[1-(Anthracen-9-ylmeth­yl)-1,4,7,10-tetra­aza­cyclododeca­ne]chlorido­zinc(II) nitrate

Yoshimi Ichimaru; Kirara Sugiura; Koichi Kato; Yuki Kondo; Masaaki Kurihara; Wanchun Jin; Masanori Imai; Hiromasa Kurosaki

doi:10.1107/S2414314624006655

. 2024 Jul 12;9(Pt 7):x240665. doi: 10.1107/S2414314624006655

[1-(Anthracen-9-ylmethyl)-1,4,7,10-tetraazacyclododecane]chloridozinc(II) nitrate

Yoshimi Ichimaru ^a, Kirara Sugiura ^b, Koichi Kato ^a, Yuki Kondo ^b, Masaaki Kurihara ^a, Wanchun Jin ^b, Masanori Imai ^b, Hiromasa Kurosaki ^b,^*

Editor: M Weil^c

PMCID: PMC11299653 PMID: 39108938

The Zn^II atom in the complex cation of the title salt has a square-pyramidal coordination environment defined by four nitrogen atoms from cyclen (1,4,7,10-tetraazacyclododecane) in the basal plane and one chlorido ligand in the apical position.

Keywords: crystal structure, cyclen, [12]aneN₄, anthracene, T-shaped π interactions

Abstract

In the title salt, [ZnCl(C₂₃H₃₀N₄)]NO₃, the central Zn^II atom of the complex cation is coordinated in a square-pyramidal arrangement by four nitrogen atoms from cyclen (1,4,7,10-tetraazacyclododecane) in the basal plane and one chlorido ligand in the apical position. The anthracene group attached to cyclen contributes to the crystal packing through intermolecular T-shaped π interactions. Additionally, the nitrate anion participates in intermolecular N—H⋯O hydrogen bonds with cyclen.

Structure description

Complexes of 1,4,7,10-tetraazacyclododecane (cyclen or [12]aneN₄) derivatives with Zn^II have been used as biological probes to elucidate the intrinsic roles of Zn^II in enzyme models such as phosphatase, alcohol dehydrogenase, and β-lactamase (Koike & Kimura, 1991 ▸; Koike et al., 1994 ▸; Kimura et al., 1992 ▸). Cyclen conjugated with the anthracenyl methyl group, 1-(anthracen-9-ylmethyl)-1,4,7,10-tetraazacyclododecane, has been developed as a fluorescent chemosensor for detecting pH and transition-metal cations in aqueous solution (Akkaya et al., 1990 ▸; Huston et al., 1990 ▸). In this context, we present the crystal structure of the title salt, [ZnCl(C₂₃H₃₀N₄)]NO₃.

The crystal structure of the title compound comprises a [Zn(C₂₃H₃₀N₄)Cl]⁺ complex cation and a nitrate anion (Fig. 1 ▸). The coordination environment around the Zn^II atom is slightly distorted square-pyramidal, with the coordination geometry index (Addison et al., 1984 ▸), τ = (β − α) / 60° = 0.08, where α [132.23 (9)°] and β [136.98 (8)°] are the second-largest and largest angles around the central Zn^II atom, respectively. A τ value of 0 corresponds to an ideal square pyramid, while a value of 1 corresponds to an ideal trigonal bipyramid. The four nitrogen atoms N1, N2, N3, and N4 of cyclen form the basal plane, with the chlorido ligand occupying the apical position. The mean Zn1—N bond length of 2.16 Å (Fig. 2 ▸) is comparable to that (2.13 Å) observed in the crystal structure of the salt Zn(C₂₃H₃₀N₄)]⁺(ClO₄)²⁻ (Ichimaru et al., 2021 ▸). The Zn^II atom is displaced by 0.8306 (12) Å above the mean basal plane toward the apical chlorido ligand. The Zn—Cl bond length of 2.2464 (7) Å is comparable to that found in other Zn^II–polyamine complexes with chlorido ligands, such as chlorido(1,4,7,11-tetraazacyclotetradecane-N,N′,N′′,N′′′)zinc(II) perchlorate [2.2734 (8) Å; Lu et al., 1997 ▸] or bis[μ-chlorido-(1,4,8,11-tetracyclotetradecane)zinc(II)] tetrachloridozincate(II) hemihydrate [2.288 (5) Å; Alcock et al., 1992 ▸]. The presence of Cl⁻ as a ligand can be deduced from the synthesis conditions (see Synthesis and crystallization). The bromine salt of the ligand was freed by an anion-exchange resin. In this process, hydrochloric acid was employed to regenerate the resin to its chloride anion form, which is the source of Cl⁻ binding to the Zn^II atom.

The molecular structures of the complex cation and the anion in the title salt with displacement ellipsoids drawn at the 50% probability level. C-bound H atoms are omitted for clarity; the hydrogen bond is represented as a red dotted line.

The coordination polyhedron around Zn1, with displacement ellipsoids drawn at the 50% probability level. Bond angles are depicted in red, whereas bond lengths are shown in black.

The anthracene group exhibits a slight deviation from planarity, with fold angles of 4.69 (10)° between the A (C2–C7) and B (C1, C2, C7, C8, C9, C14) rings and 2.78 (11)° between the B and C (C9–C14) rings. The torsion angle defined by Zn1—N1—C15—C1 is 170.33 (18)°, positioning the anthracene group away from the macrocyclic ring, thereby preventing repulsive interactions with the Cl atom. In the crystal, nitrate O1 forms intermolecular hydrogen bonds with H2 of the Zn^II complex and H3 of a neighboring molecule. The hydrogen-bond distances O1⋯H2 and O1ⁱ⋯H3 are 1.985 and 2.16 Å (Table 1 ▸). These interactions contribute to the formation of a spiral structure extending parallel to the b axis direction of the crystal. Additionally, intermolecular T-shaped π interactions (Jin et al., 2022 ▸) occur between the anthracene ring and a neighboring anthracene ring [symmetry code: (ii): −x, Inline graphic + y, − z] (Fig. 3 ▸). The distance between H8 and the centroid (Cg) of the middle ring of the neighboring anthracene ring is 2.96 Å, and the angle C8—H8⋯Cg is 152°.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O1	1.00	1.98	2.983 (3)	175
N3—H3⋯O1ⁱ	1.00	2.16	3.025 (3)	144

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Symmetry code: (i) Inline graphic .

A schematic drawing of the T-shaped π–π interactions, with displacement ellipsoids drawn at the 50% probability level. Methylene H atoms of cyclen rings and nitrate ions were omitted for clarity; T-shaped π–π interactions are depicted as green dotted lines.

Synthesis and crystallization

Under a nitrogen atmosphere, 9-chloromethylanthracene (2.40 g, 10.6 mmol) and 1,4,7-tris(tert-butyloxycarbonyl)-1,4,7,10-tetraazacyclododecane (3Boc-cyclen) (5.0 g, 10.6 mmol) (Kimura et al., 1997 ▸) were dissolved in a mixture of acetonitrile (130 ml) and DMF (40 ml) and stirred at 373 K for 18 h in the presence of Na₂CO₃ (2.20 g, 12.1 mmol). After the reaction, CH₂Cl₂ (150 ml) was added to the reaction solution and extracted, the organic layer was washed with water (200 ml × 3) and dried with anhydrous Na₂SO₄, and the organic solvent was removed in vacuo to obtain the crude product. The residue was purified by silica gel column chromatography (3% MeOH–CH₂Cl₂) to obtain N-(9-anthracenylmethyl)-N′,N′′,N′′′-tris(tert-butyloxycarbonyl)-1,4,7,10-tetraazacyclododecane, N-Ant-(3Boc-cyclen), as a yellow solid (3.27 g, 47%). To an EtOH solution (30 ml) of N-Ant-(3Boc-cyclen) (1.00 g, 1.5 mmol), aqueous HBr (47%_wt, 6 ml) was added and stirred at 273 K overnight. The resulting mixture was concentrated in vacuo below 308 K. The obtained residue was dissolved in water (2 ml) and washed with Et₂O (10 ml × 3). Then, the aqueous layer was evaporated to dryness. The residue was neutralized by anion-exchange resin (Amberlite IRA-400, OH⁻ form), and the eluant was evaporated to obtain the desired ligand, N-Ant-cyclen, as a yellow amorphous solid (287 mg, 53%).

The title complex was prepared by adding a MeOH solution (1 ml) of Zn(NO₃)₂·6H₂O (235 mg, 0.8 mmol) to a MeOH solution (5 ml) of N-Ant-cyclen (287 mg, 0.8 mmol). The mixture was heated, with stirring, at 323 K for 2 h and then concentrated. After the resulting residue was dissolved in a MeOH–water mixture (v/v = 1/1; 2 ml each) and filtrated, the filtrate was allowed to stand for 10 days at room temperature to obtain the title salt (286 mg, 84%).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸.

Table 2. Experimental details.

Crystal data
Chemical formula	[ZnCl(C₂₃H₃₀N₄)]NO₃
M _r	525.34
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	93
a, b, c (Å)	15.9086 (1), 7.8088 (1), 19.5342 (2)
β (°)	106.157 (1)
V (Å³)	2330.83 (4)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	2.81
Crystal size (mm)	0.35 × 0.25 × 0.12

Data collection
Diffractometer	Rigaku XtaLAB Synergy-i
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2022 ▸)
T_min, T_max	0.619, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	21217, 4271, 4097
R _int	0.027
(sin θ/λ)_max (Å⁻¹)	0.603

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.110, 1.05
No. of reflections	4271
No. of parameters	298
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.65, −0.68

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Computer programs: CrysAlis PRO (Rigaku OD, 2022 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸), OLEX2 (Dolomanov et al., 2009 ▸) and publCIF (Westrip, 2010 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314624006655/wm4217sup1.cif

x-09-x240665-sup1.cif^{(663.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314624006655/wm4217Isup2.hkl

x-09-x240665-Isup2.hkl^{(340.4KB, hkl)}

CCDC reference: 2368358

Additional supporting information: crystallographic information; 3D view; checkCIF report

full crystallographic data