Crystal structures of di-μ-chlorido-bis-({(E)-5-(ethyl-amino)-4-methyl-2-[(pyridin-2-yl)diazen-yl]phen-o-lato}copper(II)) and chlorido-bis-(1,10-phen-anthroline)copper(II) chloride tetra-hydrate

Abstract

The dark-red title complex crystallized from an equimolar methanol solution of (E)-5-(ethyl-amino)-4-methyl-2-[(pyridin-2-yl)diazen-yl]phenol and CuCl₂(phen) (phen = 1,10-phenanthroline) as a centrosymmetric dimer, [CuCl(C₁₄H₁₅N₄O)]₂. The Cu atoms are bridged by two Cl ligands and have a slightly distorted square-pyramidal coordination, where two N atoms from the azo and the pyridine moieties, a phenolic O and a Cl atom comprise the base and the other Cl occupies the apex position. The apical Cu-Cl bond, 2.6192 (4) Å, is longer than the basal one, 2.2985 (3) Å, due to Jahn-Teller distortion. The dimers are associated via weak inter-molecular hydrogen bonds and π-π stacking inter-actions between phenyl and pyridine rings. A monomeric by-product of the same reaction, [CuCl(phen)₂]Cl·4H₂O, has a trigonal-bipyramidal coordination of Cu with equatorial Cl ligand, and extensive outer-sphere disorder. In the structure of 4, the packing of cations leaves continuous channels containing disordered Cl^- anions and solvent mol-ecules. The identity of the solvent (water or a water/methanol mixture) was not certain. The disordered anion/solvent regions comprise 28% of the unit-cell volume. The disorder was approximated by five partly occupied positions of the Cl^- anion and ten positions of O atoms with a total occupancy of 3, giving a total of 48 electrons per asymmetric unit, in agreement with the integral electron density of 47.8 electrons in the disordered region, as was estimated using the BYPASS-type solvent-masking program [van der Sluis & Spek (1990). Acta Cryst. A46, 194-201].

Keywords: X-ray crystallography; chlorido bridge; copper(II) complex; supra­molecular features.

Figure 1

(a) The covalent modification of the LTQ cofactor of LOXL2 by 2HP. After the tautomerization of the hydrazone to the azo form, LTQ-2HP ligates to the active site Cu²⁺. The 2HP-modified LTQ (LTQ-2HP) containing the peptide was detected by mass spectrometry (Meier, Go, et al., 2022 ▸). Based on the close resemblances of UV–vis and resonance Raman spectra of 2HP-inhibited LOXL2 and the model compound 2, we hypothesize that LTQ-2HP serves as a tridentate ligand to the active site Cu^II in LOXL2 (Meier, Moon et al., 2022 ▸). The +2 charge of Cu^II is expected to be canceled out by the 4-oxoanion of LTQ-2HP and a nearby acidic residue or a water mol­ecule (Meier, Kuczera et al., 2022 ▸). (b) During the recrystallization of the dark red solids (2) isolated from an equimolar mixture of the LTQ-2HP model compound (1) and CuCl₂(phen) in anhydrous methanol, we first isolated dark-red crystals (3), then also isolated (4) from the mother liquor that was left for a week at room temperature.

Figure 2

Mol­ecular structure of 3 in different aspects (a, c), showing the coordination polyhedra of Cu (b) and intra­molecular hydrogen bonds (a). Atomic displacement ellipsoids are drawn at the 50% probability level. Primed atoms are generated by inversion, symmetry operation 1 − x, 1 − y, −z.

Figure 3

The cation and ordered water mol­ecule in the structure of 4. Atomic displacement ellipsoids are drawn at the 50% probability level.

Figure 4

Crystal packing of 3 (a), showing inter­molecular hydrogen bonds (b) and phen­yl–phenyl π–π stacking inter­actions (c) (α is the angle between the ring normal and centroid–centroid vector, d is the displacement between the rings).

Figure 5

UV–vis spectra of 2HP-inhibited LOXL2 (LOXL2–2HP) (in black) (Meier, Moon et al., 2022 ▸), crystalline 3 isolated from a 1:1 mixture of 2 with CuCl₂(phen) (in blue), and crystalline 3 isolated from a 1:1 mixture of 2 with CuCl₂ (in red). All spectra were recorded in 50 mM HEPBS buffer (pH 8.0).