An anomalous racemate of naringenin at 120 K

Unlike a previously reported structure for racemic naringenin [systematic name: 2,3-di­hydro-5,6-di­hydroxy-2-(4-hydroxy­phenyl)-4H-1-benzo­pyran-4-one], C₁₅H₁₂O₅, both S and R enantiomers appear to occupy somewhat randomly the four crystallographic sites of the unit cell in an approximate 3:1/1:3 ratio.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.067
• wR factor = 0.155
• Data-to-parameter ratio = 15.9

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level B:



RINTA_01  Alert B The value of Rint is greater than 0.15
          Rint given   0.158


 0 Alert Level A = Potentially serious problem

 1 Alert Level B = Potential problem

 0 Alert Level C = Please check

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Computing details

Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SIR97 (Altomare et al.,1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek,2001).

2,3-Dihydro-5,6-dihydroxy-2-(4-hydroxyphenyl)-4H-1-benzopyran-4-one

Crystal data

C15H12O5	F(000) = 568
Mr = 272.25	Dx = 1.482 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71069 Å
a = 4.8740 (5) Å	Cell parameters from 13970 reflections
b = 15.2610 (15) Å	θ = 2.9–27.5°
c = 16.423 (2) Å	µ = 0.11 mm^−1
β = 92.375 (5)°	T = 120 K
V = 1220.5 (2) Å^3	Needle, colourless
Z = 4	0.38 × 0.06 × 0.04 mm

Data collection

Enraf-Nonius KappaCCD area-detector diffractometer	2701 independent reflections
Radiation source: Enraf-Nonius FR591 rotating anode	1099 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.158
Detector resolution: 3.89 pixels mm^-1	θmax = 27.5°, θmin = 3.7°
φ and ω scans	h = −6→6
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997)	k = −18→19
Tmin = 0.959, Tmax = 0.996	l = −20→20
11748 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.067	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.155	H-atom parameters constrained
S = 0.93	w = 1/[σ^2(Fo^2) + (0.0581P)^2] where P = (Fo^2 + 2Fc^2)/3
2701 reflections	(Δ/σ)max < 0.001
170 parameters	Δρmax = 0.21 e Å^−3
20 restraints	Δρmin = −0.27 e Å^−3

Special details

Experimental. Please note cell_measurement_ fields are not relevant to area detector data, the entire data set is used to refine the cell, which is indexed from all observed reflections in a 10 degree phi range.

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.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.6345 (4)	0.53263 (14)	0.34853 (13)	0.0308 (6)
O2	0.1441 (5)	0.31118 (16)	0.20343 (14)	0.0363 (6)
H2	0.0990	0.2998	0.2511	0.044*
O3	0.7955 (5)	0.47286 (17)	0.06527 (14)	0.0425 (7)
H3	0.9202	0.5102	0.0737	0.051*
O4	1.0686 (5)	0.59448 (17)	0.14732 (14)	0.0394 (7)
O5A	0.9458 (11)	0.7747 (3)	0.6503 (3)	0.033 (2)*	0.775 (8)
H5A	0.8200	0.8122	0.6520	0.039*	0.775 (8)
C2A	0.8986 (9)	0.5767 (3)	0.3593 (3)	0.0302 (14)*	0.775 (8)
H2A	1.0440	0.5308	0.3660	0.036*	0.775 (8)
C3A	0.9565 (15)	0.6295 (5)	0.2838 (4)	0.037 (3)*	0.775 (8)
H3A	0.8257	0.6790	0.2792	0.045*	0.775 (8)
H3B	1.1442	0.6542	0.2895	0.045*	0.775 (8)
C1A'	0.8991 (12)	0.6294 (3)	0.4359 (3)	0.0270 (13)*	0.775 (8)
C2A'	0.7198 (11)	0.6976 (4)	0.4453 (3)	0.0330 (14)*	0.775 (8)
H2A'	0.5866	0.7104	0.4031	0.040*	0.775 (8)
C3A'	0.7304 (12)	0.7485 (4)	0.5160 (3)	0.0336 (17)*	0.775 (8)
H3A'	0.6074	0.7962	0.5216	0.040*	0.775 (8)
C4A'	0.9202 (19)	0.7290 (7)	0.5775 (4)	0.0261 (14)*	0.775 (8)
C5A'	1.1014 (13)	0.6611 (5)	0.5693 (4)	0.0358 (16)*	0.775 (8)
H5A'	1.2332	0.6483	0.6118	0.043*	0.775 (8)
C6A'	1.0914 (11)	0.6114 (3)	0.4986 (3)	0.0321 (14)*	0.775 (8)
H6A'	1.2173	0.5645	0.4930	0.038*	0.775 (8)
O5B	0.899 (4)	0.7676 (12)	0.6539 (9)	0.031 (7)*	0.225 (8)
H5B	0.8880	0.8224	0.6505	0.038*	0.225 (8)
C2B	0.756 (3)	0.6186 (10)	0.3414 (8)	0.025 (5)*	0.225 (8)
H2B	0.6138	0.6568	0.3135	0.030*	0.225 (8)
C3B	1.002 (4)	0.6187 (16)	0.2887 (12)	0.018 (7)*	0.225 (8)
H3X	1.1550	0.5867	0.3168	0.022*	0.225 (8)
H3Y	1.0623	0.6797	0.2797	0.022*	0.225 (8)
C1B'	0.803 (4)	0.6545 (13)	0.4257 (8)	0.029 (3)*	0.225 (8)
C2B'	0.653 (4)	0.7248 (12)	0.4493 (9)	0.029 (3)*	0.225 (8)
H2B'	0.5206	0.7494	0.4118	0.035*	0.225 (8)
C3B'	0.686 (4)	0.7607 (14)	0.5248 (10)	0.029 (3)*	0.225 (8)
H3B'	0.5660	0.8058	0.5413	0.035*	0.225 (8)
C4B'	0.892 (7)	0.732 (2)	0.5768 (14)	0.029 (3)*	0.225 (8)
C5B'	1.057 (4)	0.6613 (15)	0.5576 (11)	0.029 (3)*	0.225 (8)
H5B'	1.1952	0.6396	0.5948	0.035*	0.225 (8)
C6B'	1.008 (4)	0.6231 (11)	0.4788 (10)	0.029 (3)*	0.225 (8)
H6B'	1.1181	0.5752	0.4627	0.035*	0.225 (8)
C4	0.9327 (7)	0.5759 (2)	0.2079 (2)	0.0303 (9)
C5	0.6660 (7)	0.4584 (2)	0.1346 (2)	0.0332 (9)
C6	0.4647 (7)	0.3942 (2)	0.1341 (2)	0.0346 (9)
H6	0.4160	0.3631	0.0855	0.041*
C7	0.3366 (7)	0.3765 (2)	0.2055 (2)	0.0299 (9)
C8	0.3964 (6)	0.4220 (2)	0.2772 (2)	0.0295 (9)
H8	0.3051	0.4082	0.3256	0.035*
C9	0.5906 (6)	0.4876 (2)	0.2770 (2)	0.0276 (9)
C10	0.7324 (6)	0.5072 (2)	0.2061 (2)	0.0284 (8)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0330 (14)	0.0286 (15)	0.0307 (15)	−0.0057 (11)	0.0010 (11)	−0.0028 (11)
O2	0.0407 (14)	0.0354 (15)	0.0325 (15)	−0.0077 (12)	−0.0008 (12)	−0.0027 (13)
O3	0.0478 (17)	0.053 (2)	0.0277 (15)	−0.0108 (13)	0.0086 (13)	−0.0055 (12)
O4	0.0477 (16)	0.0389 (16)	0.0321 (15)	−0.0048 (12)	0.0106 (13)	0.0006 (13)
C4	0.034 (2)	0.030 (2)	0.027 (2)	0.0077 (17)	0.0029 (17)	0.0022 (17)
C5	0.035 (2)	0.036 (2)	0.030 (2)	0.0053 (18)	0.0042 (18)	−0.0001 (18)
C6	0.039 (2)	0.035 (2)	0.029 (2)	0.0012 (18)	−0.0041 (18)	−0.0023 (18)
C7	0.0274 (19)	0.028 (2)	0.033 (2)	0.0036 (17)	−0.0038 (17)	0.0027 (17)
C8	0.0263 (19)	0.034 (2)	0.028 (2)	0.0019 (17)	−0.0006 (15)	0.0006 (18)
C9	0.0263 (19)	0.025 (2)	0.031 (2)	0.0058 (16)	−0.0033 (17)	−0.0031 (17)
C10	0.0251 (18)	0.029 (2)	0.031 (2)	0.0007 (16)	0.0021 (16)	0.0017 (17)

Geometric parameters (Å, º)

O1—C9	1.370 (4)	O5B—H5B	0.840
O1—C2B	1.446 (14)	C2B—C3B	1.508 (15)
O1—C2A	1.457 (5)	C2B—C1B'	1.499 (14)
O2—C7	1.368 (4)	C2B—H2B	1.000
O2—H2	0.840	C3B—C4	1.50 (2)
O3—C5	1.343 (4)	C3B—H3X	0.990
O3—H3	0.840	C3B—H3Y	0.990
O4—C4	1.251 (4)	C1B'—C2B'	1.365 (16)
O5A—C4A'	1.385 (5)	C1B'—C6B'	1.384 (16)
O5A—H5A	0.840	C2B'—C3B'	1.359 (15)
C2A—C3A	1.515 (7)	C2B'—H2B'	0.950
C2A—C1A'	1.493 (6)	C3B'—C4B'	1.363 (15)
C2A—H2A	1.000	C3B'—H3B'	0.950
C3A—C4	1.491 (8)	C4B'—C5B'	1.388 (15)
C3A—H3A	0.990	C5B'—C6B'	1.431 (15)
C3A—H3B	0.990	C5B'—H5B'	0.950
C1A'—C2A'	1.372 (6)	C6B'—H6B'	0.950
C1A'—C6A'	1.391 (6)	C4—C10	1.432 (5)
C2A'—C3A'	1.396 (6)	C5—C6	1.386 (5)
C2A'—H2A'	0.950	C5—C10	1.417 (5)
C3A'—C4A'	1.374 (6)	C6—C7	1.378 (5)
C3A'—H3A'	0.950	C6—H6	0.950
C4A'—C5A'	1.371 (6)	C7—C8	1.388 (5)
C5A'—C6A'	1.386 (6)	C8—C9	1.378 (5)
C5A'—H5A'	0.950	C8—H8	0.950
C6A'—H6A'	0.950	C9—C10	1.411 (4)
O5B—C4B'	1.378 (14)
C9—O1—C2B	115.8 (5)	C2B—C3B—H3Y	109.5
C9—O1—C2A	116.2 (3)	C4—C3B—H3Y	109.5
C7—O2—H2	109.5	H3X—C3B—H3Y	108.1
C5—O3—H3	109.5	C2B'—C1B'—C6B'	118.4 (12)
C4A'—O5A—H5A	109.5	C2B'—C1B'—C2B	119.0 (14)
O1—C2A—C3A	109.9 (4)	C6B'—C1B'—C2B	122.4 (15)
O1—C2A—C1A'	108.8 (3)	C3B'—C2B'—C1B'	122.0 (14)
C3A—C2A—C1A'	114.2 (4)	C3B'—C2B'—H2B'	119.0
O1—C2A—H2A	107.9	C1B'—C2B'—H2B'	119.0
C3A—C2A—H2A	107.9	C2B'—C3B'—C4B'	119.9 (16)
C1A'—C2A—H2A	107.9	C2B'—C3B'—H3B'	120.1
C4—C3A—C2A	112.5 (5)	C4B'—C3B'—H3B'	120.1
C4—C3A—H3A	109.1	C3B'—C4B'—O5B	116.0 (15)
C2A—C3A—H3A	109.1	C3B'—C4B'—C5B'	121.8 (15)
C4—C3A—H3B	109.1	O5B—C4B'—C5B'	121.4 (16)
C2A—C3A—H3B	109.1	C4B'—C5B'—C6B'	116.4 (15)
H3A—C3A—H3B	107.8	C4B'—C5B'—H5B'	121.8
C2A'—C1A'—C6A'	118.7 (4)	C6B'—C5B'—H5B'	121.8
C2A'—C1A'—C2A	121.6 (5)	C1B'—C6B'—C5B'	121.1 (14)
C6A'—C1A'—C2A	119.6 (5)	C1B'—C6B'—H6B'	119.4
C1A'—C2A'—C3A'	120.9 (5)	C5B'—C6B'—H6B'	119.4
C1A'—C2A'—H2A'	119.5	O4—C4—C10	122.1 (3)
C3A'—C2A'—H2A'	119.5	O4—C4—C3A	121.0 (4)
C4A'—C3A'—C2A'	119.4 (5)	C10—C4—C3A	116.6 (4)
C4A'—C3A'—H3A'	120.3	O4—C4—C3B	119.8 (7)
C2A'—C3A'—H3A'	120.3	C10—C4—C3B	117.7 (7)
C5A'—C4A'—C3A'	120.5 (5)	O3—C5—C6	118.0 (3)
C5A'—C4A'—O5A	115.5 (5)	O3—C5—C10	121.1 (3)
C3A'—C4A'—O5A	124.0 (5)	C6—C5—C10	120.9 (3)
C4A'—C5A'—C6A'	119.7 (5)	C7—C6—C5	118.6 (3)
C4A'—C5A'—H5A'	120.1	C7—C6—H6	120.7
C6A'—C5A'—H5A'	120.1	C5—C6—H6	120.7
C5A'—C6A'—C1A'	120.7 (4)	O2—C7—C6	117.1 (3)
C5A'—C6A'—H6A'	119.7	O2—C7—C8	120.4 (3)
C1A'—C6A'—H6A'	119.7	C6—C7—C8	122.5 (3)
C4B'—O5B—H5B	109.5	C9—C8—C7	118.8 (3)
C3B—C2B—O1	112.6 (13)	C9—C8—H8	120.6
C3B—C2B—C1B'	115.7 (13)	C7—C8—H8	120.6
O1—C2B—C1B'	107.8 (11)	O1—C9—C8	116.4 (3)
C3B—C2B—H2B	106.8	O1—C9—C10	122.5 (3)
O1—C2B—H2B	106.8	C8—C9—C10	121.1 (3)
C1B'—C2B—H2B	106.8	C9—C10—C5	118.0 (3)
C2B—C3B—C4	110.6 (13)	C9—C10—C4	119.7 (3)
C2B—C3B—H3X	109.5	C5—C10—C4	122.3 (3)
C4—C3B—H3X	109.5
C9—O1—C2A—C3A	48.7 (5)	C2B'—C1B'—C6B'—C5B'	2 (3)
C9—O1—C2A—C1A'	174.3 (3)	C2B—C1B'—C6B'—C5B'	177.0 (18)
O1—C2A—C3A—C4	−53.1 (7)	C4B'—C5B'—C6B'—C1B'	−1 (4)
C1A'—C2A—C3A—C4	−175.6 (5)	C2A—C3A—C4—O4	−151.8 (4)
O1—C2A—C1A'—C2A'	−62.8 (5)	C2A—C3A—C4—C10	32.9 (7)
C3A—C2A—C1A'—C2A'	60.3 (6)	C2B—C3B—C4—O4	156.0 (12)
O1—C2A—C1A'—C6A'	119.4 (4)	C2B—C3B—C4—C10	−31 (2)
C3A—C2A—C1A'—C6A'	−117.5 (6)	O3—C5—C6—C7	177.8 (3)
C6A'—C1A'—C2A'—C3A'	0.4 (8)	C10—C5—C6—C7	−2.3 (5)
C2A—C1A'—C2A'—C3A'	−177.4 (5)	C5—C6—C7—O2	−178.3 (3)
C1A'—C2A'—C3A'—C4A'	−1.1 (11)	C5—C6—C7—C8	1.7 (5)
C2A'—C3A'—C4A'—C5A'	1.1 (15)	O2—C7—C8—C9	−179.8 (3)
C2A'—C3A'—C4A'—O5A	−179.4 (9)	C6—C7—C8—C9	0.2 (5)
C3A'—C4A'—C5A'—C6A'	−0.6 (16)	C2B—O1—C9—C8	−158.2 (7)
O5A—C4A'—C5A'—C6A'	179.9 (8)	C2A—O1—C9—C8	157.5 (3)
C4A'—C5A'—C6A'—C1A'	−0.1 (11)	C2B—O1—C9—C10	20.9 (8)
C2A'—C1A'—C6A'—C5A'	0.2 (8)	C2A—O1—C9—C10	−23.3 (5)
C2A—C1A'—C6A'—C5A'	178.0 (6)	C7—C8—C9—O1	177.6 (3)
C9—O1—C2B—C3B	−47.7 (15)	C7—C8—C9—C10	−1.6 (5)
C9—O1—C2B—C1B'	−176.5 (9)	O1—C9—C10—C5	−178.1 (3)
O1—C2B—C3B—C4	52 (2)	C8—C9—C10—C5	1.0 (5)
C1B'—C2B—C3B—C4	176.3 (14)	O1—C9—C10—C4	0.7 (5)
C3B—C2B—C1B'—C2B'	120.7 (19)	C8—C9—C10—C4	179.9 (3)
O1—C2B—C1B'—C2B'	−112.3 (15)	O3—C5—C10—C9	−179.1 (3)
C3B—C2B—C1B'—C6B'	−55 (2)	C6—C5—C10—C9	1.0 (5)
O1—C2B—C1B'—C6B'	72.4 (17)	O3—C5—C10—C4	2.1 (5)
C6B'—C1B'—C2B'—C3B'	−4 (3)	C6—C5—C10—C4	−177.9 (3)
C2B—C1B'—C2B'—C3B'	−179.8 (19)	O4—C4—C10—C9	178.3 (3)
C1B'—C2B'—C3B'—C4B'	6 (4)	C3A—C4—C10—C9	−6.5 (6)
C2B'—C3B'—C4B'—O5B	−176 (3)	C3B—C4—C10—C9	5.7 (12)
C2B'—C3B'—C4B'—C5B'	−5 (6)	O4—C4—C10—C5	−2.9 (5)
C3B'—C4B'—C5B'—C6B'	3 (5)	C3A—C4—C10—C5	172.3 (5)
O5B—C4B'—C5B'—C6B'	173 (3)	C3B—C4—C10—C5	−175.5 (11)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O4	0.84	1.89	2.624 (3)	145
O2—H2···O5A^i	0.84	2.00	2.788 (6)	156
O5A—H5A···O4^ii	0.84	1.88	2.713 (6)	172
O5B—H5B···O4^ii	0.84	2.01	2.651 (18)	133

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−1/2, −y+3/2, z+1/2.