Bis­[2,6-bis(1H-benzimidazol-2-yl-κN³)pyridinato-κN]zinc(II)

The structure of [Zn(C₁₉H₁₂N₅)₂], which is monomeric and consists of neutral Zn(bbip-H)₂ entities [bbip-H is the anionic form of bis­(benz­imidazolyl)­pyridine, formed by the loss of one H atom], has been solved from a racemic twin. The Zn atom lies at a site with imposed 222 symmetry and the bbip-H ligand has imposed twofold symmetry. The imidazolyl H atom is disordered over two symmetry-related positions, thus raising the molecular symmetry as required by the space group. The angle between the planes of the two coordinated bbip-H ligands is 84.6 (3)°, so defining a distorted octahedral environment around the metal atom.

S1. Comment

The fact that metal complexes with benzimidazol derivatives can mimic the behavior of metal ion sites in biological systems, both in structure and in reactivity (Sundberg et al.,1974; Hendriks et al., 1982; Alagna et al., 1984; Rijn et al., 1987), has made the study of these complexes increasingly attractive. One of these derivatives with better coordination properties is 2,6-bis(benzimidazol-2-yl)pyridine, which is a potentially active tridentate ligand through its two benzimidazol and one pyridine N atoms. In most of the metal complexes reported so far [15 entries in the November 2002 release of the Cambridge Structural Database (CSD; Allen, 2003), the group behaves as a neutral ligand (hereafter bbip), but in a few complexes, the group behaves as an anion (hereafter bbip-H) [e.g. Mn(bbip-H)₂ (Rajan et al., 1996), (II), Cd(bbip-H)₂ (Wang et al., 1994a), (III), and Lu(bbip-H)(CH₄O)₂(NO₃)₂ (Wang et al., 1994b), (IV)]. We present here a new Zn complex, Zn(bbip-H)₂, (I), in which the ligand displays this uncommon anionic behavior.

The building block of the structure is a Zn(bbip-H)₂ monomer that, because of the space group symmetry, makes up a quarter of a molecule of the asymmetric unit or two molecules in the unit cell?. The Zn cation lies at the origin, at the intersection of three twofold axes. The tridentate N,N',N''-bbip-H unit is bisected by one of the diads, thus rendering only half of the ligand independent, the rest being generated by symmetry (Fig. 1).

To make this situation compatible with the existence of a single nitrogen-bound H atom, there are only two possible options, viz. either the H atom is ordered and occupies a special position on the two fold axis, midway betwen two symmetry-related N atoms (which then would share the H atom in a symmetric N···H···N interaction), or the H atom is bonded to only one of the two otherwise equivalent N atoms, in a disordered fashion. In this case, the average image would be that of a double half H atom at both sides of the diad. Both models were analyzed using least-squares refinement. The first model, with an H atom on the twofold axis, 1.37 Å from each N atom, resulted in a large displacement parameter for the H atom? (ca 0.15 Å2). The second option converged with a reasonable H-atom position, ca 0.78 Å from N3, with a normal displacement parameter, so the disordered model was used in the subsequent refinement. This disorder was not the only anomaly present in the structure, since the model also had to be refined as a racemic twin [final Flack parameter = 0.48 (3)], and the effects of this special kind of disorder are manifested in unusually large displacement parameters for atoms C9 and C10.

In the bbip-H unit, the most significant departure from planarity is the dihedral angle of 5.5 (1)° between the lateral imidazolyl planes [mean deviation = 0.015 (3) Å] and the central pyridine [mean deviation = 0.001 (1) Å]. Hydrogen-bonding interactions, in turn, push the two coordinated bbip-H ligands into each other, the dihedral angle between their planes being 84.6 (3)° and that between neighboring imidazolyl groups being 69.7 (1)°. The strain imposed by coordination is apparent in the distorted geometry of the Zn octahedron, in which the angles that would ideally be right angles are actually in the range 75.91 (7)–104.09 (7)°, and opposite N atoms subtend angles of 151.83 (14) and 180.00 (17)° to the cation. Evidence of this strain can also be found in the bbip-H molecular geometry, since the N···N distance between the outermost coordinated N atoms [4.231 (6) Å] is shorter than the equivalent distance in non-coordinated bbip. In the three unstrained moieties reported by Freire et al. (2003), this separation is larger [4.550 (3)–4.580 (3) Å], irrespective of the presence or absence of strong hydrogen-bonding interactions. However, since the free ligand crystallizes with its two protonated N atoms pointing inwards, in a cis mode, any eventual N—N···H—N repulsion might tend to `open' the molecular skeleton, thus impairing this comparison. The non-interacting H···H distances found in free bbip (> 3 Å), however, suggest that the above comparison is reasonable.

The charged character of bbip-H does not seem to specifically favor coordination to the positive cation, as is reported to happen, for example, in (III). In the present case, the Zn—N coordination distances [Zn—N_pyridine = 2.090 (3) Å x 2 and Zn—N_benzimidazol = 2.181 (3) Å x 4] are almost identical to those found in similarly coordinated ZnN₆ cores with tridentate neutral ligands [the average values for eight ligands in four structures found in the CSD are <Zn—N_central> = 2.076 (11) Å and <Zn—N_lateral> = 2.187 (20) Å], sharing the typical marked difference in bonding distances for the two types of coordinated N atoms.

The Zn(bbip-H)₂ molecular entity is neutral, as the ligand behaves as an anion, thus balancing the charge on the cation. This situation has already been observed in the homologous Mn, (II), and Cd, (III), bbip-H complexes, although there are some structural differences; namely, in (II) and (III), there in no disorder and the hydrogen interactions are distributed evenly in space, defining a homogeneous three-dimensional hydrogen-bonded structure. The effect of hydrogen bonding in (II) and (II) is instead restricted to linking monomers in two directions perpendicular to [001], in order to form broad two-dimensional structures, parallel to the (001) plane. Fig. 2 shows a packing view of (I), in which these `planes' can be seen in projection as broad horizontal `strips', at heights z=0, 0.5 and 1. The resulting two-dimensional supramolecular arrangements are not directly connected and interact with each other through much weaker forces. Inspection of Fig. 2 also reveals that the coordination polyhedra look like `crosses' when projected along [110] and [−110], and the parallel stacking along the view directions determines well defined channels, ca 4 Å in diameter, as estimated by a simple `point atom' approximation.

The coordination geometry and the packing interactions result in the aromatic groups being too far from each other to allow any kind of π interaction between them.

S2. Experimental

The title compound was obtained by diffusion of a solution of bbip in dimethylformamide into a solution of zinc acetate dihydrate and potassium peroxidisulfate in a (1:3) mixture of methanol–water, with all reagents in a 0.025 M concentration and used as purchased. After one week, two different types of crystals appeared, namely a majority of highly unstable colorless needles, presumably of a complex containing the peroxidisulfate anion, and a few tiny colorless crystals of the title compound, in the form of square bipyramids. The former were not of adequate quality? for X-ray analysis, while the latter were suitable for data collection.

S3. Refinement

H atoms attached to C atoms were placed at idealized positions and allowed to ride on the parent atoms. The H atom on the protonated N atom in bbip-H was found in a difference Fourier map, very close a twofold axis, and refined using an isotropic displacement factor with a split disordered model (50% occupancy at 0.78 Å to each of the two non-coordinated benzimidazol N atoms). The final structural model was refined as a racemic twin, resulting in almost equal populations [48 (3)/52 (3)%].

Computing details

Data collection: SMART-NT (Bruker, 2001); cell refinement: SMART-NT (Bruker, 2001); data reduction: SAINT-NT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL-PC (Sheldrick,1994); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures

	Fig. 1. : An XP plot (Sheldrick, 1994) of the Zn coordination polyhedron, with the crystallographically independent part of the molecule represented by highlighted displacement ellipsoids (40% probability level).
	Fig. 2. : A view of the crystal packing, showing how the (disordered) hydrogen bonds build two-diemnsional supramolecular arrays parallel to (001). Channels nearly parallel to the projection direction are clearly visible. Benzimidazol H atoms have been omitted for clarity.

bis(2,6-bis(Benzimidazol-2-yl)pyridine)-zinc(ii)

Crystal data

[Zn(C19H12N5)2]	Dx = 1.404 Mg m^−3
Mr = 686.04	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P42212	Cell parameters from 84 reflections
Hall symbol: P 4n 2n	θ = 3.7–24.5°
a = 9.7411 (8) Å	µ = 0.80 mm^−1
c = 17.108 (2) Å	T = 293 K
V = 1623.3 (3) Å^3	Square bipyramid, colorless
Z = 2	0.22 × 0.12 × 0.12 mm
F(000) = 704

Data collection

Bruker CCD area-detector diffractometer	1866 independent reflections
Radiation source: fine-focus sealed tube	778 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.071
ϕ and ω scans	θmax = 28.0°, θmin = 2.4°
Absorption correction: multi-scan SADABS (Sheldrick, 1996) in SAINT-NT (Bruker, 2000)	h = −12→11
Tmin = 0.86, Tmax = 0.89	k = −6→12
9552 measured reflections	l = −21→21

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.078	w = 1/[σ^2(Fo^2) + (0.034P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.86	(Δ/σ)max = 0.002
1866 reflections	Δρmax = 0.24 e Å^−3
118 parameters	Δρmin = −0.23 e Å^−3
0 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.48 (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.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
Zn1	0.0000	0.0000	0.0000	0.0672 (3)
N1	0.1533 (3)	0.0763 (3)	0.08216 (16)	0.0550 (8)
N2	0.1517 (2)	−0.1517 (2)	0.0000	0.0503 (9)
N3	0.3659 (3)	0.0460 (3)	0.13001 (19)	0.0604 (10)
H3N	0.437 (3)	0.013 (7)	0.139 (2)	0.013 (15)*	0.50
C1	0.1887 (4)	0.1916 (4)	0.12441 (17)	0.0558 (8)
C2	0.1164 (5)	0.3131 (4)	0.1363 (2)	0.0800 (14)
H2	0.0292	0.3272	0.1158	0.096*
C3	0.1827 (5)	0.4114 (5)	0.1805 (3)	0.0952 (15)
H3	0.1386	0.4947	0.1892	0.114*
C4	0.3113 (5)	0.3919 (5)	0.2123 (3)	0.0867 (16)
H4	0.3499	0.4611	0.2426	0.104*
C5	0.3837 (5)	0.2728 (4)	0.2003 (2)	0.0738 (14)
H5	0.4704	0.2599	0.2219	0.089*
C6	0.3216 (4)	0.1719 (4)	0.1545 (2)	0.0551 (10)
C7	0.2638 (3)	−0.0054 (4)	0.08668 (18)	0.0531 (8)
C8	0.2633 (4)	−0.1349 (4)	0.0433 (2)	0.0605 (10)
C9	0.3651 (4)	−0.2332 (4)	0.0448 (3)	0.1220 (19)
H9	0.4430	−0.2213	0.0755	0.146*
C10	0.3488 (4)	−0.3488 (4)	0.0000	0.175 (4)
H10	0.4163	−0.4163	0.0000	0.210*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Zn1	0.0667 (4)	0.0667 (4)	0.0683 (5)	0.0350 (5)	0.000	0.000
N1	0.0477 (17)	0.0536 (18)	0.0637 (19)	0.0175 (16)	0.0029 (15)	−0.0029 (15)
N2	0.0411 (13)	0.0411 (13)	0.069 (2)	0.0084 (19)	−0.002 (2)	−0.002 (2)
N3	0.045 (2)	0.058 (3)	0.078 (2)	0.0127 (19)	−0.007 (2)	0.0006 (19)
C1	0.060 (3)	0.051 (3)	0.057 (2)	0.0186 (18)	0.004 (3)	0.000 (3)
C2	0.095 (4)	0.065 (3)	0.080 (3)	0.018 (3)	0.000 (3)	−0.025 (3)
C3	0.111 (4)	0.078 (4)	0.097 (4)	0.043 (3)	−0.007 (3)	−0.019 (3)
C4	0.108 (4)	0.067 (3)	0.085 (3)	0.001 (3)	0.000 (3)	−0.023 (3)
C5	0.063 (3)	0.070 (3)	0.089 (3)	0.004 (3)	−0.006 (3)	−0.009 (3)
C6	0.059 (3)	0.046 (3)	0.060 (3)	0.004 (2)	0.007 (2)	−0.009 (2)
C7	0.045 (2)	0.051 (2)	0.063 (2)	0.009 (2)	−0.0021 (19)	−0.003 (3)
C8	0.051 (2)	0.047 (2)	0.083 (3)	0.011 (2)	−0.004 (2)	−0.004 (2)
C9	0.071 (3)	0.084 (3)	0.210 (5)	0.043 (3)	−0.068 (3)	−0.062 (3)
C10	0.095 (3)	0.095 (3)	0.334 (12)	0.060 (4)	−0.119 (7)	−0.119 (7)

Geometric parameters (Å, º)

Zn1—N2	2.090 (3)	C2—C3	1.380 (5)
Zn1—N2^i	2.090 (3)	C2—H2	0.9300
Zn1—N1^ii	2.181 (3)	C3—C4	1.379 (6)
Zn1—N1	2.181 (3)	C3—H3	0.9300
Zn1—N1^i	2.181 (3)	C4—C5	1.373 (4)
Zn1—N1^iii	2.181 (3)	C4—H4	0.9300
N1—C7	1.340 (4)	C5—C6	1.396 (5)
N1—C1	1.380 (4)	C5—H5	0.9300
N2—C8^ii	1.325 (3)	C7—C8	1.464 (5)
N2—C8	1.325 (3)	C8—C9	1.378 (4)
N3—C7	1.338 (4)	C9—C10	1.372 (4)
N3—C6	1.366 (4)	C9—H9	0.9300
N3—H3N	0.78 (4)	C10—C9^ii	1.372 (4)
C1—C2	1.392 (5)	C10—H10	0.9300
C1—C6	1.406 (5)
N2—Zn1—N2^i	180.00 (17)	C3—C2—C1	115.7 (4)
N2—Zn1—N1^ii	75.91 (7)	C3—C2—H2	122.2
N2^i—Zn1—N1^ii	104.09 (7)	C1—C2—H2	122.2
N2—Zn1—N1	75.91 (7)	C4—C3—C2	123.0 (5)
N2^i—Zn1—N1	104.09 (7)	C4—C3—H3	118.5
N1^ii—Zn1—N1	151.83 (14)	C2—C3—H3	118.5
N2—Zn1—N1^i	104.09 (7)	C5—C4—C3	121.6 (5)
N2^i—Zn1—N1^i	75.91 (7)	C5—C4—H4	119.2
N1^ii—Zn1—N1^i	87.07 (13)	C3—C4—H4	119.2
N1—Zn1—N1^i	99.76 (14)	C4—C5—C6	117.1 (4)
N2—Zn1—N1^iii	104.09 (7)	C4—C5—H5	121.4
N2^i—Zn1—N1^iii	75.91 (7)	C6—C5—H5	121.4
N1^ii—Zn1—N1^iii	99.76 (14)	N3—C6—C5	131.8 (4)
N1—Zn1—N1^iii	87.07 (13)	N3—C6—C1	107.6 (4)
N1^i—Zn1—N1^iii	151.83 (14)	C5—C6—C1	120.6 (4)
C7—N1—C1	104.6 (3)	N3—C7—N1	114.1 (3)
C7—N1—Zn1	112.6 (2)	N3—C7—C8	127.3 (3)
C1—N1—Zn1	141.8 (3)	N1—C7—C8	118.7 (3)
C8^ii—N2—C8	120.9 (4)	N2—C8—C9	121.0 (4)
C8^ii—N2—Zn1	119.5 (2)	N2—C8—C7	113.1 (3)
C8—N2—Zn1	119.5 (2)	C9—C8—C7	125.9 (3)
C7—N3—C6	105.7 (3)	C10—C9—C8	118.4 (4)
C7—N3—H3N	128 (5)	C10—C9—H9	120.8
C6—N3—H3N	126 (5)	C8—C9—H9	120.8
N1—C1—C2	130.0 (4)	C9^ii—C10—C9	120.2 (6)
N1—C1—C6	108.1 (4)	C9^ii—C10—H10	119.9
C2—C1—C6	121.9 (4)	C9—C10—H10	119.9

Symmetry codes: (i) −x, −y, z; (ii) −y, −x, −z; (iii) y, x, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N3^iv	0.78 (4)	2.01 (3)	2.761 (6)	162 (5)

Symmetry code: (iv) −x+1, −y, z.