Crystal structure of an aryl cyclo­hexyl nona­noid, an anti­proliferative mol­ecule isolated from the spice Myristica malabarica

An aryl cyclo­hexyl nona­noid, an anti­proliferative compound, has been extracted from spice from M. myristica using gradient solvent elution. In the crystal, inter­molecular hy­droxy O—H...O_carbon­yl hydrogen-bonding inter­actions generate large 36-membered centrosymmetric cyclic dimers, which are then extended into one-dimensional ribbons along [11].

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.071
• wR factor = 0.178
• Data-to-parameter ratio = 14.0

checkCIF/PLATON results

No syntax errors found



Datablock: I


Alert level C
PLAT241_ALERT_2_C High   'MainMol' Ueq as Compared to Neighbors of         C3 Check
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00415 Ang.
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......     13.356 Check
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      2.191 Check
PLAT910_ALERT_3_C Missing # of FCF Reflection(s) Below Theta(Min)           5 Note
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600         35 Report
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density           0 Note

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          6 Note
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          4 Report
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical          ? Check
PLAT154_ALERT_1_G The s.u.'s on the Cell Angles are Equal ..(Note)       0.01 Degree
PLAT176_ALERT_4_G The CIF-Embedded .res File Contains SADI Records          3 Report
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT300_ALERT_4_G Atom Site Occupancy of >O2     is Constrained at     0.6972 Check
PLAT300_ALERT_4_G Atom Site Occupancy of <O2'    is Constrained at     0.3028 Check
PLAT300_ALERT_4_G Atom Site Occupancy of >C4     is Constrained at     0.6972 Check
PLAT300_ALERT_4_G Atom Site Occupancy of <C4'    is Constrained at     0.3028 Check
PLAT300_ALERT_4_G Atom Site Occupancy of >H2A    is Constrained at     0.6972 Check
PLAT300_ALERT_4_G Atom Site Occupancy of <H2B    is Constrained at     0.3028 Check
PLAT301_ALERT_3_G Main Residue  Disorder ............ Percentage =          8 Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          3 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          3 Note
PLAT933_ALERT_2_G Number of OMIT records in Embedded RES .........          2 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   7 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  17 ALERT level G = General information/check it is not something unexpected

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 ALERT type 2 Indicator that the structure model may be wrong or deficient
   7 ALERT type 3 Indicator that the structure quality may be low
   8 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

---

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS2014 (Sheldrick, 2015); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).

3,5-Dihydroxy-2-[9-(4-hydroxyphenyl)nonanoyl]cyclohexa-2,4-dien-1-one

Crystal data

C21H26O5	Z = 2
Mr = 358.42	F(000) = 384
Triclinic, P1	Dx = 1.213 Mg m^−3
a = 5.6630 (8) Å	Mo Kα radiation, λ = 0.71073 Å
b = 8.707 (1) Å	Cell parameters from 2139 reflections
c = 20.152 (3) Å	θ = 2.9–27.7°
α = 81.69 (1)°	µ = 0.09 mm^−1
β = 86.48 (1)°	T = 293 K
γ = 88.48 (1)°	Prism, yellow
V = 981.2 (2) Å^3	0.48 × 0.48 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur diffractometer with Sapphire CCD detector	2638 reflections with I > 2σ(I)
Radiation source: Enhance (Mo) X-ray source	Rint = 0.013
Rotation method data acquisition using ω scans	θmax = 25.4°, θmin = 2.9°
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2009)	h = −6→6
Tmin = 0.960, Tmax = 0.983	k = −10→10
6013 measured reflections	l = −21→24
3552 independent reflections

Refinement

Refinement on F^2	3 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.071	H-atom parameters constrained
wR(F^2) = 0.178	w = 1/[σ^2(Fo^2) + (0.0517P)^2 + 0.9321P] where P = (Fo^2 + 2Fc^2)/3
S = 1.10	(Δ/σ)max < 0.001
3552 reflections	Δρmax = 0.36 e Å^−3
254 parameters	Δρmin = −0.20 e Å^−3

Special details

Experimental. Absorption correction: CrysAlis RED (Oxford Diffraction, 2009) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	−0.0508 (4)	−0.0225 (3)	0.83338 (11)	0.0664 (7)
O2	0.1863 (14)	−0.3525 (8)	1.0267 (3)	0.0655 (19)	0.6972
H2A	0.2365	−0.2936	1.0510	0.079*	0.6972
O2'	0.254 (4)	−0.310 (2)	1.0277 (7)	0.069 (5)	0.3028
H2B	0.2933	−0.2259	1.0380	0.083*	0.3028
O3	0.6549 (4)	−0.3272 (3)	0.82020 (11)	0.0658 (7)
H3O	0.6550	−0.2796	0.7798	0.079*
O4	0.5334 (4)	−0.1694 (3)	0.71742 (10)	0.0673 (7)
O5	−0.5995 (4)	0.8647 (2)	0.10839 (10)	0.0617 (6)
H5O	−0.7128	0.9054	0.1283	0.074*
C1	0.3066 (5)	−0.1679 (3)	0.81894 (13)	0.0427 (6)
C2	0.1065 (5)	−0.1099 (3)	0.85825 (14)	0.0481 (7)
C3	0.0917 (6)	−0.1598 (4)	0.93293 (15)	0.0742 (11)
H3	0.0167	−0.0988	0.9625	0.089*
C4	0.2009 (10)	−0.3083 (6)	0.9562 (2)	0.0636 (14)	0.6972
C4'	0.3050 (18)	−0.2280 (11)	0.9622 (4)	0.046 (2)	0.3028
C5	0.4429 (6)	−0.3327 (4)	0.92481 (15)	0.0605 (9)
H5A	0.5567	−0.2819	0.9480	0.073*
H5B	0.4808	−0.4430	0.9313	0.073*
C6	0.4698 (5)	−0.2731 (3)	0.85166 (14)	0.0470 (7)
C7	0.3503 (5)	−0.1185 (3)	0.74718 (14)	0.0467 (7)
C8	0.1815 (5)	−0.0110 (3)	0.70682 (14)	0.0501 (7)
H8A	0.1566	0.0819	0.7279	0.060*
H8B	0.0303	−0.0616	0.7084	0.060*
C9	0.2634 (6)	0.0367 (4)	0.63382 (14)	0.0566 (8)
H9A	0.3025	−0.0553	0.6131	0.068*
H9B	0.4049	0.0981	0.6314	0.068*
C10	0.0701 (6)	0.1314 (4)	0.59556 (15)	0.0598 (8)
H10A	−0.0672	0.0670	0.5959	0.072*
H10B	0.0231	0.2186	0.6187	0.072*
C11	0.1480 (6)	0.1921 (4)	0.52332 (15)	0.0627 (9)
H11A	0.2042	0.1053	0.5010	0.075*
H11B	0.2796	0.2612	0.5232	0.075*
C12	−0.0481 (6)	0.2792 (4)	0.48314 (15)	0.0614 (9)
H12A	−0.1808	0.2108	0.4836	0.074*
H12B	−0.1027	0.3672	0.5048	0.074*
C13	0.0332 (6)	0.3360 (4)	0.41130 (15)	0.0599 (8)
H13A	0.0865	0.2474	0.3899	0.072*
H13B	0.1679	0.4026	0.4113	0.072*
C14	−0.1574 (6)	0.4262 (3)	0.36914 (14)	0.0528 (7)
H14A	−0.2963	0.3627	0.3705	0.063*
H14B	−0.2036	0.5197	0.3880	0.063*
C15	−0.0638 (5)	0.4693 (4)	0.29700 (15)	0.0553 (8)
H15A	−0.0314	0.3738	0.2783	0.066*
H15B	0.0863	0.5201	0.2975	0.066*
C16	−0.2175 (5)	0.5731 (3)	0.24928 (14)	0.0433 (6)
C17	−0.4281 (5)	0.6465 (3)	0.26883 (14)	0.0486 (7)
H17	−0.4819	0.6297	0.3138	0.058*
C18	−0.5602 (5)	0.7439 (3)	0.22330 (14)	0.0492 (7)
H18	−0.7001	0.7906	0.2376	0.059*
C19	−0.4795 (5)	0.7697 (3)	0.15660 (14)	0.0458 (7)
C20	−0.2681 (5)	0.6987 (3)	0.13615 (14)	0.0528 (8)
H20	−0.2128	0.7169	0.0913	0.063*
C21	−0.1409 (5)	0.6019 (3)	0.18188 (14)	0.0502 (7)
H21	−0.0015	0.5550	0.1673	0.060*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0639 (14)	0.0742 (15)	0.0563 (13)	0.0366 (12)	−0.0044 (10)	0.0007 (11)
O2	0.082 (5)	0.068 (4)	0.043 (2)	0.013 (3)	0.005 (2)	−0.001 (2)
O2'	0.107 (13)	0.067 (9)	0.032 (5)	−0.021 (6)	−0.013 (5)	0.004 (5)
O3	0.0579 (13)	0.0792 (15)	0.0541 (12)	0.0328 (12)	0.0045 (10)	0.0024 (11)
O4	0.0666 (15)	0.0829 (16)	0.0474 (12)	0.0210 (12)	0.0073 (10)	−0.0015 (11)
O5	0.0625 (14)	0.0668 (14)	0.0496 (12)	0.0272 (11)	−0.0018 (10)	0.0066 (10)
C1	0.0426 (15)	0.0434 (15)	0.0404 (14)	0.0073 (12)	−0.0031 (11)	−0.0018 (11)
C2	0.0477 (16)	0.0482 (16)	0.0463 (16)	0.0125 (13)	−0.0043 (13)	−0.0017 (13)
C3	0.073 (2)	0.099 (3)	0.0426 (17)	0.044 (2)	0.0076 (16)	0.0028 (17)
C4	0.078 (4)	0.070 (3)	0.036 (2)	0.032 (3)	0.010 (2)	0.006 (2)
C4'	0.068 (7)	0.040 (5)	0.030 (5)	−0.002 (5)	−0.007 (4)	−0.005 (4)
C5	0.062 (2)	0.068 (2)	0.0464 (17)	0.0210 (16)	−0.0074 (14)	0.0038 (15)
C6	0.0430 (16)	0.0492 (16)	0.0470 (16)	0.0106 (13)	−0.0005 (12)	−0.0041 (13)
C7	0.0523 (17)	0.0438 (15)	0.0437 (15)	0.0036 (13)	−0.0044 (13)	−0.0053 (12)
C8	0.0565 (18)	0.0486 (16)	0.0429 (15)	0.0030 (14)	−0.0080 (13)	0.0019 (12)
C9	0.071 (2)	0.0545 (18)	0.0433 (16)	0.0027 (15)	−0.0105 (14)	0.0005 (13)
C10	0.078 (2)	0.0532 (18)	0.0467 (17)	0.0009 (16)	−0.0139 (15)	0.0031 (14)
C11	0.081 (2)	0.0580 (19)	0.0471 (17)	0.0033 (17)	−0.0151 (16)	0.0034 (14)
C12	0.081 (2)	0.0522 (18)	0.0492 (17)	0.0053 (16)	−0.0117 (16)	0.0014 (14)
C13	0.074 (2)	0.0544 (18)	0.0488 (17)	0.0063 (16)	−0.0148 (15)	0.0037 (14)
C14	0.0605 (19)	0.0465 (16)	0.0492 (17)	0.0035 (14)	−0.0075 (14)	0.0018 (13)
C15	0.0510 (18)	0.0560 (18)	0.0542 (18)	0.0050 (14)	−0.0073 (14)	0.0082 (14)
C16	0.0428 (15)	0.0400 (14)	0.0455 (15)	0.0013 (12)	−0.0052 (12)	0.0001 (12)
C17	0.0486 (17)	0.0539 (17)	0.0400 (15)	0.0034 (13)	0.0017 (12)	0.0012 (13)
C18	0.0437 (16)	0.0503 (17)	0.0518 (17)	0.0084 (13)	0.0025 (13)	−0.0048 (13)
C19	0.0462 (16)	0.0431 (15)	0.0461 (15)	0.0081 (13)	−0.0040 (12)	−0.0003 (12)
C20	0.0544 (18)	0.0581 (18)	0.0424 (15)	0.0147 (15)	0.0031 (13)	−0.0009 (13)
C21	0.0461 (17)	0.0520 (17)	0.0504 (16)	0.0140 (13)	0.0004 (13)	−0.0039 (13)

Geometric parameters (Å, º)

O1—C2	1.238 (3)	C10—C11	1.518 (4)
O2—C4	1.415 (7)	C10—H10A	0.9700
O2—H2A	0.8256	C10—H10B	0.9700
O2'—H2B	0.8247	C11—C12	1.534 (4)
O3—C6	1.305 (3)	C11—H11A	0.9700
O3—H3O	0.8588	C11—H11B	0.9700
O4—C7	1.268 (3)	C12—C13	1.509 (4)
O5—C19	1.382 (3)	C12—H12A	0.9700
O5—H5O	0.8342	C12—H12B	0.9700
C1—C6	1.408 (4)	C13—C14	1.543 (4)
C1—C7	1.456 (4)	C13—H13A	0.9700
C1—C2	1.463 (4)	C13—H13B	0.9700
C2—C3	1.503 (4)	C14—C15	1.514 (4)
C3—C4	1.446 (5)	C14—H14A	0.9700
C3—C4'	1.452 (10)	C14—H14B	0.9700
C3—H3	0.9300	C15—C16	1.519 (4)
C4—C5	1.497 (5)	C15—H15A	0.9700
C4'—C5	1.449 (9)	C15—H15B	0.9700
C5—C6	1.490 (4)	C16—C21	1.390 (4)
C5—H5A	0.9700	C16—C17	1.400 (4)
C5—H5B	0.9700	C17—C18	1.395 (4)
C7—C8	1.510 (4)	C17—H17	0.9300
C8—C9	1.517 (4)	C18—C19	1.382 (4)
C8—H8A	0.9700	C18—H18	0.9300
C8—H8B	0.9700	C19—C20	1.400 (4)
C9—C10	1.531 (4)	C20—C21	1.379 (4)
C9—H9A	0.9700	C20—H20	0.9300
C9—H9B	0.9700	C21—H21	0.9300
C4—O2—H2A	119.3	C10—C11—C12	113.8 (3)
C6—O3—H3O	105.4	C10—C11—H11A	108.8
C19—O5—H5O	107.1	C12—C11—H11A	108.8
C6—C1—C7	117.7 (2)	C10—C11—H11B	108.8
C6—C1—C2	119.2 (2)	C12—C11—H11B	108.8
C7—C1—C2	123.1 (2)	H11A—C11—H11B	107.7
O1—C2—C1	123.6 (3)	C13—C12—C11	112.6 (3)
O1—C2—C3	118.4 (3)	C13—C12—H12A	109.1
C1—C2—C3	118.0 (2)	C11—C12—H12A	109.1
C4—C3—C2	116.1 (3)	C13—C12—H12B	109.1
C4'—C3—C2	116.5 (4)	C11—C12—H12B	109.1
C4—C3—H3	122.0	H12A—C12—H12B	107.8
C2—C3—H3	122.0	C12—C13—C14	114.5 (3)
O2—C4—C3	115.1 (5)	C12—C13—H13A	108.6
O2—C4—C5	113.0 (5)	C14—C13—H13A	108.6
C3—C4—C5	114.4 (4)	C12—C13—H13B	108.6
C5—C4'—C3	117.1 (6)	C14—C13—H13B	108.6
C4'—C5—C6	112.4 (4)	H13A—C13—H13B	107.6
C6—C5—C4	114.3 (3)	C15—C14—C13	110.4 (3)
C6—C5—H5A	108.7	C15—C14—H14A	109.6
C4—C5—H5A	108.7	C13—C14—H14A	109.6
C6—C5—H5B	108.7	C15—C14—H14B	109.6
C4—C5—H5B	108.7	C13—C14—H14B	109.6
H5A—C5—H5B	107.6	H14A—C14—H14B	108.1
O3—C6—C1	122.7 (3)	C14—C15—C16	118.1 (3)
O3—C6—C5	114.7 (2)	C14—C15—H15A	107.8
C1—C6—C5	122.6 (2)	C16—C15—H15A	107.8
O4—C7—C1	119.1 (2)	C14—C15—H15B	107.8
O4—C7—C8	119.0 (2)	C16—C15—H15B	107.8
C1—C7—C8	122.0 (2)	H15A—C15—H15B	107.1
C7—C8—C9	114.7 (3)	C21—C16—C17	117.4 (2)
C7—C8—H8A	108.6	C21—C16—C15	118.1 (3)
C9—C8—H8A	108.6	C17—C16—C15	124.5 (3)
C7—C8—H8B	108.6	C18—C17—C16	122.4 (3)
C9—C8—H8B	108.6	C18—C17—H17	118.8
H8A—C8—H8B	107.6	C16—C17—H17	118.8
C8—C9—C10	110.7 (3)	C19—C18—C17	118.8 (3)
C8—C9—H9A	109.5	C19—C18—H18	120.6
C10—C9—H9A	109.5	C17—C18—H18	120.6
C8—C9—H9B	109.5	O5—C19—C18	122.4 (2)
C10—C9—H9B	109.5	O5—C19—C20	117.9 (2)
H9A—C9—H9B	108.1	C18—C19—C20	119.7 (2)
C11—C10—C9	113.2 (3)	C21—C20—C19	120.6 (3)
C11—C10—H10A	108.9	C21—C20—H20	119.7
C9—C10—H10A	108.9	C19—C20—H20	119.7
C11—C10—H10B	108.9	C20—C21—C16	121.2 (3)
C9—C10—H10B	108.9	C20—C21—H21	119.4
H10A—C10—H10B	107.8	C16—C21—H21	119.4
C6—C1—C2—O1	−176.9 (3)	C6—C1—C7—C8	177.6 (3)
C7—C1—C2—O1	5.0 (5)	C2—C1—C7—C8	−4.3 (4)
C6—C1—C2—C3	3.0 (4)	O4—C7—C8—C9	−5.2 (4)
C7—C1—C2—C3	−175.1 (3)	C1—C7—C8—C9	176.1 (3)
O1—C2—C3—C4	152.2 (4)	C7—C8—C9—C10	174.2 (3)
C1—C2—C3—C4	−27.6 (5)	C8—C9—C10—C11	176.0 (3)
O1—C2—C3—C4'	−164.8 (5)	C9—C10—C11—C12	176.6 (3)
C1—C2—C3—C4'	15.4 (7)	C10—C11—C12—C13	−179.1 (3)
C2—C3—C4—O2	179.6 (5)	C11—C12—C13—C14	−179.2 (3)
C2—C3—C4—C5	46.1 (6)	C12—C13—C14—C15	−176.4 (3)
C2—C3—C4'—C5	−40.0 (10)	C13—C14—C15—C16	−173.8 (3)
C3—C4'—C5—C6	43.6 (9)	C14—C15—C16—C21	−174.6 (3)
O2—C4—C5—C6	−174.4 (5)	C14—C15—C16—C17	7.6 (5)
C3—C4—C5—C6	−39.9 (6)	C21—C16—C17—C18	0.6 (4)
C7—C1—C6—O3	−0.4 (4)	C15—C16—C17—C18	178.4 (3)
C2—C1—C6—O3	−178.6 (3)	C16—C17—C18—C19	−0.4 (5)
C7—C1—C6—C5	−179.6 (3)	C17—C18—C19—O5	−179.9 (3)
C2—C1—C6—C5	2.2 (5)	C17—C18—C19—C20	−0.2 (4)
C4'—C5—C6—O3	155.7 (5)	O5—C19—C20—C21	−179.6 (3)
C4—C5—C6—O3	−163.2 (4)	C18—C19—C20—C21	0.7 (5)
C4'—C5—C6—C1	−25.0 (6)	C19—C20—C21—C16	−0.5 (5)
C4—C5—C6—C1	16.1 (5)	C17—C16—C21—C20	−0.1 (4)
C6—C1—C7—O4	−1.1 (4)	C15—C16—C21—C20	−178.1 (3)
C2—C1—C7—O4	177.0 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···O5^i	0.83	2.18	3.004 (7)	174
O2′—H2B···O5^i	0.82	1.86	2.565 (16)	143
O3—H3O···O4	0.86	1.64	2.440 (3)	153
O5—H5O···O1^ii	0.83	1.86	2.687 (3)	172

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