(±)-exo-2-Hydr­oxy-5-oxo-4,8-dioxatricyclo­[4.2.1.03,7]nonane-9-exo-carboxylic acid

Sadeghi-Khomami, A.; Thomas, N.R.; Wilson, C.

doi:10.1107/S1600536806030649

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 62| Part 9| September 2006| Pages o3759-o3761

https://doi.org/10.1107/S1600536806030649

(±)-exo-2-Hydroxy-5-oxo-4,8-dioxatricyclo[4.2.1.0^3,7]nonane-9-exo-carboxylic acid

Ali Sadeghi-Khomami,^a Neil R. Thomas ^a and Claire Wilson ^b ^*

^aCentre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, England, and ^bSchool of Chemistry, University of Nottingham, Nottingham NG7 2RD, England
^*Correspondence e-mail: claire.wilson@nottingham.ac.uk

(Received 14 June 2006; accepted 4 August 2006; online 9 August 2006)

The title compound, C₈H₉NO₅, was prepared as a by-product in synthetic efforts to prepare a carbasugar analogue of a putative intermediate, viz. (±)-6-hydroxymethyl-7-oxabicyclo[2.2.1]hept-2-exo-3-endo-diol, in the uridine diphosphate–galactopyranose mutase-catalysed reaction. The structure shows extensive hydrogen bonding involving N—H⋯O and O—H⋯O as well as C—H⋯O interactions.

Comment

The title compound, (I), was prepared as a by-product in synthetic efforts to prepare a carbasugar analogue of a putative intermediate, viz. (±)-6-hydroxymethyl-7-oxabicyclo[2.2.1]hept-2-exo-3-endo-diol in the uridine diphosphate–galactopyranose mutase-catalysed reaction, and was synthesized from racemic exo-5,6-epoxy-7-oxabicyclo[2.2.1]heptan-trans-2,3-dicarboxylic acid dimethyl ester (Sadeghi-Khomami et al., 2005 ) through treatment with concentrated ammonia solution (30% w/v).

The molecular structure of (I) is shown in Fig. 1. There is extensive hydrogen bonding in the structure (see Table 1). N—H⋯O interactions form a ribbon structure (Fig. 2), which lies parallel to the ac plane and propagates along the c-axis direction. These ribbons can be considered to be linked by O—H⋯O interactions, forming a two-dimensional layer parallel to the bc plane (Fig. 3). In addition, there are C—H⋯O interactions in the structure (Table 1) which conform to the geometric conditions for the weak hydrogen bonds given by Desiraju & Steiner (1999 ).

Figure 1
View showing the molecular structure and atom-labelling scheme of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

Figure 2
View showing N—H⋯O hydrogen-bonding interactions (dashed lines), leading to a ribbon structure parallel to the ac plane and propagating parallel to the c axis.

Figure 3
View showing linkage of the N—H⋯O ribbons (each shown as a single colour) by O—H⋯O interactions (dashed lines), forming a sheet in the bc plane.

Experimental

Formation of the title compound occurred via hydrolysis of the endo-methyl carboxylate, followed by a 5-exo-Tet lactonization on to the exo-epoxide. Concurrently, the exo-methyl carboxylate is hydrolysed and, somewhat surprisingly, forms the carboxamide rather than the expected ammonium salt of the carboxylic acid. The resulting solution was neutralized to pH 7.0 after 16 h at room temperature by dropwise addition of glacial acetic acid and the solvent removed by lyophilization (see scheme). This procedure gave the amide-lactone product (R_F = 0.5, 2-propanol/MeOH 2:1), which crystallized from methanol as colourless blocks. The IR spectrum of the title compound clearly revealed carbonyl bands for the lactone (1780 cm⁻¹) and carboxamide functional groups (1670 cm⁻¹).

Crystal data

C₈H₉NO₅
M_r = 199.16
Monoclinic, P 2₁ /c
a = 8.3843 (6) Å
b = 9.1844 (6) Å
c = 10.1638 (7) Å
β = 97.525 (1)°
V = 775.92 (9) Å³
Z = 4
D_x = 1.705 Mg m⁻³
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 150 (2) K
Block, colourless
0.67 × 0.49 × 0.31 mm

Data collection

Bruker SMART1000 CCD area-detector diffractometer
ω scans
Absorption correction: none
6671 measured reflections
1744 independent reflections
1665 reflections with I > 2σ(I)
R_int = 0.051
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.096
S = 1.03
1744 reflections
140 parameters
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ²(F_o²) + (0.0546P)² + 0.3811P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.40 e Å⁻³
Δρ_min = −0.24 e Å⁻³
Extinction correction: SHELXL97
Extinction coefficient: 0.025 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N10—H10A⋯O2ⁱ	0.84 (2)	2.30 (2)	3.0871 (15)	156.1 (17)
N10—H10B⋯O5ⁱⁱ	0.88 (2)	2.39 (2)	3.1743 (15)	149.8 (16)
O2—H2⋯O11ⁱⁱⁱ	0.84 (2)	2.06 (2)	2.8841 (13)	167 (2)
C2—H2A⋯O11^iv	1.00	2.55	3.4779 (15)	154
C1—H1A⋯O11ⁱⁱⁱ	1.00	2.38	2.9723 (14)	117
C7—H7A⋯O4^v	1.00	2.43	3.2000 (14)	133
C7—H7A⋯O5^vi	1.00	2.60	3.2862 (15)	126
Symmetry codes: (i) -x+1, -y+2, -z+2; (ii) -x+1, -y+2, -z+1; (iii) $[x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iv) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (v) $[-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (vi) -x, -y+2, -z+1.

All H atoms could be located in a difference Fourier map. However, the H atoms bound to carbon were subsequently placed in idealized positions and included as part of a riding model, with C—H = 1.00 Å and U_iso(H) = 1.2U_eq(C). Positional and U_iso parameters were refined for H atoms bound to nitrogen and oxygen.

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT (Bruker, 2000 ); data reduction: SAINT and SHELXTL (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: MERCURY (Version 1.4.1; Macrae et al., 2006 ); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536806030649/fb2008sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806030649/fb2008Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT and SHELXTL (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Mercury (Version 1.4.1; Macrae et al., 2006); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).

(±)-exo-2-Hydroxy-5-oxo-4,8-dioxatricyclo[4.2.1.03,7]nonane-9-exo-carboxylic acid top

Crystal data top

C₈H₉NO₅	F(000) = 416
M_r = 199.16	D_x = 1.705 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 5318 reflections
a = 8.3843 (6) Å	θ = 2.2–27.5°
b = 9.1844 (6) Å	µ = 0.14 mm⁻¹
c = 10.1638 (7) Å	T = 150 K
β = 97.525 (1)°	Block, colourless
V = 775.92 (9) Å³	0.67 × 0.49 × 0.31 mm
Z = 4

Data collection top

Bruker SMART1000 CCD area-detector diffractometer	1665 reflections with I > 2σ(I)
Radiation source: normal-focus sealed tube	R_int = 0.051
Graphite monochromator	θ_max = 27.5°, θ_min = 2.5°
ω scans	h = −10→10
6671 measured reflections	k = −11→11
1744 independent reflections	l = −13→13

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.036	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.096	w = 1/[σ²(F_o²) + (0.0546P)² + 0.3811P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max = 0.001
1744 reflections	Δρ_max = 0.40 e Å⁻³
140 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.025 (4)

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.39752 (13)	0.90298 (12)	0.83551 (11)	0.0162 (2)
H1A	0.5033	0.8833	0.8904	0.019*
O2	0.27189 (11)	0.91959 (10)	1.03823 (8)	0.0221 (2)
H2	0.329 (3)	0.843 (2)	1.040 (2)	0.046 (6)*
C2	0.27728 (14)	0.98325 (13)	0.91116 (11)	0.0184 (3)
H2A	0.3023	1.0896	0.9187	0.022*
C3	0.11901 (14)	0.95537 (14)	0.81764 (12)	0.0203 (3)
H3A	0.0316	0.9169	0.8661	0.024*
O4	0.06852 (11)	1.08301 (10)	0.73785 (9)	0.0251 (2)
O5	0.10540 (11)	1.17205 (10)	0.53941 (9)	0.0272 (2)
C5	0.13596 (14)	1.08018 (13)	0.62312 (12)	0.0205 (3)
C6	0.24340 (13)	0.94895 (13)	0.62351 (11)	0.0171 (3)
H6A	0.2473	0.9071	0.5332	0.020*
C7	0.17366 (13)	0.84289 (13)	0.71936 (11)	0.0185 (3)
H7A	0.0875	0.7762	0.6771	0.022*
O8	0.30882 (10)	0.77254 (9)	0.79295 (8)	0.0184 (2)
C9	0.41311 (13)	0.97821 (12)	0.70168 (11)	0.0155 (2)
H9A	0.4365	1.0846	0.7126	0.019*
C10	0.54303 (13)	0.89808 (12)	0.63801 (11)	0.0163 (2)
N10	0.69432 (13)	0.92649 (13)	0.68952 (12)	0.0243 (3)
H10A	0.715 (2)	0.989 (2)	0.7503 (19)	0.038 (5)*
O11	0.50958 (10)	0.80859 (11)	0.54905 (9)	0.0258 (2)
H10B	0.769 (2)	0.881 (2)	0.6526 (18)	0.035 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0159 (5)	0.0172 (5)	0.0153 (5)	−0.0015 (4)	0.0017 (4)	0.0003 (4)
O2	0.0267 (5)	0.0245 (5)	0.0161 (4)	0.0012 (3)	0.0063 (3)	0.0021 (3)
C2	0.0200 (6)	0.0192 (5)	0.0165 (5)	−0.0004 (4)	0.0043 (4)	0.0008 (4)
C3	0.0176 (5)	0.0241 (6)	0.0197 (5)	0.0018 (4)	0.0046 (4)	0.0022 (4)
O4	0.0242 (5)	0.0295 (5)	0.0224 (5)	0.0107 (4)	0.0055 (3)	0.0031 (3)
O5	0.0257 (5)	0.0292 (5)	0.0263 (5)	0.0087 (4)	0.0020 (4)	0.0065 (4)
C5	0.0163 (5)	0.0243 (6)	0.0208 (6)	0.0022 (4)	0.0016 (4)	−0.0009 (4)
C6	0.0156 (5)	0.0192 (5)	0.0163 (5)	0.0009 (4)	0.0013 (4)	0.0005 (4)
C7	0.0153 (5)	0.0209 (6)	0.0191 (5)	−0.0011 (4)	0.0019 (4)	0.0006 (4)
O8	0.0186 (4)	0.0161 (4)	0.0203 (4)	−0.0009 (3)	0.0012 (3)	0.0010 (3)
C9	0.0147 (5)	0.0164 (5)	0.0153 (5)	0.0008 (4)	0.0021 (4)	0.0004 (4)
C10	0.0170 (5)	0.0160 (5)	0.0162 (5)	0.0002 (4)	0.0037 (4)	0.0025 (4)
N10	0.0159 (5)	0.0285 (6)	0.0287 (6)	0.0011 (4)	0.0030 (4)	−0.0103 (4)
O11	0.0199 (4)	0.0308 (5)	0.0270 (5)	−0.0007 (4)	0.0044 (3)	−0.0123 (4)

Geometric parameters (Å, º) top

C1—O8	1.4460 (13)	C5—C6	1.5044 (16)
C1—C2	1.5344 (15)	C6—C7	1.5457 (16)
C1—C9	1.5464 (15)	C6—C9	1.5594 (15)
C1—H1A	1.0000	C6—H6A	1.0000
O2—C2	1.4238 (14)	C7—O8	1.4279 (14)
O2—H2	0.84 (2)	C7—H7A	1.0000
C2—C3	1.5491 (16)	C9—C10	1.5270 (15)
C2—H2A	1.0000	C9—H9A	1.0000
C3—O4	1.4565 (14)	C10—O11	1.2269 (14)
C3—C7	1.5476 (16)	C10—N10	1.3332 (15)
C3—H3A	1.0000	N10—H10A	0.84 (2)
O4—C5	1.3612 (15)	N10—H10B	0.88 (2)
O5—C5	1.2018 (15)

O8—C1—C2	101.66 (9)	C5—C6—C9	111.68 (9)
O8—C1—C9	101.92 (8)	C7—C6—C9	100.53 (8)
C2—C1—C9	111.28 (9)	C5—C6—H6A	113.4
O8—C1—H1A	113.6	C7—C6—H6A	113.4
C2—C1—H1A	113.6	C9—C6—H6A	113.4
C9—C1—H1A	113.6	O8—C7—C6	105.99 (9)
C2—O2—H2	105.8 (14)	O8—C7—C3	104.22 (9)
O2—C2—C1	110.99 (9)	C6—C7—C3	98.89 (9)
O2—C2—C3	111.24 (9)	O8—C7—H7A	115.3
C1—C2—C3	100.33 (9)	C6—C7—H7A	115.3
O2—C2—H2A	111.3	C3—C7—H7A	115.3
C1—C2—H2A	111.3	C7—O8—C1	97.10 (8)
C3—C2—H2A	111.3	C10—C9—C1	107.73 (9)
O4—C3—C7	105.48 (9)	C10—C9—C6	110.79 (9)
O4—C3—C2	111.82 (10)	C1—C9—C6	101.22 (8)
C7—C3—C2	101.78 (9)	C10—C9—H9A	112.2
O4—C3—H3A	112.4	C1—C9—H9A	112.2
C7—C3—H3A	112.4	C6—C9—H9A	112.2
C2—C3—H3A	112.4	O11—C10—N10	122.30 (11)
C5—O4—C3	109.79 (9)	O11—C10—C9	121.89 (10)
O5—C5—O4	121.27 (11)	N10—C10—C9	115.73 (10)
O5—C5—C6	129.53 (11)	C10—N10—H10A	121.0 (13)
O4—C5—C6	109.20 (10)	C10—N10—H10B	115.9 (12)
C5—C6—C7	103.34 (9)	H10A—N10—H10B	122.9 (17)

O8—C1—C2—O2	76.24 (11)	O4—C3—C7—O8	142.70 (9)
C9—C1—C2—O2	−175.90 (9)	C2—C3—C7—O8	25.84 (11)
O8—C1—C2—C3	−41.43 (10)	O4—C3—C7—C6	33.59 (11)
C9—C1—C2—C3	66.43 (11)	C2—C3—C7—C6	−83.27 (10)
O2—C2—C3—O4	139.66 (10)	C6—C7—O8—C1	51.80 (10)
C1—C2—C3—O4	−102.85 (10)	C3—C7—O8—C1	−51.99 (10)
O2—C2—C3—C7	−108.18 (10)	C2—C1—O8—C7	58.46 (9)
C1—C2—C3—C7	9.31 (11)	C9—C1—O8—C7	−56.51 (9)
C7—C3—O4—C5	−20.84 (12)	O8—C1—C9—C10	−76.25 (10)
C2—C3—O4—C5	88.98 (11)	C2—C1—C9—C10	176.06 (9)
C3—O4—C5—O5	176.83 (11)	O8—C1—C9—C6	40.06 (10)
C3—O4—C5—C6	−2.27 (13)	C2—C1—C9—C6	−67.62 (11)
O5—C5—C6—C7	−154.72 (13)	C5—C6—C9—C10	−145.28 (10)
O4—C5—C6—C7	24.28 (12)	C7—C6—C9—C10	105.67 (10)
O5—C5—C6—C9	98.04 (15)	C5—C6—C9—C1	100.68 (10)
O4—C5—C6—C9	−82.96 (12)	C7—C6—C9—C1	−8.38 (10)
C5—C6—C7—O8	−141.71 (9)	C1—C9—C10—O11	100.73 (12)
C9—C6—C7—O8	−26.23 (11)	C6—C9—C10—O11	−9.14 (15)
C5—C6—C7—C3	−34.04 (11)	C1—C9—C10—N10	−76.22 (12)
C9—C6—C7—C3	81.44 (9)	C6—C9—C10—N10	173.92 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N10—H10A···O2ⁱ	0.84 (2)	2.30 (2)	3.0871 (15)	156.1 (17)
N10—H10B···O5ⁱⁱ	0.88 (2)	2.39 (2)	3.1743 (15)	149.8 (16)
O2—H2···O11ⁱⁱⁱ	0.84 (2)	2.06 (2)	2.8841 (13)	167 (2)
C2—H2A···O11^iv	1.00	2.55	3.4779 (15)	154
C1—H1A···O11ⁱⁱⁱ	1.00	2.38	2.9723 (14)	117
C7—H7A···O4^v	1.00	2.43	3.2000 (14)	133
C7—H7A···O5^vi	1.00	2.60	3.2862 (15)	126

Symmetry codes: (i) −x+1, −y+2, −z+2; (ii) −x+1, −y+2, −z+1; (iii) x, −y+3/2, z+1/2; (iv) −x+1, y+1/2, −z+3/2; (v) −x, y−1/2, −z+3/2; (vi) −x, −y+2, −z+1.

Acknowledgements

We thank the Iranian Government for financial support to Dr Ali Sadeghi-Khomani.

References

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