tert-Butyl 6-oxo-2,7-diaza­spiro[4.4]nonane-2-carboxyl­ate

Abstract

In the title mol­ecule, C₁₂H₂₀N₂O₃, both five-membered rings are in envelope conformations. In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into chains along [010].

Related literature

For applications of substituted pyrrolidines, see: Domagala et al. (1993 ▶); Pedder et al. (1976 ▶); Blanco & Sardina (1994 ▶); Husinec & Savic (2005 ▶). For standard bond lengths, see: Allen et al. (1987 ▶).

Experimental

Crystal data

• C₁₂H₂₀N₂O₃

• M _r = 240.30

• Monoclinic,

• a = 10.495 (5) Å

• b = 6.283 (3) Å

• c = 19.247 (10) Å

• β = 97.029 (8)°

• V = 1259.7 (11) ų

• Z = 4

• Mo Kα radiation

• μ = 0.09 mm⁻¹

• T = 173 K

• 0.21 × 0.15 × 0.06 mm

Data collection

• Rigaku Saturn 724+ diffractometer

• Absorption correction: multi-scan (CrystalClear; Rigaku, 2007 ▶) T _min = 0.981, T _max = 0.995

• 3265 measured reflections

• 1557 independent reflections

• 1452 reflections with I > 2σ(I)

• R _int = 0.039

Refinement

• R[F ² > 2σ(F ²)] = 0.050

• wR(F ²) = 0.105

• S = 1.09

• 1557 reflections

• 157 parameters

• 1 restraint

• H-atom parameters constrained

• Δρ_max = 0.23 e Å⁻³

• Δρ_min = −0.18 e Å⁻³

Data collection: CrystalClear (Rigaku, 2007 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; 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.

Supplementary Material

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

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1i	0.88	1.97	2.848 (3)	175

Symmetry code: (i) .

supplementary crystallographic information

Comment

Depending on the substitution pattern and functionalization, different substituted pyrrolidines have been shown to be effective antibacterials or fungicides agents and glycosidase inhibitors (Domagala et al., 1993; Pedder et al., 1976; Blanco et al., 1994); Husinec et al., 2005). The crystal structure of the title compound is reportede herein.

In the molecule (Fig. 1), all bond lengths and angles are within normal ranges (Allen et al., 1987). Both five-membered rings are in envelope conformations with C3 and C5 forming the flap. Atoms C6-C8/O2/O3/N2 are essentially planar, with a maximum deviation of 0.0082 (24) Å. In the crystal, N—H···O hydrogen bonds link molecules to form one dimensional chains along [010] (see Table 1).

Experimental

Tert-butyl 6-oxo-2,7-diazasiro[4.4]nonane-2-carboxylate was synthesized with methyl 1-tert-butyl 3-ethyl 3-(cyanomethyl)pyrrolidine-1,3-dicarboxylate (13.4g) and Raney Ni (3.4g) in methanol under H2(50 Psi) atmosphere at room temperature.

Single crystals of the compound suitable for X-ray measurements were obtained by recrystallization from ethanol at room temperature. In the absence of anomalous dispersion effects the Friedel pairs were merged.

Refinement

All H atoms were fixed geometrically and allowed to ride on their attached atoms, with C—H distances in the range 0.98–0.99 Å, and with U_iso(H) = 1.2U_eq(C) or U_iso(H) = 1.5U_eq(C_methyl). The N—H distance is 0.88 Å, with U_iso(H) = 1.2U_eq(N).

Figures

Fig. 1.

The molecular structure of the title compound with displacement ellipsoids are drawn at the 30% probability level.

Crystal data

C12H20N2O3	F(000) = 520
Mr = 240.30	Dx = 1.267 Mg m−3
Monoclinic, C2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2y	Cell parameters from 2422 reflections
a = 10.495 (5) Å	θ = 1.1–27.5°
b = 6.283 (3) Å	µ = 0.09 mm−1
c = 19.247 (10) Å	T = 173 K
β = 97.029 (8)°	Platelet, colorless
V = 1259.7 (11) Å3	0.21 × 0.15 × 0.06 mm
Z = 4

Data collection

Rigaku Saturn 724+ diffractometer	1557 independent reflections
Radiation source: rotating anode	1452 reflections with I > 2σ(I)
Confocal	Rint = 0.039
ω scans at fixed χ = 45°	θmax = 27.5°, θmin = 2.1°
Absorption correction: multi-scan (CrystalClear; Rigaku, 2007)	h = −13→7
Tmin = 0.981, Tmax = 0.995	k = −8→8
3265 measured reflections	l = −23→25

Refinement

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)] = 0.050	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105	H-atom parameters constrained
S = 1.09	w = 1/[σ2(Fo2) + (0.032P)2 + 0.9713P] where P = (Fo2 + 2Fc2)/3
1557 reflections	(Δ/σ)max < 0.001
157 parameters	Δρmax = 0.23 e Å−3
1 restraint	Δρmin = −0.18 e Å−3

Special details

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.Absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.2715 (2)	0.4600 (3)	0.43850 (10)	0.0313 (5)
O2	0.33362 (17)	0.2042 (3)	0.18571 (9)	0.0289 (5)
O3	0.55006 (19)	0.1382 (4)	0.19625 (10)	0.0332 (5)
N1	0.3406 (2)	0.8081 (4)	0.44345 (11)	0.0255 (5)
H1	0.3028	0.8474	0.4798	0.031*
N2	0.4618 (2)	0.3546 (4)	0.27139 (12)	0.0275 (5)
C1	0.3315 (3)	0.6117 (5)	0.41741 (13)	0.0219 (6)
C2	0.4181 (3)	0.9527 (5)	0.40704 (14)	0.0279 (6)
H2B	0.5037	0.9751	0.4339	0.033*
H2A	0.3750	1.0920	0.3984	0.033*
C3	0.4286 (3)	0.8347 (5)	0.33812 (13)	0.0234 (6)
H3B	0.5134	0.8596	0.3220	0.028*
H3A	0.3605	0.8813	0.3011	0.028*
C4	0.4118 (3)	0.5993 (5)	0.35651 (13)	0.0209 (5)
C5	0.5419 (3)	0.4915 (5)	0.38093 (13)	0.0241 (6)
H5B	0.6051	0.5963	0.4027	0.029*
H5A	0.5317	0.3766	0.4150	0.029*
C6	0.5835 (3)	0.4018 (5)	0.31360 (15)	0.0303 (7)
H6B	0.6336	0.5078	0.2902	0.036*
H6A	0.6357	0.2714	0.3230	0.036*
C7	0.3515 (2)	0.4573 (5)	0.29695 (13)	0.0233 (6)
H7B	0.2936	0.3505	0.3143	0.028*
H7A	0.3024	0.5428	0.2596	0.028*
C8	0.4568 (2)	0.2247 (5)	0.21527 (13)	0.0244 (6)
C9	0.3028 (3)	0.0912 (5)	0.11865 (14)	0.0290 (7)
C10	0.3776 (3)	0.1875 (7)	0.06389 (15)	0.0461 (9)
H10A	0.3444	0.1321	0.0176	0.069*
H10C	0.4686	0.1501	0.0745	0.069*
H10B	0.3683	0.3427	0.0641	0.069*
C11	0.3283 (3)	−0.1464 (6)	0.12960 (17)	0.0381 (8)
H11B	0.2717	−0.2031	0.1620	0.057*
H11C	0.4180	−0.1680	0.1492	0.057*
H11A	0.3117	−0.2205	0.0846	0.057*
C12	0.1607 (3)	0.1350 (7)	0.10196 (17)	0.0419 (8)
H12A	0.1281	0.0648	0.0579	0.063*
H12C	0.1466	0.2888	0.0974	0.063*
H12B	0.1154	0.0799	0.1398	0.063*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0348 (12)	0.0317 (11)	0.0293 (10)	−0.0073 (10)	0.0115 (8)	0.0027 (10)
O2	0.0228 (10)	0.0378 (11)	0.0253 (9)	0.0021 (10)	0.0002 (7)	−0.0106 (10)
O3	0.0261 (11)	0.0410 (13)	0.0335 (10)	0.0050 (10)	0.0074 (8)	−0.0098 (10)
N1	0.0263 (12)	0.0276 (13)	0.0234 (11)	0.0030 (11)	0.0066 (9)	−0.0023 (11)
N2	0.0190 (11)	0.0345 (13)	0.0284 (11)	0.0033 (11)	0.0004 (9)	−0.0091 (11)
C1	0.0200 (13)	0.0256 (13)	0.0200 (11)	−0.0001 (12)	0.0015 (10)	0.0016 (11)
C2	0.0280 (15)	0.0235 (13)	0.0322 (14)	0.0000 (13)	0.0033 (11)	0.0014 (13)
C3	0.0197 (13)	0.0265 (14)	0.0247 (12)	0.0022 (12)	0.0059 (10)	0.0037 (12)
C4	0.0193 (12)	0.0224 (13)	0.0211 (11)	0.0013 (12)	0.0025 (10)	0.0009 (11)
C5	0.0206 (13)	0.0249 (14)	0.0262 (13)	−0.0010 (12)	0.0001 (10)	−0.0014 (12)
C6	0.0183 (13)	0.0383 (18)	0.0336 (14)	0.0040 (13)	0.0001 (11)	−0.0076 (13)
C7	0.0181 (13)	0.0271 (13)	0.0252 (12)	0.0021 (12)	0.0053 (10)	−0.0021 (12)
C8	0.0219 (13)	0.0270 (14)	0.0248 (13)	0.0016 (12)	0.0048 (10)	−0.0003 (12)
C9	0.0309 (15)	0.0351 (16)	0.0212 (13)	−0.0022 (14)	0.0033 (11)	−0.0045 (13)
C10	0.048 (2)	0.062 (3)	0.0283 (15)	−0.009 (2)	0.0058 (14)	0.0031 (17)
C11	0.0388 (18)	0.0359 (17)	0.0394 (17)	−0.0022 (16)	0.0030 (14)	−0.0081 (15)
C12	0.0337 (18)	0.050 (2)	0.0395 (17)	0.0044 (17)	−0.0073 (14)	−0.0070 (17)

Geometric parameters (Å, °)

O1—C1	1.238 (3)	C5—C6	1.525 (4)
O2—C8	1.353 (3)	C5—H5B	0.9900
O2—C9	1.474 (3)	C5—H5A	0.9900
O3—C8	1.214 (3)	C6—H6B	0.9900
N1—C1	1.331 (4)	C6—H6A	0.9900
N1—C2	1.454 (4)	C7—H7B	0.9900
N1—H1	0.8800	C7—H7A	0.9900
N2—C8	1.350 (3)	C9—C12	1.511 (4)
N2—C6	1.458 (4)	C9—C10	1.516 (4)
N2—C7	1.462 (3)	C9—C11	1.526 (5)
C1—C4	1.527 (4)	C10—H10A	0.9800
C2—C3	1.535 (4)	C10—H10C	0.9800
C2—H2B	0.9900	C10—H10B	0.9800
C2—H2A	0.9900	C11—H11B	0.9800
C3—C4	1.536 (4)	C11—H11C	0.9800
C3—H3B	0.9900	C11—H11A	0.9800
C3—H3A	0.9900	C12—H12A	0.9800
C4—C7	1.527 (4)	C12—H12C	0.9800
C4—C5	1.545 (4)	C12—H12B	0.9800
C8—O2—C9	120.7 (2)	N2—C6—H6A	111.1
C1—N1—C2	114.6 (2)	C5—C6—H6A	111.1
C1—N1—H1	122.7	H6B—C6—H6A	109.1
C2—N1—H1	122.7	N2—C7—C4	103.8 (2)
C8—N2—C6	121.0 (2)	N2—C7—H7B	111.0
C8—N2—C7	125.5 (2)	C4—C7—H7B	111.0
C6—N2—C7	113.5 (2)	N2—C7—H7A	111.0
O1—C1—N1	127.3 (3)	C4—C7—H7A	111.0
O1—C1—C4	124.3 (3)	H7B—C7—H7A	109.0
N1—C1—C4	108.4 (2)	O3—C8—N2	123.9 (3)
N1—C2—C3	102.6 (2)	O3—C8—O2	126.5 (3)
N1—C2—H2B	111.2	N2—C8—O2	109.6 (2)
C3—C2—H2B	111.2	O2—C9—C12	101.8 (2)
N1—C2—H2A	111.2	O2—C9—C10	109.8 (3)
C3—C2—H2A	111.2	C12—C9—C10	111.2 (3)
H2B—C2—H2A	109.2	O2—C9—C11	109.5 (2)
C2—C3—C4	104.1 (2)	C12—C9—C11	111.1 (3)
C2—C3—H3B	110.9	C10—C9—C11	112.9 (3)
C4—C3—H3B	110.9	C9—C10—H10A	109.5
C2—C3—H3A	110.9	C9—C10—H10C	109.5
C4—C3—H3A	110.9	H10A—C10—H10C	109.5
H3B—C3—H3A	109.0	C9—C10—H10B	109.5
C1—C4—C7	112.9 (2)	H10A—C10—H10B	109.5
C1—C4—C3	102.6 (2)	H10C—C10—H10B	109.5
C7—C4—C3	116.0 (2)	C9—C11—H11B	109.5
C1—C4—C5	109.8 (2)	C9—C11—H11C	109.5
C7—C4—C5	104.0 (2)	H11B—C11—H11C	109.5
C3—C4—C5	111.7 (2)	C9—C11—H11A	109.5
C6—C5—C4	103.8 (2)	H11B—C11—H11A	109.5
C6—C5—H5B	111.0	H11C—C11—H11A	109.5
C4—C5—H5B	111.0	C9—C12—H12A	109.5
C6—C5—H5A	111.0	C9—C12—H12C	109.5
C4—C5—H5A	111.0	H12A—C12—H12C	109.5
H5B—C5—H5A	109.0	C9—C12—H12B	109.5
N2—C6—C5	103.1 (2)	H12A—C12—H12B	109.5
N2—C6—H6B	111.1	H12C—C12—H12B	109.5
C5—C6—H6B	111.1
C2—N1—C1—O1	−179.7 (3)	C7—N2—C6—C5	15.7 (3)
C2—N1—C1—C4	1.7 (3)	C4—C5—C6—N2	−30.5 (3)
C1—N1—C2—C3	15.7 (3)	C8—N2—C7—C4	−175.1 (3)
N1—C2—C3—C4	−25.8 (3)	C6—N2—C7—C4	5.9 (3)
O1—C1—C4—C7	37.5 (4)	C1—C4—C7—N2	−143.8 (2)
N1—C1—C4—C7	−143.8 (2)	C3—C4—C7—N2	98.2 (3)
O1—C1—C4—C3	163.1 (3)	C5—C4—C7—N2	−24.9 (3)
N1—C1—C4—C3	−18.2 (3)	C6—N2—C8—O3	0.5 (4)
O1—C1—C4—C5	−78.0 (3)	C7—N2—C8—O3	−178.4 (3)
N1—C1—C4—C5	100.7 (3)	C6—N2—C8—O2	179.2 (3)
C2—C3—C4—C1	26.7 (3)	C7—N2—C8—O2	0.3 (4)
C2—C3—C4—C7	150.2 (2)	C9—O2—C8—O3	−8.6 (4)
C2—C3—C4—C5	−90.8 (2)	C9—O2—C8—N2	172.7 (2)
C1—C4—C5—C6	155.7 (2)	C8—O2—C9—C12	−172.4 (3)
C7—C4—C5—C6	34.6 (3)	C8—O2—C9—C10	−54.6 (4)
C3—C4—C5—C6	−91.2 (3)	C8—O2—C9—C11	69.9 (3)
C8—N2—C6—C5	−163.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1i	0.88	1.97	2.848 (3)	175.

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