Crystal structure of benzyl 3-oxo-2-oxa-5-aza­bicyclo­[2.2.1]heptane-5-carboxyl­ate

Suvratha Krishnamurthy; Venkataprasad Jalli; Tarun Chand Vagvala; Tetsuji Moriguchi; Akihiko Tsuge

doi:10.1107/S2056989015010464

. 2015 Jun 6;71(Pt 7):o447–o448. doi: 10.1107/S2056989015010464

Crystal structure of benzyl 3-oxo-2-oxa-5-azabicyclo[2.2.1]heptane-5-carboxylate

Suvratha Krishnamurthy ^a,^*, Venkataprasad Jalli ^a, Tarun Chand Vagvala ^b, Tetsuji Moriguchi ^a, Akihiko Tsuge ^a

PMCID: PMC4518953 PMID: 26279900

Abstract

The title compound, C₁₃H₁₃NO₄ (also known as N-benzyloxycarbonyl-4-hydroxy-l-proline lactone), crystallizes with two molecules in the asymmetric unit. They have slightly different conformations: the fused ring systems almost overlap, but different C—O—C—C torsion angles for the central chains of −155.5 (2) and −178.6 (2)° lead to different twists for the terminal benzene ring. In the crystal, the molecules are linked by C—H⋯O interactions, generating a three-dimensional network. The absolute structure was established based on an unchanging chiral centre in the synthesis.

Keywords: crystal structure, 4-hydroxyproline, C—H⋯O interactions

Related literature

For biological background, see: Dickens et al. (2008 ▸); Erdmann & Wennemers (2011 ▸); Krishnamurthy et al. (2014 ▸); Gómez-Vidal & Silverman (2001 ▸). For the synthesis, see: Lombardo et al. (2012 ▸). graphic file with name e-71-0o447-scheme1.jpg

Experimental

Crystal data

C₁₃H₁₃NO₄
M _r = 247.24
Monoclinic,
a = 11.212 (2) Å
b = 8.8943 (16) Å
c = 12.258 (2) Å
β = 105.345 (2)°
V = 1178.8 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 90 K
0.40 × 0.35 × 0.30 mm

Data collection

Bruker APEX II KY CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T _min = 0.709, T _max = 0.969
11252 measured reflections
4157 independent reflections
4079 reflections with I > 2σ(I)
R _int = 0.035

Refinement

R[F ² > 2σ(F ²)] = 0.027
wR(F ²) = 0.073
S = 1.06
4157 reflections
325 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT (Bruker, 2009 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: Mercury (Macrae et al., 2008 ▸); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015010464/hb7435sup1.cif

e-71-0o447-sup1.cif^{(29.9KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010464/hb7435Isup2.hkl

e-71-0o447-Isup2.hkl^{(203.7KB, hkl)}

Click here for additional data file.^{(1.2MB, tif)}

. DOI: 10.1107/S2056989015010464/hb7435fig1.tif

Molecular configuration for the title compound with displacement ellipsoids drawn at the 50% probability level. Hydrogen atoms are omitted for clarity.

Click here for additional data file.^{(1.5MB, tif)}

. DOI: 10.1107/S2056989015010464/hb7435fig2.tif

Crystal packing diagram of the title compound.

Click here for additional data file.^{(15.8KB, tif)}

. DOI: 10.1107/S2056989015010464/hb7435fig3.tif

Synthetic scheme for the title compound (I)

CCDC reference: 1402251

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C1H1O5ⁱ	0.98	2.42	3.3493(18)	159
C2H2AO7ⁱⁱ	0.97	2.46	3.2116(18)	134
C3H3O5ⁱⁱⁱ	0.98	2.37	3.2816(18)	155
C4H4BO7ⁱⁱⁱ	0.97	2.39	3.3408(18)	168
C15H15AO3^iv	0.97	2.44	3.1382(19)	128
C16H16O1^v	0.98	2.49	3.2207(18)	131
C26H26O6^vi	0.93	2.58	3.4584(19)	157

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

Acknowledgments

We are grateful to the Center for Instrumental Analysis, Kyushu Institute of Technology (KITCIA), for the ¹H NMR and X-ray analysis.

supplementary crystallographic information

S1. Chemical context

Four possible stereoisomers exists for 4-hydroxyproline. The (2S,4R)-isomer is mainly found in collagen and its presence in collagen is a very important factor for its triple helix stabilization (Erdmann & Wennemers, 2011). Moreover (2S,4S)- of 4-hydroxyproline isomer was found to have anticancer activity (Dickens et al. 2008)

For related derivatives and synthesis see (Krishnamurthy et al. 2014, Gomez-Vidal and Silverman, 2001)

S2. Synthesis and crystallization

(I) was prepared in exactly the same manner as described by (Lombardo et al. 2012). To a solution of Z-Hyp-OH (3.0 g, 11.3 mmol) and triphenylphosphine (3.5 g, 13.3 mmol) in dry THF (50 mL) at 0 °C, was added DEAD (40% in toluene, 5.7 mL, 12.4 mmol), under argon. The resulting solution was warmed to room temperature and stirred. After 12 h, the solvent was evaporated to give a crude residue which was purified directly by flash chromatography on silica gel (EtOAc:hexane, 40:60, v/v) to give I as a white solid ( 2 g, 72 %). (¹H NMR matched Lombardo et al. 2012)

Single crystals were obtained by vapour diffusion method at room temperature, i.e., pentane vapour was allowed to slowly diffuse into a EtOAc (0.3 ml) solution of I at room temperature. Single crystals were obtained after three days.

S3. Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 1.