 (10)	0.32642 (14)	0.0293 (3)
N4	0.27460 (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*
C2	0.03721 (9)	0.31392 (13)	0.23569 (16)	0.0276 (3)
C3	0.11676 (9)	0.47080 (12)	0.40835 (18)	0.0301 (3)
H31	0.0971	0.4604	0.5177	0.036*
H32	0.0760	0.5337	0.3568	0.036*
C4	0.17261 (10)	0.25284 (13)	0.38538 (18)	0.0317 (3)
H41	0.1681	0.1763	0.3188	0.038*
H42	0.1561	0.2287	0.4931	0.038*
C5	0.21342 (9)	0.51824 (13)	0.40729 (18)	0.0322 (3)
H51	0.2304	0.5397	0.2990	0.039*
H52	0.2188	0.5960	0.4717	0.039*
C6	0.26896 (10)	0.30251 (13)	0.38538 (19)	0.0349 (4)
H61	0.3104	0.2399	0.4357	0.042*
H62	0.2886	0.3150	0.2763	0.042*
C7	0.33775 (9)	0.43825 (12)	0.58409 (16)	0.0259 (3)
C8	0.39795 (9)	0.59837 (13)	0.76528 (15)	0.0275 (3)
C9	0.36780 (11)	0.73381 (14)	0.79087 (18)	0.0387 (4)
H91	0.3721	0.7811	0.6927	0.058*
H92	0.4073	0.7734	0.8707	0.058*
H93	0.3045	0.7346	0.8258	0.058*
C10	0.49473 (10)	0.59327 (15)	0.70952 (17)	0.0354 (4)
H101	0.4989	0.6386	0.6099	0.053*
H102	0.5129	0.5047	0.6951	0.053*
H103	0.5354	0.6333	0.7873	0.053*
C11	0.38403 (10)	0.52052 (14)	0.91124 (17)	0.0351 (4)
H111	0.3190	0.5190	0.9358	0.053*
H112	0.4186	0.5583	0.9987	0.053*
H113	0.4055	0.4337	0.8939	0.053*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0331 (6)	0.0239 (5)	0.0487 (6)	−0.0044 (4)	−0.0025 (5)	−0.0072 (5)
O2	0.0298 (5)	0.0242 (5)	0.0348 (5)	0.0047 (4)	−0.0017 (4)	0.0004 (4)
O3	0.0326 (5)	0.0217 (5)	0.0336 (5)	0.0019 (4)	−0.0074 (4)	−0.0042 (4)
N1	0.0446 (8)	0.0565 (10)	0.0665 (10)	−0.0058 (7)	−0.0207 (8)	−0.0054 (8)
N2	0.0320 (7)	0.0341 (7)	0.0469 (8)	−0.0010 (5)	−0.0060 (6)	−0.0007 (6)
N3	0.0279 (6)	0.0200 (6)	0.0398 (7)	0.0018 (5)	−0.0042 (5)	−0.0041 (5)
N4	0.0304 (6)	0.0239 (6)	0.0503 (8)	0.0057 (5)	−0.0125 (6)	−0.0096 (5)
C1	0.0297 (8)	0.0281 (8)	0.0390 (8)	−0.0023 (6)	−0.0063 (6)	−0.0020 (6)
C2	0.0257 (7)	0.0241 (7)	0.0332 (7)	−0.0038 (5)	0.0042 (6)	−0.0018 (6)
C3	0.0324 (8)	0.0204 (7)	0.0373 (8)	0.0039 (6)	−0.0050 (6)	−0.0041 (6)
C4	0.0342 (8)	0.0202 (7)	0.0406 (8)	0.0031 (6)	−0.0035 (6)	−0.0040 (6)
C5	0.0341 (8)	0.0224 (7)	0.0396 (8)	−0.0002 (6)	−0.0089 (6)	−0.0014 (6)
C6	0.0325 (8)	0.0264 (7)	0.0455 (9)	0.0053 (6)	−0.0054 (7)	−0.0121 (6)
C7	0.0241 (7)	0.0237 (7)	0.0300 (7)	−0.0013 (5)	0.0030 (5)	−0.0008 (6)
C8	0.0314 (7)	0.0259 (7)	0.0249 (7)	−0.0041 (6)	−0.0037 (6)	−0.0013 (5)
C9	0.0523 (10)	0.0268 (8)	0.0367 (8)	−0.0006 (7)	−0.0048 (7)	−0.0049 (6)
C10	0.0346 (8)	0.0390 (8)	0.0325 (8)	−0.0078 (7)	−0.0006 (6)	0.0005 (6)
C11	0.0398 (8)	0.0354 (8)	0.0302 (8)	−0.0032 (7)	0.0025 (6)	0.0019 (6)

Geometric parameters (Å, °) top

O1—C2	1.2303 (17)	C4—H41	0.9900
O2—C7	1.2099 (16)	C4—H42	0.9900
O3—C7	1.3422 (17)	C5—H51	0.9900
O3—C8	1.4722 (16)	C5—H52	0.9900
N1—N2	1.1189 (18)	C6—H61	0.9900
N2—C1	1.3099 (19)	C6—H62	0.9900
N3—C2	1.3515 (18)	C8—C10	1.506 (2)
N3—C4	1.4600 (18)	C8—C11	1.511 (2)
N3—C3	1.4635 (18)	C8—C9	1.513 (2)
N4—C7	1.3483 (18)	C9—H91	0.9800
N4—C5	1.4490 (18)	C9—H92	0.9800
N4—C6	1.4494 (19)	C9—H93	0.9800
C1—C2	1.450 (2)	C10—H101	0.9800
C1—H1	0.946 (17)	C10—H102	0.9800
C3—C5	1.503 (2)	C10—H103	0.9800
C3—H31	0.9900	C11—H111	0.9800
C3—H32	0.9900	C11—H112	0.9800
C4—C6	1.506 (2)	C11—H113	0.9800

C7—O3—C8	120.57 (10)	N4—C6—H61	109.6
N1—N2—C1	179.04 (18)	C4—C6—H61	109.6
C2—N3—C4	119.35 (12)	N4—C6—H62	109.6
C2—N3—C3	124.53 (11)	C4—C6—H62	109.6
C4—N3—C3	113.83 (11)	H61—C6—H62	108.1
C7—N4—C5	125.93 (12)	O2—C7—O3	125.31 (12)
C7—N4—C6	120.26 (11)	O2—C7—N4	124.15 (13)
C5—N4—C6	113.59 (12)	O3—C7—N4	110.52 (11)
N2—C1—C2	114.68 (13)	O3—C8—C10	110.59 (12)
N2—C1—H1	115.7 (9)	O3—C8—C11	109.89 (11)
C2—C1—H1	129.6 (9)	C10—C8—C11	112.67 (12)
O1—C2—N3	122.08 (12)	O3—C8—C9	101.68 (11)
O1—C2—C1	120.21 (13)	C10—C8—C9	111.04 (12)
N3—C2—C1	117.64 (12)	C11—C8—C9	110.43 (13)
N3—C3—C5	110.49 (12)	C8—C9—H91	109.5
N3—C3—H31	109.6	C8—C9—H92	109.5
C5—C3—H31	109.6	H91—C9—H92	109.5
N3—C3—H32	109.6	C8—C9—H93	109.5
C5—C3—H32	109.6	H91—C9—H93	109.5
H31—C3—H32	108.1	H92—C9—H93	109.5
N3—C4—C6	110.29 (12)	C8—C10—H101	109.5
N3—C4—H41	109.6	C8—C10—H102	109.5
C6—C4—H41	109.6	H101—C10—H102	109.5
N3—C4—H42	109.6	C8—C10—H103	109.5
C6—C4—H42	109.6	H101—C10—H103	109.5
H41—C4—H42	108.1	H102—C10—H103	109.5
N4—C5—C3	109.92 (12)	C8—C11—H111	109.5
N4—C5—H51	109.7	C8—C11—H112	109.5
C3—C5—H51	109.7	H111—C11—H112	109.5
N4—C5—H52	109.7	C8—C11—H113	109.5
C3—C5—H52	109.7	H111—C11—H113	109.5
H51—C5—H52	108.2	H112—C11—H113	109.5
N4—C6—C4	110.27 (12)

C4—N3—C2—O1	−4.1 (2)	C7—N4—C6—C4	128.14 (15)
C3—N3—C2—O1	−165.84 (14)	C5—N4—C6—C4	−57.04 (17)
C4—N3—C2—C1	178.83 (13)	N3—C4—C6—N4	53.39 (17)
C3—N3—C2—C1	17.1 (2)	C8—O3—C7—O2	2.4 (2)
N2—C1—C2—O1	−3.6 (2)	C8—O3—C7—N4	−178.51 (11)
N2—C1—C2—N3	173.55 (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—C5	54.32 (16)	C5—N4—C7—O3	3.0 (2)
C2—N3—C4—C6	142.52 (13)	C6—N4—C7—O3	177.17 (13)
C3—N3—C4—C6	−53.89 (17)	C7—O3—C8—C10	62.39 (16)
C7—N4—C5—C3	−128.35 (15)	C7—O3—C8—C11	−62.62 (16)
C6—N4—C5—C3	57.18 (17)	C7—O3—C8—C9	−179.61 (12)
N3—C3—C5—N4	−53.86 (17)

Hydrogen-bond geometry (Å, °) top

D—H···A	D—H	H···A	D···A	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 codes: (i) −x, y+1/2, −z+1/2.

Table 1
Hydrogen-bond geometry (Å, °) top

D—H···A	D—H	H···A	D···A	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 codes: (i) −x, y+1/2, −z+1/2.

supplementary materials

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

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