trans-Bis(3-hydroxy-2-phenyl-4H-1-benzo­pyran-4-onato)­bis­(pyridine)copper(II)

The title complex, [Cu(C₁₅H₉O₃)₂(C₅H₅N)₂], has a distorted octahedral coordination in which the Cu^II atom lies on a center of symmetry. The bidentate ligands lie in trans positions with respect to one another, forming the equatorial plane, with two pyridyl ligands occupying the axial positions.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.043
• wR factor = 0.152
• Data-to-parameter ratio = 16.3

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)  Cu1    -   O2     =      11.62 su

Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ..       2.33

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

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

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S1. Comment

Flavonol (3-hydroxyflavone) is the model compound of quercetin (3'-4',5,7-tetrahydroxyflavonol) which is the component of rutin and oxygenated to the corresponding phenolic carboxylic acid ester catalysed by the copper-containing quercetin 2,3-dioxygenase (Fusetti et al., 2002). The copper complex of flavonol is also degradated to the corresponding depside catalysed by Cu^I and Cu^II flavonolate complexes (Balogh-Hergovich et al., 1991). The molecular structures of Cu^I complex (Speier et al., 1990) and Cu^II complex (Balogh-Hergovich et al., 1991) of flavonol have been determined to understand the coordination modes. In the case of Cu^I complex, one flavonol ligand coordinates to the central Cu^I by its 3-hydroxy and 4-carbonyl groups together with two triphenylphosphines to form a distorted tetrahedron (Speier et al., 1990). While two flavonolate ligands are coordinated to Cu^II by their 3-hydroxy and 4-carbonyl groups to form a square-planar geometry (Balogh-Hergovich, 1991). In the modeling of the substrate into the active site of the copper containing quercetin 2,3-dioxygenase from Aspergillus japonicus, the Cu atom is surrounded by six coordinated atoms (Fusetti, 2002) in which the 3-hydroxy and 4-carbonyl groups of the quercetin molecule are ligated to the Cu atom. In this study, we report the structure of a copper complex of flavonol, (I).

The molecular structure of (I) is shown in Fig. 1. The Cu^II atom has a distorted octahedral coordination geometry in the trans form defined by two O atoms of 3-hydroxy and 4-carbonyl groups of two bidentate ligands in the equatorial plane, and two axial N atoms of two pyridyl ligands. The Cu atom lies on a center of symmetry. The geometric parameters are listed in Table 1. The 3-hydroxyl group is deprotonated, and the coordination bond distance, C1—O1, is shorter than the others. While the short bond distance of C2—O2 reflects the ketonic form of the 4-carbonyl group. The coordination bond distance in the axial direction, Cu1—N1, is longer than those in the equatorial plane. This is ordinally observed in the distorted octahedral coordination geometry of the copper complex and explained by a Jahn–Teller effect. Flavonol moiety is almost planar [C1—C9—C10—C15 = −8.0 (5)°], and atoms Cu1, O1, C1, C2 and O2 forms a five-membered ring.

S2. Experimental

The yellow prismatic crystals of (I) were obtained by slow evaporation of the mixture of flavonol and Cu(OH)₂ in pyridine solution (molar ratio 2: 1).

S3. Refinement

After checking the presence in a difference map, all H atoms were placed at calculated positions [C—H = 0.93 Å and U_iso(H) = 1.5U_eq(C)].

Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation and Rigaku, 2000); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation and Rigaku, 2000); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Scheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: TEXSAN.

Figures

Fig. 1. ORTEPII (Johnson, 1976) drawing of (I) with the atomic numbering scheme. Ellipsoids for non-H atoms are drawn at the 50% probability level. Atoms marked with an asterisk are at the symmetry position (-x, −y, 1 − z).

(I)

Crystal data

[Cu(C15H9O3)2(C5H5N)2]	Z = 1
Mr = 696.19	F(000) = 359.0
Triclinic, P1	Dx = 1.460 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.7107 Å
a = 8.539 (2) Å	Cell parameters from 25 reflections
b = 10.029 (2) Å	θ = 13.9–14.9°
c = 11.098 (2) Å	µ = 0.74 mm^−1
α = 114.70 (1)°	T = 296 K
β = 97.18 (2)°	Prismatic, yellow
γ = 107.00 (1)°	0.30 × 0.30 × 0.20 mm
V = 791.6 (3) Å^3

Data collection

Rigaku AFC-5R diffractometer	Rint = 0.018
ω–2θ scans	θmax = 27.5°
Absorption correction: psi scan (North et al., 1968)	h = −11→10
Tmin = 0.799, Tmax = 0.859	k = 0→13
3834 measured reflections	l = −14→13
3632 independent reflections	3 standard reflections every 150 reflections
2303 reflections with I > 2σ(I)	intensity decay: 0.5%

Refinement

Refinement on F^2	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.043	w = 1/[σ^2(Fo^2) + (0.1P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.152	(Δ/σ)max = −0.001
S = 0.95	Δρmax = 0.56 e Å^−3
3632 reflections	Δρmin = −0.24 e Å^−3
223 parameters

Special details

Refinement. Refinement using reflections with F² > −10.0 σ(F²). The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

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

	x	y	z	Uiso*/Ueq
Cu1	0.0000	0.0000	0.5000	0.0542 (2)
O1	0.0333 (3)	0.2204 (2)	0.6062 (2)	0.0506 (5)
O2	0.1504 (3)	0.0412 (2)	0.6797 (2)	0.0521 (5)
O3	0.2376 (3)	0.4857 (2)	0.9725 (2)	0.0513 (5)
N1	0.2583 (4)	0.0735 (4)	0.4218 (3)	0.0766 (9)
C1	0.1173 (3)	0.2812 (3)	0.7364 (3)	0.0425 (6)
C2	0.1818 (3)	0.1795 (3)	0.7724 (3)	0.0436 (6)
C3	0.2793 (3)	0.2421 (3)	0.9131 (3)	0.0462 (6)
C4	0.3512 (4)	0.1570 (4)	0.9585 (3)	0.0551 (7)
C5	0.4420 (5)	0.2231 (5)	1.0934 (4)	0.0666 (9)
C6	0.4641 (5)	0.3774 (4)	1.1866 (3)	0.0689 (9)
C7	0.3965 (4)	0.4648 (4)	1.1459 (3)	0.0617 (8)
C8	0.3023 (4)	0.3960 (3)	1.0077 (3)	0.0477 (6)
C9	0.1448 (3)	0.4309 (3)	0.8382 (3)	0.0430 (6)
C10	0.0889 (4)	0.5495 (3)	0.8252 (3)	0.0464 (6)
C11	0.1125 (4)	0.6898 (3)	0.9434 (3)	0.0587 (8)
C12	0.0621 (5)	0.8034 (4)	0.9317 (4)	0.0694 (10)
C13	−0.0101 (5)	0.7845 (4)	0.8060 (4)	0.0709 (10)
C14	−0.0333 (5)	0.6481 (4)	0.6879 (4)	0.0723 (10)
C15	0.0139 (5)	0.5311 (4)	0.6983 (3)	0.0631 (9)
C16	0.3649 (5)	0.2228 (5)	0.4778 (4)	0.076 (1)
C17	0.5329 (6)	0.2696 (5)	0.4706 (4)	0.083 (1)
C18	0.5886 (5)	0.1509 (6)	0.3976 (4)	0.079 (1)
C19	0.4754 (5)	−0.0011 (6)	0.3372 (4)	0.078 (1)
C20	0.3146 (5)	−0.0351 (5)	0.3504 (4)	0.077 (1)
H4	0.3371	0.0543	0.8962	0.0661*
H5	0.4889	0.1654	1.1230	0.0800*
H6	0.5262	0.4218	1.2784	0.0827*
H7	0.4127	0.5679	1.2089	0.0740*
H11	0.1625	0.7062	1.0305	0.0705*
H12	0.0778	0.8951	1.0114	0.0833*
H13	−0.0434	0.8624	0.7999	0.0850*
H14	−0.0804	0.6345	0.6014	0.0868*
H15	−0.0054	0.4383	0.6183	0.0757*
H16	0.3257	0.3018	0.5249	0.0917*
H17	0.6046	0.3762	0.5131	0.1002*
H18	0.6996	0.1749	0.3904	0.0950*
H19	0.5083	−0.0834	0.2860	0.0938*
H20	0.2402	−0.1411	0.3066	0.0920*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0637 (4)	0.0376 (3)	0.0367 (3)	0.0255 (2)	−0.0054 (2)	−0.0024 (2)
O1	0.059 (1)	0.0375 (10)	0.0371 (9)	0.0207 (9)	0.0028 (8)	0.0030 (8)
O2	0.054 (1)	0.038 (1)	0.046 (1)	0.0207 (9)	0.0063 (9)	0.0045 (8)
O3	0.060 (1)	0.0355 (10)	0.0348 (9)	0.0110 (9)	0.0065 (8)	0.0031 (8)
N1	0.064 (2)	0.075 (2)	0.064 (2)	0.033 (2)	0.003 (1)	0.010 (2)
C1	0.041 (1)	0.033 (1)	0.038 (1)	0.010 (1)	0.012 (1)	0.007 (1)
C2	0.037 (1)	0.036 (1)	0.039 (1)	0.009 (1)	0.009 (1)	0.006 (1)
C3	0.039 (1)	0.044 (1)	0.041 (1)	0.008 (1)	0.009 (1)	0.014 (1)
C4	0.053 (2)	0.052 (2)	0.055 (2)	0.018 (1)	0.013 (1)	0.023 (1)
C5	0.068 (2)	0.070 (2)	0.061 (2)	0.023 (2)	0.009 (2)	0.036 (2)
C6	0.068 (2)	0.070 (2)	0.044 (2)	0.009 (2)	0.000 (1)	0.022 (2)
C7	0.066 (2)	0.050 (2)	0.038 (1)	0.004 (1)	0.003 (1)	0.009 (1)
C8	0.048 (2)	0.041 (1)	0.039 (1)	0.007 (1)	0.010 (1)	0.013 (1)
C9	0.044 (1)	0.034 (1)	0.035 (1)	0.010 (1)	0.009 (1)	0.0069 (10)
C10	0.047 (2)	0.031 (1)	0.048 (1)	0.010 (1)	0.017 (1)	0.008 (1)
C11	0.075 (2)	0.034 (1)	0.051 (2)	0.017 (1)	0.023 (2)	0.007 (1)
C12	0.086 (3)	0.034 (2)	0.073 (2)	0.022 (2)	0.030 (2)	0.010 (1)
C13	0.081 (2)	0.042 (2)	0.092 (3)	0.028 (2)	0.033 (2)	0.029 (2)
C14	0.087 (3)	0.061 (2)	0.067 (2)	0.036 (2)	0.016 (2)	0.026 (2)
C15	0.080 (2)	0.044 (2)	0.050 (2)	0.028 (2)	0.011 (2)	0.009 (1)
C16	0.077 (3)	0.074 (2)	0.068 (2)	0.040 (2)	0.016 (2)	0.019 (2)
C17	0.088 (3)	0.071 (3)	0.072 (2)	0.020 (2)	0.010 (2)	0.028 (2)
C18	0.070 (2)	0.101 (3)	0.076 (2)	0.039 (2)	0.029 (2)	0.044 (2)
C19	0.078 (3)	0.091 (3)	0.073 (2)	0.046 (2)	0.032 (2)	0.035 (2)
C20	0.071 (2)	0.078 (3)	0.060 (2)	0.033 (2)	0.015 (2)	0.013 (2)

Geometric parameters (Å, º)

Cu1—O1	1.931 (2)	C7—C8	1.400 (4)
Cu1—O1^i	1.931 (2)	C7—H7	0.93
Cu1—O2	2.039 (2)	C9—C10	1.457 (5)
Cu1—O2^i	2.039 (2)	C10—C11	1.403 (4)
Cu1—N1	2.495 (4)	C10—C15	1.384 (5)
Cu1—N1^i	2.495 (4)	C11—C12	1.377 (6)
O1—C1	1.312 (3)	C11—H11	0.93
O2—C2	1.255 (3)	C12—C13	1.363 (7)
O3—C8	1.341 (5)	C12—H12	0.93
O3—C9	1.385 (3)	C13—C14	1.381 (5)
N1—C16	1.320 (5)	C13—H13	0.93
N1—C20	1.314 (6)	C14—C15	1.390 (7)
C1—C2	1.455 (5)	C14—H14	0.93
C1—C9	1.377 (3)	C15—H15	0.93
C2—C3	1.441 (4)	C16—C17	1.397 (7)
C3—C4	1.395 (6)	C16—H16	0.93
C3—C8	1.393 (4)	C17—C18	1.386 (7)
C4—C5	1.365 (5)	C17—H17	0.93
C4—H4	0.93	C18—C19	1.353 (6)
C5—C6	1.394 (5)	C18—H18	0.93
C5—H5	0.93	C19—C20	1.357 (6)
C6—C7	1.366 (7)	C19—H19	0.93
C6—H6	0.93	C20—H20	0.93
O2···C18^ii	3.320 (6)	C6···C9^v	3.441 (5)
O2···C19^ii	3.353 (6)	C7···C8^v	3.530 (5)
O2···C13^iii	3.450 (6)	C8···C8^v	3.480 (6)
O3···C11^iv	3.450 (4)	C8···C12^iv	3.484 (5)
O3···C7^v	3.521 (4)	C8···C11^iv	3.559 (5)
O3···C6^v	3.549 (5)	C18···C20^ii	3.542 (8)
C3···C12^iv	3.579 (6)	C19···C20^ii	3.518 (7)
C4···C12^iii	3.546 (5)	C19···C19^ii	3.57 (1)
O1—Cu1—O1^i	180.0	C8—C7—H7	120.7
O1—Cu1—O2	83.29 (9)	O3—C8—C3	122.7 (3)
O1—Cu1—O2^i	96.71 (9)	O3—C8—C7	116.7 (3)
O1—Cu1—N1	91.3 (1)	C3—C8—C7	120.7 (4)
O1—Cu1—N1^i	88.7 (1)	O3—C9—C1	120.3 (3)
O1^i—Cu1—O2	96.71 (9)	O3—C9—C10	111.6 (2)
O1^i—Cu1—O2^i	83.29 (9)	C1—C9—C10	128.2 (3)
O1^i—Cu1—N1	88.7 (1)	C9—C10—C11	120.3 (3)
O1^i—Cu1—N1^i	91.3 (1)	C9—C10—C15	122.4 (3)
O2—Cu1—O2^i	180.0	C11—C10—C15	117.4 (3)
O2—Cu1—N1	90.1 (1)	C10—C11—C12	120.5 (3)
O2—Cu1—N1^i	89.9 (1)	C10—C11—H11	119.7
O2^i—Cu1—N1	89.9 (1)	C12—C11—H11	119.7
O2^i—Cu1—N1^i	90.1 (1)	C11—C12—C13	121.5 (3)
N1—Cu1—N1^i	180.0	C11—C12—H12	119.2
Cu1—O1—C1	112.0 (2)	C13—C12—H12	119.2
Cu1—O2—C2	109.4 (2)	C12—C13—C14	119.1 (4)
C8—O3—C9	121.6 (2)	C12—C13—H13	120.4
Cu1—N1—C16	120.9 (3)	C14—C13—H13	120.5
Cu1—N1—C20	120.5 (3)	C13—C14—C15	120.0 (4)
C16—N1—C20	116.6 (4)	C13—C14—H14	120.0
O1—C1—C2	116.3 (2)	C15—C14—H14	120.0
O1—C1—C9	124.5 (3)	C10—C15—C14	121.4 (3)
C2—C1—C9	119.3 (3)	C10—C15—H15	119.3
O2—C2—C1	118.7 (3)	C14—C15—H15	119.3
O2—C2—C3	122.8 (3)	N1—C16—C17	124.0 (4)
C1—C2—C3	118.6 (2)	N1—C16—H16	118.0
C2—C3—C4	123.5 (3)	C17—C16—H16	118.0
C2—C3—C8	117.6 (3)	C16—C17—C18	117.4 (4)
C4—C3—C8	118.9 (3)	C16—C17—H17	121.3
C3—C4—C5	120.6 (3)	C18—C17—H17	121.3
C3—C4—H4	119.7	C17—C18—C19	117.5 (4)
C5—C4—H4	119.7	C17—C18—H18	121.2
C4—C5—C6	119.7 (4)	C19—C18—H18	121.2
C4—C5—H5	120.1	C18—C19—C20	120.8 (5)
C6—C5—H5	120.1	C18—C19—H19	119.6
C5—C6—C7	121.4 (3)	C20—C19—H19	119.6
C5—C6—H6	119.3	N1—C20—C19	123.5 (4)
C7—C6—H6	119.3	N1—C20—H20	118.2
C6—C7—C8	118.7 (3)	C19—C20—H20	118.2
C6—C7—H7	120.7
Cu1—O1—C1—C2	5.5 (3)	N1—Cu1—O1—C1	−95.4 (2)
Cu1—O1—C1—C9	−173.5 (2)	N1—Cu1—O1^i—C1^i	−84.6 (2)
Cu1—O1^i—C1^i—C2^i	−5.5 (3)	N1—Cu1—O2—C2	95.8 (2)
Cu1—O1^i—C1^i—C9^i	173.5 (2)	N1—Cu1—O2^i—C2^i	84.2 (2)
Cu1—O2—C2—C1	−2.8 (3)	N1—C16—C17—C18	1.3 (8)
Cu1—O2—C2—C3	177.3 (2)	N1—C20—C19—C18	−0.6 (8)
Cu1—O2^i—C2^i—C1^i	2.8 (3)	C1—C2—C3—C4	−178.2 (3)
Cu1—O2^i—C2^i—C3^i	−177.3 (2)	C1—C2—C3—C8	1.7 (4)
Cu1—N1—C16—C17	160.7 (4)	C1—C9—O3—C8	−0.4 (4)
Cu1—N1—C20—C19	−161.1 (4)	C1—C9—C10—C11	173.0 (3)
Cu1—N1^i—C16^i—C17^i	−160.7 (4)	C1—C9—C10—C15	−8.0 (5)
Cu1—N1^i—C20^i—C19^i	161.1 (4)	C2—C1—C9—C10	−178.7 (3)
O1—Cu1—O2—C2	4.5 (2)	C2—C3—C4—C5	−179.9 (3)
O1—Cu1—O2^i—C2^i	175.5 (2)	C2—C3—C8—C7	−179.6 (3)
O1—Cu1—N1—C16	10.3 (4)	C3—C2—C1—C9	−2.8 (4)
O1—Cu1—N1—C20	173.5 (3)	C3—C4—C5—C6	−0.4 (6)
O1—Cu1—N1^i—C16^i	169.7 (4)	C3—C8—O3—C9	−0.8 (4)
O1—Cu1—N1^i—C20^i	6.5 (3)	C3—C8—C7—C6	−0.6 (5)
O1—C1—C2—O2	−1.7 (4)	C4—C3—C8—C7	0.3 (5)
O1—C1—C2—C3	178.2 (3)	C4—C5—C6—C7	0.1 (6)
O1—C1—C9—O3	−179.0 (3)	C5—C4—C3—C8	0.3 (5)
O1—C1—C9—C10	0.3 (5)	C5—C6—C7—C8	0.5 (6)
O2—Cu1—O1—C1	−5.4 (2)	C7—C8—O3—C9	178.9 (3)
O2—Cu1—O1^i—C1^i	−174.6 (2)	C8—O3—C9—C10	−179.7 (3)
O2—Cu1—N1—C16	−73.0 (4)	C9—C10—C11—C12	179.1 (3)
O2—Cu1—N1—C20	90.2 (3)	C9—C10—C15—C14	−177.8 (3)
O2—Cu1—N1^i—C16^i	−107.0 (4)	C10—C11—C12—C13	−0.7 (6)
O2—Cu1—N1^i—C20^i	89.8 (3)	C10—C15—C14—C13	−1.9 (6)
O2—C2—C1—C9	177.4 (3)	C11—C10—C15—C14	1.2 (5)
O2—C2—C3—C4	1.7 (5)	C11—C12—C13—C14	0.0 (6)
O2—C2—C3—C8	−178.4 (3)	C12—C11—C10—C15	0.0 (5)
O3—C8—C3—C2	0.0 (5)	C12—C13—C14—C15	1.2 (6)
O3—C8—C3—C4	179.9 (3)	C16—N1—C20—C19	2.8 (7)
O3—C8—C7—C6	179.7 (3)	C16—C17—C18—C19	0.9 (8)
O3—C9—C1—C2	2.1 (4)	C17—C16—N1—C20	−3.1 (7)
O3—C9—C10—C11	−7.7 (4)	C17—C18—C19—C20	−1.3 (8)
O3—C9—C10—C15	171.2 (3)	C17—C18—C19—C20	−1.3 (8)

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