[1R-(1α,2α,4α,5β,6α,7α)]-4-Benzoyl­oxymethyl-5,6-dihy­droxy-3,8-dioxa­tricyclo­[5.1.0.02,4]octan-5-yl acetate (3-deacetyl­crotepoxide) from Kaempferia rotunda Val.

Sirat, H.M.; Feng, Y.S.; Awang, K.; Ng, S.W.

doi:10.1107/S1600536810042686

[1R-(1α,2α,4α,5β,6α,7α)]-4-Benzoyloxymethyl-5,6-dihydroxy-3,8-dioxatricyclo[5.1.0.0^2,4]octan-5-yl acetate (3-deacetylcrotepoxide) from Kaempferia rotunda Val.

H. M. Sirat, Y. S. Feng, K. Awang and S. W. Ng

The title compound, C₁₆H₁₆O₇, isolated from Kaempferia rotunda rhizomes, features a six-membered cyclohexane ring that adopts a twisted-boat conformation owing to the presence of two adjacent epoxide attachments that lock in four of the six axial positions. The CH₃CO₂– and HO– substituents occupy equatorial positions. However, the bond angles at the ring carbon connected to the C₆H₅CO₂CH₂– substituent deviate signifcantly from the idealized tetrahedral angles as the carbon atom is part of an epoxide ring. In the crystal, the molecules are linked into chains by O—H

O hydrogen bonds.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536810042686/bt5386sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536810042686/bt5386Isup2.hkl Contains datablock I

CCDC reference: 799699

checkCIF report

Key indicators

Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.004 Å
R factor = 0.038
wR factor = 0.117
Data-to-parameter ratio = 9.4

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT919_ALERT_3_B Reflection(s) # Likely Affected by the Beamstop           1

Alert level C
PLAT338_ALERT_4_C Small Average Tau in cyclohexane C9     -C14          31.55 Deg.

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.50
           From the CIF: _reflns_number_total               2011
           Count of symmetry unique reflns         2011
           Completeness (_total/calc)            100.00%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT791_ALERT_4_G Note: The Model has Chirality at C9     (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C10    (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C11    (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C12    (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C13    (Verify)          R
PLAT791_ALERT_4_G Note: The Model has Chirality at C14    (Verify)          S

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   7 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 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
   8 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

Kaempferia rotunda is one of the four Malaysian Kaempferia of the Zingiberaceae family; among the constitutents isolated is 3-deacetylcrotepoxide (Scheme I), which was first reported by Pancharoen et al. (1996). 3-Deacetylcrotepoxide (Scheme I) features a six-membered cyclohexane ring that adopts a twisted boat conformation owing to the presence of two adjacent epoxide attachements that tie up four of the six axial positions. The CH₃CO₂– and HO– substituents occupy regular equatorial positions as each is connected to a methine carbon atom (Fig. 1). However, the bond angles at the ring carbon connected to the C₆H₅CO₂CH₂– substituent deviate signifcantly from the idealized tetrahedral angles as the carbon atom is part of an epoxide ring [112.4 (2), 117.9 (2), 120.3 (3) °].

Related literature top

For the isolation of the compound from Kaempferia rotunda, see: Pancharoen et al. (1996).

Experimental top

Kaempferia rotunda rhizomes were purchased from a market in Kempas, Johor. The rhizomes were dried and then grounded. The grounded rhizomes were extracted with n-hexane (4.5 L), ethyl acetate (4.5 L) and methanol (4.5 L) in a soxhlet extractor for 16 h. The extracts were concentrated to give a dark brown semi-solid from the n-hexane extract (2.32 g), a dark brown oil from the ethyl acetate extract (6.80 g) and a dark brown viscous liquid from the methanol extract (15.27 g). The ethyl acetate extract (6.80 g) was fractionated by VLC (260 g, column size: 10 x 12 cm) by using petroleum ether, ether and ethyl acetate to afford four fractions, (0.02 g, 0.15 g, 2.70 g and 2.50 g. Evaporation of the solvent of the third fraction yielded 3-deacetylcrotepoxide (0.145 g, 2.13%) as colorless crystals.

The absolute configuration was assumed from that obtained from spectroscopic measurements (Pancharoen et al., 1996).

Structure description top

For the isolation of the compound from Kaempferia rotunda, see: Pancharoen et al. (1996).

Computing details top

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: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

Fig. 1. Anisotropic displacement ellipsoid plot (Barbour, 2001) of C₁₆H₁₆O₇ at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.

[1R-(1α,2α,4α,5β,6α,7α)]-4-Benzoyloxymethyl-5,6-dihydroxy- 3,8-dioxatricyclo[5.1.0.0^2,4]octan-5-yl acetate top

Crystal data top

C₁₆H₁₆O₇	F(000) = 672
M_r = 320.29	D_x = 1.445 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1788 reflections
a = 5.7451 (7) Å	θ = 3.1–20.0°
b = 7.1746 (9) Å	µ = 0.12 mm⁻¹
c = 35.708 (5) Å	T = 100 K
V = 1471.9 (3) Å³	Prism, colorless
Z = 4	0.35 × 0.05 × 0.05 mm

Data collection top

Bruker SMART APEX diffractometer	1730 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.073
Graphite monochromator	θ_max = 27.5°, θ_min = 1.1°
ω scans	h = −7→7
14228 measured reflections	k = −9→9
2011 independent reflections	l = −46→46

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) = 0.117	H atoms treated by a mixture of independent and constrained refinement
S = 1.12	w = 1/[σ²(F_o²) + (0.0674P)²] where P = (F_o² + 2F_c²)/3
2011 reflections	(Δ/σ)_max = 0.001
213 parameters	Δρ_max = 0.37 e Å⁻³
1 restraint	Δρ_min = −0.33 e Å⁻³

Crystal data top

C₁₆H₁₆O₇	V = 1471.9 (3) Å³
M_r = 320.29	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.7451 (7) Å	µ = 0.12 mm⁻¹
b = 7.1746 (9) Å	T = 100 K
c = 35.708 (5) Å	0.35 × 0.05 × 0.05 mm

Data collection top

Bruker SMART APEX diffractometer	1730 reflections with I > 2σ(I)
14228 measured reflections	R_int = 0.073
2011 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	1 restraint
wR(F²) = 0.117	H atoms treated by a mixture of independent and constrained refinement
S = 1.12	Δρ_max = 0.37 e Å⁻³
2011 reflections	Δρ_min = −0.33 e Å⁻³
213 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.4671 (3)	0.4022 (3)	0.89359 (5)	0.0161 (4)
O2	0.1026 (4)	0.3085 (3)	0.88101 (5)	0.0237 (5)
O3	0.5062 (3)	0.3882 (3)	0.78913 (5)	0.0166 (4)
O4	0.1819 (4)	0.5944 (3)	0.74537 (5)	0.0204 (5)
O5	0.4387 (4)	0.9627 (3)	0.80058 (6)	0.0220 (5)
H5	0.541 (5)	0.999 (5)	0.7854 (8)	0.032 (10)*
O6	0.6886 (3)	0.7118 (3)	0.84539 (5)	0.0164 (4)
O7	0.5199 (4)	0.8762 (3)	0.89191 (6)	0.0251 (5)
C1	0.1872 (5)	0.4312 (4)	0.94156 (7)	0.0152 (6)
C2	0.3442 (5)	0.5291 (4)	0.96376 (8)	0.0177 (6)
H2	0.4890	0.5684	0.9536	0.021*
C3	0.2893 (6)	0.5693 (4)	1.00069 (8)	0.0208 (6)
H3	0.3963	0.6364	1.0158	0.025*
C4	0.0783 (6)	0.5115 (4)	1.01552 (8)	0.0207 (6)
H4	0.0423	0.5364	1.0410	0.025*
C5	−0.0805 (5)	0.4172 (4)	0.99317 (8)	0.0203 (6)
H5A	−0.2256	0.3789	1.0034	0.024*
C6	−0.0289 (5)	0.3787 (4)	0.95618 (8)	0.0183 (6)
H6	−0.1395	0.3169	0.9408	0.022*
C7	0.2420 (5)	0.3749 (4)	0.90243 (7)	0.0163 (6)
C8	0.5387 (5)	0.3349 (4)	0.85715 (7)	0.0162 (6)
H8A	0.4820	0.2058	0.8537	0.019*
H8B	0.7108	0.3329	0.8558	0.019*
C9	0.4444 (5)	0.4570 (4)	0.82602 (7)	0.0143 (6)
C10	0.2631 (5)	0.3857 (4)	0.80053 (7)	0.0167 (6)
H10	0.1942	0.2615	0.8067	0.020*
C11	0.1072 (5)	0.5236 (4)	0.78182 (7)	0.0177 (6)
H11	−0.0640	0.5067	0.7856	0.021*
C12	0.1917 (5)	0.7166 (4)	0.77788 (7)	0.0173 (6)
H12	0.0699	0.8160	0.7790	0.021*
C13	0.4278 (6)	0.7684 (4)	0.79357 (7)	0.0170 (6)
H13	0.5530	0.7316	0.7756	0.020*
C14	0.4611 (5)	0.6656 (4)	0.83081 (7)	0.0141 (6)
H14	0.3394	0.7078	0.8490	0.017*
C15	0.6928 (6)	0.8232 (4)	0.87612 (7)	0.0183 (6)
C16	0.9378 (6)	0.8664 (5)	0.88744 (9)	0.0274 (7)
H16A	0.9366	0.9530	0.9087	0.041*
H16B	1.0202	0.9235	0.8663	0.041*
H16C	1.0169	0.7510	0.8947	0.041*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0167 (10)	0.0203 (11)	0.0112 (9)	−0.0012 (9)	0.0016 (8)	0.0001 (8)
O2	0.0184 (11)	0.0360 (13)	0.0167 (10)	−0.0048 (10)	−0.0022 (9)	−0.0016 (9)
O3	0.0193 (10)	0.0184 (10)	0.0120 (9)	0.0009 (9)	0.0021 (7)	−0.0031 (8)
O4	0.0252 (11)	0.0239 (11)	0.0122 (9)	−0.0022 (10)	−0.0031 (8)	0.0016 (8)
O5	0.0331 (13)	0.0125 (10)	0.0202 (10)	−0.0010 (10)	0.0035 (10)	0.0003 (8)
O6	0.0171 (10)	0.0177 (10)	0.0146 (9)	−0.0014 (9)	0.0000 (8)	−0.0013 (8)
O7	0.0250 (12)	0.0321 (13)	0.0182 (10)	0.0011 (11)	0.0004 (9)	−0.0079 (9)
C1	0.0159 (13)	0.0173 (14)	0.0124 (12)	0.0034 (12)	0.0009 (11)	0.0031 (10)
C2	0.0170 (14)	0.0161 (14)	0.0201 (13)	−0.0001 (12)	0.0029 (11)	0.0032 (11)
C3	0.0270 (16)	0.0167 (14)	0.0189 (14)	0.0011 (13)	−0.0008 (12)	−0.0014 (11)
C4	0.0282 (17)	0.0182 (15)	0.0158 (13)	0.0065 (13)	0.0048 (13)	0.0011 (11)
C5	0.0178 (15)	0.0201 (16)	0.0229 (15)	0.0016 (12)	0.0029 (12)	0.0044 (11)
C6	0.0152 (14)	0.0208 (14)	0.0190 (14)	0.0000 (13)	−0.0029 (11)	0.0042 (12)
C7	0.0168 (14)	0.0166 (14)	0.0155 (13)	−0.0006 (12)	−0.0017 (11)	0.0038 (11)
C8	0.0170 (14)	0.0183 (14)	0.0132 (12)	0.0021 (12)	0.0000 (11)	0.0006 (10)
C9	0.0160 (13)	0.0176 (14)	0.0094 (12)	0.0012 (12)	0.0015 (10)	−0.0011 (10)
C10	0.0178 (14)	0.0186 (14)	0.0137 (12)	−0.0004 (12)	0.0004 (11)	−0.0015 (11)
C11	0.0171 (14)	0.0237 (15)	0.0122 (12)	−0.0013 (12)	−0.0012 (11)	0.0001 (11)
C12	0.0207 (14)	0.0203 (14)	0.0110 (12)	0.0057 (13)	−0.0010 (11)	0.0009 (11)
C13	0.0232 (15)	0.0144 (14)	0.0133 (12)	−0.0008 (12)	−0.0003 (12)	−0.0007 (10)
C14	0.0131 (13)	0.0173 (14)	0.0120 (12)	0.0001 (11)	0.0017 (10)	−0.0005 (10)
C15	0.0236 (15)	0.0173 (15)	0.0141 (13)	0.0008 (13)	−0.0023 (12)	−0.0007 (11)
C16	0.0241 (16)	0.0281 (17)	0.0300 (16)	−0.0003 (15)	−0.0067 (14)	−0.0071 (14)

Geometric parameters (Å, º) top

O1—C7	1.345 (3)	C5—C6	1.382 (4)
O1—C8	1.448 (3)	C5—H5A	0.9500
O2—C7	1.206 (3)	C6—H6	0.9500
O3—C9	1.451 (3)	C8—C9	1.515 (4)
O3—C10	1.455 (3)	C8—H8A	0.9900
O4—C12	1.455 (3)	C8—H8B	0.9900
O4—C11	1.462 (3)	C9—C10	1.475 (4)
O5—C13	1.418 (3)	C9—C14	1.509 (4)
O5—H5	0.84 (3)	C10—C11	1.492 (4)
O6—C15	1.358 (3)	C10—H10	1.0000
O6—C14	1.445 (3)	C11—C12	1.474 (4)
O7—C15	1.204 (4)	C11—H11	1.0000
C1—C2	1.391 (4)	C12—C13	1.514 (4)
C1—C6	1.398 (4)	C12—H12	1.0000
C1—C7	1.488 (4)	C13—C14	1.532 (4)
C2—C3	1.386 (4)	C13—H13	1.0000
C2—H2	0.9500	C14—H14	1.0000
C3—C4	1.387 (4)	C15—C16	1.497 (4)
C3—H3	0.9500	C16—H16A	0.9800
C4—C5	1.388 (4)	C16—H16B	0.9800
C4—H4	0.9500	C16—H16C	0.9800

C7—O1—C8	115.8 (2)	O3—C10—C11	116.3 (2)
C9—O3—C10	61.00 (17)	C9—C10—C11	118.1 (3)
C12—O4—C11	60.70 (18)	O3—C10—H10	116.9
C13—O5—H5	103 (3)	C9—C10—H10	116.9
C15—O6—C14	116.2 (2)	C11—C10—H10	116.9
C2—C1—C6	119.9 (3)	O4—C11—C12	59.43 (17)
C2—C1—C7	122.3 (3)	O4—C11—C10	116.9 (2)
C6—C1—C7	117.7 (3)	C12—C11—C10	117.9 (3)
C3—C2—C1	120.0 (3)	O4—C11—H11	116.7
C3—C2—H2	120.0	C12—C11—H11	116.7
C1—C2—H2	120.0	C10—C11—H11	116.7
C2—C3—C4	120.0 (3)	O4—C12—C11	59.86 (18)
C2—C3—H3	120.0	O4—C12—C13	118.5 (2)
C4—C3—H3	120.0	C11—C12—C13	119.3 (2)
C3—C4—C5	120.1 (3)	O4—C12—H12	115.9
C3—C4—H4	120.0	C11—C12—H12	115.9
C5—C4—H4	120.0	C13—C12—H12	115.9
C6—C5—C4	120.4 (3)	O5—C13—C12	110.3 (3)
C6—C5—H5A	119.8	O5—C13—C14	108.3 (2)
C4—C5—H5A	119.8	C12—C13—C14	108.3 (2)
C5—C6—C1	119.6 (3)	O5—C13—H13	110.0
C5—C6—H6	120.2	C12—C13—H13	110.0
C1—C6—H6	120.2	C14—C13—H13	110.0
O2—C7—O1	123.2 (3)	O6—C14—C9	109.0 (2)
O2—C7—C1	124.2 (3)	O6—C14—C13	108.4 (2)
O1—C7—C1	112.6 (2)	C9—C14—C13	111.8 (2)
O1—C8—C9	111.4 (2)	O6—C14—H14	109.2
O1—C8—H8A	109.3	C9—C14—H14	109.2
C9—C8—H8A	109.3	C13—C14—H14	109.2
O1—C8—H8B	109.3	O7—C15—O6	123.3 (3)
C9—C8—H8B	109.3	O7—C15—C16	125.7 (3)
H8A—C8—H8B	108.0	O6—C15—C16	110.9 (3)
O3—C9—C10	59.64 (16)	C15—C16—H16A	109.5
O3—C9—C14	115.2 (2)	C15—C16—H16B	109.5
C10—C9—C14	117.3 (3)	H16A—C16—H16B	109.5
O3—C9—C8	112.4 (2)	C15—C16—H16C	109.5
C10—C9—C8	120.3 (3)	H16A—C16—H16C	109.5
C14—C9—C8	117.9 (2)	H16B—C16—H16C	109.5
O3—C10—C9	59.37 (17)

C6—C1—C2—C3	2.1 (4)	O3—C10—C11—O4	23.0 (4)
C7—C1—C2—C3	−176.5 (3)	C9—C10—C11—O4	90.6 (3)
C1—C2—C3—C4	0.2 (4)	O3—C10—C11—C12	−44.9 (3)
C2—C3—C4—C5	−1.5 (4)	C9—C10—C11—C12	22.7 (4)
C3—C4—C5—C6	0.6 (4)	C11—O4—C12—C13	109.2 (3)
C4—C5—C6—C1	1.6 (4)	C10—C11—C12—O4	106.4 (3)
C2—C1—C6—C5	−2.9 (4)	O4—C11—C12—C13	−107.9 (3)
C7—C1—C6—C5	175.7 (3)	C10—C11—C12—C13	−1.5 (4)
C8—O1—C7—O2	−4.1 (4)	O4—C12—C13—O5	133.7 (2)
C8—O1—C7—C1	174.5 (2)	C11—C12—C13—O5	−156.8 (2)
C2—C1—C7—O2	−171.5 (3)	O4—C12—C13—C14	−107.9 (3)
C6—C1—C7—O2	9.9 (4)	C11—C12—C13—C14	−38.4 (3)
C2—C1—C7—O1	9.9 (4)	C15—O6—C14—C9	−128.9 (2)
C6—C1—C7—O1	−168.7 (2)	C15—O6—C14—C13	109.2 (2)
C7—O1—C8—C9	72.9 (3)	O3—C9—C14—O6	−93.0 (3)
C10—O3—C9—C14	−108.2 (3)	C10—C9—C14—O6	−160.3 (2)
C10—O3—C9—C8	113.0 (3)	C8—C9—C14—O6	43.4 (3)
O1—C8—C9—O3	−177.7 (2)	O3—C9—C14—C13	26.7 (4)
O1—C8—C9—C10	−110.8 (3)	C10—C9—C14—C13	−40.6 (4)
O1—C8—C9—C14	44.7 (4)	C8—C9—C14—C13	163.2 (2)
C9—O3—C10—C11	108.5 (3)	O5—C13—C14—O6	−61.7 (3)
C14—C9—C10—O3	104.6 (3)	C12—C13—C14—O6	178.7 (2)
C8—C9—C10—O3	−99.8 (3)	O5—C13—C14—C9	178.2 (3)
O3—C9—C10—C11	−105.5 (3)	C12—C13—C14—C9	58.6 (3)
C14—C9—C10—C11	−0.9 (4)	C14—O6—C15—O7	3.2 (4)
C8—C9—C10—C11	154.7 (3)	C14—O6—C15—C16	−177.8 (2)
C12—O4—C11—C10	−108.0 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O5—H5···O4ⁱ	0.84 (3)	2.05 (3)	2.887 (3)	172 (4)

Symmetry code: (i) −x+1, y+1/2, −z+3/2.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₆O₇
M_r	320.29
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	100
a, b, c (Å)	5.7451 (7), 7.1746 (9), 35.708 (5)
V (Å³)	1471.9 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.35 × 0.05 × 0.05

Data collection
Diffractometer	Bruker SMART APEX
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	14228, 2011, 1730
R_int	0.073
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.117, 1.12
No. of reflections	2011
No. of parameters	213
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.37, −0.33

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).