Malabaricone C monohydrate

The crystal structure of the title compound, 1-(2,6-dihydroxy­phen­yl)-9-(3,4-dihydroxy­phen­yl)nonan-1-one monohydrate, also known as malabaricone C, C₂₁H₂₆O₅·H₂O, is stabilized by both intra- and inter­molecular O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 299 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.048
• wR factor = 0.137
• Data-to-parameter ratio = 13.6

checkCIF/PLATON results

No syntax errors found



Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           66.96
           From the CIF: _reflns_number_total               3566
           Count of symmetry unique reflns         2162
           Completeness (_total/calc)            164.94%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1404
           Fraction of Friedel pairs measured     0.649
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 ALERT level C = Check and explain
   1 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
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

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.

1-(2,6-dihydroxyphenyl)-9-(3,4-dihydroxyphenyl)nonan-1-one monohydrate

Crystal data

C21H26O5·H2O	Dx = 1.227 Mg m^−3
Mr = 376.43	Melting point: 396 K
Orthorhombic, P212121	Cu Kα radiation, λ = 1.54180 Å
Hall symbol: P 2ac 2ab	Cell parameters from 25 reflections
a = 5.4549 (6) Å	θ = 5.8–20.2°
b = 9.176 (1) Å	µ = 0.73 mm^−1
c = 40.718 (3) Å	T = 299 K
V = 2038.1 (3) Å^3	Long needle, dark yellow
Z = 4	0.55 × 0.25 × 0.20 mm
F(000) = 808

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.032
Radiation source: fine-focus sealed tube	θmax = 67.0°, θmin = 2.2°
Graphite monochromator	h = −6→6
Ω/2θ scans	k = −10→0
3822 measured reflections	l = −48→0
3566 independent reflections	3 standard reflections every 120 min
3323 reflections with I > 2σ(I)	intensity decay: 1%

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.048	w = 1/[σ^2(Fo^2) + (0.1014P)^2 + 0.1804P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.137	(Δ/σ)max = 0.007
S = 1.04	Δρmax = 0.20 e Å^−3
3566 reflections	Δρmin = −0.21 e Å^−3
263 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
7 restraints	Extinction coefficient: 0.0035 (6)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1404 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.1 (2)

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
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*
C13	−0.2052 (6)	0.1386 (4)	0.23178 (6)	0.0796 (8)
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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0632 (9)	0.0797 (9)	0.0448 (7)	0.0219 (8)	0.0085 (7)	0.0129 (7)
O2	0.0601 (9)	0.0758 (9)	0.0488 (8)	0.0267 (8)	0.0075 (6)	0.0119 (7)
O3	0.0544 (8)	0.0711 (8)	0.0479 (7)	0.0219 (7)	0.0061 (6)	0.0044 (6)
O4	0.0550 (8)	0.0776 (9)	0.0532 (7)	−0.0258 (8)	−0.0089 (7)	0.0019 (7)
O5	0.0384 (7)	0.0987 (11)	0.0503 (7)	−0.0172 (8)	0.0003 (6)	0.0144 (7)
C1	0.0427 (10)	0.0542 (10)	0.0428 (9)	0.0007 (8)	0.0021 (7)	0.0012 (7)
C2	0.0468 (11)	0.0707 (12)	0.0460 (10)	−0.0008 (9)	0.0087 (8)	−0.0003 (8)
C3	0.0386 (10)	0.0741 (12)	0.0552 (10)	0.0038 (10)	0.0096 (9)	−0.0083 (9)
C4	0.0372 (9)	0.0626 (10)	0.0556 (10)	0.0078 (9)	0.0017 (8)	−0.0040 (8)
C5	0.0373 (9)	0.0554 (9)	0.0431 (9)	0.0032 (8)	−0.0013 (7)	−0.0020 (7)
C6	0.0380 (9)	0.0510 (9)	0.0398 (8)	0.0002 (7)	0.0003 (7)	−0.0027 (7)
C7	0.0397 (9)	0.0497 (9)	0.0427 (8)	0.0012 (8)	0.0021 (7)	−0.0009 (7)
C8	0.0497 (11)	0.0683 (12)	0.0447 (10)	0.0106 (10)	0.0075 (8)	0.0032 (8)
C9	0.0522 (11)	0.0652 (11)	0.0453 (10)	0.0077 (9)	0.0102 (9)	0.0028 (9)
C10	0.0842 (18)	0.0978 (17)	0.0503 (12)	0.0294 (15)	0.0232 (12)	0.0174 (12)
C11	0.0699 (15)	0.0972 (17)	0.0474 (11)	0.0173 (14)	0.0143 (10)	0.0097 (11)
C12	0.0891 (19)	0.124 (2)	0.0533 (12)	0.0291 (19)	0.0269 (13)	0.0203 (14)
C13	0.0754 (16)	0.114 (2)	0.0496 (12)	0.0199 (16)	0.0140 (11)	0.0096 (13)
C14	0.0762 (17)	0.116 (2)	0.0476 (11)	0.0223 (16)	0.0157 (12)	0.0094 (13)
C15	0.0749 (16)	0.1142 (19)	0.0510 (12)	0.0250 (16)	0.0081 (12)	0.0108 (13)
C16	0.0553 (12)	0.0888 (15)	0.0426 (9)	0.0128 (12)	0.0079 (9)	−0.0002 (10)
C17	0.0496 (11)	0.0663 (12)	0.0520 (11)	−0.0054 (9)	0.0084 (9)	0.0031 (9)
C18	0.0399 (9)	0.0576 (10)	0.0447 (9)	−0.0062 (8)	0.0013 (7)	−0.0052 (8)
C19	0.0346 (9)	0.0644 (10)	0.0431 (8)	−0.0027 (8)	0.0018 (7)	−0.0025 (8)
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
C4—C3—H3	119.2	C12—C13—H13B	108.8
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)
O1—C1—C2—C3	−179.60 (19)	C8—C9—C10—C11	177.0 (2)
C6—C1—C2—C3	0.3 (3)	C9—C10—C11—C12	173.7 (3)
C1—C2—C3—C4	0.8 (3)	C10—C11—C12—C13	179.2 (3)
C2—C3—C4—C5	−0.9 (3)	C11—C12—C13—C14	−179.8 (3)
C3—C4—C5—O2	179.42 (18)	C12—C13—C14—C15	178.0 (3)
C3—C4—C5—C6	0.0 (3)	C13—C14—C15—C16	−175.8 (3)
O2—C5—C6—C1	−178.48 (17)	C14—C15—C16—C21	−97.2 (3)
C4—C5—C6—C1	1.0 (3)	C14—C15—C16—C17	81.0 (3)
O2—C5—C6—C7	2.4 (3)	C21—C16—C17—C18	−2.7 (3)
C4—C5—C6—C7	−178.13 (18)	C15—C16—C17—C18	179.0 (2)
O1—C1—C6—C5	178.75 (18)	C16—C17—C18—O4	−178.5 (2)
C2—C1—C6—C5	−1.1 (3)	C16—C17—C18—C19	−0.1 (3)
O1—C1—C6—C7	−2.1 (3)	C17—C18—C19—O5	−178.80 (19)
C2—C1—C6—C7	178.05 (17)	O4—C18—C19—O5	−0.4 (3)
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···O4^i	0.84 (2)	1.92 (2)	2.748 (2)	173 (3)
O4—H4O···O6^ii	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···O6^iii	0.80 (2)	1.95 (2)	2.724 (2)	164 (3)
O6—H61O···O1^iv	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) −x+1, y−1/2, −z+1/2; (ii) −x, y−1/2, −z+1/2; (iii) −x−1, y−1/2, −z+1/2; (iv) x−1/2, −y+1/2, −z.