Malabaricone A isolated from a methanol extract of Myristica malabarica

The title compound, malabaricone A [systematic name: 1-(2,6-dihydroxy­phen­yl)-9-phenyl­nonan-1-one], C₂₁H₂₆O₃, contains two benzene rings linked through a C₉ alkyl chain. Both intra- and inter­molecular O—H...O hydrogen-bonding inter­actions stabilize the packing. The inter­molecular hydrogen bonds result in the formation of an infinite zigzag chain.

Key indicators

• Single-crystal X-ray study
• T = 299 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.046
• wR factor = 0.143
• Data-to-parameter ratio = 11.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.65 mm

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 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
   0 ALERT type 4 Improvement, methodology, query or suggestion

---

Computing details

Data collection: CAD-4-PC Software (Enraf–Nonius, 1993); cell refinement: CAD-4-PC Software; 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: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97.

1-(2,6-dihydroxyphenyl)-9-phenylnonan-1-one

Crystal data

C21H26O3	F(000) = 704
Mr = 326.47	Dx = 1.181 Mg m^−3
Monoclinic, P21/n	Melting point: 82 K
Hall symbol: -P 2yn	Cu Kα radiation, λ = 1.54180 Å
a = 4.1831 (6) Å	Cell parameters from 25 reflections
b = 32.562 (2) Å	θ = 8.2–23.9°
c = 13.627 (1) Å	µ = 0.61 mm^−1
β = 98.43 (1)°	T = 299 K
V = 1836.1 (3) Å^3	Prism, yellow
Z = 4	0.65 × 0.18 × 0.10 mm

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.044
Radiation source: fine-focus sealed tube	θmax = 67.1°, θmin = 2.7°
Graphite monochromator	h = −4→4
ω/2θ scans	k = −38→0
6403 measured reflections	l = −16→16
3251 independent reflections	3 standard reflections every 120 min
2092 reflections with I > 2σ(I)	intensity decay: 3.4%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.046	Only H-atom coordinates refined
wR(F^2) = 0.143	w = 1/[σ^2(Fo^2) + (0.075P)^2 + 0.1143P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max = 0.004
3251 reflections	Δρmax = 0.22 e Å^−3
296 parameters	Δρmin = −0.14 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0029 (5)

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.5983 (5)	0.23683 (5)	0.74737 (12)	0.0564 (5)
C2	0.4480 (6)	0.27300 (7)	0.76589 (15)	0.0724 (6)
H2	0.430 (6)	0.2779 (7)	0.8348 (18)	0.087*
C3	0.3309 (6)	0.29818 (7)	0.68817 (16)	0.0791 (7)
H3	0.205 (6)	0.3231 (8)	0.7024 (18)	0.095*
C4	0.3579 (6)	0.28770 (6)	0.59201 (15)	0.0664 (6)
H4	0.283 (5)	0.3044 (7)	0.5354 (17)	0.080*
C5	0.5065 (5)	0.25163 (5)	0.57254 (12)	0.0522 (5)
C6	0.6333 (4)	0.22460 (5)	0.64985 (11)	0.0489 (4)
C7	0.7913 (5)	0.18532 (5)	0.63489 (12)	0.0547 (5)
C8	0.8362 (5)	0.16898 (6)	0.53494 (12)	0.0528 (5)
H8A	0.969 (5)	0.1877 (6)	0.5064 (14)	0.063*
H8B	0.620 (5)	0.1696 (6)	0.4916 (15)	0.063*
C9	0.9689 (6)	0.12557 (6)	0.53724 (14)	0.0585 (5)
H9A	0.817 (5)	0.1066 (6)	0.5671 (15)	0.070*
H9B	1.180 (5)	0.1248 (6)	0.5789 (16)	0.070*
C10	0.9993 (6)	0.10955 (6)	0.43458 (14)	0.0608 (5)
H10A	1.141 (5)	0.1259 (7)	0.4035 (15)	0.073*
H10B	0.772 (5)	0.1126 (6)	0.3936 (15)	0.073*
C11	1.1054 (6)	0.06497 (6)	0.43418 (15)	0.0639 (5)
H11A	0.945 (5)	0.0468 (7)	0.4672 (15)	0.077*
H11B	1.319 (6)	0.0625 (6)	0.4796 (16)	0.077*
C12	1.1379 (6)	0.04837 (6)	0.33239 (16)	0.0669 (6)
H12A	1.283 (6)	0.0656 (7)	0.3032 (16)	0.080*
H12B	0.937 (6)	0.0522 (7)	0.2896 (16)	0.080*
C13	1.2285 (6)	0.00328 (6)	0.33126 (16)	0.0656 (5)
H13A	1.081 (6)	−0.0145 (7)	0.3608 (15)	0.079*
H13B	1.434 (6)	−0.0010 (6)	0.3749 (16)	0.079*
C14	1.2676 (6)	−0.01268 (6)	0.22933 (16)	0.0656 (5)
H14A	1.434 (6)	0.0043 (7)	0.2005 (16)	0.079*
H14B	1.068 (6)	−0.0086 (6)	0.1851 (16)	0.079*
C15	1.3578 (6)	−0.05754 (6)	0.22743 (15)	0.0658 (5)
H15A	1.175 (5)	−0.0734 (7)	0.2524 (15)	0.079*
H15B	1.563 (6)	−0.0610 (6)	0.2773 (16)	0.079*
C16	1.4310 (5)	−0.07410 (5)	0.13030 (14)	0.0592 (5)
C17	1.3497 (7)	−0.05446 (7)	0.04123 (17)	0.0845 (7)
H17	1.240 (6)	−0.0288 (8)	0.0385 (18)	0.101*
C18	1.4231 (9)	−0.07179 (10)	−0.04660 (19)	0.1030 (10)
H18	1.365 (7)	−0.0581 (9)	−0.106 (2)	0.124*
C19	1.5807 (7)	−0.10865 (9)	−0.0450 (2)	0.0972 (9)
H19	1.627 (7)	−0.1202 (8)	−0.115 (2)	0.117*
C20	1.6604 (7)	−0.12841 (9)	0.0436 (2)	0.0918 (8)
H20	1.767 (7)	−0.1553 (8)	0.034 (2)	0.110*
C21	1.5883 (6)	−0.11141 (6)	0.12899 (18)	0.0731 (6)
H21	1.622 (6)	−0.1248 (7)	0.1918 (18)	0.088*
O1	0.7132 (4)	0.21311 (4)	0.82672 (9)	0.0729 (5)
H1O	0.813 (6)	0.1912 (7)	0.8009 (18)	0.088*
O2	0.5361 (4)	0.24107 (4)	0.47867 (9)	0.0715 (5)
H2O	0.437 (6)	0.2597 (7)	0.4385 (18)	0.086*
O3	0.8903 (4)	0.16382 (4)	0.70806 (9)	0.0849 (5)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0767 (13)	0.0515 (10)	0.0382 (8)	−0.0098 (8)	−0.0006 (8)	−0.0001 (7)
C2	0.1009 (18)	0.0685 (12)	0.0483 (10)	0.0073 (11)	0.0130 (10)	−0.0096 (9)
C3	0.1042 (19)	0.0663 (13)	0.0664 (13)	0.0217 (12)	0.0115 (12)	−0.0038 (10)
C4	0.0849 (16)	0.0592 (11)	0.0531 (10)	0.0108 (10)	0.0037 (10)	0.0064 (8)
C5	0.0643 (12)	0.0509 (9)	0.0396 (8)	−0.0042 (8)	0.0020 (8)	0.0025 (7)
C6	0.0617 (12)	0.0449 (8)	0.0381 (8)	−0.0070 (8)	0.0007 (7)	−0.0001 (7)
C7	0.0684 (13)	0.0495 (9)	0.0429 (8)	−0.0046 (8)	−0.0032 (8)	0.0009 (7)
C8	0.0615 (13)	0.0501 (10)	0.0455 (9)	−0.0024 (8)	0.0032 (8)	−0.0001 (7)
C9	0.0649 (14)	0.0551 (11)	0.0545 (10)	0.0023 (9)	0.0057 (9)	−0.0035 (8)
C10	0.0652 (14)	0.0588 (11)	0.0579 (11)	0.0012 (9)	0.0068 (10)	−0.0072 (8)
C11	0.0672 (14)	0.0601 (12)	0.0637 (11)	0.0043 (9)	0.0076 (10)	−0.0067 (9)
C12	0.0727 (16)	0.0601 (12)	0.0674 (12)	0.0049 (10)	0.0087 (11)	−0.0077 (9)
C13	0.0670 (15)	0.0598 (11)	0.0702 (12)	0.0028 (10)	0.0111 (10)	−0.0051 (9)
C14	0.0693 (15)	0.0563 (11)	0.0707 (12)	0.0030 (10)	0.0088 (11)	−0.0055 (9)
C15	0.0752 (15)	0.0553 (11)	0.0665 (12)	0.0025 (10)	0.0087 (11)	−0.0012 (9)
C16	0.0597 (13)	0.0509 (9)	0.0652 (11)	−0.0052 (8)	0.0034 (9)	−0.0052 (8)
C17	0.118 (2)	0.0627 (13)	0.0718 (14)	0.0058 (13)	0.0112 (13)	0.0006 (11)
C18	0.149 (3)	0.095 (2)	0.0645 (14)	−0.0257 (18)	0.0138 (16)	−0.0014 (13)
C19	0.112 (2)	0.0920 (19)	0.0929 (19)	−0.0279 (16)	0.0327 (16)	−0.0355 (16)
C20	0.0898 (19)	0.0794 (16)	0.107 (2)	0.0020 (13)	0.0170 (15)	−0.0320 (15)
C21	0.0769 (16)	0.0596 (12)	0.0801 (14)	0.0056 (10)	0.0028 (12)	−0.0079 (10)
O1	0.1218 (13)	0.0581 (8)	0.0352 (6)	0.0012 (8)	−0.0009 (7)	−0.0005 (5)
O2	0.1088 (12)	0.0657 (8)	0.0382 (6)	0.0199 (8)	0.0048 (7)	0.0069 (6)
O3	0.1419 (15)	0.0638 (9)	0.0441 (7)	0.0267 (9)	−0.0033 (8)	0.0044 (6)

Geometric parameters (Å, º)

C1—O1	1.358 (2)	C12—C13	1.517 (3)
C1—C2	1.376 (3)	C12—H12A	0.95 (2)
C1—C6	1.415 (2)	C12—H12B	0.96 (2)
C2—C3	1.372 (3)	C13—C14	1.514 (3)
C2—H2	0.97 (2)	C13—H13A	0.97 (2)
C3—C4	1.375 (3)	C13—H13B	0.98 (2)
C3—H3	1.00 (2)	C14—C15	1.510 (3)
C4—C5	1.373 (3)	C14—H14A	1.01 (2)
C4—H4	0.96 (2)	C14—H14B	0.97 (2)
C5—O2	1.348 (2)	C15—C16	1.502 (3)
C5—C6	1.415 (2)	C15—H15A	1.02 (2)
C6—C7	1.468 (2)	C15—H15B	1.02 (2)
C7—O3	1.239 (2)	C16—C17	1.370 (3)
C7—C8	1.499 (2)	C16—C21	1.383 (3)
C8—C9	1.517 (3)	C17—C18	1.397 (4)
C8—H8A	0.95 (2)	C17—H17	0.95 (3)
C8—H8B	1.00 (2)	C18—C19	1.368 (4)
C9—C10	1.516 (3)	C18—H18	0.92 (3)
C9—H9A	1.01 (2)	C19—C20	1.366 (4)
C9—H9B	0.98 (2)	C19—H19	1.07 (3)
C10—C11	1.518 (3)	C20—C21	1.361 (3)
C10—H10A	0.94 (2)	C20—H20	1.00 (3)
C10—H10B	1.03 (2)	C21—H21	0.95 (2)
C11—C12	1.513 (3)	O1—H1O	0.92 (2)
C11—H11A	1.04 (2)	O2—H2O	0.88 (2)
C11—H11B	1.01 (2)
O1—C1—C2	117.30 (16)	C11—C12—C13	114.28 (18)
O1—C1—C6	120.96 (16)	C11—C12—H12A	108.7 (13)
C2—C1—C6	121.74 (16)	C13—C12—H12A	112.9 (14)
C3—C2—C1	119.41 (18)	C11—C12—H12B	108.9 (14)
C3—C2—H2	125.5 (14)	C13—C12—H12B	108.5 (13)
C1—C2—H2	115.1 (14)	H12A—C12—H12B	102.9 (19)
C2—C3—C4	121.2 (2)	C14—C13—C12	113.71 (18)
C2—C3—H3	118.2 (14)	C14—C13—H13A	109.6 (13)
C4—C3—H3	120.3 (14)	C12—C13—H13A	113.4 (14)
C5—C4—C3	119.95 (18)	C14—C13—H13B	107.8 (13)
C5—C4—H4	115.6 (13)	C12—C13—H13B	109.2 (12)
C3—C4—H4	124.4 (13)	H13A—C13—H13B	102.5 (18)
O2—C5—C4	120.59 (15)	C15—C14—C13	114.11 (18)
O2—C5—C6	118.12 (16)	C15—C14—H14A	109.5 (13)
C4—C5—C6	121.29 (16)	C13—C14—H14A	109.9 (12)
C5—C6—C1	116.42 (16)	C15—C14—H14B	108.6 (13)
C5—C6—C7	124.48 (15)	C13—C14—H14B	109.0 (13)
C1—C6—C7	119.10 (14)	H14A—C14—H14B	105.3 (18)
O3—C7—C6	119.01 (15)	C16—C15—C14	116.50 (18)
O3—C7—C8	117.31 (16)	C16—C15—H15A	111.8 (12)
C6—C7—C8	123.66 (14)	C14—C15—H15A	106.4 (13)
C7—C8—C9	113.95 (15)	C16—C15—H15B	106.8 (12)
C7—C8—H8A	107.7 (12)	C14—C15—H15B	106.5 (12)
C9—C8—H8A	111.9 (12)	H15A—C15—H15B	108.6 (17)
C7—C8—H8B	107.8 (11)	C17—C16—C21	117.1 (2)
C9—C8—H8B	109.0 (11)	C17—C16—C15	123.86 (19)
H8A—C8—H8B	106.1 (16)	C21—C16—C15	119.05 (19)
C10—C9—C8	112.42 (16)	C16—C17—C18	120.9 (2)
C10—C9—H9A	107.7 (11)	C16—C17—H17	120.0 (15)
C8—C9—H9A	109.1 (12)	C18—C17—H17	119.1 (15)
C10—C9—H9B	109.7 (12)	C19—C18—C17	120.4 (3)
C8—C9—H9B	109.4 (12)	C19—C18—H18	120.2 (19)
H9A—C9—H9B	108.6 (17)	C17—C18—H18	119.4 (19)
C9—C10—C11	113.35 (17)	C20—C19—C18	118.8 (3)
C9—C10—H10A	111.4 (13)	C20—C19—H19	124.8 (15)
C11—C10—H10A	109.6 (14)	C18—C19—H19	116.3 (15)
C9—C10—H10B	105.8 (11)	C21—C20—C19	120.5 (3)
C11—C10—H10B	109.5 (11)	C21—C20—H20	129.2 (16)
H10A—C10—H10B	106.9 (17)	C19—C20—H20	110.3 (16)
C12—C11—C10	114.23 (18)	C20—C21—C16	122.2 (2)
C12—C11—H11A	110.0 (12)	C20—C21—H21	124.0 (15)
C10—C11—H11A	109.5 (12)	C16—C21—H21	113.6 (15)
C12—C11—H11B	110.0 (12)	C1—O1—H1O	105.3 (14)
C10—C11—H11B	107.9 (12)	C5—O2—H2O	108.3 (15)
H11A—C11—H11B	104.8 (16)
O1—C1—C2—C3	179.3 (2)	C6—C7—C8—C9	−172.95 (18)
C6—C1—C2—C3	−0.5 (4)	C7—C8—C9—C10	177.90 (18)
C1—C2—C3—C4	0.7 (4)	C8—C9—C10—C11	−175.3 (2)
C2—C3—C4—C5	−0.5 (4)	C9—C10—C11—C12	−179.90 (19)
C3—C4—C5—O2	−179.7 (2)	C10—C11—C12—C13	−177.3 (2)
C3—C4—C5—C6	0.2 (3)	C11—C12—C13—C14	−178.7 (2)
O2—C5—C6—C1	179.84 (17)	C12—C13—C14—C15	180.0 (2)
C4—C5—C6—C1	0.0 (3)	C13—C14—C15—C16	−174.3 (2)
O2—C5—C6—C7	−1.0 (3)	C14—C15—C16—C17	−15.8 (3)
C4—C5—C6—C7	179.15 (19)	C14—C15—C16—C21	164.5 (2)
O1—C1—C6—C5	−179.70 (17)	C21—C16—C17—C18	0.2 (4)
C2—C1—C6—C5	0.2 (3)	C15—C16—C17—C18	−179.5 (2)
O1—C1—C6—C7	1.1 (3)	C16—C17—C18—C19	−0.6 (5)
C2—C1—C6—C7	−179.01 (19)	C17—C18—C19—C20	1.0 (5)
C5—C6—C7—O3	−179.16 (19)	C18—C19—C20—C21	−0.9 (4)
C1—C6—C7—O3	0.0 (3)	C19—C20—C21—C16	0.6 (4)
C5—C6—C7—C8	−0.2 (3)	C17—C16—C21—C20	−0.2 (4)
C1—C6—C7—C8	178.87 (18)	C15—C16—C21—C20	179.5 (2)
O3—C7—C8—C9	6.0 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1O···O3	0.92 (2)	1.62 (2)	2.4681 (19)	151 (2)
O2—H2O···O1^i	0.88 (2)	1.89 (2)	2.7419 (18)	164 (2)

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