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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1366.
Published online 2009 May 23. doi:  10.1107/S1600536809018820
PMCID: PMC2969635

2-Butyl-5-pentyl­benzene-1,3-diol

Abstract

In the title compound, C15H24O2, a natural dialkyl­resorcinol commonly named stemphol, the mol­ecules are linked into C(6) and C 2 2(4) chains and R 4 4(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 [triangle]); Andersen & Frisvad (2004 [triangle]); Marumo et al. (1985 [triangle]); Solfrizzo et al. (1994 [triangle]); Stodola et al. (1973 [triangle]). For structural discussion, see: Etter (1990 [triangle]); Bernstein et al. (1995 [triangle]).

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Object name is e-65-o1366-scheme1.jpg

Experimental

Crystal data

  • C15H24O2
  • M r = 236.34
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1366-efi1.jpg
  • a = 4.654 (2) Å
  • b = 25.450 (5) Å
  • c = 12.790 (4) Å
  • β = 108.12 (1)°
  • V = 1439.8 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.07 mm−1
  • T = 293 K
  • 0.50 × 0.10 × 0.08 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997 [triangle]) T min = 0.881, T max = 0.994
  • 15852 measured reflections
  • 2631 independent reflections
  • 1703 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.048
  • wR(F 2) = 0.131
  • S = 1.04
  • 2631 reflections
  • 158 parameters
  • H-atom parameters constrained
  • Δρmax = 0.18 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: DENZO (Otwinowski & Minor, 1997 [triangle]) and COLLECT (Nonius, 1999 [triangle]); cell refinement: DENZO; data reduction: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]) and CrystalBuilder (Welter, 2006 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018820/dn2455sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018820/dn2455Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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.

Experimental

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 column chromatography 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).

Refinement

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].

Figures

Fig. 1.
Molecular view of the compound with the atom labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small spheres of arbitrary radii.
Fig. 2.
The crystal packing of the title molecule, viewed down the b axis, showing the molecules connected by O—H···O hydrogen bonds in dotted lines. H atoms not involved in hydrogen bondings have been omitted for clarity.
Fig. 3.
The crystal packing of the title molecule, viewed down the a axis, showing the segregration between alkyl chains and resorcinol moieties; H atoms are omitted for clarity.

Crystal data

C15H24O2F(000) = 520
Mr = 236.34Dx = 1.090 Mg m3
Monoclinic, P21/cMelting point: 364 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71069 Å
a = 4.654 (2) ÅCell parameters from 2700 reflections
b = 25.450 (5) Åθ = 0.4–25.4°
c = 12.790 (4) ŵ = 0.07 mm1
β = 108.12 (1)°T = 293 K
V = 1439.8 (8) Å3Needle, colourless
Z = 40.50 × 0.10 × 0.08 mm

Data collection

Nonius KappaCCD diffractometer2631 independent reflections
Radiation source: fine-focus sealed tube1703 reflections with I > 2σ(I)
graphiteRint = 0.029
[var phi] and ω scansθmax = 25.3°, θmin = 2.3°
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997)h = −5→5
Tmin = 0.881, Tmax = 0.994k = −30→30
15852 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: difference Fourier map
wR(F2) = 0.131H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0625P)2 + 0.1805P] where P = (Fo2 + 2Fc2)/3
2631 reflections(Δ/σ)max < 0.001
158 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = −0.15 e Å3

Special details

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)

xyzUiso*/Ueq
O10.0951 (3)0.27129 (5)0.28490 (10)0.0555 (4)
H10.26480.27190.32990.083*
O2−0.2986 (2)0.22721 (5)−0.09324 (9)0.0517 (4)
H2−0.20740.2253−0.13860.077*
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)
C30.0994 (4)0.17495 (7)0.02531 (14)0.0428 (4)
H30.10000.1542−0.03450.051*
C40.3006 (3)0.16426 (7)0.12888 (14)0.0414 (4)
C50.2925 (3)0.19620 (7)0.21530 (14)0.0432 (5)
H50.42330.18960.28550.052*
C60.0935 (3)0.23774 (7)0.19898 (13)0.0394 (4)
C7−0.3211 (4)0.29564 (7)0.07705 (15)0.0454 (5)
H7A−0.36740.30380.14410.054*
H7B−0.50920.28710.02070.054*
C8−0.1801 (4)0.34346 (7)0.04135 (17)0.0557 (5)
H8A0.00200.35280.09990.067*
H8B−0.12100.3341−0.02260.067*
C9−0.3832 (5)0.39095 (8)0.0136 (2)0.0756 (7)
H9A−0.56250.3822−0.04680.091*
H9B−0.44720.39990.07660.091*
C10−0.2332 (6)0.43810 (9)−0.0182 (3)0.1069 (10)
H10A−0.07210.45000.04450.160*
H10B−0.37900.4657−0.04300.160*
H10C−0.15290.4286−0.07620.160*
C110.5085 (4)0.11754 (7)0.14655 (16)0.0523 (5)
H11A0.67580.12280.21340.063*
H11B0.59100.11510.08580.063*
C120.3515 (4)0.06650 (7)0.15543 (18)0.0604 (6)
H12A0.17670.06280.09050.073*
H12B0.27830.06870.21850.073*
C130.5435 (4)0.01760 (7)0.16697 (17)0.0594 (5)
H13A0.61710.01530.10400.071*
H13B0.71780.02110.23220.071*
C140.3833 (5)−0.03251 (8)0.1752 (2)0.0848 (8)
H14A0.3137−0.03040.23910.102*
H14B0.2060−0.03540.11090.102*
C150.5672 (6)−0.08146 (9)0.1840 (2)0.0970 (9)
H15A0.6319−0.08480.12000.145*
H15B0.4468−0.11140.18920.145*
H15C0.7409−0.07960.24850.145*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0453 (7)0.0768 (9)0.0399 (8)0.0016 (7)0.0069 (6)−0.0146 (7)
O20.0446 (7)0.0744 (9)0.0314 (7)0.0080 (6)0.0052 (5)0.0047 (7)
C10.0292 (8)0.0443 (10)0.0339 (9)−0.0028 (7)0.0099 (7)0.0024 (8)
C20.0316 (8)0.0488 (10)0.0311 (9)−0.0041 (8)0.0046 (7)0.0039 (8)
C30.0432 (9)0.0484 (11)0.0367 (10)0.0004 (9)0.0120 (8)−0.0031 (8)
C40.0345 (8)0.0442 (10)0.0442 (11)−0.0015 (8)0.0104 (8)0.0053 (8)
C50.0333 (9)0.0552 (11)0.0350 (10)−0.0007 (8)0.0018 (7)0.0063 (9)
C60.0342 (9)0.0511 (11)0.0325 (10)−0.0050 (8)0.0101 (7)−0.0029 (8)
C70.0369 (9)0.0538 (11)0.0450 (11)0.0028 (8)0.0119 (8)−0.0009 (9)
C80.0491 (10)0.0527 (12)0.0640 (13)0.0043 (9)0.0156 (9)0.0016 (10)
C90.0815 (15)0.0596 (14)0.0889 (17)0.0159 (12)0.0310 (13)0.0062 (13)
C100.131 (2)0.0567 (16)0.138 (3)0.0108 (15)0.050 (2)0.0224 (16)
C110.0440 (10)0.0511 (11)0.0592 (12)0.0069 (9)0.0124 (8)0.0052 (10)
C120.0517 (11)0.0524 (12)0.0753 (14)0.0037 (9)0.0168 (10)0.0068 (11)
C130.0604 (12)0.0521 (12)0.0638 (14)0.0075 (10)0.0167 (10)0.0006 (10)
C140.0828 (16)0.0543 (14)0.113 (2)0.0030 (12)0.0242 (15)0.0058 (13)
C150.118 (2)0.0560 (15)0.113 (2)0.0078 (14)0.0293 (17)−0.0002 (14)

Geometric parameters (Å, °)

O1—C61.3899 (19)C9—H9A0.9700
O1—H10.8200C9—H9B0.9700
O2—C21.3924 (18)C10—H10A0.9600
O2—H20.8200C10—H10B0.9600
C1—C21.388 (2)C10—H10C0.9600
C1—C61.394 (2)C11—C121.512 (3)
C1—C71.503 (2)C11—H11A0.9700
C2—C31.381 (2)C11—H11B0.9700
C3—C41.391 (2)C12—C131.512 (3)
C3—H30.9300C12—H12A0.9700
C4—C51.382 (2)C12—H12B0.9700
C4—C111.505 (2)C13—C141.497 (3)
C5—C61.378 (2)C13—H13A0.9700
C5—H50.9300C13—H13B0.9700
C7—C81.519 (3)C14—C151.496 (3)
C7—H7A0.9700C14—H14A0.9700
C7—H7B0.9700C14—H14B0.9700
C8—C91.507 (3)C15—H15A0.9600
C8—H8A0.9700C15—H15B0.9600
C8—H8B0.9700C15—H15C0.9600
C9—C101.506 (3)
C6—O1—H1109.5H9A—C9—H9B107.8
C2—O2—H2109.5C9—C10—H10A109.5
C2—C1—C6115.59 (15)C9—C10—H10B109.5
C2—C1—C7121.63 (14)H10A—C10—H10B109.5
C6—C1—C7122.55 (15)C9—C10—H10C109.5
C3—C2—C1122.97 (15)H10A—C10—H10C109.5
C3—C2—O2119.73 (15)H10B—C10—H10C109.5
C1—C2—O2117.29 (14)C4—C11—C12112.77 (14)
C2—C3—C4120.13 (16)C4—C11—H11A109.0
C2—C3—H3119.9C12—C11—H11A109.0
C4—C3—H3119.9C4—C11—H11B109.0
C5—C4—C3117.98 (15)C12—C11—H11B109.0
C5—C4—C11121.38 (16)H11A—C11—H11B107.8
C3—C4—C11120.57 (17)C11—C12—C13115.46 (16)
C6—C5—C4120.95 (15)C11—C12—H12A108.4
C6—C5—H5119.5C13—C12—H12A108.4
C4—C5—H5119.5C11—C12—H12B108.4
C5—C6—O1120.90 (14)C13—C12—H12B108.4
C5—C6—C1122.35 (16)H12A—C12—H12B107.5
O1—C6—C1116.74 (14)C14—C13—C12114.58 (17)
C1—C7—C8111.85 (14)C14—C13—H13A108.6
C1—C7—H7A109.2C12—C13—H13A108.6
C8—C7—H7A109.2C14—C13—H13B108.6
C1—C7—H7B109.2C12—C13—H13B108.6
C8—C7—H7B109.2H13A—C13—H13B107.6
H7A—C7—H7B107.9C15—C14—C13115.4 (2)
C9—C8—C7114.57 (16)C15—C14—H14A108.4
C9—C8—H8A108.6C13—C14—H14A108.4
C7—C8—H8A108.6C15—C14—H14B108.4
C9—C8—H8B108.6C13—C14—H14B108.4
C7—C8—H8B108.6H14A—C14—H14B107.5
H8A—C8—H8B107.6C14—C15—H15A109.5
C10—C9—C8113.16 (18)C14—C15—H15B109.5
C10—C9—H9A108.9H15A—C15—H15B109.5
C8—C9—H9A108.9C14—C15—H15C109.5
C10—C9—H9B108.9H15A—C15—H15C109.5
C8—C9—H9B108.9H15B—C15—H15C109.5
C6—C1—C2—C31.2 (2)C7—C1—C6—C5−176.77 (15)
C7—C1—C2—C3175.85 (15)C2—C1—C6—O1176.89 (14)
C6—C1—C2—O2−177.88 (13)C7—C1—C6—O12.3 (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—C890.4 (2)
O2—C2—C3—C4179.01 (14)C1—C7—C8—C9176.41 (17)
C2—C3—C4—C5−0.2 (2)C7—C8—C9—C10178.26 (19)
C2—C3—C4—C11176.65 (15)C5—C4—C11—C1298.0 (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—C13176.76 (17)
C4—C5—C6—O1−177.00 (15)C11—C12—C13—C14−179.8 (2)
C4—C5—C6—C12.0 (2)C12—C13—C14—C15178.6 (2)
C2—C1—C6—C5−2.2 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.821.962.767 (2)167
O2—H2···O1ii0.821.952.750 (2)165

Symmetry codes: (i) x+1, −y+1/2, z+1/2; (ii) x, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2455).

References

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