Crystal structure of (1R,4R)-tert-butyl 3-oxo-2-oxa-5-aza­bicyclo­[2.2.2]octane-5-carboxyl­ate

In the title compound, C₁₁H₁₇NO₄, commonly known as N-tert-but­oxy­carbonyl-5-hy­droxy-D-pipecolic acid lactone, the absolute configuration is (1R,4R) due to the enantiomeric purity of the starting material which remains unchanged during the course of the reaction. In the crystal there no inter­molecular hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 90 K
• Mean [sigma](C-C) = 0.001 Å
• R factor = 0.030
• wR factor = 0.081
• Data-to-parameter ratio = 18.9

checkCIF/PLATON results

No syntax errors found



Alert level C
STRVA01_ALERT_4_C           Flack test results are meaningless.
           From the CIF: _refine_ls_abs_structure_Flack    0.100
           From the CIF: _refine_ls_abs_structure_Flack_su    0.700
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......      0.960 Note
PLAT230_ALERT_2_C Hirshfeld Test Diff for    O3     --  C7      ..        5.2 su

Alert level G
PLAT032_ALERT_4_G Std. Uncertainty on Flack Parameter Value High .      0.700 Report
PLAT791_ALERT_4_G The Model has Chirality at C1      (Chiral SPGR)          R Verify
PLAT791_ALERT_4_G The Model has Chirality at C4      (Chiral SPGR)          R Verify
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         63 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   4 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   5 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

5-Hydroxypipecolic acid is a higher homologue of 4-hydroxyproline, which is found in dates (Witkop & Foltz, 1957). 4-Hydroxyproline is formed by post-translational modification of proline in collagen and is responsible for enhancing its stability. Literature reports the synthesis of 5-hydroxypipecolic acid derivatives (Hoarau et al., 1996; Sun et al., 2008), generally forming diastereomeric mixtures of cis- and trans-5-hydroxypipecolic acids. Therefore such syntheses suffer from disadvantages of separation of the diasteromers making the procedure very tedious. A facile procedure to isolate this amino acid was desirable.

Our previous communication reported the synthesis of a 4-hydroxyproline derivative from an amino acid bearing epoxide (Krishnamurthy et al. 2014). It is reported in this study that the cis-isomer undergoes intramolecular lactonization to tert-butyl- 3-oxo-2-oxa-5-azabicyclo[2.2.1]heptane-5-carboxylate, making the isolation from the trans ester highly feasible. Based on this observation it can be expected that cis-5-hydroxypipecolic acids would also undergo in situ intramolecular lactonization. In fact, when a mixture of a cis- and trans-5-hydroxypipecolic acid derivatives was reacted under acidic conditions, the cis-isomer successfully converted to the lactone (I), subsequently readily separated from the remaining trans--isomer. We had previously reported the crystal structure of racemic tert-butyl- 3-oxo-2-oxa-5-azabicyclo[2.2.2]octane-5-carboxylate (Moriguchi, Krishnamurthy, Arai, Tsuge et al., 2014) and (1S,4S)-tert-butyl 3-oxo-2-oxa-5-azabicyclo[2.2.2]octane-5-carboxylate (Moriguchi, Krishnamurthy, Arai, & Tsuge, 2014). Herein we would like to report the crystal structure of enantiomerically pure (1R,4R)-tert-butyl- 3-oxo-2-oxa-5-azabicyclo[2.2.2]octane-5-carboxylate, C₁₁H₁₇N O₄, (I).

The title compound (I), commonly known as N-tert- butoxycarbonyl-5-hydroxy-D-pipecolic acid lactone, was derived from a starting product having a cis configuration for both hydroxyl and carboxyl groups, leading to lactone formation (Fig. 1). The nitrogen atom N1 appears next to the bridge-head atom within the bicyclic ring system. The absolute configuration of the compound was found to be (1R,4R) due to the configuration of the starting material (Fig. 3). The Flack structure parameter (Flack, 1983) determined for (I) [0.1 (7)], although not definitive because of the uncertainty factor, is considered to provide adequate supporting evidence for this configuration. The desired hydrophobic conformer (1R,4R), (I) was easily isolated from hydrophylic (1R,4S)–(4) (Fig. 3). The intramolecular lactonization is possible only in (1R,4R)–(3) isomer due to its configuration. The hydroxyl and the carboxyl groups are in close proximity due to the cis- configuration of (1R,4R)–(3), which leads to the intamolecular lactonization with loss of EtOH. With the (1R,4S)–(4) isomer the hydroxyl and the carboxyl groups are far apart due to the trans- configuration, thus preventing the lactonization. In the crystal there no formal intramolecular hydrogen bonds (Fig. 2).

This work represents the first structural characterization of this (1R,4R)- aza and oxa bicyclic chiral lactone characterized by X-ray analysis.

Related literature

For background information on 5-hydroxypipecolic acid and related compounds, see: Witkop & Foltz (1957); Hoarau et al. (1996); Sun et al. (2008). For the synthesis of a related compound, see: Krishnamurthy et al. (2014). For crystal structures of related lactones, including the (1S,4S) conformer, see: Moriguchi, Krishnamurthy, Arai & Tsuge (2014); Moriguchi, Krishnamurthy, Arai, Matsumoto et al. (2014).

S2. Experimental

The basic reaction scheme for preparation of the title compound (I) is shown in Fig. 3. To a ice cooled solution of 4 mol/L HCl in 1,4-dioxane (16 mL), a solution of diastereomeric (1) ( 0.97 g, 3.56 mmol) in 0.5 mL of 1,4-dioxane was added. This reaction mixture was then warmed to room temperature and stirred. After 3 h most of the volatile materials were removed under vacuum resulting in a crude oily mixture. Trituration with diethyl ether followed by decantation resulted in (2) as a foam (0.71 g, 95 %). DIEA (0.89 mL, 5.07 mmol) was added to a solution of (2) ( 0.71 g, 3.38 mmol) in DMF (13 mL) and stirred at 50 °C. After 6 h the solution was warmed to room temperature, followed by addition of Boc₂O (3.96 g, 18.1 mmol), additional DIEA (0.3 mL, 1.69 mmol) and stirred at room temperature for 18 h. The DMF was evaporated and the crude mixture was subsequently washed with 10% aqueous citric acid, 4% aqueous NaHCO₃, brine, dried (MgSO₄), filtered and evaporated to obtain an oil. The crude product was purified by silica gel column chromatography with (CHCl₃/MeOH, 100:0 to 98:2, v/v) to yield (1R,4R), (I) (0.18 g, 23%) as a white solid. Single crystals were obtained by vapour diffusion method at room temperature, i.e., hexane vapour was allowed to diffuse into an EtOAc (0.5 ml) solution of (1R,4R), (I) at room temperature. Single crystals suitable for analysis were obtained after a week.

¹H NMR 4.61-4.82 (2H, m), 3.63 (1H, m), 3.45 (1H, m), 2.22 (1H, br s), 2.11 (1H, m), 2.00 (1H, m), 1.80 (1H, m), 1.47 (9H, s); MS (FAB m/z): 228 (74), 190 (44), 172 (100), 137 (50), 128 (68), 55 (47). HRMS(FAB) calcd for C₁₁H₁₈N₁O₄ [M + H]⁺ 228.12358, found 228.1243

S3. Refinement

All hydrogen atoms were placed in calculated positions (C—H = 0.98–1.00 Å) and allowed to ride, with U_isoH = 1.5U_eqC(methyl) or 1.2U_eqC(methine and methylene). The absolute structure parameter (Flack, 1983) for (I) [0.01 (7) for 2933 Friedel pairs], although not definitive is sufficient to confirm the (1R,4R) identity, as distinct from that of the known (1S,4S) conformer (Moriguchi, Krishnamurthy, Arai & Tsuge, 2014).

Computing details

Data collection: APEX2 (Bruker,2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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: SHELXL97 (Sheldrick, 2008).

Figures

	Fig. 1. Molecular configuration and atom numbering scheme for the title compound with displacement ellipsoids drawn at the 50% probability level. Hydrogen atoms are omitted for clarity.
	Fig. 2. Crystal packing diagram of the title compound.
	Fig. 3. Synthetic scheme for the title compound (I).

(1R,4R)-tert-butyl 3-oxo-2-oxa-5-azabicyclo[2.2.2]octane-5-carboxylate

Crystal data

C11H17NO4	Dx = 1.318 Mg m^−3
Mr = 227.26	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 9630 reflections
a = 9.6472 (4) Å	θ = 2.7–28.7°
b = 9.7084 (4) Å	µ = 0.10 mm^−1
c = 12.2323 (5) Å	T = 90 K
V = 1145.66 (8) Å^3	Prism, colorless
Z = 4	0.45 × 0.40 × 0.40 mm
F(000) = 488

Data collection

Bruker APEX2 KY CCD diffractometer	2791 independent reflections
Radiation source: fine-focus sealed tube	2728 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
Detector resolution: 16.6666 pixels mm^-1	θmax = 28.7°, θmin = 2.7°
ϕ and ω–scans	h = −12→12
Absorption correction: multi-scan SADABS (Bruker, 2009)	k = −12→12
Tmin = 0.870, Tmax = 0.961	l = −16→16
13518 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.030	w = 1/[σ^2(Fo^2) + (0.0583P)^2 + 0.1302P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.081	(Δ/σ)max < 0.001
S = 1.02	Δρmax = 0.24 e Å^−3
2791 reflections	Δρmin = −0.27 e Å^−3
148 parameters	Extinction correction: SHELXL97
0 restraints	Extinction coefficient: 0.0015
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 2933 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.1 (7)

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.

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

	x	y	z	Uiso*/Ueq
C1	0.65404 (10)	0.31574 (9)	0.06026 (7)	0.01427 (18)
H1	0.71	0.2937	−0.0063	0.017*
C2	0.49996 (10)	0.33409 (10)	0.03171 (8)	0.0176 (2)
H2A	0.4628	0.2485	−0.0011	0.021*
H2B	0.4883	0.41	−0.0215	0.021*
C3	0.42204 (10)	0.36786 (11)	0.13907 (9)	0.0206 (2)
H3B	0.378	0.4597	0.1335	0.025*
H3A	0.3485	0.2987	0.1521	0.025*
C4	0.52501 (11)	0.36654 (10)	0.23335 (8)	0.01785 (19)
H4	0.475	0.3836	0.3037	0.021*
C5	0.63878 (10)	0.47291 (11)	0.21909 (8)	0.0178 (2)
H5B	0.5993	0.567	0.2175	0.021*
H5A	0.7064	0.4671	0.2798	0.021*
C6	0.66134 (10)	0.19956 (10)	0.14366 (8)	0.01762 (19)
C7	0.81399 (10)	0.51222 (9)	0.07261 (8)	0.01444 (19)
C8	0.96933 (10)	0.70326 (10)	0.12123 (8)	0.01618 (19)
C9	1.10001 (11)	0.61760 (12)	0.11084 (11)	0.0276 (2)
H9A	1.0964	0.5638	0.0431	0.041*
H9B	1.1072	0.5551	0.1735	0.041*
H9C	1.181	0.6785	0.1092	0.041*
C10	0.94288 (14)	0.79172 (11)	0.02135 (10)	0.0272 (3)
H10A	0.8622	0.8507	0.0345	0.041*
H10B	0.925	0.7324	−0.0419	0.041*
H10C	1.0243	0.8492	0.0069	0.041*
C11	0.97332 (14)	0.79157 (13)	0.22359 (10)	0.0311 (3)
H11A	0.9866	0.7325	0.2877	0.047*
H11B	0.8858	0.842	0.2307	0.047*
H11C	1.0502	0.8572	0.2184	0.047*
N1	0.70560 (9)	0.44009 (8)	0.11448 (7)	0.01612 (17)
O1	0.71703 (8)	0.08995 (8)	0.13238 (7)	0.02526 (18)
O2	0.59161 (8)	0.23044 (8)	0.23684 (6)	0.01975 (16)
O3	0.86922 (8)	0.48744 (7)	−0.01469 (6)	0.01893 (16)
O4	0.84801 (7)	0.61426 (7)	0.14236 (6)	0.01846 (16)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0141 (4)	0.0119 (4)	0.0168 (4)	−0.0019 (3)	0.0008 (3)	−0.0028 (3)
C2	0.0155 (5)	0.0172 (4)	0.0201 (4)	−0.0010 (4)	−0.0030 (3)	−0.0007 (3)
C3	0.0129 (4)	0.0230 (5)	0.0259 (5)	0.0005 (4)	0.0000 (4)	−0.0014 (4)
C4	0.0160 (4)	0.0179 (4)	0.0196 (4)	−0.0001 (4)	0.0032 (4)	−0.0012 (4)
C5	0.0166 (4)	0.0198 (4)	0.0172 (4)	−0.0019 (4)	0.0050 (3)	−0.0052 (3)
C6	0.0143 (4)	0.0171 (4)	0.0215 (5)	−0.0016 (3)	−0.0017 (4)	−0.0002 (4)
C7	0.0145 (4)	0.0126 (4)	0.0162 (4)	0.0002 (3)	−0.0017 (3)	0.0000 (3)
C8	0.0151 (4)	0.0155 (4)	0.0179 (4)	−0.0058 (4)	−0.0001 (3)	−0.0001 (3)
C9	0.0166 (5)	0.0241 (5)	0.0421 (6)	−0.0010 (4)	−0.0024 (4)	0.0012 (5)
C10	0.0361 (6)	0.0179 (5)	0.0275 (5)	−0.0039 (4)	−0.0051 (4)	0.0051 (4)
C11	0.0330 (6)	0.0349 (6)	0.0255 (6)	−0.0171 (5)	0.0039 (5)	−0.0126 (5)
N1	0.0161 (4)	0.0161 (4)	0.0162 (4)	−0.0040 (3)	0.0032 (3)	−0.0056 (3)
O1	0.0252 (4)	0.0171 (3)	0.0334 (4)	0.0050 (3)	−0.0025 (4)	0.0002 (3)
O2	0.0211 (4)	0.0186 (3)	0.0195 (3)	0.0009 (3)	0.0015 (3)	0.0029 (3)
O3	0.0219 (4)	0.0184 (3)	0.0165 (3)	−0.0038 (3)	0.0041 (3)	−0.0022 (3)
O4	0.0175 (3)	0.0185 (3)	0.0194 (3)	−0.0073 (3)	0.0040 (3)	−0.0059 (3)

Geometric parameters (Å, º)

C1—N1	1.4645 (11)	C6—O2	1.3570 (12)
C1—C6	1.5225 (13)	C7—O3	1.2175 (12)
C1—C2	1.5373 (14)	C7—O4	1.3481 (11)
C1—H1	1.0	C7—N1	1.3587 (12)
C2—C3	1.5482 (14)	C8—O4	1.4776 (11)
C2—H2A	0.99	C8—C9	1.5156 (15)
C2—H2B	0.99	C8—C10	1.5150 (14)
C3—C4	1.5222 (15)	C8—C11	1.5180 (14)
C3—H3B	0.99	C9—H9A	0.98
C3—H3A	0.99	C9—H9B	0.98
C4—O2	1.4699 (13)	C9—H9C	0.98
C4—C5	1.5171 (13)	C10—H10A	0.98
C4—H4	1.0	C10—H10B	0.98
C5—N1	1.4677 (12)	C10—H10C	0.98
C5—H5B	0.99	C11—H11A	0.98
C5—H5A	0.99	C11—H11B	0.98
C6—O1	1.2000 (12)	C11—H11C	0.98
N1—C1—C6	106.95 (7)	O3—C7—O4	126.43 (9)
N1—C1—C2	109.62 (8)	O3—C7—N1	124.45 (9)
C6—C1—C2	106.43 (8)	O4—C7—N1	109.12 (8)
N1—C1—H1	111.2	O4—C8—C9	110.65 (8)
C6—C1—H1	111.2	O4—C8—C10	109.82 (8)
C2—C1—H1	111.2	C9—C8—C10	112.55 (9)
C1—C2—C3	107.54 (8)	O4—C8—C11	101.89 (8)
C1—C2—H2A	110.2	C9—C8—C11	110.98 (10)
C3—C2—H2A	110.2	C10—C8—C11	110.44 (9)
C1—C2—H2B	110.2	C8—C9—H9A	109.5
C3—C2—H2B	110.2	C8—C9—H9B	109.5
H2A—C2—H2B	108.5	H9A—C9—H9B	109.5
C4—C3—C2	108.91 (8)	C8—C9—H9C	109.5
C4—C3—H3B	109.9	H9A—C9—H9C	109.5
C2—C3—H3B	109.9	H9B—C9—H9C	109.5
C4—C3—H3A	109.9	C8—C10—H10A	109.5
C2—C3—H3A	109.9	C8—C10—H10B	109.5
H3B—C3—H3A	108.3	H10A—C10—H10B	109.5
O2—C4—C5	107.40 (8)	C8—C10—H10C	109.5
O2—C4—C3	108.35 (8)	H10A—C10—H10C	109.5
C5—C4—C3	112.29 (9)	H10B—C10—H10C	109.5
O2—C4—H4	109.6	C8—C11—H11A	109.5
C5—C4—H4	109.6	C8—C11—H11B	109.5
C3—C4—H4	109.6	H11A—C11—H11B	109.5
N1—C5—C4	105.68 (8)	C8—C11—H11C	109.5
N1—C5—H5B	110.6	H11A—C11—H11C	109.5
C4—C5—H5B	110.6	H11B—C11—H11C	109.5
N1—C5—H5A	110.6	C7—N1—C1	121.03 (8)
C4—C5—H5A	110.6	C7—N1—C5	123.69 (8)
H5B—C5—H5A	108.7	C1—N1—C5	115.13 (8)
O1—C6—O2	120.96 (9)	C6—O2—C4	113.01 (7)
O1—C6—C1	126.91 (9)	C7—O4—C8	120.79 (7)
O2—C6—C1	112.10 (8)
N1—C1—C2—C3	−56.55 (10)	C6—C1—N1—C7	123.18 (10)
C6—C1—C2—C3	58.77 (10)	C2—C1—N1—C7	−121.84 (9)
C1—C2—C3—C4	−1.58 (11)	C6—C1—N1—C5	−52.53 (11)
C2—C3—C4—O2	−57.69 (10)	C2—C1—N1—C5	62.46 (10)
C2—C3—C4—C5	60.76 (11)	C4—C5—N1—C7	−179.64 (9)
O2—C4—C5—N1	61.20 (10)	C4—C5—N1—C1	−4.06 (11)
C3—C4—C5—N1	−57.81 (10)	O1—C6—O2—C4	−177.27 (9)
N1—C1—C6—O1	−126.60 (11)	C1—C6—O2—C4	0.91 (11)
C2—C1—C6—O1	116.29 (11)	C5—C4—O2—C6	−61.30 (10)
N1—C1—C6—O2	55.36 (10)	C3—C4—O2—C6	60.21 (10)
C2—C1—C6—O2	−61.75 (10)	O3—C7—O4—C8	−4.98 (15)
O3—C7—N1—C1	5.74 (15)	N1—C7—O4—C8	175.60 (8)
O4—C7—N1—C1	−174.83 (8)	C10—C8—O4—C7	67.57 (11)
O3—C7—N1—C5	−178.93 (9)	C9—C8—O4—C7	−57.30 (12)
O4—C7—N1—C5	0.50 (13)	C11—C8—O4—C7	−175.35 (9)