organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

Santal monohydrate, an isoflavone isolated from Wye­thia mollis

aDepartment of Chemistry, The University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA, and bCrystallographic Systems, Bruker AXS Inc., 4565 East Cheryl Parkway, Madison, WI 53711, USA
*Correspondence e-mail: kyle-knight@utc.edu

(Received 4 February 2014; accepted 5 February 2014; online 8 February 2014)

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 ππ inter­actions within the layers.

Related literature

For the discovery and structural identification of isoflavones, see: Raudnitz & Perlmann (1935[Raudnitz, H. & Perlmann, G. (1935). Ber. Dtsch Chem. Ges. B, 68, 1862-1866.]); Robertson et al. (1949[Robertson, A., Suckling, C. W. & Whalley, W. B. (1949). J. Chem. Soc. pp. 1571-1578.]). Santal was isolated following the method of Waddell et al. (1982[Waddell, T. G., Thomasson, M. H., Moore, M. W., White, H. W., Swanson-Bean, D., Green, M. E., Van, H. G. S. & Fales, H. M. (1982). Phytochemistry, 21, 1631-1633.]). For the structure of the triterpene component of Wye­thia mollis, see: Smith et al. (2013[Smith, C. T., Noll, B., Waddell, T. G. & Knight, K. S. (2013). Nat. Prod. Commun. 8, 299-300.]).

[Scheme 1]

Experimental

Crystal data
  • C16H12O6·H2O

  • Mr = 318.28

  • Orthorhombic, P c a 21

  • a = 16.494 (3) Å

  • b = 13.082 (3) Å

  • c = 6.6008 (12) Å

  • V = 1424.3 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 200 K

  • 0.46 × 0.41 × 0.4 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2004[Sheldrick, G. M. (2004). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.518, Tmax = 0.958

  • 8545 measured reflections

  • 2478 independent reflections

  • 2002 reflections with I > 2σ(I)

  • Rint = 0.060

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.110

  • S = 0.85

  • 2478 reflections

  • 221 parameters

  • 3 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.14 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯O4i 0.84 1.98 2.777 (4) 157
O4—H4⋯O1S 0.84 1.88 2.708 (4) 169
O1S—H1SA⋯O5ii 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+{\script{1\over 2}}]; (ii) [-x+{\script{1\over 2}}, y, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]); software used to prepare material for publication: OLEX2.

Supporting information


Comment top

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 ππ interactions inside the layers.

Related literature top

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).

Experimental top

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.

Refinement top

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 Uiso(H)= 1.5Ueq (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 Uiso(H)= 1.2–1.5Ueq of the parent atom.

Computing details top

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 top
[Figure 1] 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 top
Crystal data top
C16H12O6·H2ODx = 1.484 Mg m3
Mr = 318.28Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pca21Cell parameters from 2745 reflections
a = 16.494 (3) Åθ = 2.5–24.8°
b = 13.082 (3) ŵ = 0.12 mm1
c = 6.6008 (12) ÅT = 200 K
V = 1424.3 (5) Å3Prism, yellow
Z = 40.46 × 0.41 × 0.4 mm
F(000) = 664
Data collection top
Bruker APEXII CCD
diffractometer
2002 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.060
φ and ω scansθmax = 25.0°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
h = 1819
Tmin = 0.518, Tmax = 0.958k = 1415
8545 measured reflectionsl = 77
2478 independent reflections
Refinement top
Refinement on F23 restraints
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.039 w = 1/[σ2(Fo2) + (0.0829P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.110(Δ/σ)max < 0.001
S = 0.85Δρmax = 0.14 e Å3
2478 reflectionsΔρmin = 0.18 e Å3
221 parameters
Crystal data top
C16H12O6·H2OV = 1424.3 (5) Å3
Mr = 318.28Z = 4
Orthorhombic, Pca21Mo Kα radiation
a = 16.494 (3) ŵ = 0.12 mm1
b = 13.082 (3) ÅT = 200 K
c = 6.6008 (12) Å0.46 × 0.41 × 0.4 mm
Data collection top
Bruker APEXII CCD
diffractometer
2478 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
2002 reflections with I > 2σ(I)
Tmin = 0.518, Tmax = 0.958Rint = 0.060
8545 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0393 restraints
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 0.85Δρmax = 0.14 e Å3
2478 reflectionsΔρmin = 0.18 e Å3
221 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
O10.00097 (18)0.5170 (2)0.8482 (5)0.0495 (7)
H10.03150.49720.93800.074*
O20.05990 (13)1.09967 (17)1.0156 (4)0.0349 (6)
O30.25286 (16)1.36978 (18)1.0531 (5)0.0496 (7)
O40.10095 (17)0.6010 (2)0.5878 (4)0.0519 (8)
H40.13430.63360.51660.078*
O50.24167 (15)0.88921 (18)0.9502 (4)0.0410 (6)
O60.34600 (14)1.0348 (2)0.9842 (4)0.0387 (6)
C10.0235 (2)0.6152 (3)0.8869 (6)0.0359 (8)
C20.0036 (2)0.6707 (3)1.0506 (6)0.0391 (8)
H20.03990.64031.14480.047*
C30.0222 (2)0.7715 (3)1.0786 (5)0.0380 (8)
H30.00360.80901.19280.046*
C40.0746 (2)0.8173 (2)0.9417 (5)0.0316 (7)
C50.1003 (2)0.9250 (2)0.9674 (5)0.0306 (7)
C60.0442 (2)0.9991 (3)0.9915 (5)0.0335 (7)
H6A0.01110.97880.99140.040*
C70.13907 (18)1.1317 (2)1.0132 (4)0.0282 (7)
C80.1518 (2)1.2363 (3)1.0322 (5)0.0339 (7)
H80.10771.28261.04320.041*
C90.2307 (2)1.2700 (3)1.0344 (5)0.0343 (8)
C100.1904 (3)1.4455 (3)1.0619 (9)0.0680 (14)
H10A0.15721.44160.93900.102*
H10B0.21501.51351.07180.102*
H10C0.15621.43321.18080.102*
C110.1018 (2)0.7603 (3)0.7752 (5)0.0342 (8)
H110.13800.79050.68080.041*
C120.0764 (2)0.6607 (3)0.7470 (5)0.0356 (8)
C130.18522 (19)0.9544 (2)0.9687 (4)0.0284 (7)
C140.20191 (18)1.0609 (2)0.9938 (4)0.0271 (7)
C150.29629 (19)1.2025 (3)1.0181 (5)0.0350 (8)
H150.35031.22781.02070.042*
C160.28220 (19)1.1001 (2)0.9983 (5)0.0297 (7)
O1S0.1966 (2)0.6972 (2)0.3142 (5)0.0571 (8)
H1SA0.225 (3)0.755 (3)0.345 (9)0.086*
H1SB0.162 (3)0.711 (4)0.214 (7)0.086*
H60.323 (2)0.975 (3)0.975 (6)0.044 (12)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0547 (17)0.0299 (15)0.0639 (18)0.0135 (12)0.0080 (13)0.0013 (13)
O20.0262 (12)0.0265 (12)0.0520 (13)0.0019 (10)0.0011 (11)0.0010 (11)
O30.0511 (16)0.0283 (14)0.0694 (18)0.0072 (13)0.0025 (14)0.0057 (13)
O40.0612 (19)0.0411 (17)0.0534 (16)0.0198 (13)0.0149 (13)0.0138 (12)
O50.0322 (13)0.0305 (14)0.0602 (16)0.0054 (11)0.0029 (10)0.0060 (12)
O60.0266 (12)0.0382 (15)0.0513 (15)0.0031 (11)0.0018 (11)0.0011 (11)
C10.0334 (19)0.0228 (19)0.051 (2)0.0029 (14)0.0024 (15)0.0019 (15)
C20.0356 (19)0.031 (2)0.050 (2)0.0014 (14)0.0092 (15)0.0066 (16)
C30.039 (2)0.034 (2)0.0418 (19)0.0042 (15)0.0063 (15)0.0018 (15)
C40.0251 (16)0.0293 (18)0.0404 (16)0.0022 (14)0.0030 (13)0.0021 (13)
C50.0332 (18)0.0258 (18)0.0329 (17)0.0015 (13)0.0004 (12)0.0011 (12)
C60.0295 (17)0.0310 (19)0.0401 (17)0.0025 (13)0.0017 (13)0.0006 (14)
C70.0262 (16)0.0308 (18)0.0276 (14)0.0018 (13)0.0005 (13)0.0005 (13)
C80.0345 (18)0.0284 (18)0.0387 (17)0.0032 (13)0.0001 (15)0.0023 (14)
C90.041 (2)0.0302 (18)0.0320 (17)0.0054 (14)0.0017 (15)0.0026 (14)
C100.063 (3)0.027 (2)0.114 (4)0.0008 (19)0.009 (3)0.012 (2)
C110.0331 (18)0.0303 (19)0.0392 (19)0.0076 (14)0.0003 (13)0.0005 (13)
C120.0366 (19)0.032 (2)0.0381 (18)0.0019 (15)0.0003 (14)0.0045 (14)
C130.0280 (16)0.0305 (18)0.0268 (15)0.0021 (14)0.0009 (12)0.0016 (12)
C140.0259 (16)0.0297 (18)0.0256 (15)0.0010 (13)0.0004 (12)0.0011 (12)
C150.0299 (17)0.040 (2)0.0350 (16)0.0056 (14)0.0031 (14)0.0012 (15)
C160.0272 (16)0.0359 (18)0.0262 (15)0.0020 (14)0.0018 (12)0.0002 (13)
O1S0.065 (2)0.0485 (18)0.0582 (17)0.0161 (14)0.0047 (15)0.0012 (14)
Geometric parameters (Å, º) top
O1—H10.8400C5—C61.350 (5)
O1—C11.362 (4)C5—C131.453 (5)
O2—C61.351 (4)C6—H6A0.9500
O2—C71.371 (4)C7—C81.390 (4)
O3—C91.361 (4)C7—C141.396 (4)
O3—C101.430 (5)C8—H80.9500
O4—H40.8400C8—C91.374 (5)
O4—C121.370 (4)C9—C151.401 (5)
O5—C131.268 (4)C10—H10A0.9800
O6—C161.359 (4)C10—H10B0.9800
O6—H60.87 (4)C10—H10C0.9800
C1—C21.376 (5)C11—H110.9500
C1—C121.402 (5)C11—C121.382 (5)
C2—H20.9500C13—C141.430 (4)
C2—C31.398 (5)C14—C161.420 (4)
C3—H30.9500C15—H150.9500
C3—C41.387 (5)C15—C161.366 (5)
C4—C51.480 (4)O1S—H1SA0.91 (3)
C4—C111.402 (5)O1S—H1SB0.89 (3)
C1—O1—H1109.5O3—C9—C8124.3 (3)
C6—O2—C7118.6 (2)O3—C9—C15113.8 (3)
C9—O3—C10118.3 (3)C8—C9—C15121.9 (3)
C12—O4—H4109.5O3—C10—H10A109.5
C16—O6—H6104 (3)O3—C10—H10B109.5
O1—C1—C2123.7 (3)O3—C10—H10C109.5
O1—C1—C12116.5 (3)H10A—C10—H10B109.5
C2—C1—C12119.7 (3)H10A—C10—H10C109.5
C1—C2—H2119.9H10B—C10—H10C109.5
C1—C2—C3120.2 (3)C4—C11—H11119.6
C3—C2—H2119.9C12—C11—C4120.7 (3)
C2—C3—H3119.6C12—C11—H11119.6
C4—C3—C2120.8 (3)O4—C12—C1116.6 (3)
C4—C3—H3119.6O4—C12—C11123.5 (3)
C3—C4—C5121.0 (3)C11—C12—C1120.0 (3)
C3—C4—C11118.7 (3)O5—C13—C5122.0 (3)
C11—C4—C5120.3 (3)O5—C13—C14121.6 (3)
C6—C5—C4120.1 (3)C14—C13—C5116.4 (3)
C6—C5—C13118.0 (3)C7—C14—C13120.9 (3)
C13—C5—C4121.9 (3)C7—C14—C16116.8 (3)
O2—C6—H6A117.2C16—C14—C13122.3 (3)
C5—C6—O2125.6 (3)C9—C15—H15120.2
C5—C6—H6A117.2C16—C15—C9119.6 (3)
O2—C7—C8116.3 (3)C16—C15—H15120.2
O2—C7—C14120.4 (3)O6—C16—C14119.6 (3)
C8—C7—C14123.3 (3)O6—C16—C15119.4 (3)
C7—C8—H8121.3C15—C16—C14121.0 (3)
C9—C8—C7117.4 (3)H1SA—O1S—H1SB108 (5)
C9—C8—H8121.3
O1—C1—C2—C3179.6 (3)C5—C13—C14—C16179.9 (3)
O1—C1—C12—O41.0 (5)C6—O2—C7—C8178.0 (3)
O1—C1—C12—C11179.7 (3)C6—O2—C7—C142.4 (4)
O2—C7—C8—C9178.7 (3)C6—C5—C13—O5178.9 (3)
O2—C7—C14—C132.3 (4)C6—C5—C13—C140.6 (4)
O2—C7—C14—C16178.3 (3)C7—O2—C6—C51.0 (5)
O3—C9—C15—C16179.9 (3)C7—C8—C9—O3179.6 (3)
O5—C13—C14—C7179.8 (3)C7—C8—C9—C150.1 (5)
O5—C13—C14—C160.4 (4)C7—C14—C16—O6178.7 (3)
C1—C2—C3—C40.6 (5)C7—C14—C16—C150.8 (4)
C2—C1—C12—O4180.0 (3)C8—C7—C14—C13178.1 (3)
C2—C1—C12—C110.7 (5)C8—C7—C14—C161.3 (4)
C2—C3—C4—C5178.3 (3)C8—C9—C15—C160.3 (5)
C2—C3—C4—C110.5 (5)C9—C15—C16—O6179.5 (3)
C3—C4—C5—C652.6 (5)C9—C15—C16—C140.1 (5)
C3—C4—C5—C13127.1 (3)C10—O3—C9—C83.0 (6)
C3—C4—C11—C120.5 (5)C10—O3—C9—C15177.3 (4)
C4—C5—C6—O2179.8 (3)C11—C4—C5—C6126.2 (4)
C4—C5—C13—O50.8 (4)C11—C4—C5—C1354.1 (5)
C4—C5—C13—C14179.7 (3)C12—C1—C2—C30.7 (5)
C4—C11—C12—O4179.8 (3)C13—C5—C6—O20.5 (5)
C4—C11—C12—C10.6 (5)C13—C14—C16—O61.9 (4)
C5—C4—C11—C12178.3 (3)C13—C14—C16—C15178.6 (3)
C5—C13—C14—C70.8 (4)C14—C7—C8—C90.9 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O4i0.841.982.777 (4)157
O4—H4···O1S0.841.882.708 (4)169
O1S—H1SA···O5ii0.91 (3)1.97 (3)2.855 (4)164 (5)
O6—H6···O50.87 (4)1.76 (4)2.577 (4)155 (4)
Symmetry codes: (i) x, y+1, z+1/2; (ii) x+1/2, y, z1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O4i0.841.982.777 (4)156.8
O4—H4···O1S0.841.882.708 (4)168.7
O1S—H1SA···O5ii0.91 (3)1.97 (3)2.855 (4)164 (5)
O6—H6···O50.87 (4)1.76 (4)2.577 (4)155 (4)
Symmetry codes: (i) x, y+1, z+1/2; (ii) x+1/2, y, z1/2.
 

Acknowledgements

Acknowledgements are made to the National Science Foundation MRI Program (CHE-0951711) and the Grote Chemistry Fund at the University of Tennessee at Chattanooga for their generous support of our work. The authors would like to thank Dr Daron Janzen for helpful discussions.

References

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