organic papers
o2202
Bauriet al. C21H26O5H2O doi:10.1107/S1600536806015273 Acta Cryst.(2006). E62, o2202–o2203
Acta Crystallographica Section E
Structure Reports
Online
ISSN 1600-5368
Malabaricone C monohydrate
A. K. Bauri,aS. K. Nayak,aSabine Forob* and Hans-Jo¨rg Lindnerb
a
Bioorganic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India, and b
Clemens Scho¨pf-Institut fu¨r Organische Chemie und Biochemie, Technische Universita¨t Darm-stadt, Petersenstrasse 22, D-64287 DarmDarm-stadt, Germany
Correspondence e-mail: [email protected]
Key indicators
Single-crystal X-ray study
T= 299 K
Mean(C–C) = 0.003 A˚
Rfactor = 0.048
wRfactor = 0.137
Data-to-parameter ratio = 13.6
For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.
Received 13 April 2006 Accepted 26 April 2006
#2006 International Union of Crystallography
All rights reserved
The crystal structure of the title compound, 1-(2,6-dihydroxy-phenyl)-9-(3,4-dihydroxyphenyl)nonan-1-one monohydrate, also known as malabaricone C, C21H26O5H2O, is stabilized
by both intra- and intermolecular O—H O hydrogen bonds.
Comment
The fruit rind of Myristica malabarica, popularly known as Rampatri in Mumbai (India), is used as an exotic spice in various Indian cuisines, as well as in phytomedicine (Forrest & Heacock, 1972, and references therein). It is credited with hepatoprotective, anticarcinogenic and antithrombotic prop-erties and is found as a constituent in many ayurvedic preparations such as Pasupasi. Previous phytochemical investigations of M. malabarica fruit rinds revealed the presence of four novel diarylnonanoids named as malabar-icone A–D (Purushothamanet al., 1977). In addition, a lignan malabericanol A and an isoflavone were also isolated from heart wood of the plant (Purushothamanet al., 1974; Talukdar
et al., 2000). During our studies of the antioxidant activity of methanol extracts of M. malabarica fruit rinds, we have isolated malabaricone C as a major product. The compound was assayed against breast and colon cancer cells, and the result was quite promising (Patroet al., 2005).
[image:1.610.209.458.609.722.2]A view of the title compound, (I), is shown in Fig. 1 and a packing diagram depicting the hydrogen bonds is shown in Fig. 2. Details of hydrogen bonding are given in Table 1.
Figure 1
Experimental
The title compound was isolated as a major product from a methanol extract ofM. malabaricaby column chromatography over silica gel with gradient elution by changing the polarity of the solvent system using ethyl acetate in petroleum ether followed by purification by preparative thin-layer chromatography. Crystals suitable for X-ray data collection were obtained by recrystallization from aqueous methanol at room temperature by slow evaporation.
Crystal data
C21H26O5H2O
Mr= 376.43
Orthorhombic,P212121
a= 5.4549 (6) A˚
b= 9.176 (1) A˚
c= 40.718 (3) A˚
V= 2038.1 (3) A˚3
Z= 4
Dx= 1.227 Mg m
3
CuKradiation = 0.73 mm1
T= 299 (2) K
Long needle, dark yellow 0.550.250.20 mm
Data collection
Enraf–Nonius CAD-4 diffractometer !/2scans
Absorption correction: none 3822 measured reflections 3566 independent reflections
3323 reflections withI> 2(I)
Rint= 0.032
max= 67.0
3 standard reflections frequency: 120 min intensity decay: 1%
Refinement
Refinement onF2
R[F2> 2(F2)] = 0.048
wR(F2) = 0.137
S= 1.04 3566 reflections 263 parameters
H atoms treated by a mixture of independent and constrained refinement
w= 1/[2(F
o2) + (0.1014P)2
+ 0.1804P]
whereP= (Fo2+ 2Fc2)/3
(/)max= 0.007
max= 0.20 e A˚
3
min=0.21 e A˚
3
Extinction correction:SHELXL97
Extinction coefficient: 0.0035 (6) Absolute structure: Flack (1983),
[image:2.610.45.300.73.178.2]1404 Friedel pairs Flack parameter:0.1 (2)
Table 1
Hydrogen-bond geometry (A˚ ,).
D—H A D—H H A D A D—H A
O1—H1O O3 0.86 (2) 1.67 (2) 2.4938 (19) 160 (3) O2—H2O O4i
0.84 (2) 1.92 (2) 2.748 (2) 173 (3) O4—H4O O6ii
0.87 (2) 1.98 (2) 2.788 (2) 153 (3) O4—H4O O5 0.87 (2) 2.34 (3) 2.675 (2) 103 (2) O5—H5O O6iii 0.80 (2) 1.95 (2) 2.724 (2) 164 (3) O6—H61O O1iv
0.85 (2) 1.96 (2) 2.8006 (19) 169 (3) O6—H62O O3 0.82 (2) 2.12 (2) 2.788 (2) 138 (2)
Symmetry codes: (i) xþ1;y1 2;zþ
1
2; (ii) x;y 1 2;zþ
1 2; (iii) x1;y1
2;zþ 1 2; (iv)x
1 2;yþ
1 2;z.
The O-bound H atoms were located in a difference map and their coordinates were refined. The H atoms of the water molecule were refined with geometry restraints (Nardelli, 1999),viz. O—H distances were restrained to 0.85 (2) A˚ and the H H distance was restrained to 1.36 (2) A˚ . The C-bound H atoms were positioned with idealized geometry using a riding model, with C—H = 0.93 A˚ (aromatic) and 0.97 A˚ (methylene groups). For all H atoms,Uiso(H) = 1.2Ueq(C,O).
Data collection:CAD-4-PC(Enraf–Nonius, 1996); cell refinement:
CAD-4-PC; data reduction:REDU4(Stoe & Cie, 1987); program(s) used to solve structure: SHELXS97(Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics:PLATON(Spek, 2003); software used to prepare material for publication:SHELXL97.
The authors thank Professor Dr Hartmut Fuess, FG Strukturforschung, FB Material- und Geowissenschaften, Technische Universita¨t Darmstadt, Germany, for diffract-ometer time.
References
Enraf–Nonius (1996). CAD-4-PC. Version 1.2. Enraf–Nonius, Delft, The Netherlands.
Flack, H. D. (1983).Acta Cryst.A39, 876–881.
Forrest, J. E. & Heacock, R. A. (1972).Lloydia,35, 440–490. Nardelli, M. (1999).J. Appl. Cryst.32, 563–571.
Patro, B. S., Bauri, A. K., Mishra, S. & Chattopadhyay, S. (2005).J. Agric. Food Chem.53, 6912–6918.
Purushothaman, K. K., Sarada, A. & Connolly, J. D. (1974).Indian J. Chem. Sect. B,23, 46–48.
Purushothaman, K. K., Sarada, A. & Connolly, J. D. (1977).J. Chem. Soc. Perkin Trans. 1, pp. 587–588.
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Go¨ttingen, Germany.
Spek, A. L. (2003).J. Appl. Cryst.36, 7–13.
Stoe & Cie (1987).REDU4. Version 6.2c. Stoe & Cie GmbH, Darmstadt, Germany.
Talukdar, A. C., Jain, N., De, S. & Krishnamurthy, H. G. (2000). Phyto-chemistry,53, 155–157.
Figure 2
supporting information
sup-1 Acta Cryst. (2006). E62, o2202–o2203
supporting information
Acta Cryst. (2006). E62, o2202–o2203 [https://doi.org/10.1107/S1600536806015273]
Malabaricone C monohydrate
A. K. Bauri, S. K. Nayak, Sabine Foro and Hans-J
ö
rg Lindner
1-(2,6-dihydroxyphenyl)-9-(3,4-dihydroxyphenyl)nonan-1-one monohydrate
Crystal data
C21H26O5·H2O Mr = 376.43
Orthorhombic, P212121
Hall symbol: P 2ac 2ab
a = 5.4549 (6) Å
b = 9.176 (1) Å
c = 40.718 (3) Å
V = 2038.1 (3) Å3 Z = 4
F(000) = 808
Dx = 1.227 Mg m−3
Melting point: 396 K
Cu Kα radiation, λ = 1.54180 Å Cell parameters from 25 reflections
θ = 5.8–20.2°
µ = 0.73 mm−1 T = 299 K
Long needle, dark yellow 0.55 × 0.25 × 0.20 mm
Data collection
Enraf–Nonius CAD-4 diffractometer
Radiation source: fine-focus sealed tube Graphite monochromator
Ω/2θ scans
3822 measured reflections 3566 independent reflections 3323 reflections with I > 2σ(I)
Rint = 0.032
θmax = 67.0°, θmin = 2.2° h = −6→6
k = −10→0
l = −48→0
3 standard reflections every 120 min intensity decay: 1%
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.048 wR(F2) = 0.137 S = 1.04 3566 reflections 263 parameters 7 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ2(F
o2) + (0.1014P)2 + 0.1804P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max = 0.007
Δρmax = 0.20 e Å−3
Δρmin = −0.21 e Å−3
Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Extinction coefficient: 0.0035 (6)
Absolute structure: Flack (1983), 1404 Friedel pairs
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)
x y z Uiso*/Ueq
O1 0.5695 (3) 0.13747 (18) 0.00484 (3) 0.0626 (4) H1O 0.489 (5) 0.157 (3) 0.0223 (5) 0.075* O2 0.8195 (3) −0.18660 (18) 0.09091 (3) 0.0616 (4) H2O 0.910 (5) −0.260 (2) 0.0932 (6) 0.074* O3 0.3470 (3) 0.13347 (17) 0.05833 (3) 0.0578 (4) O4 −0.1463 (3) 0.08933 (17) 0.39972 (4) 0.0619 (4) H4O −0.140 (5) 0.023 (2) 0.4151 (5) 0.074* O5 −0.5390 (3) −0.0720 (2) 0.41482 (4) 0.0625 (4) H5O −0.664 (4) −0.111 (3) 0.4200 (7) 0.075* C1 0.7187 (4) 0.0343 (2) 0.01766 (4) 0.0466 (4) C2 0.9055 (4) −0.0157 (2) −0.00246 (5) 0.0545 (5)
H2 0.9247 0.0216 −0.0235 0.065*
C3 1.0616 (4) −0.1209 (2) 0.00913 (5) 0.0560 (5)
H3 1.1883 −0.1537 −0.0043 0.067*
C4 1.0358 (4) −0.1792 (2) 0.04005 (5) 0.0518 (4)
H4 1.1426 −0.2514 0.0473 0.062*
C5 0.8483 (3) −0.1294 (2) 0.06060 (4) 0.0453 (4) C6 0.6848 (3) −0.01972 (19) 0.04996 (4) 0.0429 (4) C7 0.4870 (3) 0.04190 (19) 0.07041 (4) 0.0440 (4) C8 0.4482 (4) −0.0006 (2) 0.10564 (4) 0.0542 (5)
H8A 0.6019 0.0106 0.1173 0.065*
H8B 0.4036 −0.1028 0.1065 0.065*
C9 0.2524 (4) 0.0871 (2) 0.12326 (5) 0.0542 (5)
H9A 0.3006 0.1889 0.1238 0.065*
H9B 0.0995 0.0802 0.1112 0.065*
C10 0.2127 (6) 0.0335 (3) 0.15806 (5) 0.0774 (8)
H10A 0.1582 −0.0671 0.1572 0.093*
H10B 0.3689 0.0349 0.1695 0.093*
C11 0.0299 (5) 0.1199 (3) 0.17788 (5) 0.0715 (7)
H11A −0.1215 0.1275 0.1655 0.086*
H11B 0.0930 0.2178 0.1810 0.086*
C12 −0.0255 (6) 0.0537 (4) 0.21116 (6) 0.0888 (9)
H12A −0.0897 −0.0438 0.2079 0.107*
H12B 0.1269 0.0447 0.2233 0.107*
supporting information
sup-3 Acta Cryst. (2006). E62, o2202–o2203
H13A −0.3583 0.1471 0.2198 0.096*
H13B −0.1416 0.2362 0.2351 0.096*
C14 −0.2562 (6) 0.0701 (4) 0.26498 (6) 0.0799 (8)
H14A −0.3247 −0.0262 0.2615 0.096*
H14B −0.1019 0.0583 0.2765 0.096*
C15 −0.4280 (6) 0.1558 (4) 0.28632 (5) 0.0800 (7)
H15A −0.5865 0.1613 0.2756 0.096*
H15B −0.3659 0.2543 0.2885 0.096*
C16 −0.4616 (4) 0.0910 (3) 0.32025 (5) 0.0622 (6) C17 −0.2887 (4) 0.1160 (2) 0.34476 (5) 0.0560 (5)
H17 −0.1506 0.1717 0.3401 0.067*
C18 −0.3184 (4) 0.0598 (2) 0.37576 (5) 0.0474 (4) C19 −0.5231 (3) −0.0236 (2) 0.38351 (4) 0.0473 (4) C20 −0.6911 (4) −0.0536 (3) 0.35898 (5) 0.0629 (6)
H20 −0.8266 −0.1118 0.3635 0.076*
C21 −0.6581 (4) 0.0028 (3) 0.32784 (5) 0.0712 (7)
H21 −0.7716 −0.0193 0.3115 0.085*
O6 −0.0078 (3) 0.35116 (19) 0.06311 (3) 0.0577 (4) H61O −0.004 (5) 0.359 (2) 0.0424 (4) 0.069* H62O 0.041 (5) 0.269 (2) 0.0683 (5) 0.069*
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
C20 0.0390 (10) 0.0949 (15) 0.0549 (11) −0.0118 (11) −0.0032 (8) −0.0038 (11) C21 0.0478 (12) 0.118 (2) 0.0474 (11) 0.0003 (14) −0.0088 (9) −0.0085 (12) O6 0.0441 (7) 0.0834 (9) 0.0455 (7) 0.0200 (7) 0.0034 (6) −0.0011 (7)
Geometric parameters (Å, º)
O1—C1 1.353 (2) C10—H10B 0.9700
O1—H1O 0.857 (17) C11—C12 1.515 (3)
O2—C5 1.350 (2) C11—H11A 0.9700
O2—H2O 0.836 (17) C11—H11B 0.9700
O3—C7 1.237 (2) C12—C13 1.507 (4)
O4—C18 1.381 (2) C12—H12A 0.9700
O4—H4O 0.874 (17) C12—H12B 0.9700
O5—C19 1.353 (2) C13—C14 1.516 (3)
O5—H5O 0.795 (18) C13—H13A 0.9700
C1—C2 1.386 (3) C13—H13B 0.9700
C1—C6 1.418 (3) C14—C15 1.501 (4)
C2—C3 1.372 (3) C14—H14A 0.9700
C2—H2 0.9300 C14—H14B 0.9700
C3—C4 1.375 (3) C15—C16 1.515 (3)
C3—H3 0.9300 C15—H15A 0.9700
C4—C5 1.398 (3) C15—H15B 0.9700
C4—H4 0.9300 C16—C21 1.379 (4)
C5—C6 1.413 (3) C16—C17 1.392 (3)
C6—C7 1.476 (2) C17—C18 1.373 (3)
C7—C8 1.501 (2) C17—H17 0.9300
C8—C9 1.518 (3) C18—C19 1.390 (3)
C8—H8A 0.9700 C19—C20 1.383 (3)
C8—H8B 0.9700 C20—C21 1.381 (3)
C9—C10 1.516 (3) C20—H20 0.9300
C9—H9A 0.9700 C21—H21 0.9300
C9—H9B 0.9700 O6—H61O 0.847 (15)
C10—C11 1.508 (3) O6—H62O 0.824 (16)
C10—H10A 0.9700
C1—O1—H1O 97.7 (18) C10—C11—H11B 108.9
C5—O2—H2O 110.1 (18) C12—C11—H11B 108.9 C18—O4—H4O 113.3 (19) H11A—C11—H11B 107.7 C19—O5—H5O 117 (2) C13—C12—C11 114.9 (2) O1—C1—C2 116.48 (17) C13—C12—H12A 108.5 O1—C1—C6 121.62 (17) C11—C12—H12A 108.5 C2—C1—C6 121.90 (18) C13—C12—H12B 108.5 C3—C2—C1 119.11 (18) C11—C12—H12B 108.5
C3—C2—H2 120.4 H12A—C12—H12B 107.5
C1—C2—H2 120.4 C12—C13—C14 113.7 (2)
C2—C3—C4 121.69 (18) C12—C13—H13A 108.8
C2—C3—H3 119.2 C14—C13—H13A 108.8
supporting information
sup-5 Acta Cryst. (2006). E62, o2202–o2203
C3—C4—C5 119.72 (18) C14—C13—H13B 108.8
C3—C4—H4 120.1 H13A—C13—H13B 107.7
C5—C4—H4 120.1 C15—C14—C13 114.5 (2)
O2—C5—C4 120.36 (17) C15—C14—H14A 108.6 O2—C5—C6 118.90 (16) C13—C14—H14A 108.6 C4—C5—C6 120.74 (17) C15—C14—H14B 108.6 C5—C6—C1 116.82 (16) C13—C14—H14B 108.6 C5—C6—C7 124.18 (16) H14A—C14—H14B 107.6 C1—C6—C7 118.99 (16) C14—C15—C16 113.5 (2) O3—C7—C6 119.16 (16) C14—C15—H15A 108.9 O3—C7—C8 117.98 (16) C16—C15—H15A 108.9 C6—C7—C8 122.86 (16) C14—C15—H15B 108.9 C7—C8—C9 114.40 (17) C16—C15—H15B 108.9
C7—C8—H8A 108.7 H15A—C15—H15B 107.7
C9—C8—H8A 108.7 C21—C16—C17 117.6 (2)
C7—C8—H8B 108.7 C21—C16—C15 121.9 (2)
C9—C8—H8B 108.7 C17—C16—C15 120.5 (2)
H8A—C8—H8B 107.6 C18—C17—C16 121.1 (2)
C10—C9—C8 111.71 (18) C18—C17—H17 119.4
C10—C9—H9A 109.3 C16—C17—H17 119.4
C8—C9—H9A 109.3 C17—C18—O4 119.71 (18)
C10—C9—H9B 109.3 C17—C18—C19 120.69 (17)
C8—C9—H9B 109.3 O4—C18—C19 119.58 (17)
H9A—C9—H9B 107.9 O5—C19—C20 124.96 (18)
C11—C10—C9 115.1 (2) O5—C19—C18 116.49 (16) C11—C10—H10A 108.5 C20—C19—C18 118.53 (17)
C9—C10—H10A 108.5 C21—C20—C19 120.2 (2)
C11—C10—H10B 108.5 C21—C20—H20 119.9
C9—C10—H10B 108.5 C19—C20—H20 119.9
H10A—C10—H10B 107.5 C16—C21—C20 121.8 (2) C10—C11—C12 113.5 (2) C16—C21—H21 119.1
C10—C11—H11A 108.9 C20—C21—H21 119.1
C12—C11—H11A 108.9 H61O—O6—H62O 109 (2)
C5—C6—C7—O3 −177.03 (18) C17—C18—C19—C20 2.6 (3) C1—C6—C7—O3 3.9 (3) O4—C18—C19—C20 −179.1 (2) C5—C6—C7—C8 3.6 (3) O5—C19—C20—C21 179.4 (2) C1—C6—C7—C8 −175.53 (18) C18—C19—C20—C21 −2.1 (3) O3—C7—C8—C9 −5.7 (3) C17—C16—C21—C20 3.2 (4) C6—C7—C8—C9 173.77 (17) C15—C16—C21—C20 −178.6 (3) C7—C8—C9—C10 176.9 (2) C19—C20—C21—C16 −0.8 (4)
Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
O1—H1O···O3 0.86 (2) 1.67 (2) 2.4938 (19) 160 (3) O2—H2O···O4i 0.84 (2) 1.92 (2) 2.748 (2) 173 (3)
O4—H4O···O6ii 0.87 (2) 1.98 (2) 2.788 (2) 153 (3)
O4—H4O···O5 0.87 (2) 2.34 (3) 2.675 (2) 103 (2) O5—H5O···O6iii 0.80 (2) 1.95 (2) 2.724 (2) 164 (3)
O6—H61O···O1iv 0.85 (2) 1.96 (2) 2.8006 (19) 169 (3)
O6—H62O···O3 0.82 (2) 2.12 (2) 2.788 (2) 138 (2)
