Santal monohydrate, an isoflavone isolated from Wye­thia mollis

The title compound [systematic name: 3-(3,4-di­hydroxy­phen­yl)-5-hy­droxy-7-meth­oxy-4H-chromen-4-one monohydrate], C₁₆H₁₂O₆·H₂O, is a monohydrate of a natural product santal isolated from Wye­thia mollis. In the santal mol­ecule, the dihedral angle between the benzo­quinone and di­hydroxy­phenyl fragments is 53.9 (1)° and an intra­molecular O—H...O hydrogen bond occurs. In the crystal, O—H...O hydrogen bonds link the components into corrugated layers parallel to the ac plane. The short distance of 3.474 (5) Å between the centroids of the benzene rings in neighbouring santal mol­ecules reveals then existence of π–π inter­actions within the layers.

Key indicators

• Single-crystal X-ray study
• T = 200 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.039
• wR factor = 0.110
• Data-to-parameter ratio = 11.2

checkCIF/PLATON results

No syntax errors found



Alert level B
            Crystal system given = orthorhombic
PLAT420_ALERT_2_B D-H Without Acceptor       O1S    -   H1SB   ...     Please Check

Author Response: H1SB is stabilized by interation with the \p system of the dihydroxyphenyl ring of an adjacent santal molecule.

Alert level C
PLAT019_ALERT_1_C Check _diffrn_measured_fraction_theta_full/_max       0.982
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........       6.25
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0048 Ang.

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF     Please Do !
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Why ?
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          2
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          3 Note
PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still          54 %
PLAT910_ALERT_3_G Missing # of FCF Reflections Below Th(Min) .....          2 Why ?

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

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

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S1. Comment

Santal, C₁₆H₁₂O₆, is an isoflavone isolated from Wyethia mollis, a species once used in folk medicine to treat contusions, pain, fevers, and colds. Santal (Figure 1), has a benzoquinone core with an appended dihydroxyphenyl group. The benzoquinone core is substituted with hydroxyl and methoxy substituents. In the santal molecule of the title compound, which is a monohydrate, the flat planes created by the benzoquinone core and the dihydroxyphenyl group are twisted dramatically relative to each other with a dihedral angle of 53.9 (1)°. The torsion angle C11—C4—C5—C13 is 54.1 (5)°. This twisting breaks conjugation between the rings, but is likely necessitated by steric interactions between O5 and H11.

The molecule stacks together with the benzoquinone rings parallel to each other and with the dihydroxyphenyl rings pointing in toward the center of the unit cell. The crystal structure shows the presence of linking external water molecules. The water interacts uniquely with three separate santal molecules. It acts as a hydrogen bond donor (H1SA) with O5 and as a hydrogen bond acceptor with O4H of a second santal molecule (Table 1). The second hydrogen on the water (H1SB) is stabilized by interaction with the electron rich π system of the dihydroxyphenyl ring of a third santal molecule. Additionally, O4 acts as a hydrogen bond acceptor to O1H in another santal unit. There is an intramolecular hydrogen bond in which the hydroxyl group at O6 acts as the donor and O5 as the acceptor (Table 1).

In the crystal, intermolecular O—H···O hydrogen bonds link all moieties into corrugated layers parallel to ac plane. The short distances of 3.474 (5) Å between the centroids of benzene rings from the neighbouring santal molecules reveal an existence of π–π interactions inside the layers.

Related literature

For the discovery and structural identification of isoflavones, see: Raudnitz & Perlmann (1935); Robertson et al. (1949). Santal was isolated following the method of Waddell et al. (1982). For the structure of the triterpene component of Wyethia mollis, see: Smith et al. (2013).

S2. Experimental

Santal was isolated as described previously (Waddell et al., 1982). Suitable crystals of the title compound were obtained by slow evaporation of a water solution of the santal.

S3. Refinement

H6 was located in a difference Fourier map and refined freely. H1SA and H1SB (H₂O) were located in a difference Fourier map and refined with O—H distance restrained to 0.91 (3) Å, with U_iso(H)= 1.5U_eq (O). All other H atoms were positioned geometrically, with bond distances of 0.85 Å for hydroxyl, 0.98 Å for methyl and 0.95 Å for those bound to aromatic rings and were refined as riding, with U_iso(H)= 1.2–1.5U_eq of the parent atom.

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXS97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures

Fig. 1. View of the title compound showing the atomic numbering and 50% probability displacement ellipsoids. Dashed lines denote hydrogen bonds.

3-(3,4-Dihydroxyphenyl)-5-hydroxy-7-methoxy-4H-chromen-4-one monohydrate

Crystal data

C16H12O6·H2O	Dx = 1.484 Mg m^−3
Mr = 318.28	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pca21	Cell parameters from 2745 reflections
a = 16.494 (3) Å	θ = 2.5–24.8°
b = 13.082 (3) Å	µ = 0.12 mm^−1
c = 6.6008 (12) Å	T = 200 K
V = 1424.3 (5) Å^3	Prism, yellow
Z = 4	0.46 × 0.41 × 0.4 mm
F(000) = 664

Data collection

Bruker APEXII CCD diffractometer	2002 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.060
φ and ω scans	θmax = 25.0°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	h = −18→19
Tmin = 0.518, Tmax = 0.958	k = −14→15
8545 measured reflections	l = −7→7
2478 independent reflections

Refinement

Refinement on F^2	3 restraints
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.039	w = 1/[σ^2(Fo^2) + (0.0829P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.110	(Δ/σ)max < 0.001
S = 0.85	Δρmax = 0.14 e Å^−3
2478 reflections	Δρmin = −0.18 e Å^−3
221 parameters

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.

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

	x	y	z	Uiso*/Ueq
O1	0.00097 (18)	0.5170 (2)	0.8482 (5)	0.0495 (7)
H1	−0.0315	0.4972	0.9380	0.074*
O2	0.05990 (13)	1.09967 (17)	1.0156 (4)	0.0349 (6)
O3	0.25286 (16)	1.36978 (18)	1.0531 (5)	0.0496 (7)
O4	0.10095 (17)	0.6010 (2)	0.5878 (4)	0.0519 (8)
H4	0.1343	0.6336	0.5166	0.078*
O5	0.24167 (15)	0.88921 (18)	0.9502 (4)	0.0410 (6)
O6	0.34600 (14)	1.0348 (2)	0.9842 (4)	0.0387 (6)
C1	0.0235 (2)	0.6152 (3)	0.8869 (6)	0.0359 (8)
C2	−0.0036 (2)	0.6707 (3)	1.0506 (6)	0.0391 (8)
H2	−0.0399	0.6403	1.1448	0.047*
C3	0.0222 (2)	0.7715 (3)	1.0786 (5)	0.0380 (8)
H3	0.0036	0.8090	1.1928	0.046*
C4	0.0746 (2)	0.8173 (2)	0.9417 (5)	0.0316 (7)
C5	0.1003 (2)	0.9250 (2)	0.9674 (5)	0.0306 (7)
C6	0.0442 (2)	0.9991 (3)	0.9915 (5)	0.0335 (7)
H6A	−0.0111	0.9788	0.9914	0.040*
C7	0.13907 (18)	1.1317 (2)	1.0132 (4)	0.0282 (7)
C8	0.1518 (2)	1.2363 (3)	1.0322 (5)	0.0339 (7)
H8	0.1077	1.2826	1.0432	0.041*
C9	0.2307 (2)	1.2700 (3)	1.0344 (5)	0.0343 (8)
C10	0.1904 (3)	1.4455 (3)	1.0619 (9)	0.0680 (14)
H10A	0.1572	1.4416	0.9390	0.102*
H10B	0.2150	1.5135	1.0718	0.102*
H10C	0.1562	1.4332	1.1808	0.102*
C11	0.1018 (2)	0.7603 (3)	0.7752 (5)	0.0342 (8)
H11	0.1380	0.7905	0.6808	0.041*
C12	0.0764 (2)	0.6607 (3)	0.7470 (5)	0.0356 (8)
C13	0.18522 (19)	0.9544 (2)	0.9687 (4)	0.0284 (7)
C14	0.20191 (18)	1.0609 (2)	0.9938 (4)	0.0271 (7)
C15	0.29629 (19)	1.2025 (3)	1.0181 (5)	0.0350 (8)
H15	0.3503	1.2278	1.0207	0.042*
C16	0.28220 (19)	1.1001 (2)	0.9983 (5)	0.0297 (7)
O1S	0.1966 (2)	0.6972 (2)	0.3142 (5)	0.0571 (8)
H1SA	0.225 (3)	0.755 (3)	0.345 (9)	0.086*
H1SB	0.162 (3)	0.711 (4)	0.214 (7)	0.086*
H6	0.323 (2)	0.975 (3)	0.975 (6)	0.044 (12)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0547 (17)	0.0299 (15)	0.0639 (18)	−0.0135 (12)	0.0080 (13)	−0.0013 (13)
O2	0.0262 (12)	0.0265 (12)	0.0520 (13)	0.0019 (10)	0.0011 (11)	−0.0010 (11)
O3	0.0511 (16)	0.0283 (14)	0.0694 (18)	−0.0072 (13)	−0.0025 (14)	−0.0057 (13)
O4	0.0612 (19)	0.0411 (17)	0.0534 (16)	−0.0198 (13)	0.0149 (13)	−0.0138 (12)
O5	0.0322 (13)	0.0305 (14)	0.0602 (16)	0.0054 (11)	−0.0029 (10)	−0.0060 (12)
O6	0.0266 (12)	0.0382 (15)	0.0513 (15)	0.0031 (11)	−0.0018 (11)	−0.0011 (11)
C1	0.0334 (19)	0.0228 (19)	0.051 (2)	−0.0029 (14)	−0.0024 (15)	0.0019 (15)
C2	0.0356 (19)	0.031 (2)	0.050 (2)	−0.0014 (14)	0.0092 (15)	0.0066 (16)
C3	0.039 (2)	0.034 (2)	0.0418 (19)	0.0042 (15)	0.0063 (15)	0.0018 (15)
C4	0.0251 (16)	0.0293 (18)	0.0404 (16)	−0.0022 (14)	−0.0030 (13)	0.0021 (13)
C5	0.0332 (18)	0.0258 (18)	0.0329 (17)	−0.0015 (13)	−0.0004 (12)	0.0011 (12)
C6	0.0295 (17)	0.0310 (19)	0.0401 (17)	−0.0025 (13)	0.0017 (13)	0.0006 (14)
C7	0.0262 (16)	0.0308 (18)	0.0276 (14)	0.0018 (13)	−0.0005 (13)	−0.0005 (13)
C8	0.0345 (18)	0.0284 (18)	0.0387 (17)	0.0032 (13)	−0.0001 (15)	−0.0023 (14)
C9	0.041 (2)	0.0302 (18)	0.0320 (17)	−0.0054 (14)	−0.0017 (15)	−0.0026 (14)
C10	0.063 (3)	0.027 (2)	0.114 (4)	0.0008 (19)	−0.009 (3)	−0.012 (2)
C11	0.0331 (18)	0.0303 (19)	0.0392 (19)	−0.0076 (14)	0.0003 (13)	0.0005 (13)
C12	0.0366 (19)	0.032 (2)	0.0381 (18)	−0.0019 (15)	0.0003 (14)	−0.0045 (14)
C13	0.0280 (16)	0.0305 (18)	0.0268 (15)	0.0021 (14)	−0.0009 (12)	−0.0016 (12)
C14	0.0259 (16)	0.0297 (18)	0.0256 (15)	0.0010 (13)	−0.0004 (12)	0.0011 (12)
C15	0.0299 (17)	0.040 (2)	0.0350 (16)	−0.0056 (14)	−0.0031 (14)	0.0012 (15)
C16	0.0272 (16)	0.0359 (18)	0.0262 (15)	0.0020 (14)	−0.0018 (12)	−0.0002 (13)
O1S	0.065 (2)	0.0485 (18)	0.0582 (17)	−0.0161 (14)	0.0047 (15)	−0.0012 (14)

Geometric parameters (Å, º)

O1—H1	0.8400	C5—C6	1.350 (5)
O1—C1	1.362 (4)	C5—C13	1.453 (5)
O2—C6	1.351 (4)	C6—H6A	0.9500
O2—C7	1.371 (4)	C7—C8	1.390 (4)
O3—C9	1.361 (4)	C7—C14	1.396 (4)
O3—C10	1.430 (5)	C8—H8	0.9500
O4—H4	0.8400	C8—C9	1.374 (5)
O4—C12	1.370 (4)	C9—C15	1.401 (5)
O5—C13	1.268 (4)	C10—H10A	0.9800
O6—C16	1.359 (4)	C10—H10B	0.9800
O6—H6	0.87 (4)	C10—H10C	0.9800
C1—C2	1.376 (5)	C11—H11	0.9500
C1—C12	1.402 (5)	C11—C12	1.382 (5)
C2—H2	0.9500	C13—C14	1.430 (4)
C2—C3	1.398 (5)	C14—C16	1.420 (4)
C3—H3	0.9500	C15—H15	0.9500
C3—C4	1.387 (5)	C15—C16	1.366 (5)
C4—C5	1.480 (4)	O1S—H1SA	0.91 (3)
C4—C11	1.402 (5)	O1S—H1SB	0.89 (3)
C1—O1—H1	109.5	O3—C9—C8	124.3 (3)
C6—O2—C7	118.6 (2)	O3—C9—C15	113.8 (3)
C9—O3—C10	118.3 (3)	C8—C9—C15	121.9 (3)
C12—O4—H4	109.5	O3—C10—H10A	109.5
C16—O6—H6	104 (3)	O3—C10—H10B	109.5
O1—C1—C2	123.7 (3)	O3—C10—H10C	109.5
O1—C1—C12	116.5 (3)	H10A—C10—H10B	109.5
C2—C1—C12	119.7 (3)	H10A—C10—H10C	109.5
C1—C2—H2	119.9	H10B—C10—H10C	109.5
C1—C2—C3	120.2 (3)	C4—C11—H11	119.6
C3—C2—H2	119.9	C12—C11—C4	120.7 (3)
C2—C3—H3	119.6	C12—C11—H11	119.6
C4—C3—C2	120.8 (3)	O4—C12—C1	116.6 (3)
C4—C3—H3	119.6	O4—C12—C11	123.5 (3)
C3—C4—C5	121.0 (3)	C11—C12—C1	120.0 (3)
C3—C4—C11	118.7 (3)	O5—C13—C5	122.0 (3)
C11—C4—C5	120.3 (3)	O5—C13—C14	121.6 (3)
C6—C5—C4	120.1 (3)	C14—C13—C5	116.4 (3)
C6—C5—C13	118.0 (3)	C7—C14—C13	120.9 (3)
C13—C5—C4	121.9 (3)	C7—C14—C16	116.8 (3)
O2—C6—H6A	117.2	C16—C14—C13	122.3 (3)
C5—C6—O2	125.6 (3)	C9—C15—H15	120.2
C5—C6—H6A	117.2	C16—C15—C9	119.6 (3)
O2—C7—C8	116.3 (3)	C16—C15—H15	120.2
O2—C7—C14	120.4 (3)	O6—C16—C14	119.6 (3)
C8—C7—C14	123.3 (3)	O6—C16—C15	119.4 (3)
C7—C8—H8	121.3	C15—C16—C14	121.0 (3)
C9—C8—C7	117.4 (3)	H1SA—O1S—H1SB	108 (5)
C9—C8—H8	121.3
O1—C1—C2—C3	−179.6 (3)	C5—C13—C14—C16	179.9 (3)
O1—C1—C12—O4	−1.0 (5)	C6—O2—C7—C8	178.0 (3)
O1—C1—C12—C11	179.7 (3)	C6—O2—C7—C14	−2.4 (4)
O2—C7—C8—C9	178.7 (3)	C6—C5—C13—O5	178.9 (3)
O2—C7—C14—C13	2.3 (4)	C6—C5—C13—C14	−0.6 (4)
O2—C7—C14—C16	−178.3 (3)	C7—O2—C6—C5	1.0 (5)
O3—C9—C15—C16	−179.9 (3)	C7—C8—C9—O3	−179.6 (3)
O5—C13—C14—C7	179.8 (3)	C7—C8—C9—C15	0.1 (5)
O5—C13—C14—C16	0.4 (4)	C7—C14—C16—O6	178.7 (3)
C1—C2—C3—C4	0.6 (5)	C7—C14—C16—C15	−0.8 (4)
C2—C1—C12—O4	180.0 (3)	C8—C7—C14—C13	−178.1 (3)
C2—C1—C12—C11	0.7 (5)	C8—C7—C14—C16	1.3 (4)
C2—C3—C4—C5	178.3 (3)	C8—C9—C15—C16	0.3 (5)
C2—C3—C4—C11	−0.5 (5)	C9—C15—C16—O6	−179.5 (3)
C3—C4—C5—C6	−52.6 (5)	C9—C15—C16—C14	0.1 (5)
C3—C4—C5—C13	127.1 (3)	C10—O3—C9—C8	−3.0 (6)
C3—C4—C11—C12	0.5 (5)	C10—O3—C9—C15	177.3 (4)
C4—C5—C6—O2	−179.8 (3)	C11—C4—C5—C6	126.2 (4)
C4—C5—C13—O5	−0.8 (4)	C11—C4—C5—C13	−54.1 (5)
C4—C5—C13—C14	179.7 (3)	C12—C1—C2—C3	−0.7 (5)
C4—C11—C12—O4	−179.8 (3)	C13—C5—C6—O2	0.5 (5)
C4—C11—C12—C1	−0.6 (5)	C13—C14—C16—O6	−1.9 (4)
C5—C4—C11—C12	−178.3 (3)	C13—C14—C16—C15	178.6 (3)
C5—C13—C14—C7	−0.8 (4)	C14—C7—C8—C9	−0.9 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O4^i	0.84	1.98	2.777 (4)	157
O4—H4···O1S	0.84	1.88	2.708 (4)	169
O1S—H1SA···O5^ii	0.91 (3)	1.97 (3)	2.855 (4)	164 (5)
O6—H6···O5	0.87 (4)	1.76 (4)	2.577 (4)	155 (4)

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