Chlorido­[5,10,15,20-tetra­kis­(quinoline-7-carboxamido)­porphinato]iron(III)

Jun Yang; Cuijuan Zhang; Jiaxiang Chu

doi:10.1107/S2414314624004966

. 2024 Jun 4;9(Pt 6):x240496. doi: 10.1107/S2414314624004966

Chlorido[5,10,15,20-tetrakis(quinoline-7-carboxamido)porphinato]iron(III)

Jun Yang ^a, Cuijuan Zhang ^a,^*, Jiaxiang Chu ^a,^*

Editor: W T A Harrison^b

PMCID: PMC11223685 PMID: 38974845

The porphyrin macrocycle shows a characteristic ruffled-shape distortion. The central Fe^III cation (site symmetry 2) is coordinated in a fivefold manner, with four pyrrole N atoms of the porphyrin core in the basal sites and one Cl atom (site symmetry 2) in the apical position.

Keywords: crystal structure, iron, porphyrin derivative, hydrogen bonds

Abstract

The title compound, [Fe(C₈₄H₅₂N₁₂O₄)Cl], crystallizes in space group C2/c. The central Fe^III cation (site symmetry 2) is coordinated in a fivefold manner, with four pyrrole N atoms of the porphyrin core in the basal sites and one Cl atom (site symmetry 2) in the apical position, which completes a slightly distorted square-pyramidal environment. The porphyrin macrocycle shows a characteristic ruffled-shape distortion and the iron atom is displaced out of the porphyrin plane by 0.42 Å with the average Fe—N distance being 2.054 (4) Å; the Fe—Cl bond length is 2.2042 (7) Å. Intermolecular C—H⋯N and C—H⋯O hydrogen bonds occur in the crystal structure.

Structure description

The relationship between the structural variations of iron porphyrins and the functional diversity of hemoproteins has been investigated extensively in the literature (Adam et al., 2018 ▸). As an exemplar porphyrin model, the molecular structure of the ‘picket-fence’ porphyrin, 5,10,15,20-tetrakis(o-pivalamidophenyl)porphyrin (referred to as TpivPP) has been thoroughly investigated. The Collman group first reported the crystal structure of a picket-fence metalloporphyrin, [Fe(TpivPP)(1-MeIm)(O₂)] (1-MeIm = 1-methylimidazole; Collman et al., 1975 ▸). Subsequently, several analogues of picket-fence compounds have been synthesized. The Gunter group devised a model compound, 5,10,15,20-tetrakis(o-nicotinamidophenyl)porphyrin, modeled after the classical picket-fence porphyrin, with the substitution of the tert-butyl group at the terminus by a pyridine group (Gunter et al., 1980 ▸). Similarly, Yao and co-workers developed 5,10,15,20-tetrakis(5-imidazolecarboxylaminophenyl)porphyrin by substituting the tert-butyl group at the terminus with an imidazole group (Yao et al., 2020 ▸). In this study, we replaced the terminal tert-butyl group with a 7-quinoline group, and determined the crystal structure of the title compound [Fe(C₈₄H₅₂N₁₂O₄)Cl].

The asymmetric unit contains one Fe atom and one Cl atom (both site symmetry 2) and half of the porphyrin ligand, which is completed by crystallographic twofold symmetry. There are no solvent molecules present in the crystal. As depicted in Fig. 1 ▸, the new crystal demonstrates a five-coordinate structure of the metal atom with a significant out-of-plane displacement. The axial chloride ligand is positioned within the molecular cavity on the hindered porphyrin side. Further structural details are presented in supplementary Fig. 1 ▸, including the specific displacements of each porphyrin core atom from the 24-atom mean plane. Additionally, averaged values of the chemically unique bond lengths (Å) and angles (°) are provided. Notably, the porphyrin macrocycle exhibits a characteristic ruffled-shaped distortion, with the Fe^III atom displaced out of the porphyrin plane by 0.42 Å, and an average Fe—N_p distance of 2.054 (4) Å (N_p represents a porphyrin N atom). The Fe—Cl bond length is 2.2042 (7) Å (Table 1 ▸).

The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. Hydrogen atoms have been omitted for clarity.

Table 1. Selected geometric parameters (Å, °).

Fe1—Cl1	2.2042 (7)	Fe1—N2	2.0581 (13)
Fe1—N1	2.0508 (13)

N1—Fe1—Cl1	102.93 (4)	N2—Fe1—Cl1	101.67 (4)
N1ⁱ—Fe1—N1	154.14 (8)	N2ⁱ—Fe1—N2	156.66 (7)
N1—Fe1—N2ⁱ	87.60 (5)

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Symmetry code: (i) Inline graphic .

Several intra- and inter-molecular interactions are identified in the title compound, as presented in Table 2 ▸ and Fig. 2 ▸. The distance between C3 and N5 and the C3—H3A⋯N5 angle are 3.411 (2) Å and 166°, respectively. These value are consistent with literature data where the C⋯N separation of C—H⋯N hydrogen bonds ranges from 2.4–3.9 Å (Rabaça et al., 2022 ▸) with angles of 100–171° (Shivakumar et al., 2012 ▸). Furthermore, the distances between C15 and O2, and C31 and O1 are 2.871 (3) Å and 2.867 (2) Å, respectively, which align with literature data where the C⋯O separation of C—H⋯O bonds ranges from 3.00–4.00 Å (Desiraju, 1996 ▸) with angles of 120–180° (Thakur et al., 2015 ▸). The molecular packing arrangement is illustrated in Fig. 3 ▸.

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C15—H15⋯O2	0.95	2.25	2.871 (3)	122
C31—H31⋯O1	0.95	2.25	2.867 (2)	122
C42—H42⋯Cl1	0.95	2.77	3.3596 (18)	121
C3—H3A⋯N5ⁱⁱ	0.95	2.48	3.411 (2)	166
C14—H14⋯O1ⁱⁱⁱ	0.95	2.45	3.165 (2)	132

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Symmetry codes: (ii) Inline graphic ; (iii) .

Intra- and inter-molecular interactions in the crystal structure of the title compound.

A view of the packing of the title compound. H atoms have been omitted for clarity.

Synthesis and crystallization

All experimental procedures were carried out under an argon atmosphere using a double-manifold vacuum line, Schlenkware, and cannula techniques. Except for the solvent employed in column chromatography, all solvents used in the experimental protocols underwent thorough drying and purging under anhydrous and anaerobic conditions. Solvents utilized within the anhydrous and anaerobic operations (Schlenk system) underwent the freeze–pump–thaw method three times prior to utilization.

The synthesis of the precursor 5,10,15,20-tetrakis(quinoline-7-carboxamide)porphyrin followed the procedures outlined in a previous publication (Yao et al., 2020 ▸). Initially, oxalyl chloride (2.2 mmol) was added to a suspension of 7-quinolinecarboxylic acid (1 mmol) in a solvent mixture of 15 ml dichloromethane (DCM) and 10 µl N,N-dimethylformamide in a nitrogen-protected atmosphere. The reaction mixture was stirred at room temperature for 1 h and concentrated in vacuo. The resulting solid was used in the subsequent step without further purification. Dry DCM (25 ml) containing 7-quinolinecarboxylic acid chloride was mixed with αααα-H₂TamPP (0.2 mmol) and 2,6-lutidine (270 µmol). The resulting solution was refluxed for 90 minutes and concentrated to dryness. The obtained product was purified through chromatography on a silica gel column using an elution solvent mixture of CHCl₃:CH₃OH in a ratio of 12:1, resulting in a yield of 70%. Subsequently, the chloro-iron porphyrin compound was prepared. To a solution of the free base porphyrin (ca. 100 µmol) in tetrahydrofuran (30 ml), FeCl₂ (20 equiv) and 2,6-lutidine (50 µl) were added. The mixture was refluxed overnight and concentrated to dryness. The resulting product was purified through chromatography on a silica gel column using an elution solvent composed of CHCl₃:CH₃OH in a ratio of 9:1, resulting in a yield of 70%. To produce X-ray-quality crystals, we utilized a vapor diffusion technique, wherein n-hexane was introduced into a 3 mM dichloromethane (CH₂Cl₂) solution to initiate crystallization.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸.

Table 3. Experimental details.

Crystal data
Chemical formula	[Fe(C₈₄H₅₂N₁₂O₄)Cl]
M _r	1384.68
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	23.1771 (19), 12.7959 (10), 22.5404 (16)
β (°)	100.332 (3)
V (Å³)	6576.5 (9)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.34
Crystal size (mm)	0.47 × 0.24 × 0.24

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	56518, 6685, 5979
R _int	0.041
(sin θ/λ)_max (Å⁻¹)	0.626

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.088, 1.07
No. of reflections	6685
No. of parameters	469
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.46

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Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), OLEX2.solve (Bourhis et al., 2015 ▸), OLEX2 (Dolomanov et al., 2009 ▸) and SHELXL2018/3 (Sheldrick, 2015 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314624004966/hb4470sup1.cif

x-09-x240496-sup1.cif^{(1.6MB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314624004966/hb4470Isup2.hkl

x-09-x240496-Isup2.hkl^{(531.6KB, hkl)}

x-09-x240496-sup3.docx^{(185.4KB, docx)}

Porphyrin ring displacement data. DOI: 10.1107/S2414314624004966/hb4470sup3.docx

CCDC reference: 2358334

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

full crystallographic data