Cynarine mono­hy­drate from synchrotron powder X-ray diffraction data

Kaduk, J.A.; Boaz, N.C.; Markun, E.L.; Gindhart, A.M.; Blanton, T.N.

doi:10.1107/S2053229622000687

Cynarine monohydrate from synchrotron powder X-ray diffraction data

J. A. Kaduk, N. C. Boaz, E. L. Markun, A. M. Gindhart and T. N. Blanton

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—H

O 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.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229622000687/cu3179sup1.cif Contains datablocks global, cynarine_5, cynarine_5_VASP.cif
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229622000687/cu3179cynarine_5sup2.cml Supplementary material
	Rietveld powder data file (CIF format) https://doi.org/10.1107/S2053229622000687/cu3179cynarine_5sup3.rtv Contains datablock cynarine_5

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
M_r = 534.47	Z = 2
Monoclinic, P2₁	D_x = 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	2θ_min = 0.500°, 2θ_max = 49.997°, 2θ_step = 0.001°

Refinement top

Least-squares matrix: full	146 parameters
R_p = 0.057	95 restraints
R_wp = 0.070	4 constraints
R_exp = 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	U_iso*/U_eq
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