Investigating the properties and biological activity of a new Cu(II) complex with a 2-Dimethyaminopyridinium cation (C₇H₁₂N₂)₂[CuCl₄]

2.1 (C₇H₁₂N₂)₂[CuCl₄] preparation

(C₇H₁₂N₂)₂[CuCl₄] or bis-(2-dimethylaminopyrimidinium) tetrachloridecuprate (II) (Mw = 453.71 g.mol⁻¹) was synthesized by the slow evaporation technique. An aqueous solution of CuCl₂·2H₂O (1 mmol) and 2-dimethylaminopyridine (2 mmol in 5 mL of pure ethanol) were mixed in a round-bottom flask. Then, 10 mL of concentrated hydrochloric acid was added to the solution, which was allowed to stir mechanically for about two hours at 50 °C. After a few days of progressively evaporating, prismatic crystals appropriate for X-ray research were formed. Recrystallization of the crystals from the water was required to increase their quality.

2.2 Instrumentation

3.1 Powder XRD and SEM/EDX observations

SEM image examination reveals that the hybrid's surfaces seem to be flat. Areas of strong contrast were used for EDX analysis during SEM. To verify the existence of heavy element compositions in the crystal. As may be seen by the presence of the typical signals from the elements carbon, copper, chloride, and nitrogen (Fig. 1A). In addition, there were no differences discovered between the simulated and experimental XRPD patterns of (C₇H₁₂N₂)₂[CuCl₄] when comparing both sets (Fig. 1B). This provides further evidence that the product that was synthesized is pure and confirms the crystal data that was used in the process of synthesizing it.

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Fig. 1

SEM image observation and related EDX analysis from three separate zones (A) and experimental and theoretical X-ray diffractograms of (C₇H₁₂N₂)₂[CuCl₄] (B).

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3.2 Structure of the crystal

Fig. 2A shows the asymmetric unit of the structure generated with 50% probability thermal ellipsoids for non-hydrogen atoms, which contains two non-equivalent cations: bis-(2-dimethylaminopyrimidinium) tetrachloridecuprate (II) (cation A made up by: C8-C12/N3, and cation B made by: C1-C5/N1) and one tetrahedron anions [CuCl₄]^2-. As can be observed, the N atoms of the pyridine ring are protonated, whilst the amine groups remain unprotonated. Therefore, the charge of each organic cation is increased by + 1. As a result, the structure matches each tetrachlorocuprate anion with two 2-dimethylaminopyridinium cations in order to preserve the charge balance.

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Fig. 2

(C₇H₁₂N₂)₂[CuCl₄] structure projection along the b-axis (A), atomic arrangement parallel to the [0 0 1] direction (B), interaction between two cations type A (C), C–H… π interaction (D) π…π, and interaction between two cations type B (E).

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(C₇H₁₂N₂)₂[CuCl₄] packing along the b-axis reveals that the title compound's structure is made up of mixed cation–anion layers that run parallel to the (1 1 0) plane and are held together by C11-H11…Cl1 H-bonds and Van der Waals interactions. The H-bonds, on the other hand; C5-H5…Cl1, C9-H9… Cl1, N3-H3A, Cl2, C7-H7B, Cl3, C2-H2… Cl3, C10-H10… Cl3 and Cl4 connect two neighboring layers to form a three-dimensional network (Table 2, Fig. 2B).

A mixed layer is formed by paralleling organic (cations type A) and inorganic columns to the [0 1 0] axis (Fig. 2C). Cations A generate organic columns with centroids spaced at 3.646 (Fig. 2D) and C—H… π interactions (3.299 Å) (Fig. 2E), whereas cations B interact via offset face-to-face π…π interactions with centroids spaced at 3.588 Å (Fig. 2F).

The geometric characteristics of organic cations (C₇H₁₂N₂)²⁺ are listed in Table 3. These findings are consistent with those seen in similar compounds (Kumar et al., 2020; Sundaraganesan et al., 2008; Szafran et al., 2005). The sum of the angles that surround the nitrogen atoms N(4) and N(2) in the cations A and B, respectively, is close to being equal to 360°. The C—N bond distance of the NH₂ group is 1.320 (16) Å for cation A and 1.306 (10) Å for cation B. This distance is consistent with an imino resonance form, which is often seen for a C—N single bond containing sp² hybridized C and N atoms. The delocalization of the ring density with the p-orbital electrons of the amino group is most likely the cause of the decrease in the distance between the C—N amino bond and the amino group. Because of this, the basicity of the nitrogen atoms at positions N(2) and N(4) decreases, which makes protonation of the nitrogen atoms at positions N(1) and N(3) on the pyridine ring more likely. A pyridinium cation will almost always have a larger C—N—C angle when compared to the parent pyridine molecule. Both the C1—N1—C5 angle of 120.83 (10) ° and the C8—N3—C12 angle of 122.3 (14) ° are typical for the protonated forms of pyridine that have been described in the literature (Vembu et al., 2003; Majerz et al., 1995).

The Cu—Cl distances of the tetrahedrally coordinated [CuCl₄]^2-anion range from 2.242 (3) to 2.275 (3) Å and the angle Cl—Cu—Cl ranges between 99.35 (11) ° and 133.09 (12) °. These bonding lengths and angles are consistent with those observed in other compounds (Table 3) (Nasr et al., 2016; Halvorson et al., 1990).

The values for dissociation constants (DI) were as follows: DI(Cl—Cu) = 0.0049, DI(Cl—Cl) = 0.078, and DI(Cl—Cu—Cl) = 0.124. In comparison to Cl—Cl distances, the angles Cl—Cu—Cl in these measurements are significantly distorted. The anions [CuCl₄]^2- are thought to be made up of chlorine atoms in a regular configuration, with the copper atom slightly dislocated from the tetrahedron's center of gravity. Additionally, the Yang parameter τ₄ may be utilized, with a value of zero suggesting a perfect square planar geometry and a value of one indicating a perfect tetrahedral geometry (Yang et al., 2007). The estimated value of 0.69 indicates that the tetrachlorocuprate anions have almost a tetrahedral structure.

3.3 HS surface study

The Hirshfeld surface (HS) is drawn over the d_norm surface to find the interactions between molecules in the complex's solid phase structure (Fig. 3a). The blue sections indicate distances greater than the total of the van der Waals radii of the associated atoms, while the red parts indicate lesser distances. The circular red spots are actually caused by the N—H…Cl and C–H…Cl connections, while the white spots are caused by other contacts. The HS shape-index is used to visualize the π…π stacking by detecting the presence of adjacent red and blue triangles (Fig. 3b). The title structure, (C₇H₁₂N₂)₂[CuCl₄], clearly demonstrates the presence of π…π stacking interactions, where a flat region surrounding the pyridine rings on the Hirshfeld surface, plotted against curvedness (Fig. 3c). Moreover, the 2D fingerprint graphs can be used to separate the interactions between molecules in a structure, which makes it possible to observe how much each one contributes. The overall two-dimensional fingerprint pattern is shown in Fig. 3d.

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Fig. 3

Hirshfeld surface mapped with dnorm (a), shape index (b), curvedness (c), 2D fingerprint plots (d).

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Fig. 3d depicts the 2D fingerprint of all contacts contributing to the Hirshfeld surface. The enrichment ratio computation for a pair of elements (X, Y) E_XY is presented in Table 4. According to the plot shown in Fig. 4a H…H are the most frequently detected interactions, with a relative contribution of 47.7%.and with an enrichment ratio slightly under-represented by E_H…_H = 0.92. The H…Cl/Cl…H interactions account for 36.2% of the total HS area (Fig. 4b).Due to the abundance of chloride and hydrogen on the molecular surface (S_Cl = 18.75% and S_H = 71.7%), these are significantly favored with an enrichment ratio of E_H…_Cl = 1.35. The C…H/H…C interactions account for 8.4% of the overall area (Fig. 4c), and are preferred contact in the crystal packing (E_C…_H = 0.91). The hydrophobic C…C contacts account for 1.5% of the overall surface area (Fig. 4d) and are considered as more pronounced since the associated enrichment ratio is E_C…_C = 3.60 as a result of π…π stacking between the aromatic pyridine rings. In contrast, the N…H interactions make about 2.3% of the Hirshfeld surface (Fig. 4e), followed by C…N/N…C and Cu…H/H…Cu that both count for 1.1% of the whole Hirshfeld surface area (Fig. 4f and Fig. 4g). However, the N…Cl/Cl..N (Fig. 4h), C..Cl/Cl…C (Fig. 4i), and N…N (Fig. 4f) contacts, each contribute around 0.9%, 0.4%, and 0.4% of the total surface, respectively, and are particularly poor. It is important to note that the remaining contributions do not accurately reflect their contribution to the structure's stabilization.

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Fig. 4

The 2D fngerprint map for (C₇H₁₂N₂)₂[CuCl₄] illustrating the contribution all contacts.

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We conclude from this analysis that H…H and Cl…H contacts, followed by C…H, account for most of the total surface, reflecting the driving force in this crystal packing.These findings support the notion that the presence of π…π stacking, C—H…interactions, and H-bonds plays an important role in the stability of crystalline structures (Munawar et al., 2023; Chalkha et al. 2023). Therefore, the absence of these interactions in solution may be a contributing factor to instability and subsequent dissociation.

3.4 IR-Spectroscopy of (C₇H₁₂N₂)₂[CuCl₄]

Fig. 5 depicts the IR spectra of (C₇H₁₂N₂)₂[CuCl₄], which is in excellent agreement with the structural X-ray study findings. The different vibrational modes of this compound are compared with other compounds having the same organic cation (Karaa et al., 2012; Thanigaimani et al., 2015). The two bands located at 3068 and at 2976 cm⁻¹ correspond to the vibrations of asymmetric lengthening of the C—H bond of the methyl groups-CH3 and of the C—H bond of the aromatic ring. The pyridinium N—H group's elongation vibrations can be at 3383 cm^-1and at 3245 cm⁻¹, on the other hand, the two peaks located at 1646 and at 1613 cm⁻¹ are attributed to the deformation vibrations δ(N—H). The stretching vibration of the C⚌C bond in the infrared spectrum of the title compound is characterized by a peak observed at 1547 cm⁻¹.

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Fig. 5

The infrared spectrum of (C₇H₁₂N₂)₂[CuCl₄] at room temperature.

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The –CH3 groups' deformation vibrations are positioned by three successive bands, the first at 1455 cm-1, the second at 1410 cm-1, and the last at 1383 cm⁻¹. Frequencies between 1259 and 1000 cm⁻¹ are assigned to the vibrations of ν (C—N) and ν (C—C). The remains of the bands (between 1000 and 400 cm⁻¹) are attributed to the out-of-plane bending modes for C—H, C—C and C—N bonds.

3.5 Antibacterial activity

Using the disc diffusion method, different concentrations of bis-(2-dimethylaminopyrimidinium) tetrachloridecuprate (II); 100 µg.mL⁻¹; 50 µg.mL⁻¹; 25 µg.mL⁻¹ and 12.5 µg.mL⁻¹ were tested against three opportunistic nosocomial pathogen bacterial strains: Klebsiella pneumonia and Serratiamarcescens, which are both gram-negative; and Staphylococcus aureus, which is a Gram-positive bacterial strain (Sarangi et al., 2020; Azam et al., 2021; Azam et al., 2022; Al-Resayes et al., 2017). The zone (mm) of inhibition, the compound showed high antibacterial activity against Serratiamarcescens even in small concentration 12.5 µg.mL⁻¹, whereas the antibiotics control Norfloxacin (NOR-10) and Nalidixic acid (NA30) did not inhibit cell viability but Novobiocin (NV-5); Erythromycin (E-15) agent, was observed either by using high concentrations of 50 g.mL⁻¹ and 100 µg.mL⁻¹ from the compound (C₇H₁₂N₂)₂[CuCl₄] or by the four used antibiotics (Fig. 6). The combination of the compound (C₇H₁₂N₂)₂[CuCl₄] with the four antibiotics was tested against two Gram-negative bacterial strains (Klebsiella pneumonia and Serratiamarcescens) and Gram- positive bacteria (Staphylococcus aureus) using the disc diffusion method. The zone of inhibition (mm) of different antibiotic discs with (C₇H₁₂N₂)₂[CuCl₄] against test three strains was measured and revealed that the free compound or the reference used four antibiotics had the highest antimicrobial activity. A Copper (II) complex with 12.5 μg. mL⁻¹ produced a maximum fold increase of 60% antibacterial activity against Serratiamarcescens. In the case of Klebsiella pneumonia and Staphylococcus aureus, the synthesized compound 100 μg.mL⁻¹ together with the antibiotics shows as 10% fold increase against both strains. In the current investigation, the antibiotics' synergistic efficacy against the three different pathogens was significantly increased in the presence of (C₇H₁₂N₂)₂[CuCl₄].

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Fig. 6

A) Antimicrobial activity of the compound (C₇H₁₂N₂)₂[CuCl₄]; B) Antimicrobial activity of the antibiotics Norfloxacin (NOR-10), Novobiocin (NV-5), Erythromycin (E-15), and Nalidixic acid (NA30); C) Antimicrobial activity of the compound (C₇H₁₂N₂)₂[CuCl₄] combined with the antibiotics.

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The increasing antimicrobial activity of Cu (II) compounds can be explained by the cell permeability. Because the lipid membrane surrounding the cell preferred only fat-soluble substances to pass, fat solubility is an important factor in antimicrobial control activity. Cu (II) increases the lipophilic character of the central metal atom, allowing it to penetrate the cellular fat layers membrane and inhibit bacterial growth (Anjaneyulu and Prabhakara Rao, 1986; Chandraleka et al., 2014).