Bis[1,3-bis­(benzimidazol-2-yl)propane-κ²N,N′]copper(II) dinitrate methanol disolvate

In the title compound, [Cu(C₁₇H₁₆N₄)₂](NO₃)₂·2C₂H₅OH, the Cu^II ion lies on a crystallographic twofold rotation axis and is in a distorted square-planar coordination geometry formed by four N atoms from two 1,3-bis­(benzimidazol-2-yl)propane ligands. The N—Cu—N angles range from 90.25 (7) to 144.89 (11)°. In the crystal structure, a two-dimensional framework is formed by a combination of N—H...O and O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 297 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.052
• wR factor = 0.130
• Data-to-parameter ratio = 17.1

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSTM02_ALERT_3_C  The ratio of Tmax/Tmin expected RT(exp) is > 1.10
            Absorption corrections should be applied.
            Tmin and Tmax expected:      0.782     0.877
            RT(exp) =      1.121
PLAT057_ALERT_3_C Correction for Absorption Required   RT(exp) ...       1.13
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for         N5

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 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
   0 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
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Interest in bis(2-benzimidazolyl)alkanes is widespread, due to their wide-ranging antiviral activity (Roderick et al., 1972). Herein, we report the crystal structure of the title compound (I). In the cation (Fig. 1), the Cu^II ion lies on a crystallogrphic twofold axis. Hence, the Cu^II ion is coordinated by four N atoms (N1, N3, N1a, N3a [symmety code: (a) 1/2 - x, 3/2 - y, z]) from two dbz ligangs. The bond anlges listed in Table 1 indicate a distorted square-planar coordination geomtry.

In the crystal structure, molecules are linked by N—H_{benzimidazole}···O_nitrate and O—H_methanol···O _nitrate hydrogen bonds, forming a two-dimensional framework structure perpendicular to the ab plane (Table 2, Fig. 2).

Related literature

For related literature, see: Albada et al. (1995); Roderick et al. (1972); Wang & Joullie (1957), Allen et al. (1987); Sun et al. (2004).

S2. Experimental

The ligand 1,3-bis(2-benzimidazolyl)propane (dbz) was synthesized from reported literature earlier (van Albada et al., 1995; Wang

& Joullie, 1957). The title compound was prepared according to the following procedure: The ligand (0.28 g, 1 mmol) in 10 ml me thanol was added slowly to a Cu(NO₃)₂^.2H₂O (0.12 g, 0.5 mmol) solution of 10 ml me thanol. The mixture was stirred for 1 h. After filtration, the brownish solution was allowed to stand at room temperature. Green block-shaped crystals of (I) were obtained after three weeks.

S3. Refinement

H atoms bonded to O and N atoms were located in difference maps and then included in the refinement with bond-length restraints of O–H = 0.82 Å and N–H = 0.78 Å, with U_iso(H)= 1.2U_eq (O) and the U_iso(H) of the N—H atoms refined. H atoms bonded to C atoms were placed in calculated positions and included in the riding-model approximation, with C–H = 0.97—0.98 Å and U _iso(H) = 1.2U_eq(C of methylene and aromatic) or 1.5U _eq(C of methyl).

Computing details

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The molecular structure of (I), with displacement ellipsoids drawn at the 50% probability level. The H atoms, anion and solvent molecules are not shown. [symmetry code: (a) 1/2 - x, 3/2 - y, z]
	Fig. 2. Part of the crystal structure of (I), showing the formation of hydrogen-bonded (dashed lines) two-dimensional layers.

Bis[1,3-bis(benzimidazol-2-yl)propane-κ²N,N']copper(II) dinitrate methanol solvate

Crystal data

[Cu(C17H16N4)2](NO3)2·2C2H6O	F(000) = 1676
Mr = 804.32	Dx = 1.441 Mg m^−3
Orthorhombic, Pccn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ab 2ac	Cell parameters from 5026 reflections
a = 14.4793 (10) Å	θ = 2.3–25.4°
b = 17.8978 (13) Å	µ = 0.66 mm^−1
c = 14.3078 (10) Å	T = 297 K
V = 3707.8 (5) Å^3	Block, green
Z = 4	0.45 × 0.32 × 0.20 mm

Data collection

Bruker APEX CCD diffractometer	3394 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.042
Graphite monochromator	θmax = 28.0°, θmin = 1.8°
φ and ω scans	h = −19→18
23966 measured reflections	k = −21→23
4453 independent reflections	l = −17→18

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0635P)^2 + 1.4161P] where P = (Fo^2 + 2Fc^2)/3
4453 reflections	(Δ/σ)max = 0.001
261 parameters	Δρmax = 0.48 e Å^−3
1 restraint	Δρmin = −0.25 e Å^−3

Special details

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
H4N	0.293 (2)	0.4833 (17)	0.041 (2)	0.048 (8)*
H2N	−0.077 (2)	0.6948 (16)	0.111 (2)	0.048 (8)*
Cu1	0.2500	0.7500	0.06676 (3)	0.03171 (13)
N1	0.11849 (13)	0.74057 (10)	0.10902 (14)	0.0352 (4)
N3	0.27403 (13)	0.64615 (10)	0.02440 (14)	0.0342 (4)
C1	0.07694 (16)	0.79298 (12)	0.16863 (16)	0.0368 (5)
C2	0.1142 (2)	0.85029 (14)	0.22291 (17)	0.0449 (6)
H2	0.1773	0.8601	0.2228	0.054*
C3	0.0542 (2)	0.89193 (15)	0.2768 (2)	0.0554 (7)
H3	0.0774	0.9310	0.3127	0.067*
C4	−0.0399 (2)	0.87695 (17)	0.2789 (2)	0.0619 (8)
H4	−0.0782	0.9062	0.3162	0.074*
C5	−0.0778 (2)	0.82015 (17)	0.2275 (2)	0.0562 (7)
H5	−0.1407	0.8098	0.2294	0.067*
C6	−0.01757 (17)	0.77856 (15)	0.17211 (18)	0.0430 (6)
C7	0.04996 (16)	0.69688 (13)	0.07935 (16)	0.0371 (5)
C8	0.05757 (17)	0.62941 (14)	0.01904 (18)	0.0434 (6)
H8A	0.1047	0.6377	−0.0280	0.052*
H8B	−0.0007	0.6213	−0.0129	0.052*
C9	0.08211 (18)	0.55980 (13)	0.07567 (19)	0.0465 (6)
H9A	0.0857	0.5173	0.0338	0.056*
H9B	0.0331	0.5501	0.1203	0.056*
C10	0.17360 (16)	0.56732 (13)	0.12819 (17)	0.0405 (5)
H10A	0.1698	0.6085	0.1721	0.049*
H10B	0.1856	0.5220	0.1633	0.049*
C11	0.25044 (16)	0.58083 (13)	0.06119 (16)	0.0371 (5)
C12	0.36087 (17)	0.55352 (13)	−0.03919 (17)	0.0396 (5)
C13	0.4271 (2)	0.52029 (15)	−0.09541 (19)	0.0516 (7)
H13	0.4376	0.4690	−0.0940	0.062*
C14	0.4766 (2)	0.56670 (17)	−0.1534 (2)	0.0568 (7)
H14	0.5219	0.5465	−0.1918	0.068*
C15	0.4603 (2)	0.64322 (17)	−0.1558 (2)	0.0543 (7)
H15	0.4951	0.6729	−0.1959	0.065*
C16	0.39374 (18)	0.67644 (14)	−0.10034 (18)	0.0465 (6)
H16	0.3825	0.7275	−0.1030	0.056*
C17	0.34427 (16)	0.63005 (13)	−0.04022 (16)	0.0363 (5)
C18	0.1719 (4)	0.1726 (3)	0.0359 (4)	0.1238 (19)
H18A	0.1675	0.2185	0.0705	0.186*
H18B	0.1110	0.1540	0.0232	0.186*
H18C	0.2035	0.1816	−0.0221	0.186*
N2	−0.03139 (15)	0.71824 (13)	0.11500 (16)	0.0444 (5)
N4	0.30001 (15)	0.52477 (12)	0.02574 (16)	0.0423 (5)
N5	0.81550 (16)	0.58786 (18)	0.1762 (2)	0.0654 (7)
O1	0.7826 (3)	0.53217 (18)	0.2119 (3)	0.1170 (11)
O2	0.81605 (17)	0.64741 (15)	0.2217 (2)	0.0854 (7)
O3	0.84823 (19)	0.58743 (19)	0.0982 (2)	0.1039 (10)
O4	0.2211 (2)	0.11977 (14)	0.08836 (19)	0.0816 (7)
H4A	0.216 (4)	0.122 (3)	0.1451 (8)	0.122*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0331 (2)	0.0260 (2)	0.0361 (2)	−0.00241 (15)	0.000	0.000
N1	0.0356 (10)	0.0323 (10)	0.0376 (10)	−0.0013 (8)	0.0028 (8)	0.0005 (8)
N3	0.0372 (10)	0.0273 (9)	0.0380 (10)	−0.0017 (7)	0.0034 (8)	−0.0023 (8)
C1	0.0435 (13)	0.0311 (12)	0.0357 (12)	0.0029 (9)	0.0047 (9)	0.0073 (9)
C2	0.0571 (16)	0.0381 (13)	0.0395 (13)	−0.0006 (11)	0.0073 (11)	0.0030 (11)
C3	0.084 (2)	0.0397 (14)	0.0424 (15)	0.0062 (14)	0.0068 (14)	0.0015 (11)
C4	0.075 (2)	0.0527 (17)	0.0581 (18)	0.0256 (15)	0.0183 (15)	0.0057 (14)
C5	0.0488 (15)	0.0561 (17)	0.0636 (18)	0.0159 (13)	0.0125 (13)	0.0094 (14)
C6	0.0441 (14)	0.0407 (13)	0.0441 (14)	0.0063 (11)	0.0030 (10)	0.0098 (11)
C7	0.0365 (12)	0.0381 (12)	0.0367 (12)	−0.0029 (10)	−0.0020 (9)	0.0079 (10)
C8	0.0415 (13)	0.0463 (14)	0.0425 (14)	−0.0091 (11)	−0.0029 (10)	−0.0071 (11)
C9	0.0459 (14)	0.0346 (13)	0.0589 (16)	−0.0109 (11)	0.0082 (11)	−0.0028 (11)
C10	0.0464 (14)	0.0302 (12)	0.0448 (14)	−0.0018 (10)	0.0081 (10)	0.0029 (10)
C11	0.0404 (12)	0.0317 (11)	0.0391 (12)	−0.0022 (10)	−0.0016 (10)	−0.0015 (9)
C12	0.0442 (13)	0.0341 (12)	0.0407 (13)	−0.0009 (10)	0.0020 (10)	−0.0012 (10)
C13	0.0596 (17)	0.0414 (14)	0.0540 (16)	0.0069 (12)	0.0091 (13)	−0.0075 (12)
C14	0.0592 (17)	0.0622 (18)	0.0491 (16)	0.0052 (14)	0.0167 (13)	−0.0060 (14)
C15	0.0610 (17)	0.0585 (17)	0.0434 (14)	−0.0055 (14)	0.0155 (13)	0.0019 (13)
C16	0.0572 (16)	0.0381 (13)	0.0441 (14)	−0.0047 (11)	0.0067 (12)	0.0026 (11)
C17	0.0391 (12)	0.0349 (12)	0.0348 (12)	−0.0031 (10)	0.0006 (9)	−0.0024 (9)
C18	0.140 (5)	0.074 (3)	0.158 (5)	0.013 (3)	0.034 (4)	0.030 (3)
N2	0.0335 (12)	0.0476 (12)	0.0521 (13)	−0.0011 (10)	−0.0017 (9)	0.0090 (11)
N4	0.0517 (13)	0.0253 (10)	0.0498 (12)	−0.0002 (9)	0.0078 (10)	−0.0003 (9)
N5	0.0395 (13)	0.0756 (19)	0.081 (2)	−0.0106 (13)	−0.0033 (13)	0.0111 (16)
O1	0.133 (3)	0.084 (2)	0.134 (3)	−0.032 (2)	0.020 (2)	0.025 (2)
O2	0.0706 (16)	0.0768 (17)	0.109 (2)	−0.0088 (13)	0.0124 (14)	0.0026 (16)
O3	0.0819 (18)	0.147 (3)	0.0829 (19)	−0.0447 (18)	0.0125 (15)	−0.0126 (18)
O4	0.114 (2)	0.0473 (13)	0.0834 (17)	0.0018 (13)	0.0006 (16)	−0.0110 (13)

Geometric parameters (Å, º)

Cu1—N3	1.9857 (18)	C9—H9B	0.9700
Cu1—N3^i	1.9857 (18)	C10—C11	1.488 (3)
Cu1—N1	2.0049 (19)	C10—H10A	0.9700
Cu1—N1^i	2.0049 (19)	C10—H10B	0.9700
N1—C7	1.333 (3)	C11—N4	1.334 (3)
N1—C1	1.403 (3)	C12—N4	1.380 (3)
N3—C11	1.327 (3)	C12—C13	1.386 (4)
N3—C17	1.404 (3)	C12—C17	1.391 (3)
C1—C6	1.393 (3)	C13—C14	1.375 (4)
C1—C2	1.395 (3)	C13—H13	0.9300
C2—C3	1.380 (4)	C14—C15	1.390 (4)
C2—H2	0.9300	C14—H14	0.9300
C3—C4	1.390 (5)	C15—C16	1.382 (4)
C3—H3	0.9300	C15—H15	0.9300
C4—C5	1.369 (5)	C16—C17	1.394 (3)
C4—H4	0.9300	C16—H16	0.9300
C5—C6	1.393 (4)	C18—O4	1.403 (5)
C5—H5	0.9300	C18—H18A	0.9600
C6—N2	1.369 (4)	C18—H18B	0.9600
C7—N2	1.339 (3)	C18—H18C	0.9600
C7—C8	1.488 (3)	N2—H2N	0.78 (3)
C8—C9	1.528 (4)	N4—H4N	0.78 (3)
C8—H8A	0.9700	N5—O3	1.213 (4)
C8—H8B	0.9700	N5—O1	1.217 (4)
C9—C10	1.529 (4)	N5—O2	1.249 (4)
C9—H9A	0.9700	O4—H4A	0.816 (10)
N3—Cu1—N3^i	144.46 (12)	H9A—C9—H9B	107.8
N3—Cu1—N1	100.35 (7)	C11—C10—C9	110.2 (2)
N3^i—Cu1—N1	90.25 (7)	C11—C10—H10A	109.6
N3—Cu1—N1^i	90.25 (7)	C9—C10—H10A	109.6
N3^i—Cu1—N1^i	100.35 (7)	C11—C10—H10B	109.6
N1—Cu1—N1^i	144.89 (11)	C9—C10—H10B	109.6
C7—N1—C1	105.46 (19)	H10A—C10—H10B	108.1
C7—N1—Cu1	131.33 (16)	N3—C11—N4	111.9 (2)
C1—N1—Cu1	122.29 (15)	N3—C11—C10	126.2 (2)
C11—N3—C17	105.48 (19)	N4—C11—C10	121.7 (2)
C11—N3—Cu1	131.19 (16)	N4—C12—C13	132.3 (2)
C17—N3—Cu1	121.32 (15)	N4—C12—C17	105.3 (2)
C6—C1—C2	119.8 (2)	C13—C12—C17	122.4 (2)
C6—C1—N1	108.6 (2)	C14—C13—C12	116.8 (2)
C2—C1—N1	131.6 (2)	C14—C13—H13	121.6
C3—C2—C1	117.7 (3)	C12—C13—H13	121.6
C3—C2—H2	121.2	C13—C14—C15	121.4 (3)
C1—C2—H2	121.2	C13—C14—H14	119.3
C2—C3—C4	121.7 (3)	C15—C14—H14	119.3
C2—C3—H3	119.2	C16—C15—C14	121.9 (3)
C4—C3—H3	119.2	C16—C15—H15	119.1
C5—C4—C3	121.6 (3)	C14—C15—H15	119.1
C5—C4—H4	119.2	C15—C16—C17	117.1 (2)
C3—C4—H4	119.2	C15—C16—H16	121.4
C4—C5—C6	116.9 (3)	C17—C16—H16	121.4
C4—C5—H5	121.6	C12—C17—C16	120.3 (2)
C6—C5—H5	121.6	C12—C17—N3	108.7 (2)
N2—C6—C5	132.0 (3)	C16—C17—N3	131.0 (2)
N2—C6—C1	105.6 (2)	O4—C18—H18A	109.5
C5—C6—C1	122.4 (3)	O4—C18—H18B	109.5
N1—C7—N2	111.5 (2)	H18A—C18—H18B	109.5
N1—C7—C8	127.3 (2)	O4—C18—H18C	109.5
N2—C7—C8	121.2 (2)	H18A—C18—H18C	109.5
C7—C8—C9	111.8 (2)	H18B—C18—H18C	109.5
C7—C8—H8A	109.3	C7—N2—C6	108.9 (2)
C9—C8—H8A	109.3	C7—N2—H2N	124 (2)
C7—C8—H8B	109.3	C6—N2—H2N	126 (2)
C9—C8—H8B	109.3	C11—N4—C12	108.6 (2)
H8A—C8—H8B	107.9	C11—N4—H4N	123 (2)
C8—C9—C10	112.97 (19)	C12—N4—H4N	128 (2)
C8—C9—H9A	109.0	O3—N5—O1	122.3 (4)
C10—C9—H9A	109.0	O3—N5—O2	118.9 (3)
C8—C9—H9B	109.0	O1—N5—O2	118.9 (3)
C10—C9—H9B	109.0	C18—O4—H4A	117 (4)
N3—Cu1—N1—C7	−30.8 (2)	N2—C7—C8—C9	−93.1 (3)
N3^i—Cu1—N1—C7	115.1 (2)	C7—C8—C9—C10	−59.3 (3)
N1^i—Cu1—N1—C7	−136.3 (2)	C8—C9—C10—C11	−59.8 (3)
N3—Cu1—N1—C1	161.87 (17)	C17—N3—C11—N4	0.3 (3)
N3^i—Cu1—N1—C1	−52.24 (18)	Cu1—N3—C11—N4	−163.27 (17)
N1^i—Cu1—N1—C1	56.35 (16)	C17—N3—C11—C10	−174.9 (2)
N3^i—Cu1—N3—C11	−146.5 (2)	Cu1—N3—C11—C10	21.5 (4)
N1—Cu1—N3—C11	−41.2 (2)	C9—C10—C11—N3	82.5 (3)
N1^i—Cu1—N3—C11	105.1 (2)	C9—C10—C11—N4	−92.3 (3)
N3^i—Cu1—N3—C17	52.10 (16)	N4—C12—C13—C14	180.0 (3)
N1—Cu1—N3—C17	157.37 (17)	C17—C12—C13—C14	−0.1 (4)
N1^i—Cu1—N3—C17	−56.28 (18)	C12—C13—C14—C15	−0.5 (5)
C7—N1—C1—C6	−0.3 (2)	C13—C14—C15—C16	0.0 (5)
Cu1—N1—C1—C6	169.84 (15)	C14—C15—C16—C17	1.1 (4)
C7—N1—C1—C2	176.9 (2)	N4—C12—C17—C16	−178.9 (2)
Cu1—N1—C1—C2	−13.0 (3)	C13—C12—C17—C16	1.2 (4)
C6—C1—C2—C3	−1.5 (3)	N4—C12—C17—N3	0.3 (3)
N1—C1—C2—C3	−178.5 (2)	C13—C12—C17—N3	−179.7 (2)
C1—C2—C3—C4	1.2 (4)	C15—C16—C17—C12	−1.6 (4)
C2—C3—C4—C5	−0.1 (4)	C15—C16—C17—N3	179.4 (3)
C3—C4—C5—C6	−0.7 (4)	C11—N3—C17—C12	−0.4 (3)
C4—C5—C6—N2	178.3 (3)	Cu1—N3—C17—C12	165.21 (16)
C4—C5—C6—C1	0.3 (4)	C11—N3—C17—C16	178.7 (3)
C2—C1—C6—N2	−177.6 (2)	Cu1—N3—C17—C16	−15.7 (4)
N1—C1—C6—N2	0.0 (3)	N1—C7—N2—C6	−0.6 (3)
C2—C1—C6—C5	0.8 (4)	C8—C7—N2—C6	176.1 (2)
N1—C1—C6—C5	178.4 (2)	C5—C6—N2—C7	−177.8 (3)
C1—N1—C7—N2	0.6 (3)	C1—C6—N2—C7	0.4 (3)
Cu1—N1—C7—N2	−168.34 (16)	N3—C11—N4—C12	−0.1 (3)
C1—N1—C7—C8	−175.9 (2)	C10—C11—N4—C12	175.4 (2)
Cu1—N1—C7—C8	15.1 (4)	C13—C12—N4—C11	179.8 (3)
N1—C7—C8—C9	83.1 (3)	C17—C12—N4—C11	−0.1 (3)

Symmetry code: (i) −x+1/2, −y+3/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4A···O2^ii	0.82 (1)	2.01 (2)	2.814 (4)	167 (5)
O4—H4A···O1^ii	0.82 (1)	2.60 (4)	3.261 (5)	139 (5)
N2—H2N···O3^iii	0.78 (3)	2.21 (3)	2.929 (4)	152 (3)
N2—H2N···O2^iii	0.78 (3)	2.37 (3)	2.969 (3)	134 (3)

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