Effects of electron-donating ability of binding sites on coordination number: the inter­actions of a cyclic Schiff base with copper ions

The stepwise addition of Cu²⁺ ions to the nonplanar cyclic Schiff base 5,9,14,18-tetra­methyl-1,4,10,13-tetra­aza­cyclo­octa­deca-5,8,14,17-tetra­ene-7,16-dione (H₄daaden, C₁₈H₂₈N₄O₂), yields a one-end-open dinuclear copper chelate. The pyri­dine adduct of the dinuclear copper chelate, namely, [μ-6,11-dimethyl-7,10-di­aza­hexa­deca-5,11-diene-2,4,13,15-tetra­olato(4−)](pyri­dine)dicopper(II), [Cu₂(C₁₆H₂₀N₂O₄)(C₅H₅N)], was characterized by single-crystal X-ray crystallography. The two Cu^II atoms of the copper chelate display different coordination modes, i.e. inner-N₂O₂ and outer-O₂O₂. The Cu atom which is bonded in the outer-O₂O₂ mode is axially bonded to a pyri­dine mol­ecule, which suggests that the electron-donating ability of the O₂O₂ site to the Cu atom is poor. As a result, the O₂O₂-bonded Cu atom has a coordination number of five, showing square-bipyramidal geometry around the Cu atom. The N₂O₂-coordinated site provides sufficient electron density to the other Cu atom to be stabilized with a coordination number of four, showing square-planar geometry around the Cu atom. The electron-donating ability of the ligand coordination sites plays a key role in determining the coordination number of the Cu atoms of the dicopper chelate.

Computing details

Data collection: APEX4 (Bruker, 2021); cell refinement: APEX4 (Bruker, 2021); data reduction: SAINT (Bruker, 2021); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXTL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020) and POV-RAY (Cason, 2004); software used to prepare material for publication: APEX4 (Bruker, 2021).

[µ-6,11-Dimethyl-7,10-diazahexadeca-5,11-diene-2,4,13,15-tetraolato(4-)-1κ⁴O²,O⁴,O¹³,O¹⁵:2κ⁴N⁷,N¹⁰,O⁴,O¹³](pyridine-1κN)dicopper(II)

Crystal data

[Cu2(C16H20N2O4)(C5H5N)]	Z = 2
Mr = 510.52	F(000) = 524
Triclinic, P1	Dx = 1.671 Mg m^−3
a = 8.0549 (5) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.8811 (6) Å	Cell parameters from 1540 reflections
c = 13.7189 (8) Å	θ = 1.6–28.5°
α = 106.451 (1)°	µ = 2.13 mm^−1
β = 103.271 (1)°	T = 296 K
γ = 91.482 (1)°	Prism frag, colorless
V = 1014.40 (11) Å^3	0.30 × 0.08 × 0.08 mm

Data collection

Bruker D8 Venture diffractometer	4293 reflections with I > 2σ(I)
profile data from θ/2θ scans	Rint = 0.015
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θmax = 28.5°, θmin = 1.6°
Tmin = 0.567, Tmax = 0.848	h = −10→10
12405 measured reflections	k = −13→13
4680 independent reflections	l = −18→17

Refinement

Refinement on F^2	Primary atom site location: dual
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.021	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.055	H-atom parameters constrained
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0266P)^2 + 0.5267P] where P = (Fo^2 + 2Fc^2)/3
4680 reflections	(Δ/σ)max = 0.002
275 parameters	Δρmax = 0.34 e Å^−3
0 restraints	Δρmin = −0.31 e Å^−3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. A brown-coloured plate-like single crystal of Cu2(daaen)(py), having approximate dimensions 0.080 × 0.080 × 0.300 mm was selected for the X-ray crystallographic analysis and mounted on a cryo-loop using an oil cryo-protectant. The X-ray intensity data were measured at T = 296 K, using a three-circle goniometer platform geometry with a fixed χ angle = 54.74°. A Bruker SMART 1000 diffractometer, equipped with a CCD detector. Monochromatic Mo X-ray radiation (λ = 0.71073 Å) was selected for the measurement. All frames were integrated with the aid of the Bruker SAINT software using a narrow-frame algorithm. The integration of the data using a triclinic unit cell yielded a total of 12405 reflections to a maximum θ angle of 28.50° (0.74 Å resolution), of which 4680 were independent (average redundancy = 2.651, completeness = 91.1%, R_int = 1.53%, R_sig = 1.74%) and 4293 (91.73%) were greater than 2σ (F²). The final unit-cell constants of a = 8.0549 (5) Å, b = 9.8811 (6) Å, c = 13.7189 (8)Å, α = 106.4510 (10)°, β = 103.2710 (10)°, γ = 91.4820 (10)° and V = 1014.40 (11) ų, are based upon the refinement of the 1540 XYZ-centroids of reflections above 20σ(I). The calculated minimum and maximum transmission coefficients (based on crystal size) are 0.5670 and 0.8480. The structure was solved in a triclinic unit cell; ppace group: P1, with Z = 2 for the formula unit, C₂₁H₂₅Cu₂N₃O₄. Using the Bruker SHELXT software package, refinement of the structure was carried out by least-squares procedures on weighted F² values using the SHELXTL2018 (Sheldrick, 2015b) included in the APEX4 (Bruker, 2021) program.

The final anisotropic full-matrix least-squares refinement on F² with 276 variables converged at R1 = 2.05%, for the observed data and wR2 = 5.53% for all data. The goodness-of-fit was 1.044. The largest peak in the final difference electron density synthesis was 0.340 e^- Å^-3 and the largest hole was -0.306 e^- Å^-3 with an r.m.s. deviation of 0.054 e^- Å^-3. Based on the final model, the calculated density was 1.671 g cm^-3 and F(000) = 524 e^-. Graphics were performed using software Mercury V.4.2.0: (https://www.ccdc.cam.ac.uk/) and POV-Ray v 3.7: (The Persistence of Vision Raytracer, high quality, Free Software tool).

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

	x	y	z	Uiso*/Ueq
Cu1	0.67560 (2)	0.69842 (2)	0.78376 (2)	0.01441 (5)
Cu2	0.74398 (2)	0.47982 (2)	0.59601 (2)	0.01529 (5)
N1	0.84460 (16)	0.30766 (13)	0.57589 (10)	0.0174 (2)
N2	0.74679 (16)	0.47544 (14)	0.45833 (10)	0.0187 (3)
N3	0.94332 (16)	0.81239 (13)	0.84007 (10)	0.0180 (2)
O1	0.65027 (13)	0.67677 (11)	0.91465 (8)	0.0181 (2)
O2	0.74876 (14)	0.50802 (11)	0.74018 (8)	0.0174 (2)
O3	0.66075 (14)	0.66147 (11)	0.63315 (8)	0.0183 (2)
O4	0.55647 (13)	0.86413 (11)	0.78924 (8)	0.0188 (2)
C1	0.6968 (2)	0.59164 (17)	1.06208 (12)	0.0215 (3)
H1A	0.798563	0.647035	1.109045	0.032*
H1B	0.688525	0.500378	1.073311	0.032*
H1C	0.598137	0.639346	1.075005	0.032*
C2	0.70478 (18)	0.57295 (16)	0.94990 (11)	0.0171 (3)
C3	0.7684 (2)	0.45196 (16)	0.89819 (12)	0.0191 (3)
H3	0.802498	0.388154	0.935667	0.023*
C4	0.78706 (18)	0.41521 (15)	0.79329 (11)	0.0165 (3)
C5	0.8455 (2)	0.28646 (16)	0.74729 (12)	0.0200 (3)
H13	0.867341	0.225331	0.788305	0.024*
C6	0.87582 (19)	0.23728 (16)	0.64569 (12)	0.0192 (3)
C7	0.8840 (2)	0.25573 (17)	0.47290 (12)	0.0213 (3)
H7A	0.830832	0.159632	0.438267	0.026*
H7B	1.006961	0.253681	0.482675	0.026*
C8	0.8191 (2)	0.35063 (16)	0.40248 (12)	0.0207 (3)
H8A	0.913531	0.381478	0.378369	0.025*
H8B	0.732266	0.295644	0.341362	0.025*
C9	0.68559 (19)	0.57112 (17)	0.41322 (12)	0.0194 (3)
C10	0.6165 (2)	0.69437 (17)	0.46544 (12)	0.0217 (3)
H10	0.569839	0.751143	0.424439	0.026*
C11	0.61003 (19)	0.74071 (16)	0.57067 (12)	0.0180 (3)
C12	0.5485 (2)	0.87312 (16)	0.61445 (12)	0.0207 (3)
H12	0.521759	0.930978	0.571213	0.025*
C13	0.52491 (18)	0.92382 (16)	0.71465 (12)	0.0189 (3)
C14	0.4520 (2)	1.06472 (18)	0.74577 (14)	0.0275 (4)
H14A	0.346067	1.051050	0.764106	0.041*
H14B	0.431660	1.103913	0.688040	0.041*
H14C	0.532032	1.128651	0.804933	0.041*
C15	0.9508 (2)	0.09704 (18)	0.61936 (14)	0.0276 (4)
H15A	0.872528	0.030649	0.560754	0.041*
H15B	0.970034	0.061321	0.678814	0.041*
H15C	1.057625	0.109900	0.601769	0.041*
C16	0.6906 (2)	0.55399 (18)	0.30118 (12)	0.0234 (3)
H16A	0.807382	0.565340	0.297329	0.035*
H16B	0.628017	0.624467	0.276943	0.035*
H16C	0.639422	0.461260	0.257930	0.035*
C17	0.9586 (2)	0.95341 (16)	0.86038 (12)	0.0210 (3)
H17	0.861655	0.997153	0.839373	0.025*
C18	1.1110 (2)	1.03733 (17)	0.91091 (13)	0.0241 (3)
H18	1.115733	1.135193	0.924179	0.029*
C19	1.2563 (2)	0.97349 (18)	0.94140 (14)	0.0276 (4)
H19	1.360332	1.027555	0.976354	0.033*
C20	1.2440 (2)	0.82729 (19)	0.91890 (14)	0.0293 (4)
H20	1.340221	0.780985	0.936801	0.035*
C21	1.0856 (2)	0.75152 (17)	0.86922 (13)	0.0222 (3)
H21	1.077474	0.653523	0.855383	0.027*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.01791 (9)	0.01383 (9)	0.01186 (9)	0.00351 (6)	0.00342 (7)	0.00444 (7)
Cu2	0.01905 (10)	0.01593 (9)	0.01119 (9)	0.00390 (7)	0.00379 (7)	0.00424 (7)
N1	0.0187 (6)	0.0174 (6)	0.0152 (6)	0.0025 (5)	0.0048 (5)	0.0028 (5)
N2	0.0194 (6)	0.0221 (6)	0.0145 (6)	0.0023 (5)	0.0045 (5)	0.0053 (5)
N3	0.0187 (6)	0.0194 (6)	0.0160 (6)	0.0019 (5)	0.0045 (5)	0.0054 (5)
O1	0.0238 (5)	0.0165 (5)	0.0147 (5)	0.0038 (4)	0.0054 (4)	0.0050 (4)
O2	0.0247 (5)	0.0153 (5)	0.0132 (5)	0.0048 (4)	0.0048 (4)	0.0054 (4)
O3	0.0247 (5)	0.0178 (5)	0.0137 (5)	0.0059 (4)	0.0042 (4)	0.0066 (4)
O4	0.0205 (5)	0.0195 (5)	0.0176 (5)	0.0058 (4)	0.0048 (4)	0.0071 (4)
C1	0.0294 (8)	0.0216 (7)	0.0145 (7)	0.0021 (6)	0.0066 (6)	0.0060 (6)
C2	0.0178 (7)	0.0186 (7)	0.0143 (7)	−0.0010 (5)	0.0026 (5)	0.0053 (6)
C3	0.0247 (7)	0.0186 (7)	0.0168 (7)	0.0051 (6)	0.0054 (6)	0.0092 (6)
C4	0.0172 (7)	0.0166 (7)	0.0156 (7)	0.0017 (5)	0.0023 (5)	0.0062 (6)
C5	0.0260 (8)	0.0183 (7)	0.0191 (7)	0.0065 (6)	0.0076 (6)	0.0090 (6)
C6	0.0187 (7)	0.0172 (7)	0.0209 (8)	0.0030 (5)	0.0047 (6)	0.0045 (6)
C7	0.0222 (7)	0.0247 (8)	0.0166 (7)	0.0067 (6)	0.0065 (6)	0.0036 (6)
C8	0.0245 (8)	0.0210 (7)	0.0164 (7)	0.0004 (6)	0.0082 (6)	0.0029 (6)
C9	0.0168 (7)	0.0267 (8)	0.0152 (7)	−0.0007 (6)	0.0029 (5)	0.0080 (6)
C10	0.0232 (8)	0.0272 (8)	0.0190 (8)	0.0057 (6)	0.0054 (6)	0.0130 (6)
C11	0.0172 (7)	0.0212 (7)	0.0182 (7)	0.0023 (5)	0.0031 (6)	0.0108 (6)
C12	0.0228 (7)	0.0219 (7)	0.0229 (8)	0.0060 (6)	0.0070 (6)	0.0140 (6)
C13	0.0155 (7)	0.0188 (7)	0.0238 (8)	0.0029 (5)	0.0047 (6)	0.0087 (6)
C14	0.0336 (9)	0.0244 (8)	0.0316 (9)	0.0127 (7)	0.0136 (7)	0.0138 (7)
C15	0.0387 (10)	0.0242 (8)	0.0253 (8)	0.0149 (7)	0.0146 (7)	0.0092 (7)
C16	0.0260 (8)	0.0297 (8)	0.0167 (7)	0.0023 (6)	0.0063 (6)	0.0093 (6)
C17	0.0213 (7)	0.0206 (7)	0.0226 (8)	0.0025 (6)	0.0040 (6)	0.0100 (6)
C18	0.0268 (8)	0.0201 (7)	0.0250 (8)	−0.0014 (6)	0.0049 (6)	0.0077 (6)
C19	0.0192 (8)	0.0296 (9)	0.0307 (9)	−0.0037 (6)	0.0029 (7)	0.0070 (7)
C20	0.0185 (8)	0.0324 (9)	0.0357 (10)	0.0064 (6)	0.0037 (7)	0.0102 (8)
C21	0.0225 (8)	0.0186 (7)	0.0247 (8)	0.0049 (6)	0.0060 (6)	0.0047 (6)

Geometric parameters (Å, º)

Cu1—O4	1.9110 (10)	C7—C8	1.547 (2)
Cu1—O1	1.9223 (10)	C7—H7A	0.9700
Cu1—O2	1.9561 (10)	C7—H7B	0.9700
Cu1—O3	1.9682 (10)	C8—H8A	0.9700
Cu1—N3	2.2654 (13)	C8—H8B	0.9700
Cu1—Cu2	3.0275 (3)	C9—C10	1.425 (2)
Cu2—N1	1.8801 (12)	C9—C16	1.508 (2)
Cu2—N2	1.8823 (13)	C10—C11	1.399 (2)
Cu2—O3	1.9057 (10)	C10—H10	0.9300
Cu2—O2	1.9088 (10)	C11—C12	1.429 (2)
N1—C6	1.319 (2)	C12—C13	1.383 (2)
N1—C7	1.4711 (19)	C12—H12	0.9300
N2—C9	1.317 (2)	C13—C14	1.512 (2)
N2—C8	1.4679 (19)	C14—H14A	0.9600
N3—C17	1.3379 (19)	C14—H14B	0.9600
N3—C21	1.3404 (19)	C14—H14C	0.9600
O1—C2	1.2985 (18)	C15—H15A	0.9600
O2—C4	1.3255 (17)	C15—H15B	0.9600
O3—C11	1.3232 (17)	C15—H15C	0.9600
O4—C13	1.2999 (18)	C16—H16A	0.9600
C1—C2	1.514 (2)	C16—H16B	0.9600
C1—H1A	0.9600	C16—H16C	0.9600
C1—H1B	0.9600	C17—C18	1.381 (2)
C1—H1C	0.9600	C17—H17	0.9300
C2—C3	1.383 (2)	C18—C19	1.380 (2)
C3—C4	1.425 (2)	C18—H18	0.9300
C3—H3	0.9300	C19—C20	1.385 (2)
C4—C5	1.397 (2)	C19—H19	0.9300
C5—C6	1.420 (2)	C20—C21	1.384 (2)
C5—H13	0.9300	C20—H20	0.9300
C6—C15	1.508 (2)	C21—H21	0.9300
O4—Cu1—O1	96.96 (4)	C5—C6—C15	116.55 (14)
O4—Cu1—O2	163.66 (5)	N1—C7—C8	111.64 (12)
O1—Cu1—O2	92.26 (4)	N1—C7—H7A	109.3
O4—Cu1—O3	91.98 (4)	C8—C7—H7A	109.3
O1—Cu1—O3	161.95 (5)	N1—C7—H7B	109.3
O2—Cu1—O3	75.68 (4)	C8—C7—H7B	109.3
O4—Cu1—N3	96.36 (5)	H7A—C7—H7B	108.0
O1—Cu1—N3	98.64 (5)	N2—C8—C7	111.93 (12)
O2—Cu1—N3	95.55 (5)	N2—C8—H8A	109.2
O3—Cu1—N3	95.90 (5)	C7—C8—H8A	109.2
O4—Cu1—Cu2	129.40 (3)	N2—C8—H8B	109.2
O1—Cu1—Cu2	129.34 (3)	C7—C8—H8B	109.2
O2—Cu1—Cu2	37.88 (3)	H8A—C8—H8B	107.9
O3—Cu1—Cu2	37.87 (3)	N2—C9—C10	123.47 (14)
N3—Cu1—Cu2	95.51 (3)	N2—C9—C16	119.63 (14)
N1—Cu2—N2	89.11 (5)	C10—C9—C16	116.89 (14)
N1—Cu2—O3	172.95 (5)	C11—C10—C9	128.15 (14)
N2—Cu2—O3	96.15 (5)	C11—C10—H10	115.9
N1—Cu2—O2	96.14 (5)	C9—C10—H10	115.9
N2—Cu2—O2	173.15 (5)	O3—C11—C10	120.35 (14)
O3—Cu2—O2	78.27 (4)	O3—C11—C12	117.70 (13)
N1—Cu2—Cu1	134.73 (4)	C10—C11—C12	121.95 (14)
N2—Cu2—Cu1	135.12 (4)	C13—C12—C11	126.53 (14)
O3—Cu2—Cu1	39.35 (3)	C13—C12—H12	116.7
O2—Cu2—Cu1	39.00 (3)	C11—C12—H12	116.7
C6—N1—C7	122.22 (13)	O4—C13—C12	127.96 (14)
C6—N1—Cu2	124.18 (10)	O4—C13—C14	113.09 (13)
C7—N1—Cu2	113.59 (10)	C12—C13—C14	118.95 (14)
C9—N2—C8	121.97 (13)	C13—C14—H14A	109.5
C9—N2—Cu2	124.47 (11)	C13—C14—H14B	109.5
C8—N2—Cu2	113.53 (10)	H14A—C14—H14B	109.5
C17—N3—C21	117.19 (13)	C13—C14—H14C	109.5
C17—N3—Cu1	117.85 (10)	H14A—C14—H14C	109.5
C21—N3—Cu1	124.18 (10)	H14B—C14—H14C	109.5
C2—O1—Cu1	123.78 (9)	C6—C15—H15A	109.5
C4—O2—Cu2	126.53 (9)	C6—C15—H15B	109.5
C4—O2—Cu1	130.30 (9)	H15A—C15—H15B	109.5
Cu2—O2—Cu1	103.12 (5)	C6—C15—H15C	109.5
C11—O3—Cu2	126.89 (10)	H15A—C15—H15C	109.5
C11—O3—Cu1	130.31 (10)	H15B—C15—H15C	109.5
Cu2—O3—Cu1	102.78 (5)	C9—C16—H16A	109.5
C13—O4—Cu1	124.28 (10)	C9—C16—H16B	109.5
C2—C1—H1A	109.5	H16A—C16—H16B	109.5
C2—C1—H1B	109.5	C9—C16—H16C	109.5
H1A—C1—H1B	109.5	H16A—C16—H16C	109.5
C2—C1—H1C	109.5	H16B—C16—H16C	109.5
H1A—C1—H1C	109.5	N3—C17—C18	123.38 (15)
H1B—C1—H1C	109.5	N3—C17—H17	118.3
O1—C2—C3	128.09 (13)	C18—C17—H17	118.3
O1—C2—C1	113.90 (13)	C19—C18—C17	118.85 (15)
C3—C2—C1	118.01 (13)	C19—C18—H18	120.6
C2—C3—C4	126.58 (14)	C17—C18—H18	120.6
C2—C3—H3	116.7	C18—C19—C20	118.67 (15)
C4—C3—H3	116.7	C18—C19—H19	120.7
O2—C4—C5	120.43 (13)	C20—C19—H19	120.7
O2—C4—C3	117.93 (13)	C21—C20—C19	118.63 (15)
C5—C4—C3	121.63 (14)	C21—C20—H20	120.7
C4—C5—C6	128.09 (14)	C19—C20—H20	120.7
C4—C5—H13	116.0	N3—C21—C20	123.25 (15)
C6—C5—H13	116.0	N3—C21—H21	118.4
N1—C6—C5	123.86 (14)	C20—C21—H21	118.4
N1—C6—C15	119.59 (14)