research papers
The crystal structure of cynarine monohydrate (systematic name: 1,3-bis{[(E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid monohydrate), C25H24O12·H2O, has been solved and refined using synchrotron powder X-ray diffraction data, and optimized using density functional techniques. Despite being purchased as anhydrous, cynarine crystallizes as a monohydrate and the crystal structure is characterized by alternating layers of hydrocarbon and hydrogen-bonding interactions parallel to the bc plane. Hydrogen bonds are significant in the crystal structure. The carboxylic acid group forms a strong intermolecular hydrogen bond to a hydroxy group of the quinic acid ring. Most of the hydroxy groups act as donors in O—HO hydrogen bonding to carbonyl O atoms. One hydroxy group participates in bifurcated hydrogen bonds, one to a hydroxy group on the quinic acid ring and the other, an intramolecular interaction, to another hydroxy group. The powder pattern has been submitted to the International Centre for Diffraction Data (ICDD) for inclusion in the Powder Diffraction File (PDF-4).
Keywords: powder diffraction; cynarine; 1,5-dicaffeoylquinic acid; Rietveld refinement; density functional theory; crystal structure.
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229622000687/cu3179sup1.cif | |
Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229622000687/cu3179cynarine_5sup2.cml | |
Rietveld powder data file (CIF format) https://doi.org/10.1107/S2053229622000687/cu3179cynarine_5sup3.rtv |
CCDC references: 2143218; 2143219
Computing details top
Program(s) used to solve structure: FOX for cynarine_5. Program(s) used to refine structure: GSAS-II (Toby & Von Dreele, 2013) for cynarine_5. Molecular graphics: Mercury, Diamond for cynarine_5. Software used to prepare material for publication: publCIF for cynarine_5.
1,3-Bis{[(E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid monohydrate (cynarine_5) top
Crystal data top
C25H24O12·H2O | V = 1188.16 (1) Å3 |
Mr = 534.47 | Z = 2 |
Monoclinic, P21 | Dx = 1.494 Mg m−3 |
Hall symbol: P 2yb | Synchrotron radiation, λ = 0.45815 Å |
a = 13.88124 (12) Å | µ = 0.01 mm−1 |
b = 15.36081 (4) Å | T = 295 K |
c = 5.59335 (2) Å | tan |
β = 94.9763 (4)° | cylinder, 3.0 × 1.5 mm |
Data collection top
11-BM, Advanced Photon Source, Argonne National Laboratory diffractometer | Data collection mode: transmission |
Radiation source: synchrotron | Scan method: step |
Specimen mounting: Kapton capillary | 2θmin = 0.500°, 2θmax = 49.997°, 2θstep = 0.001° |
Refinement top
Least-squares matrix: full | 146 parameters |
Rp = 0.057 | 95 restraints |
Rwp = 0.070 | 4 constraints |
Rexp = 0.059 | H-atom parameters not refined |
R(F2) = 0.06417 | Weighting scheme based on measured s.u.'s |
49575 data points | (Δ/σ)max = 0.910 |
Excluded region(s): 0.5-1.8 and 30-50 | Background function: Background function: "chebyschev-1" function with 12 terms: 162.64(21), -76.0(3), 19.23(28), -0.00(28), -10.09(26), -3.82(25), 18.77(23), -18.02(24), 22.04(22), -19.66(22), 8.17(19), 0.80(16), |
Profile function: Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L: peak variance(Gauss) = Utan(Th)2+Vtan(Th)+W: peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L U, V, W in (centideg)2, X & Y in centideg 1.163, -0.126, 0.063, 0.000, 0.000, 0.002, Crystallite size in microns with "isotropic" model: parameters: Size, G/L mix 1.000, 1.000, Microstrain, "generalized" model (106 * delta Q/Q) parameters: S400, S040, S004, S220, S202, S022, S301, S103, S121, G/L mix 256.163, 72.076, 15203.783, 86.451, 2030.750, 984.854, 953.498, 297.185, -466.993, 1.000, | Preferred orientation correction: Simple spherical harmonic correction Order = 2 Coefficients: 0:0:C(2,-2) = 0.1271(31); 0:0:C(2,0) = 0.050(4); 0:0:C(2,2) = 0.0186(27) |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
O1 | 0.1728 (3) | −0.04483 | 0.1064 (8) | 0.0172* | |
O2 | 0.2516 (2) | 0.0659 (3) | 0.4396 (5) | 0.0172 (7)* | |
O3 | 0.1372 (3) | 0.2178 (3) | 0.5169 (8) | 0.0309* | |
O4 | 0.0098 (4) | 0.1885 (3) | 0.0918 (8) | 0.0309* | |
O5 | −0.0063 (4) | −0.1590 (4) | 0.3723 (7) | 0.0309* | |
O6 | 0.0118 (4) | −0.1485 (4) | −0.0173 (7) | 0.0309* | |
O7 | 0.2264 (3) | −0.1714 (3) | 0.2768 (8) | 0.0172* | |
O8 | 0.3396 (3) | 0.1266 (3) | 0.7567 (7) | 0.0172* | |
O9 | 0.7233 (3) | −0.2470 (4) | −0.0767 (8) | 0.0313* | |
O10 | 0.8222 (3) | 0.2234 (4) | 0.3131 (9) | 0.0313* | |
O11 | 0.7220 (3) | −0.1592 (4) | −0.4957 (7) | 0.0313* | |
O12 | 0.8212 (3) | 0.1230 (4) | −0.0820 (7) | 0.0313* | |
C13 | 0.0873 (2) | −0.0424 (2) | 0.2396 (6) | 0.0309 (7)* | |
C14 | 0.1179 (3) | −0.0296 (3) | 0.5077 (6) | 0.0309* | |
C15 | 0.1631 (2) | 0.0605 (3) | 0.5644 (5) | 0.0309* | |
C16 | 0.0236 (3) | 0.0338 (3) | 0.1470 (7) | 0.0309* | |
C17 | 0.0956 (2) | 0.1342 (3) | 0.4644 (6) | 0.0309* | |
C18 | 0.0723 (3) | 0.1215 (3) | 0.1967 (5) | 0.0309* | |
C19 | 0.0309 (3) | −0.1262 (3) | 0.1921 (6) | 0.0309* | |
C20 | 0.2376 (3) | −0.1098 (4) | 0.1497 (11) | 0.0172* | |
C21 | 0.3316 (3) | 0.1033 (5) | 0.5498 (7) | 0.0172* | |
C22 | 0.3200 (4) | −0.1023 (4) | −0.0002 (12) | 0.0172* | |
C23 | 0.4116 (3) | 0.0985 (5) | 0.3928 (8) | 0.0172* | |
C24 | 0.3924 (3) | −0.1592 (4) | 0.0116 (11) | 0.0172* | |
C25 | 0.5008 (3) | 0.1240 (5) | 0.4576 (7) | 0.0172* | |
C26 | 0.4808 (3) | −0.1537 (5) | −0.1110 (9) | 0.0313 (6)* | |
C27 | 0.5800 (3) | 0.1302 (4) | 0.3017 (9) | 0.0313* | |
C28 | 0.5610 (3) | −0.2045 (4) | −0.0360 (9) | 0.0313* | |
C29 | 0.4823 (3) | −0.1080 (5) | −0.3244 (9) | 0.0313* | |
C30 | 0.6641 (3) | 0.1747 (5) | 0.3821 (9) | 0.0313* | |
C31 | 0.5831 (3) | 0.0751 (4) | 0.1070 (9) | 0.0313* | |
C32 | 0.6466 (3) | −0.1962 (4) | −0.1447 (8) | 0.0313* | |
C33 | 0.5652 (3) | −0.1047 (5) | −0.4462 (9) | 0.0313* | |
C34 | 0.7454 (3) | 0.1707 (5) | 0.2560 (10) | 0.0313* | |
C35 | 0.6616 (3) | 0.0758 (5) | −0.0289 (7) | 0.0313* | |
C36 | 0.6485 (3) | −0.1475 (4) | −0.3546 (8) | 0.0313* | |
C37 | 0.7460 (3) | 0.1172 (4) | 0.0565 (8) | 0.0313* | |
H38 | 0.05196 | −0.03641 | 0.61447 | 0.0405* | |
H39 | 0.17270 | −0.08207 | 0.56884 | 0.0405* | |
H40 | 0.18056 | 0.06862 | 0.76609 | 0.0405* | |
H41 | 0.006581 | 0.02736 | −0.05529 | 0.0405* | |
H42 | −0.04692 | 0.03207 | 0.23719 | 0.0405* | |
H43 | −0.00055 | 0.13650 | 0.44616 | 0.0405* | |
H44 | 0.14282 | 0.12270 | 0.10628 | 0.0405* | |
H45 | 0.10907 | 0.24003 | 0.39027 | 0.0405* | |
H46 | −0.00194 | 0.22937 | −0.02964 | 0.0405* | |
H47 | −0.03874 | −0.21065 | 0.42906 | 0.0405* | |
H48 | 0.32303 | −0.04605 | −0.13227 | 0.0223* | |
H49 | 0.39810 | 0.07147 | 0.20304 | 0.0223* | |
H50 | 0.38904 | −0.22010 | 0.12708 | 0.0223* | |
H51 | 0.52206 | 0.14383 | 0.65142 | 0.0223* | |
H52 | 0.55658 | −0.25341 | 0.11596 | 0.0406* | |
H53 | 0.41468 | −0.07238 | −0.40248 | 0.0406* | |
H54 | 0.66638 | 0.21501 | 0.55363 | 0.0406* | |
H55 | 0.52053 | 0.02860 | 0.05747 | 0.0406* | |
H56 | 0.56494 | −0.06685 | −0.62155 | 0.0406* | |
H57 | 0.65668 | 0.04222 | −0.21131 | 0.0406* | |
H58 | 0.71189 | −0.28322 | 0.08019 | 0.0406* | |
H59 | 0.80810 | 0.25425 | 0.47297 | 0.0406* | |
H60 | 0.77235 | −0.20131 | −0.39372 | 0.0406* | |
H61 | 0.86650 | 0.14729 | −0.02780 | 0.0406* | |
O62 | 0.1631 (5) | 0.5049 (5) | 0.4284 (12) | 0.114 (3)* | |
H63 | 0.18734 | 0.44997 | 0.47321 | 0.1539* | |
H64 | 0.16863 | 0.53948 | 0.34780 | 0.1539* |
Geometric parameters (Å, º) top
O1—C13 | 1.4555 (13) | C21—C23 | 1.477 (3) |
O1—C20 | 1.352 (2) | C22—C20 | 1.479 (3) |
O2—C15 | 1.4670 (19) | C22—C24 | 1.329 (3) |
O2—C21 | 1.351 (2) | C23—C21 | 1.477 (3) |
O3—C17 | 1.428 (3) | C23—C25 | 1.319 (3) |
O4—C18 | 1.438 (2) | C24—C22 | 1.329 (3) |
O5—C19 | 1.275 (3) | C24—C26 | 1.460 (3) |
O6—C19 | 1.227 (3) | C25—C23 | 1.319 (3) |
O7—C20 | 1.202 (2) | C25—C27 | 1.465 (3) |
O8—C21 | 1.207 (2) | C26—C24 | 1.460 (3) |
O9—C32 | 1.348 (2) | C26—C28 | 1.3931 (18) |
O10—C34 | 1.354 (2) | C26—C29 | 1.387 (2) |
O11—C36 | 1.354 (2) | C27—C25 | 1.465 (3) |
O12—C37 | 1.356 (2) | C27—C30 | 1.3922 (18) |
C13—O1 | 1.4555 (13) | C27—C31 | 1.384 (2) |
C13—C14 | 1.5352 (12) | C28—C26 | 1.3931 (18) |
C13—C16 | 1.5301 (12) | C28—C32 | 1.3864 (16) |
C13—C19 | 1.5182 (15) | C29—C26 | 1.387 (2) |
C14—C13 | 1.5352 (12) | C29—C33 | 1.3883 (19) |
C14—C15 | 1.542 (2) | C30—C27 | 1.3922 (18) |
C15—O2 | 1.4670 (19) | C30—C34 | 1.3834 (16) |
C15—C14 | 1.542 (2) | C31—C27 | 1.384 (2) |
C15—C17 | 1.543 (2) | C31—C35 | 1.3811 (19) |
C16—C13 | 1.5301 (12) | C32—O9 | 1.348 (2) |
C16—C18 | 1.5217 (17) | C32—C28 | 1.3864 (16) |
C17—O3 | 1.428 (3) | C32—C36 | 1.3947 (19) |
C17—C15 | 1.543 (2) | C33—C29 | 1.3883 (19) |
C17—C18 | 1.5172 (17) | C33—C36 | 1.389 (2) |
C18—O4 | 1.438 (2) | C34—O10 | 1.354 (2) |
C18—C16 | 1.5217 (17) | C34—C30 | 1.3834 (16) |
C18—C17 | 1.5172 (17) | C34—C37 | 1.3862 (19) |
C19—O5 | 1.275 (3) | C35—C31 | 1.3811 (19) |
C19—O6 | 1.227 (3) | C35—C37 | 1.382 (2) |
C19—C13 | 1.5182 (15) | C36—O11 | 1.354 (2) |
C20—O1 | 1.352 (2) | C36—C32 | 1.3947 (19) |
C20—O7 | 1.202 (2) | C36—C33 | 1.389 (2) |
C20—C22 | 1.479 (3) | C37—O12 | 1.356 (2) |
C21—O2 | 1.351 (2) | C37—C34 | 1.3862 (19) |
C21—O8 | 1.207 (2) | C37—C35 | 1.382 (2) |
C13—O1—C20 | 119.15 (18) | C20—C22—C24 | 122.6 (2) |
C15—O2—C21 | 119.75 (15) | C21—C23—C25 | 123.9 (2) |
O1—C13—C14 | 109.5 (2) | C22—C24—C26 | 127.1 (2) |
O1—C13—C16 | 108.6 (2) | C23—C25—C27 | 126.2 (2) |
C14—C13—C16 | 109.61 (12) | C24—C26—C28 | 120.6 (2) |
O1—C13—C19 | 108.67 (16) | C24—C26—C29 | 120.6 (3) |
C14—C13—C19 | 111.96 (16) | C28—C26—C29 | 118.15 (12) |
C16—C13—C19 | 108.40 (18) | C25—C27—C30 | 119.4 (2) |
C13—C14—C15 | 112.88 (16) | C25—C27—C31 | 120.3 (3) |
O2—C15—C14 | 107.2 (2) | C30—C27—C31 | 118.18 (12) |
O2—C15—C17 | 107.08 (18) | C26—C28—C32 | 120.63 (8) |
C14—C15—C17 | 111.18 (13) | C26—C29—C33 | 121.00 (11) |
C13—C16—C18 | 112.39 (17) | C27—C30—C34 | 120.76 (8) |
O3—C17—C15 | 111.3 (2) | C27—C31—C35 | 120.57 (13) |
O3—C17—C18 | 111.5 (2) | O9—C32—C28 | 120.6 (2) |
C15—C17—C18 | 109.48 (11) | O9—C32—C36 | 118.4 (2) |
O4—C18—C16 | 108.4 (2) | C28—C32—C36 | 119.87 (10) |
O4—C18—C17 | 112.3 (2) | C29—C33—C36 | 120.08 (10) |
C16—C18—C17 | 110.35 (11) | O10—C34—C30 | 120.9 (2) |
O5—C19—O6 | 125.2 (3) | O10—C34—C37 | 119.0 (2) |
O5—C19—C13 | 115.8 (2) | C30—C34—C37 | 119.90 (9) |
O6—C19—C13 | 117.9 (2) | C31—C35—C37 | 119.88 (11) |
O1—C20—O7 | 124.65 (15) | O11—C36—C32 | 119.3 (2) |
O1—C20—C22 | 112.11 (19) | O11—C36—C33 | 119.5 (3) |
O7—C20—C22 | 122.9 (2) | C32—C36—C33 | 119.22 (10) |
O2—C21—O8 | 124.55 (17) | O12—C37—C34 | 118.7 (2) |
O2—C21—C23 | 109.80 (19) | O12—C37—C35 | 120.3 (2) |
O8—C21—C23 | 125.0 (2) | C34—C37—C35 | 119.19 (11) |
(cynarine_5_VASP.cif) top
Crystal data top
C25H26O13 | c = 5.59340 Å |
Mr = 534.47 | β = 94.98° |
Monoclinic, P21 | V = 1188.15 Å3 |
a = 13.88110 Å | Z = 2 |
b = 15.36080 Å |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
O1 | 0.15992 | −0.04973 | 0.07055 | 0.0172 | |
O2 | 0.23203 | 0.08702 | 0.38475 | 0.0172 | |
O3 | 0.10320 | 0.23044 | 0.38809 | 0.0309 | |
O4 | −0.01867 | 0.16618 | −0.03835 | 0.0309 | |
O5 | 0.00750 | −0.16010 | 0.42163 | 0.0309 | |
O6 | −0.00507 | −0.16532 | 0.01446 | 0.0309 | |
O7 | 0.21833 | −0.16963 | 0.27579 | 0.0172 | |
O8 | 0.31337 | 0.13514 | 0.73373 | 0.0172 | |
O9 | 0.72576 | −0.24113 | −0.04771 | 0.0313 | |
O10 | 0.81717 | 0.21794 | 0.33104 | 0.0313 | |
O11 | 0.73049 | −0.15396 | −0.46270 | 0.0313 | |
O12 | 0.80402 | 0.11860 | −0.09018 | 0.0313 | |
C13 | 0.07829 | −0.04408 | 0.21696 | 0.0309 | |
C14 | 0.10720 | −0.01384 | 0.47459 | 0.0309 | |
C15 | 0.14148 | 0.08035 | 0.49277 | 0.0309 | |
C16 | 0.00903 | 0.02160 | 0.09003 | 0.0309 | |
C17 | 0.06808 | 0.14154 | 0.36083 | 0.0309 | |
C18 | 0.05058 | 0.11345 | 0.09900 | 0.0309 | |
C19 | 0.02392 | −0.13113 | 0.20827 | 0.0309 | |
C20 | 0.22848 | −0.11232 | 0.12442 | 0.0172 | |
C21 | 0.31328 | 0.11272 | 0.52032 | 0.0172 | |
C22 | 0.31037 | −0.10031 | −0.01784 | 0.0172 | |
C23 | 0.39512 | 0.10706 | 0.37856 | 0.0172 | |
C24 | 0.39172 | −0.14925 | 0.02054 | 0.0172 | |
C25 | 0.48543 | 0.13387 | 0.45822 | 0.0172 | |
C26 | 0.47862 | −0.14566 | −0.10460 | 0.0313 | |
C27 | 0.56843 | 0.12884 | 0.32113 | 0.0313 | |
C28 | 0.55977 | −0.19424 | −0.01127 | 0.0313 | |
C29 | 0.48597 | −0.09749 | −0.31662 | 0.0313 | |
C30 | 0.65398 | 0.17386 | 0.39849 | 0.0313 | |
C31 | 0.56635 | 0.07985 | 0.10746 | 0.0313 | |
C32 | 0.64475 | −0.19583 | −0.12520 | 0.0313 | |
C33 | 0.57043 | −0.09949 | −0.43341 | 0.0313 | |
C34 | 0.73426 | 0.17308 | 0.26594 | 0.0313 | |
C35 | 0.64643 | 0.07693 | −0.02225 | 0.0313 | |
C36 | 0.64927 | −0.14929 | −0.34101 | 0.0313 | |
C37 | 0.73058 | 0.12353 | 0.05153 | 0.0313 | |
H38 | 0.04190 | −0.01951 | 0.57127 | 0.0405 | |
H39 | 0.16171 | −0.05712 | 0.56419 | 0.0405 | |
H40 | 0.15411 | 0.09956 | 0.68198 | 0.0405 | |
H41 | −0.00991 | 0.00151 | −0.09641 | 0.0405 | |
H42 | −0.05805 | 0.02135 | 0.18234 | 0.0405 | |
H43 | −0.00055 | 0.13650 | 0.44616 | 0.0405 | |
H44 | 0.12024 | 0.11582 | 0.01812 | 0.0405 | |
H48 | 0.30387 | −0.04831 | −0.15089 | 0.0223 | |
H49 | 0.37904 | 0.08194 | 0.19736 | 0.0223 | |
H50 | 0.39258 | −0.19701 | 0.16593 | 0.0223 | |
H51 | 0.49648 | 0.16179 | 0.63844 | 0.0223 | |
H52 | 0.55635 | −0.23147 | 0.15378 | 0.0406 | |
H53 | 0.42484 | −0.05944 | −0.39453 | 0.0406 | |
H54 | 0.65789 | 0.21186 | 0.56389 | 0.0406 | |
H55 | 0.50229 | 0.04264 | 0.04458 | 0.0406 | |
H56 | 0.57614 | −0.06373 | −0.60002 | 0.0406 | |
H57 | 0.64594 | 0.03822 | −0.18557 | 0.0406 | |
H60 | 0.77235 | −0.20131 | −0.39372 | 0.0406 | |
H61 | 0.86650 | 0.14729 | −0.02780 | 0.0406 | |
H47 | −0.03874 | −0.21065 | 0.42906 | 0.0405 | |
H45 | 0.07756 | 0.26490 | 0.24844 | 0.0405 | |
H46 | −0.00194 | 0.22937 | −0.02964 | 0.0405 | |
H59 | 0.80810 | 0.25425 | 0.47297 | 0.0406 | |
H58 | 0.71189 | −0.28322 | 0.08019 | 0.0406 | |
O62 | 0.14221 | 0.49921 | 0.46173 | 0.1140 | |
H63 | 0.18734 | 0.44997 | 0.47321 | 0.1539 | |
H64 | 0.16863 | 0.53948 | 0.34780 | 0.1539 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H47···O3 | 1.011 | 1.681 | 2.570 | 144.3 |
O4—H46···O6 | 0.998 | 1.622 | 2.611 | 170.0 |
O3—H45···O6 | 0.984 | 2.017 | 2.993 | 171.0 |
O12—H61···O4 | 1.008 | 1.626 | 2.560 | 151.9 |
O9—H58···O8 | 0.995 | 1.686 | 2.675 | 172.1 |
O10—H59···O7 | 0.987 | 1.888 | 2.872 | 174.2 |
O11—H60···O3 | 0.988 | 2.019 | 2.914 | 149.5 |
O11—H60···O9 | 0.988 | 2.181 | 2.685 | 110.1 |
O62—H64···O12 | 0.982 | 1.947 | 2.917 | 168.9 |
O62—H63···O11 | 0.981 | 1.986 | 2.942 | 173.4 |
C15—H40···O8 | 1.098 | 2.271 | 2.768 | 105.0 |
C30—H54···O7 | 1.091 | 2.608 | 3.418 | 130.4 |
C18—H44···O2 | 1.103 | 2.501 | 2.892 | 99.3 |
C16—H42···O62 | 1.103 | 2.418 | 3.424 | 150.9 |
C16—H41···O62 | 1.097 | 2.626 | 3.595 | 146.8 |
C14—H38···O62 | 1.098 | 2.562 | 3.517 | 144.7 |