organic compounds
2-Butyl-5-pentylbenzene-1,3-diol
aDepartment of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand, bInstitut de Chimie des Substances Naturelles - CNRS, 1 avenue de la Terrasse, 91198 Gif sur Yvette, France, and cDepartment of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, D-37077 Göttingen, Germany
*Correspondence e-mail: pascal.retailleau@icsn.cnrs-gif.fr, scboi009@chiangmai.ac.th
In the title compound, C15H24O2, a natural dialkylresorcinol commonly named stemphol, the molecules are linked into C(6) and C22(4) chains and R44(16) rings by intermolecular O—H⋯O hydrogen bonds, creating molecular sheets parallel to the (010) plane. The alkyl chains are directed orthogonally away from these planes in almost complete extension.
Related literature
For general background, synthesis, biological activity and related structures, see: Achenbach & Kohl (1979); Andersen & Frisvad (2004); Marumo et al. (1985); Solfrizzo et al. (1994); Stodola et al. (1973). For structural discussion, see: Etter (1990); Bernstein et al. (1995).
Experimental
Crystal data
|
Refinement
|
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Nonius, 1999); cell DENZO; data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) and CrystalBuilder (Welter, 2006); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2009).
Supporting information
10.1107/S1600536809018820/dn2455sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809018820/dn2455Isup2.hkl
Gaeumannomyces amomi BCC4066 was cultivated in 20 l of liquid culture and incubated for 21 d at room temperature (20 °C). Liquid culture was filtrated and extracted separately. The residue (5.0 g) obtained after evaporation of solvent was subjected to
over sephadex to afford 30 mg of Stemphol. Colourless needle-shaped crystals were obtained by re-crystallization from 20% EtOAc in Heptane (m.p. 91 °C).All H atoms were located in difference maps but were treated as riding on their parent atoms, with O—H = 0.82 Å, and C—H distances in the range 0.93–0.97 Å and with Uiso(H) = 1.2Ueq(carrier) [1.5 for methyl H atoms].
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Nonius, 1999); cell
DENZO (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) and CrystalBuilder (Welter, 2006); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2009).C15H24O2 | F(000) = 520 |
Mr = 236.34 | Dx = 1.090 Mg m−3 |
Monoclinic, P21/c | Melting point: 364 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71069 Å |
a = 4.654 (2) Å | Cell parameters from 2700 reflections |
b = 25.450 (5) Å | θ = 0.4–25.4° |
c = 12.790 (4) Å | µ = 0.07 mm−1 |
β = 108.12 (1)° | T = 293 K |
V = 1439.8 (8) Å3 | Needle, colourless |
Z = 4 | 0.50 × 0.10 × 0.08 mm |
Nonius KappaCCD diffractometer | 2631 independent reflections |
Radiation source: fine-focus sealed tube | 1703 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
ϕ and ω scans | θmax = 25.3°, θmin = 2.3° |
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997) | h = −5→5 |
Tmin = 0.881, Tmax = 0.994 | k = −30→30 |
15852 measured reflections | l = −15→15 |
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)] = 0.048 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.131 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0625P)2 + 0.1805P] where P = (Fo2 + 2Fc2)/3 |
2631 reflections | (Δ/σ)max < 0.001 |
158 parameters | Δρmax = 0.18 e Å−3 |
0 restraints | Δρmin = −0.16 e Å−3 |
C15H24O2 | V = 1439.8 (8) Å3 |
Mr = 236.34 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.654 (2) Å | µ = 0.07 mm−1 |
b = 25.450 (5) Å | T = 293 K |
c = 12.790 (4) Å | 0.50 × 0.10 × 0.08 mm |
β = 108.12 (1)° |
Nonius KappaCCD diffractometer | 2631 independent reflections |
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997) | 1703 reflections with I > 2σ(I) |
Tmin = 0.881, Tmax = 0.994 | Rint = 0.029 |
15852 measured reflections |
R[F2 > 2σ(F2)] = 0.048 | 0 restraints |
wR(F2) = 0.131 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.18 e Å−3 |
2631 reflections | Δρmin = −0.16 e Å−3 |
158 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.0951 (3) | 0.27129 (5) | 0.28490 (10) | 0.0555 (4) | |
H1 | 0.2648 | 0.2719 | 0.3299 | 0.083* | |
O2 | −0.2986 (2) | 0.22721 (5) | −0.09324 (9) | 0.0517 (4) | |
H2 | −0.2074 | 0.2253 | −0.1386 | 0.077* | |
C1 | −0.1145 (3) | 0.24879 (6) | 0.09661 (13) | 0.0358 (4) | |
C2 | −0.1012 (3) | 0.21631 (7) | 0.01107 (13) | 0.0383 (4) | |
C3 | 0.0994 (4) | 0.17495 (7) | 0.02531 (14) | 0.0428 (4) | |
H3 | 0.1000 | 0.1542 | −0.0345 | 0.051* | |
C4 | 0.3006 (3) | 0.16426 (7) | 0.12888 (14) | 0.0414 (4) | |
C5 | 0.2925 (3) | 0.19620 (7) | 0.21530 (14) | 0.0432 (5) | |
H5 | 0.4233 | 0.1896 | 0.2855 | 0.052* | |
C6 | 0.0935 (3) | 0.23774 (7) | 0.19898 (13) | 0.0394 (4) | |
C7 | −0.3211 (4) | 0.29564 (7) | 0.07705 (15) | 0.0454 (5) | |
H7A | −0.3674 | 0.3038 | 0.1441 | 0.054* | |
H7B | −0.5092 | 0.2871 | 0.0207 | 0.054* | |
C8 | −0.1801 (4) | 0.34346 (7) | 0.04135 (17) | 0.0557 (5) | |
H8A | 0.0020 | 0.3528 | 0.0999 | 0.067* | |
H8B | −0.1210 | 0.3341 | −0.0226 | 0.067* | |
C9 | −0.3832 (5) | 0.39095 (8) | 0.0136 (2) | 0.0756 (7) | |
H9A | −0.5625 | 0.3822 | −0.0468 | 0.091* | |
H9B | −0.4472 | 0.3999 | 0.0766 | 0.091* | |
C10 | −0.2332 (6) | 0.43810 (9) | −0.0182 (3) | 0.1069 (10) | |
H10A | −0.0721 | 0.4500 | 0.0445 | 0.160* | |
H10B | −0.3790 | 0.4657 | −0.0430 | 0.160* | |
H10C | −0.1529 | 0.4286 | −0.0762 | 0.160* | |
C11 | 0.5085 (4) | 0.11754 (7) | 0.14655 (16) | 0.0523 (5) | |
H11A | 0.6758 | 0.1228 | 0.2134 | 0.063* | |
H11B | 0.5910 | 0.1151 | 0.0858 | 0.063* | |
C12 | 0.3515 (4) | 0.06650 (7) | 0.15543 (18) | 0.0604 (6) | |
H12A | 0.1767 | 0.0628 | 0.0905 | 0.073* | |
H12B | 0.2783 | 0.0687 | 0.2185 | 0.073* | |
C13 | 0.5435 (4) | 0.01760 (7) | 0.16697 (17) | 0.0594 (5) | |
H13A | 0.6171 | 0.0153 | 0.1040 | 0.071* | |
H13B | 0.7178 | 0.0211 | 0.2322 | 0.071* | |
C14 | 0.3833 (5) | −0.03251 (8) | 0.1752 (2) | 0.0848 (8) | |
H14A | 0.3137 | −0.0304 | 0.2391 | 0.102* | |
H14B | 0.2060 | −0.0354 | 0.1109 | 0.102* | |
C15 | 0.5672 (6) | −0.08146 (9) | 0.1840 (2) | 0.0970 (9) | |
H15A | 0.6319 | −0.0848 | 0.1200 | 0.145* | |
H15B | 0.4468 | −0.1114 | 0.1892 | 0.145* | |
H15C | 0.7409 | −0.0796 | 0.2485 | 0.145* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0453 (7) | 0.0768 (9) | 0.0399 (8) | 0.0016 (7) | 0.0069 (6) | −0.0146 (7) |
O2 | 0.0446 (7) | 0.0744 (9) | 0.0314 (7) | 0.0080 (6) | 0.0052 (5) | 0.0047 (7) |
C1 | 0.0292 (8) | 0.0443 (10) | 0.0339 (9) | −0.0028 (7) | 0.0099 (7) | 0.0024 (8) |
C2 | 0.0316 (8) | 0.0488 (10) | 0.0311 (9) | −0.0041 (8) | 0.0046 (7) | 0.0039 (8) |
C3 | 0.0432 (9) | 0.0484 (11) | 0.0367 (10) | 0.0004 (9) | 0.0120 (8) | −0.0031 (8) |
C4 | 0.0345 (8) | 0.0442 (10) | 0.0442 (11) | −0.0015 (8) | 0.0104 (8) | 0.0053 (8) |
C5 | 0.0333 (9) | 0.0552 (11) | 0.0350 (10) | −0.0007 (8) | 0.0018 (7) | 0.0063 (9) |
C6 | 0.0342 (9) | 0.0511 (11) | 0.0325 (10) | −0.0050 (8) | 0.0101 (7) | −0.0029 (8) |
C7 | 0.0369 (9) | 0.0538 (11) | 0.0450 (11) | 0.0028 (8) | 0.0119 (8) | −0.0009 (9) |
C8 | 0.0491 (10) | 0.0527 (12) | 0.0640 (13) | 0.0043 (9) | 0.0156 (9) | 0.0016 (10) |
C9 | 0.0815 (15) | 0.0596 (14) | 0.0889 (17) | 0.0159 (12) | 0.0310 (13) | 0.0062 (13) |
C10 | 0.131 (2) | 0.0567 (16) | 0.138 (3) | 0.0108 (15) | 0.050 (2) | 0.0224 (16) |
C11 | 0.0440 (10) | 0.0511 (11) | 0.0592 (12) | 0.0069 (9) | 0.0124 (8) | 0.0052 (10) |
C12 | 0.0517 (11) | 0.0524 (12) | 0.0753 (14) | 0.0037 (9) | 0.0168 (10) | 0.0068 (11) |
C13 | 0.0604 (12) | 0.0521 (12) | 0.0638 (14) | 0.0075 (10) | 0.0167 (10) | 0.0006 (10) |
C14 | 0.0828 (16) | 0.0543 (14) | 0.113 (2) | 0.0030 (12) | 0.0242 (15) | 0.0058 (13) |
C15 | 0.118 (2) | 0.0560 (15) | 0.113 (2) | 0.0078 (14) | 0.0293 (17) | −0.0002 (14) |
O1—C6 | 1.3899 (19) | C9—H9A | 0.9700 |
O1—H1 | 0.8200 | C9—H9B | 0.9700 |
O2—C2 | 1.3924 (18) | C10—H10A | 0.9600 |
O2—H2 | 0.8200 | C10—H10B | 0.9600 |
C1—C2 | 1.388 (2) | C10—H10C | 0.9600 |
C1—C6 | 1.394 (2) | C11—C12 | 1.512 (3) |
C1—C7 | 1.503 (2) | C11—H11A | 0.9700 |
C2—C3 | 1.381 (2) | C11—H11B | 0.9700 |
C3—C4 | 1.391 (2) | C12—C13 | 1.512 (3) |
C3—H3 | 0.9300 | C12—H12A | 0.9700 |
C4—C5 | 1.382 (2) | C12—H12B | 0.9700 |
C4—C11 | 1.505 (2) | C13—C14 | 1.497 (3) |
C5—C6 | 1.378 (2) | C13—H13A | 0.9700 |
C5—H5 | 0.9300 | C13—H13B | 0.9700 |
C7—C8 | 1.519 (3) | C14—C15 | 1.496 (3) |
C7—H7A | 0.9700 | C14—H14A | 0.9700 |
C7—H7B | 0.9700 | C14—H14B | 0.9700 |
C8—C9 | 1.507 (3) | C15—H15A | 0.9600 |
C8—H8A | 0.9700 | C15—H15B | 0.9600 |
C8—H8B | 0.9700 | C15—H15C | 0.9600 |
C9—C10 | 1.506 (3) | ||
C6—O1—H1 | 109.5 | H9A—C9—H9B | 107.8 |
C2—O2—H2 | 109.5 | C9—C10—H10A | 109.5 |
C2—C1—C6 | 115.59 (15) | C9—C10—H10B | 109.5 |
C2—C1—C7 | 121.63 (14) | H10A—C10—H10B | 109.5 |
C6—C1—C7 | 122.55 (15) | C9—C10—H10C | 109.5 |
C3—C2—C1 | 122.97 (15) | H10A—C10—H10C | 109.5 |
C3—C2—O2 | 119.73 (15) | H10B—C10—H10C | 109.5 |
C1—C2—O2 | 117.29 (14) | C4—C11—C12 | 112.77 (14) |
C2—C3—C4 | 120.13 (16) | C4—C11—H11A | 109.0 |
C2—C3—H3 | 119.9 | C12—C11—H11A | 109.0 |
C4—C3—H3 | 119.9 | C4—C11—H11B | 109.0 |
C5—C4—C3 | 117.98 (15) | C12—C11—H11B | 109.0 |
C5—C4—C11 | 121.38 (16) | H11A—C11—H11B | 107.8 |
C3—C4—C11 | 120.57 (17) | C11—C12—C13 | 115.46 (16) |
C6—C5—C4 | 120.95 (15) | C11—C12—H12A | 108.4 |
C6—C5—H5 | 119.5 | C13—C12—H12A | 108.4 |
C4—C5—H5 | 119.5 | C11—C12—H12B | 108.4 |
C5—C6—O1 | 120.90 (14) | C13—C12—H12B | 108.4 |
C5—C6—C1 | 122.35 (16) | H12A—C12—H12B | 107.5 |
O1—C6—C1 | 116.74 (14) | C14—C13—C12 | 114.58 (17) |
C1—C7—C8 | 111.85 (14) | C14—C13—H13A | 108.6 |
C1—C7—H7A | 109.2 | C12—C13—H13A | 108.6 |
C8—C7—H7A | 109.2 | C14—C13—H13B | 108.6 |
C1—C7—H7B | 109.2 | C12—C13—H13B | 108.6 |
C8—C7—H7B | 109.2 | H13A—C13—H13B | 107.6 |
H7A—C7—H7B | 107.9 | C15—C14—C13 | 115.4 (2) |
C9—C8—C7 | 114.57 (16) | C15—C14—H14A | 108.4 |
C9—C8—H8A | 108.6 | C13—C14—H14A | 108.4 |
C7—C8—H8A | 108.6 | C15—C14—H14B | 108.4 |
C9—C8—H8B | 108.6 | C13—C14—H14B | 108.4 |
C7—C8—H8B | 108.6 | H14A—C14—H14B | 107.5 |
H8A—C8—H8B | 107.6 | C14—C15—H15A | 109.5 |
C10—C9—C8 | 113.16 (18) | C14—C15—H15B | 109.5 |
C10—C9—H9A | 108.9 | H15A—C15—H15B | 109.5 |
C8—C9—H9A | 108.9 | C14—C15—H15C | 109.5 |
C10—C9—H9B | 108.9 | H15A—C15—H15C | 109.5 |
C8—C9—H9B | 108.9 | H15B—C15—H15C | 109.5 |
C6—C1—C2—C3 | 1.2 (2) | C7—C1—C6—C5 | −176.77 (15) |
C7—C1—C2—C3 | 175.85 (15) | C2—C1—C6—O1 | 176.89 (14) |
C6—C1—C2—O2 | −177.88 (13) | C7—C1—C6—O1 | 2.3 (2) |
C7—C1—C2—O2 | −3.2 (2) | C2—C1—C7—C8 | −83.9 (2) |
C1—C2—C3—C4 | −0.1 (2) | C6—C1—C7—C8 | 90.4 (2) |
O2—C2—C3—C4 | 179.01 (14) | C1—C7—C8—C9 | 176.41 (17) |
C2—C3—C4—C5 | −0.2 (2) | C7—C8—C9—C10 | 178.26 (19) |
C2—C3—C4—C11 | 176.65 (15) | C5—C4—C11—C12 | 98.0 (2) |
C3—C4—C5—C6 | −0.8 (2) | C3—C4—C11—C12 | −78.7 (2) |
C11—C4—C5—C6 | −177.58 (15) | C4—C11—C12—C13 | 176.76 (17) |
C4—C5—C6—O1 | −177.00 (15) | C11—C12—C13—C14 | −179.8 (2) |
C4—C5—C6—C1 | 2.0 (2) | C12—C13—C14—C15 | 178.6 (2) |
C2—C1—C6—C5 | −2.2 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O2i | 0.82 | 1.96 | 2.767 (2) | 167 |
O2—H2···O1ii | 0.82 | 1.95 | 2.750 (2) | 165 |
Symmetry codes: (i) x+1, −y+1/2, z+1/2; (ii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C15H24O2 |
Mr | 236.34 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 4.654 (2), 25.450 (5), 12.790 (4) |
β (°) | 108.12 (1) |
V (Å3) | 1439.8 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.07 |
Crystal size (mm) | 0.50 × 0.10 × 0.08 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.881, 0.994 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15852, 2631, 1703 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.602 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.048, 0.131, 1.04 |
No. of reflections | 2631 |
No. of parameters | 158 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.18, −0.16 |
Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Nonius, 1999), DENZO (Otwinowski & Minor, 1997), SCALEPACK (Otwinowski & Minor, 1997), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008) and CrystalBuilder (Welter, 2006), PLATON (Spek, 2009) and Mercury (Macrae et al., 2006), SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O2i | 0.82 | 1.963 | 2.767 (2) | 166.63 |
O2—H2···O1ii | 0.82 | 1.951 | 2.750 (2) | 164.82 |
Symmetry codes: (i) x+1, −y+1/2, z+1/2; (ii) x, −y+1/2, z−1/2. |
Acknowledgements
JJ thanks the Thailand Research Fund (Royal Golden Jubilee PhD Program 4.V.CM/47/D.1) and the French Embassy for financial support. Professor H. Laatsch (Department of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Germany) is thanked for the structure elucidation.
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Stemphol was first isolated from Stemphylium majusculum (Stodola et al., 1973) and its related compounds were reported with antimicrobial activities against fungus (Mucor hiemalis), yeast (Schizosaccharomyces pombe) and Gram positive bacteria (Bacillus subtilis and Staphylococcus aureus) (Achenbach & Kohl, 1979). Later on, stemphol was isolated from Pleospora herbarum and described as self-inhibitor (Marumo et al., 1985). Five of eleven isolates of Stemphylium botryosum Wallr. from oilseed rape produced the phytotoxin, stemphol when cultured on rice (Solfrizzo et al., 1994). Stemphylium cf. lycopersici was postharvest spoiler of fresh tomatoes and was first detected of stemphols in naturally contaminated tomatoes (Andersen & Frisvad, 2004). Screening investigation for polyketide and novel substance from new endophytic fungus led to the finding of stemphol from Gaeumannomyces amomi BCC4066 isolated from healthy pseudostem of Alpinia malaccensis, which was collected in the Suthep- Pui National Park, Chiang Mai, in the northern part of Thailand. This molecule has been reported for the first time in endophytic fungus and its X-ray structure (Fig. 1) is presented herein.
The two hydroxyl groups of the stemphol molecules lead to the formation of chains and rings through O—H···O hydrogen bonds (Table 1) with graph set motifs C(6), C22(4) and R44(16) (Etter, 1990; Bernstein et al., 1995) all contained within the glide planes (Fig. 2). Both butyl and pentyl chains, directed in opposite directions and running up and down with respect to the resorcinol mean plane, adopt essentially fully extended conformations, but with 12.7 (2)° of deviation between their mean planes defined by C1–C7/C10 and C4–C12/C15 respectively (Fig. 3). The dihedral angles they form with respect to the (010) plane are 84.3 (2)° and 73.5 (2)° respectively.