(Benzoato-κ²O,O′)chlorido(di-2-pyridylamine-κ²N,N′)copper(II)

In the title complex, [Cu(C₇H₅O₂)Cl(C₁₀H₉N₃)], the Cu atom has a distorted CuN₂O₂Cl square-pyramidal geometry defined by one N,N′-bidentate 2,2′-bipyridylamine (bpa) mol­ecule, one O,O′-bidentate benzene­carboxyl­ate (BA) anion and one chloride ion, the latter in the apical position. The complete mol­ecule is generated by mirror symmetry with the NH group of bpa, the Cu atom, three C atoms of BA and the Cl atom lying on the mirror plane. The complexes are connected to each other by N—H...Cl hydrogen bonds and π–π stacking inter­actions between adjacent heterocyclic rings, with distances between the ring centroids of 3.592 (4) and 3.468 (4) Å.

Key indicators

• Single-crystal X-ray study
• T = 123 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.025
• wR factor = 0.072
• Data-to-parameter ratio = 15.9

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT148_ALERT_3_B su on the      a  - Axis is Too Large (x 1000) .         20 Ang.

Alert level C
PLAT060_ALERT_3_C Ratio Tmax/Tmin (Exp-to-Rep) (too) Large .......       1.11
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       1.02
PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X)  Cu1    -   O1      ..       7.49 su
PLAT764_ALERT_4_C Overcomplete CIF Bond List Detected (Rep/Expd) .       1.11 Ratio

Alert level G
PLAT794_ALERT_5_G Check Predicted Bond Valency for Cu1         (2)       2.30

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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

The construction of novel Cu(II) complexes are important for the development of new therapeutic drug design, because some Cu(II) complexes of 1,10-phenanthroline have antitumor activity (Selvakumar et al., 2006; Li et al., 2005; Kelland, 2005; Ranford et al., 1993).

In a previous study, we have reported the structure of the ternary Cu(II) complex with 2,2'-bipyridylamine (bpa) and p-hydroxybenzenecarboxylate (p-HB) (Wang & Okabe, 2005) in which the bpa ligand has been used as the bidentate N-donor ligand and p-HB as the bidentate O-donor. In this study, we report the structure of the Cu(II) complex with bpa and benzenecarboxylate (BA), (I).

The central Cu atom in (I) (Fig. 1) has a square-pyramidal CuN₂O₂Cl geometry. Each Cu atom is coordinated by two N atoms from one bpa and two O atoms from one BA and one chloride anion. The bond distances and angles around the Cu atom indicate that the coordination geometry is a slightly distorted square pyramidal (Table 1).

In the complex molecule, the two pyridine rings of the bpa ligand are related by mirror symmetry and distinguished as Ring I (N1/C1—C5) and Ring II (N1ⁱ/C1ⁱ—C5ⁱ) [symmetry code: (i)(x, 1/2 - y, z)]. Four ligand atoms (N1, N1ⁱ,O1 and O1ⁱ) are neary coplanar, and the Cu atom deviates from the mean square plane towards the apical Cl atom by 0.2986 (1) Å. The bite angle N1—Cu1—N1ⁱ is in the range normally observed for the Cu(II) bpa complexes (Wang & Okabe, 2005; Youngme et al., 1999, 2004) The Cu—Cl distance is intermediate between the known values from 2.336 (2) to 2.733 (2) Å (Mao et al., 2004; Brophy et al., 1999). The long Cu—Cl bond distance is explained by the well known Jahn-Teller effect. The molecular structure of (I) is similar to that of the Cu(II) complex with bpa and p-HB (Wang & Okabe, 2005), although the hydrogen bonding and the packing modes of these are different to each other.

As shown in Figs. 2a and 2 b, the crystal structure of (I) is stabilized by hydrogen bonds (Table 2) and by two kinds of π-π stacking interactions with distances between the centroids of the aromatic rings, 3.592 (4) Å between Cg1 (Ring I) and Cg3 (Ring II) at (x, y, 1 + z) and 3.468 (4) Å between Cg2 (N1/C5/N2/C5ⁱ/N1ⁱ/Cu1) [symmetry code: (i) (x, 1/2 - y, z)] and Cg4 (BA) at (1 - x, 1 - y, 1 - z).

Related literature

For related literature, see: Brophy et al. (1999); Kelland (2005); Li et al. (2005); Mao et al. (2004); Ranford et al. (1993); Selvakumar et al. (2006); Wang & Okabe (2005); Youngme et al. (2004).

For related literature, see: Youngme (1999).

S2. Experimental

2,2'-Bipyridylamine (5.0 mg, 0.03 mol) dissolved in 90%(v/v) methanol-water solution (2 ml) was reacted with benzoic acid (3.6 mg, 0.03 mol), dissolved in the same solution (2 ml) for 5 min at room temperature. This was followed by the addition of CuCl₂.2H₂O (5.0 mg, 0.03 mol) dissolved in H₂O (1 ml) and reacted for 15 min at room temperature. After several days green plates of (I) appeared from the mother liquor.

S3. Refinement

All H atoms were located from the difference Fourier maps, and then were placed in idealized positions and treated as riding, with C—H = 0.93 Å, N—H = 0.86Å and U_iso(H) = 1.2U_eq(C,N).

Computing details

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2005) and CRYSTALS (Betteridge et al., 2003); 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, 2003); software used to prepare material for publication: CrystalStructure.

Figures

	Fig. 1. View of (I) with the atomic numbering-scheme and displacement ellipsoid drawn at the 50% probability level (arbitrary spheres for the H atoms). Symmetry code: (i) x, 1/2 - y, z.
	Fig. 2. A view of the N—H···Cl hydrogen bonds (dashed lines) between the adjacent molecules of (I)
	Fig. 3. A view of the π-π stacking interaction in (I). See the text for the ring designations.

(Benzoato-κ²O,O')chlorido(di-2-pyridylamine- κ²N,N')copper(II)

Crystal data

[Cu(C7H5O2)Cl(C10H9N3)]	F(000) = 796.0
Mr = 391.31	Dx = 1.644 Mg m^−3
Orthorhombic, Pnma	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2ac 2n	Cell parameters from 13658 reflections
a = 19.31 (2) Å	θ = 3.1–27.5°
b = 11.77 (1) Å	µ = 1.57 mm^−1
c = 6.958 (6) Å	T = 123 K
V = 1581 (3) Å^3	Plate, green
Z = 4	0.40 × 0.40 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID diffractometer	1746 reflections with F^2 > 2.0σ(F^2)
Detector resolution: 10.00 pixels mm^-1	Rint = 0.015
ω scans	θmax = 27.5°
Absorption correction: multi-scan (ABSCOR : Higashi,1995)	h = −25→25
Tmin = 0.587, Tmax = 0.840	k = −15→15
15128 measured reflections	l = −8→9
1893 independent reflections

Refinement

Refinement on F^2	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.025	w = 1/[σ^2(Fo^2) + (0.0341P)^2 + 1.7191P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.072	(Δ/σ)max < 0.001
S = 1.12	Δρmax = 0.34 e Å^−3
1893 reflections	Δρmin = −1.17 e Å^−3
119 parameters

Special details

Geometry. ENTER SPECIAL DETAILS OF THE MOLECULAR GEOMETRY

Refinement. Refinement using all reflections. 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	0.61824 (1)	0.2500	0.18707 (4)	0.0144 (1)
Cl1	0.50045 (3)	0.2500	0.03740 (8)	0.0198 (1)
O1	0.67196 (6)	0.3426 (1)	−0.0121 (2)	0.0190 (3)
N1	0.60171 (7)	0.3723 (1)	0.3734 (2)	0.0148 (3)
N2	0.5622 (1)	0.2500	0.6194 (3)	0.0166 (4)
C1	0.61517 (9)	0.4801 (2)	0.3141 (3)	0.0201 (4)
C2	0.6049 (1)	0.5735 (2)	0.4273 (3)	0.0238 (4)
C3	0.57907 (9)	0.5576 (1)	0.6132 (3)	0.0210 (4)
C4	0.56524 (9)	0.4495 (2)	0.6754 (2)	0.0183 (3)
C5	0.57716 (8)	0.3570 (1)	0.5513 (2)	0.0146 (3)
C6	0.6903 (1)	0.2500	−0.0902 (3)	0.0153 (4)
C7	0.7299 (1)	0.2500	−0.2737 (3)	0.0144 (4)
C8	0.74776 (9)	0.1475 (1)	−0.3616 (3)	0.0178 (3)
C9	0.78256 (9)	0.1476 (1)	−0.5363 (3)	0.0203 (3)
C10	0.7993 (1)	0.2500	−0.6228 (4)	0.0208 (5)
H1	0.6322	0.4908	0.1905	0.024*
H2	0.6148	0.6460	0.3816	0.028*
H3	0.5714	0.6195	0.6935	0.025*
H4	0.5481	0.4373	0.7986	0.022*
H5	0.5391	0.2500	0.7250	0.020*
H6	0.7363	0.0791	−0.3030	0.021*
H7	0.7945	0.0793	−0.5948	0.024*
H8	0.8221	0.2500	−0.7405	0.025*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0185 (2)	0.0141 (2)	0.0105 (2)	0.0000	0.0030 (1)	0.0000
Cl1	0.0175 (3)	0.0296 (3)	0.0125 (3)	0.0000	0.0023 (2)	0.0000
O1	0.0228 (6)	0.0191 (6)	0.0150 (6)	0.0009 (5)	0.0050 (5)	−0.0011 (5)
N1	0.0159 (6)	0.0150 (6)	0.0136 (6)	−0.0010 (5)	0.0010 (5)	−0.0012 (5)
N2	0.020 (1)	0.021 (1)	0.0092 (9)	0.0000	0.0052 (8)	0.0000
C1	0.0234 (9)	0.0182 (9)	0.0187 (9)	−0.0028 (6)	0.0043 (6)	−0.0000 (7)
C2	0.0264 (9)	0.0156 (8)	0.0292 (9)	−0.0030 (7)	0.0046 (8)	−0.0017 (7)
C3	0.0201 (8)	0.0197 (8)	0.0233 (9)	0.0006 (7)	−0.0007 (7)	−0.0085 (7)
C4	0.0167 (7)	0.0236 (9)	0.0146 (8)	0.0020 (6)	−0.0001 (6)	−0.0040 (6)
C5	0.0124 (7)	0.0182 (8)	0.0133 (7)	0.0000 (6)	−0.0011 (6)	−0.0010 (6)
C6	0.014 (1)	0.020 (1)	0.012 (1)	0.0000	−0.0014 (9)	0.0000
C7	0.0120 (9)	0.018 (1)	0.013 (1)	0.0000	−0.0004 (9)	0.0000
C8	0.0182 (7)	0.0167 (8)	0.0185 (8)	−0.0010 (6)	0.0023 (6)	0.0009 (7)
C9	0.0212 (8)	0.0206 (8)	0.0190 (8)	0.0002 (6)	0.0036 (7)	−0.0053 (7)
C10	0.020 (1)	0.030 (1)	0.012 (1)	0.0000	0.0054 (9)	0.0000

Geometric parameters (Å, º)

Cu1—Cl1	2.502 (3)	C3—C4	1.370 (3)
Cu1—O1	2.046 (1)	C3—H3	0.9300
Cu1—O1^i	2.046 (1)	C4—C5	1.409 (2)
Cu1—N1	1.963 (1)	C4—H4	0.9300
Cu1—N1^i	1.963 (1)	C6—O1^i	1.269 (2)
C6—O1	1.269 (2)	C6—C7	1.488 (3)
N1—C1	1.359 (2)	C7—C8	1.396 (2)
N1—C5	1.338 (2)	C7—C8^i	1.396 (2)
N2—C5	1.377 (2)	C8—C9	1.389 (2)
N2—C5^i	1.377 (2)	C8—H6	0.9300
N2—H5	0.8600	C9—C10	1.386 (2)
C1—C2	1.367 (3)	C9—H7	0.9300
C1—H1	0.9300	C10—C9^i	1.386 (2)
C2—C3	1.399 (3)	C10—H8	0.9300
C2—H2	0.9299
Cl1—Cu1—O1	100.32 (4)	H2—C2—C1	120.7624
Cl1—Cu1—O1^i	100.32 (4)	C4—C3—C2	119.0 (2)
Cl1—Cu1—N1	97.30 (4)	C4—C3—H3	120.4892
Cl1—Cu1—N1^i	97.30 (4)	H3—C3—C2	120.4784
O1—Cu1—O1^i	64.43 (5)	C5—C4—C3	119.5 (2)
O1—Cu1—N1	97.97 (5)	C5—C4—H4	120.2397
O1—Cu1—N1^i	156.99 (5)	H4—C4—C3	120.2411
O1^i—Cu1—N1	156.99 (5)	O1^i—C6—O1	118.5 (2)
O1^i—Cu1—N1^i	97.97 (5)	O1^i—C6—C7	120.7 (1)
N1—Cu1—N1^i	94.33 (6)	C7—C6—O1	120.7 (1)
C6—O1—Cu1	88.5 (1)	C8—C7—C6	120.2 (1)
C1—N1—Cu1	117.0 (1)	C8—C7—C8^i	119.6 (2)
C1—N1—C5	118.3 (1)	C8^i—C7—C6	120.2 (1)
C5—N1—Cu1	124.7 (1)	C9—C8—C7	120.2 (2)
C5—N2—C5^i	132.5 (2)	C9—C8—H6	119.9074
C5—N2—H5	113.7538	H6—C8—C7	119.9042
C5^i—N2—H5	113.7538	C10—C9—C8	119.5 (2)
C2—C1—N1	123.3 (2)	C10—C9—H7	120.2314
C2—C1—H1	118.3538	H7—C9—C8	120.2290
H1—C1—N1	118.3581	C9^i—C10—C9	120.9 (2)
C3—C2—C1	118.5 (2)	C9^i—C10—H8	119.5321
C3—C2—H2	120.7669	H8—C10—C9	119.5321
Cl1—Cu1—O1—C6	−94.68 (11)	C1—C2—C3—C4	0.1 (2)
Cl1—Cu1—N1—C1	−89.35 (12)	C2—C3—C4—C5	−0.0 (2)
Cu1—O1—C6—C7	174.32 (17)	C3—C4—C5—N1	−0.1 (2)
Cu1—N1—C1—C2	178.8 (1)	C3—C4—C5—N2	−179.67 (17)
Cu1—N1—C5—N2	1.0 (2)	O1—C6—C7—C8	−177.83 (18)
Cu1—N1—C5—C4	−178.6 (1)	C6—C7—C8—C9	177.7 (3)
H5—N2—C5—N1	−168.0	C7—C8—C9—C10	−0.1 (2)
H5—N2—C5—C4	11.6	C8—C9—C10—H8	−179.2
N1—C1—C2—C3	−0.1 (2)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H5···Cl1^ii	0.86	2.3	3.144 (2)	168

Symmetry code: (ii) x, y, z+1.