Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Previous article
Next article
Previous article
Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Next article

organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2274
https://doi.org/10.1107/S1600536812028334

5-Hy­dr­oxy-6-[(E)-2-phenyl­ethen­yl]-5,6-di­hydro-2H-pyran-2-one isolated from Goniothalamus ridleyi

Samsiah Jusoh,a Laily B. Din,a Zuriati Zakariaa and Hamid Khaledib*

aSchool of Chemical Sciences and Food Technology, Faculty of Science and Technology, National University of Malaysia, 43600 UKM Bangi, Selangor, Malaysia, and bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: hamid.khaledi@gmail.com

(Received 14 June 2012; accepted 22 June 2012; online 30 June 2012)

In the title compound, C13H12O3, the pyran ring adopts a half-chair conformation with a C atom deviating from the least-squares plane of the remaining ring atoms by 0.606 (2) Å. This plane and that of the benzene ring make a dihedral angle of 44.18 (6)°. In the crystal, mol­ecules are linked through O—H⋯O hydrogen bonds into infinite chains along the b axis, and these chains are cross-linked by C—H⋯O hydrogen bonded into sheets lying parallel to the bc plane. The layers are further connected via C—H⋯π inter­actions to form a three-dimensional supra­molecular structure.

Related literature

For spectroscopic characterization of the 5β-hy­droxy­goniothalamin, see: Goh et al. (1995[Goh, S. H., Ee, G. C. L. & Chuah, C. H. (1995). Nat. Prod. Lett. 5, 255-259.]). For the crystal structures of some similar compounds, see: Fun et al. (1995[Fun, H.-K., Sivakumar, K., Ang, H.-B., Sam, T.-W. & Gan, E.-K. (1995). Acta Cryst. C51, 1330-1333.]); Tuchinda et al. (2006[Tuchinda, P., Munyoo, B., Pohmakotr, M., Thinapong, P., Sophasan, S., Santisuk, T. & Reutrakul, V. (2006). J. Nat. Prod. 69, 1728-1733.]).

[Scheme 1]

Experimental

Crystal data

  • C13H12O3

  • Mr = 216.23

  • Monoclinic, P 21

  • a = 6.5442 (8) Å

  • b = 11.0267 (14) Å

  • c = 8.0991 (10) Å

  • β = 111.402 (2)°

  • V = 544.14 (12) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 100 K

  • 0.30 × 0.18 × 0.06 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.973, Tmax = 0.994

  • 2559 measured reflections

  • 1250 independent reflections

  • 1220 reflections with I > 2σ(I)

  • Rint = 0.012
Refinement

  • R[F2 > 2σ(F2)] = 0.027

  • wR(F2) = 0.069

  • S = 1.08

  • 1250 reflections

  • 148 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C1–C6 ring.
D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H1A⋯O2i 0.87 (3) 1.95 (3) 2.8026 (19) 170 (2)
C12—H12⋯O1ii 0.95 2.53 3.427 (2) 157
C9—H9⋯Cgii 1.00 2.97 3.747 (2) 135
C10—H10⋯Cgiii 1.00 2.80 3.6561 (18) 144
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z]; (ii) x-1, y, z; (iii) [-x+2, y-{\script{1\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: X-SEED (Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.]); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536812028334/pv2562sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812028334/pv2562Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812028334/pv2562Isup3.cml

checkCIF report


Comment top

The title compound was isolated from the roots of Goniothalamus ridleyi and found to be the same styrylpyrone isolated from the stem bark of Goniothalamus dolichocarpus (Goh et al., 1995). In agreement with the structures of similar molecules (Fun et al., 1995; Tuchinda et al., 2006), the pyran ring in the title molecule adopts a half-chair conformation with C9 displaced by 0.606 (2) Å from the plane of the remaining ring atoms (C10/C11/C12/C13/O3). This plane and the benzene ring make a dihedral angle of 44.18 (6)°. The crystal packing comprises three dimensional network formed by O—H···O, C—H···O and C—H···π interactions (Table 1, Fig. 2).

Related literature top

For spectroscopic characterization of the 5β-hydroxygoniothalamin, see: Goh et al. (1995). For the crystal structures of some similar compounds, see: Fun et al. (1995); Tuchinda et al. (2006).

Experimental top

Samples of the roots of G. ridleyi were collected from Post Brooke, Gua Musang, Kelantan, Malaysia. The roots were dried in an oven (323 K), ground and extracted using cool extraction. The extraction using three types of solvents i. e., hexane, chloroform and methanol gave three crude extracts. The chloroform crude extract (9.57 g) was separated using vacuum liquid chromatography (VLC). A mixture solvent of ethyl acetate and methanol as eluent solvent gave 12 fractions. TLC profiles showed fractions 1–3 were identical. Therefore, these fractions has been selected for further separation using column chromatography (CC) with eluent solvents hexane and ethyl acetate; 178 vials were collected and vials 157–165 have been selected for preparative TLC (PTLC) using hexane:ethyl acetate (9:11). GRAB 6 (0.0617 g) with Rf 0.46 in solvent system hexane: ethyl acetate (5:5) was crystallized from a mixture of ethyl acetate and n-hexane (1:1) at room temperature.

Refinement top

The C-bound hydrogen atoms were located in the calculated positions and refined in a riding mode with C—H distances of 0.95 (Csp2) and 1.000 (Csp3) Å. The O-bound H atom was found in a difference Fourier map and refined freely. For all hydrogen atoms, Uiso were set to 1.2Ueq(carrier atom). In the absence of significant anomalous scattering effects Friedel pairs were merged.

Structure description top

The title compound was isolated from the roots of Goniothalamus ridleyi and found to be the same styrylpyrone isolated from the stem bark of Goniothalamus dolichocarpus (Goh et al., 1995). In agreement with the structures of similar molecules (Fun et al., 1995; Tuchinda et al., 2006), the pyran ring in the title molecule adopts a half-chair conformation with C9 displaced by 0.606 (2) Å from the plane of the remaining ring atoms (C10/C11/C12/C13/O3). This plane and the benzene ring make a dihedral angle of 44.18 (6)°. The crystal packing comprises three dimensional network formed by O—H···O, C—H···O and C—H···π interactions (Table 1, Fig. 2).

For spectroscopic characterization of the 5β-hydroxygoniothalamin, see: Goh et al. (1995). For the crystal structures of some similar compounds, see: Fun et al. (1995); Tuchinda et al. (2006).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius.
[Figure 2] Fig. 2. A view of the O—H···O, C—H···O and C—H···π interactions in the structure. Hydrogen atoms, except those involved in hydrogen bonding, are ommited. Symmetry codes: ' = -x + 1, y - 1/2; '' = x - 1, y, z; ''' = -x + 2, y - 1/2, -z + 1.
5-Hydroxy-6-[(E)-2-phenylethenyl]-5,6-dihydro-2H-pyran-2-one top
Crystal data top
C13H12O3F(000) = 228
Mr = 216.23Dx = 1.320 Mg m−3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1643 reflections
a = 6.5442 (8) Åθ = 2.7–29.6°
b = 11.0267 (14) ŵ = 0.09 mm−1
c = 8.0991 (10) ÅT = 100 K
β = 111.402 (2)°Plate, colorless
V = 544.14 (12) Å30.30 × 0.18 × 0.06 mm
Z = 2
Data collection top
Bruker APEXII CCD
diffractometer		1250 independent reflections
Radiation source: fine-focus sealed tube1220 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.012
φ and ω scansθmax = 27.0°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −8→8
Tmin = 0.973, Tmax = 0.994k = −12→14
2559 measured reflectionsl = −10→10
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.027H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.069 w = 1/[σ2(Fo2) + (0.0382P)2 + 0.0929P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
1250 reflectionsΔρmax = 0.18 e Å−3
148 parametersΔρmin = −0.18 e Å−3
1 restraintAbsolute structure: 749 Friedel pairs were merged
Primary atom site location: structure-invariant direct methods
Crystal data top
C13H12O3V = 544.14 (12) Å3
Mr = 216.23Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.5442 (8) ŵ = 0.09 mm−1
b = 11.0267 (14) ÅT = 100 K
c = 8.0991 (10) Å0.30 × 0.18 × 0.06 mm
β = 111.402 (2)°
Data collection top
Bruker APEXII CCD
diffractometer		1250 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		1220 reflections with I > 2σ(I)
Tmin = 0.973, Tmax = 0.994Rint = 0.012
2559 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0271 restraint
wR(F2) = 0.069H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.18 e Å−3
1250 reflectionsΔρmin = −0.18 e Å−3
148 parametersAbsolute structure: 749 Friedel pairs were merged
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
xyzUiso*/Ueq
O10.6604 (2)0.26455 (12)−0.01641 (17)0.0203 (3)
H1A0.720 (4)0.194 (2)−0.012 (3)0.024*
O20.12430 (19)0.53996 (12)−0.04165 (17)0.0225 (3)
O30.46365 (18)0.48046 (11)0.10232 (16)0.0185 (3)
C11.2436 (3)0.59025 (18)0.3976 (2)0.0217 (4)
H11.12930.62470.29940.026*
C21.4539 (3)0.63794 (18)0.4495 (2)0.0248 (4)
H21.48270.70410.38620.030*
C31.6224 (3)0.58916 (18)0.5938 (3)0.0237 (4)
H31.76660.62150.62920.028*
C41.5782 (3)0.49275 (18)0.6858 (2)0.0221 (4)
H41.69280.45910.78460.027*
C51.3677 (3)0.44522 (17)0.6346 (2)0.0187 (3)
H51.33880.38010.69970.022*
C61.1977 (3)0.49255 (16)0.4877 (2)0.0173 (3)
C70.9754 (3)0.43928 (17)0.4324 (2)0.0191 (3)
H70.93090.40560.52190.023*
C80.8338 (3)0.43534 (17)0.2661 (2)0.0186 (3)
H80.87950.46540.17520.022*
C90.6060 (3)0.38607 (15)0.2147 (2)0.0172 (3)
H90.57050.37710.32420.021*
C100.5697 (2)0.26443 (16)0.1191 (2)0.0176 (3)
H100.64230.19940.20700.021*
C110.3265 (3)0.23880 (16)0.0389 (2)0.0200 (4)
H110.27710.15730.01540.024*
C120.1802 (3)0.32814 (17)0.0004 (2)0.0203 (4)
H120.02820.3092−0.04060.024*
C130.2497 (3)0.45594 (16)0.0204 (2)0.0179 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0233 (6)0.0155 (6)0.0254 (6)0.0005 (5)0.0130 (5)−0.0002 (5)
O20.0178 (6)0.0187 (6)0.0302 (7)0.0013 (5)0.0079 (5)0.0025 (5)
O30.0136 (5)0.0159 (6)0.0237 (6)−0.0004 (4)0.0040 (4)0.0009 (5)
C10.0229 (8)0.0214 (9)0.0180 (8)0.0008 (7)0.0042 (6)0.0000 (7)
C20.0290 (9)0.0222 (9)0.0257 (9)−0.0061 (8)0.0130 (8)−0.0031 (8)
C30.0175 (7)0.0268 (10)0.0282 (9)−0.0057 (7)0.0099 (7)−0.0106 (8)
C40.0189 (8)0.0226 (9)0.0217 (8)0.0044 (7)0.0035 (6)−0.0045 (7)
C50.0197 (8)0.0184 (8)0.0180 (8)0.0023 (7)0.0068 (6)−0.0011 (7)
C60.0160 (7)0.0180 (8)0.0180 (7)0.0004 (7)0.0062 (6)−0.0035 (7)
C70.0182 (8)0.0184 (8)0.0217 (8)0.0001 (7)0.0084 (7)−0.0003 (7)
C80.0162 (7)0.0177 (8)0.0224 (8)−0.0008 (7)0.0078 (6)−0.0008 (7)
C90.0161 (8)0.0175 (8)0.0179 (8)0.0010 (6)0.0059 (6)0.0021 (6)
C100.0171 (7)0.0154 (8)0.0208 (8)−0.0001 (6)0.0075 (6)0.0022 (7)
C110.0205 (8)0.0163 (8)0.0230 (8)−0.0046 (7)0.0077 (7)−0.0006 (7)
C120.0128 (7)0.0220 (9)0.0241 (8)−0.0039 (7)0.0044 (7)0.0003 (7)
C130.0153 (7)0.0195 (9)0.0204 (8)−0.0005 (7)0.0081 (6)0.0005 (7)
Geometric parameters (Å, º) top
O1—C101.426 (2)C5—H50.9500
O1—H1A0.87 (3)C6—C71.479 (2)
O2—C131.218 (2)C7—C81.328 (2)
O3—C131.3399 (19)C7—H70.9500
O3—C91.470 (2)C8—C91.496 (2)
C1—C21.387 (2)C8—H80.9500
C1—C61.394 (3)C9—C101.523 (2)
C1—H10.9500C9—H91.0000
C2—C31.390 (3)C10—C111.510 (2)
C2—H20.9500C10—H101.0000
C3—C41.388 (3)C11—C121.329 (2)
C3—H30.9500C11—H110.9500
C4—C51.388 (2)C12—C131.471 (2)
C4—H40.9500C12—H120.9500
C5—C61.400 (2)
C10—O1—H1A106.0 (15)C7—C8—H8118.3
C13—O3—C9118.37 (13)C9—C8—H8118.3
C2—C1—C6120.93 (16)O3—C9—C8104.91 (13)
C2—C1—H1119.5O3—C9—C10111.27 (13)
C6—C1—H1119.5C8—C9—C10114.59 (14)
C1—C2—C3120.21 (18)O3—C9—H9108.6
C1—C2—H2119.9C8—C9—H9108.6
C3—C2—H2119.9C10—C9—H9108.6
C4—C3—C2119.41 (16)O1—C10—C11109.78 (13)
C4—C3—H3120.3O1—C10—C9111.02 (14)
C2—C3—H3120.3C11—C10—C9109.15 (14)
C3—C4—C5120.46 (16)O1—C10—H10109.0
C3—C4—H4119.8C11—C10—H10109.0
C5—C4—H4119.8C9—C10—H10109.0
C4—C5—C6120.50 (16)C12—C11—C10121.20 (16)
C4—C5—H5119.8C12—C11—H11119.4
C6—C5—H5119.8C10—C11—H11119.4
C1—C6—C5118.47 (15)C11—C12—C13121.12 (14)
C1—C6—C7121.66 (15)C11—C12—H12119.4
C5—C6—C7119.87 (15)C13—C12—H12119.4
C8—C7—C6124.42 (16)O2—C13—O3118.41 (16)
C8—C7—H7117.8O2—C13—C12123.25 (15)
C6—C7—H7117.8O3—C13—C12118.22 (14)
C7—C8—C9123.36 (16)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C1-C6 ring.
D—H···AD—HH···AD···AD—H···A
O1—H1A···O2i0.87 (3)1.95 (3)2.8026 (19)170 (2)
C12—H12···O1ii0.952.533.427 (2)157
C9—H9···Cgii1.002.973.747 (2)135
C10—H10···Cgiii1.002.803.6561 (18)144
Symmetry codes: (i) −x+1, y−1/2, −z; (ii) x−1, y, z; (iii) −x+2, y−1/2, −z+1.

Experimental details

Crystal data
Chemical formulaC13H12O3
Mr216.23
Crystal system, space groupMonoclinic, P21
Temperature (K)100
a, b, c (Å)6.5442 (8), 11.0267 (14), 8.0991 (10)
β (°) 111.402 (2)
V (Å3)544.14 (12)
Z2
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.30 × 0.18 × 0.06
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.973, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections		2559, 1250, 1220
Rint0.012
(sin θ/λ)max (Å−1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.069, 1.08
No. of reflections1250
No. of parameters148
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.18, −0.18
Absolute structure749 Friedel pairs were merged

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), X-SEED (Barbour, 2001), SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C1-C6 ring.
D—H···AD—HH···AD···AD—H···A
O1—H1A···O2i0.87 (3)1.95 (3)2.8026 (19)170 (2)
C12—H12···O1ii0.952.533.427 (2)156.7
C9—H9···Cgii1.002.973.747 (2)135
C10—H10···Cgiii1.002.803.6561 (18)144
Symmetry codes: (i) −x+1, y−1/2, −z; (ii) x−1, y, z; (iii) −x+2, y−1/2, −z+1.
 

Acknowledgements

This research was financially supported by UKM grant (grant No. UKM-DLP-2012–033). We are grateful to Dr Shamsul Khamis for the assistance in identifying plant material.

References

First citationBarbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.  CrossRef CAS Google Scholar
 First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationFun, H.-K., Sivakumar, K., Ang, H.-B., Sam, T.-W. & Gan, E.-K. (1995). Acta Cryst. C51, 1330–1333.  CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationGoh, S. H., Ee, G. C. L. & Chuah, C. H. (1995). Nat. Prod. Lett. 5, 255–259.  CrossRef CAS Google Scholar
 First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationTuchinda, P., Munyoo, B., Pohmakotr, M., Thinapong, P., Sophasan, S., Santisuk, T. & Reutrakul, V. (2006). J. Nat. Prod. 69, 1728–1733.  Web of Science CSD CrossRef PubMed CAS Google Scholar
 First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2274
https://doi.org/10.1107/S1600536812028334
Follow Acta Cryst. E
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS