Crystal structure and Hirshfeld-surface analysis of di­aqua­bis­(5-methyl-1H-1,2,4-triazole-3-carboxyl­ato)copper(II)

Petrenko, Y.P.; Vynohradov, O.S.; Khomenko, D.M.; Doroshchuk, R.O.; Raspertova, I.V.; Shova, S.; Lampeka, R.D.

doi:10.1107/S2056989023010770

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Volume 80| Part 1| January 2024| Pages 54-57

https://doi.org/10.1107/S2056989023010770

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Crystal structure and Hirshfeld-surface analysis of diaquabis(5-methyl-1H-1,2,4-triazole-3-carboxylato)copper(II)

Yuliia P. Petrenko,^a Oleksandr S. Vynohradov,^a ^* Dmytro M. Khomenko,^a,^b Roman O. Doroshchuk,^a,^b Ilona V. Raspertova,^a Sergiu Shova ^c and Rostyslav D. Lampeka ^a

^aDepartment of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska str. 64/13, 01601 Kyiv, Ukraine, ^bEnamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine, and ^c"PetruPoni" Institute of Macromolecular Chemistry, Aleea Gr., GhicaVoda 41A, 700487 Iasi, Romania
^*Correspondence e-mail: osvynohradov@ukr.net

Edited by S. Parkin, University of Kentucky, USA (Received 11 December 2023; accepted 14 December 2023; online 1 January 2024)

The title compound, [Cu(HL)₂(H₂O)₂] or [Cu(C₄H₄N₃O₂)₂(H₂O)₂], is a mononuclear octahedral Cu^II complex based on 5-methyl-1H-1,2,4-triazole-3-carboxylic acid (H₂L). [Cu(HL)₂(H₂O)₂] was synthesized by reaction of H₂L with copper(II) nitrate hexahydrate (2:1 stoichiometric ratio) in water under ambient conditions to produce clear light-blue crystals. The central Cu atom exhibits an N₂O₄ coordination environment in an elongated octahedral geometry provided by two bidentate HL⁻ anions in the equatorial plane and two water molecules in the axial positions. Hirshfeld surface analysis revealed that the most important contributions to the surface contacts are from H⋯O/O⋯H (33.1%), H⋯H (29.5%) and H⋯N/N⋯H (19.3%) interactions.

Keywords: copper; copper complexes; crystal structure; 1,2,4-triazole; X-ray crystallography; Hirshfeld surface analysis.

CCDC reference: 2314480

1. Chemical context

A few decades ago, 1,2,4-triazole-containing compounds became a focal point for both organic and inorganic chemists. It turned out that 1,2,4-triazoles are substances that show promising results as antibacterial, anticancer, antifungal, anti-inflammatory, and antiviral agents and have miscellaneous biological activities (Opsomer & Dehaen, 2022 ; Strzelecka & Świątek, 2021 ; Karczmarzyk et al., 2020 ). The presence of three nitrogen atoms and the possibility of being involved in metal bonding, both in their acid and deprotonated forms, resulted in the synthesis and investigation of numerous coordination compounds based on 1,2,4-triazole derivatives (Haasnoot, 2000 ). As a result of the presence of the N–N bridging function in the triazole ring, these ligands can form polynuclear complexes with specific magnetic properties (Aromí et al., 2011 ; Kitchen & Brooker, 2008 ; Klingele & Brooker, 2003 ; Petrenko et al., 2020 ; 2021 ). Meanwhile, 1,2,4-triazole used as linker in ligands for MOF construction, is not usually involved in the formation of coordination bonds (Du et al., 2005 ). The most widely used ligands of such type are 3-(2-pyridyl)-1,2,4-triazole derivatives, which readily form extremely stable planar coordination compounds with platinum (Chang et al., 2006 ; Chen et al., 2013 ) and palladium (Zakharchenko et al., 2017 ; 2019 ; 2021 ), showing promising photoelectronic and catalytic properties, respectively. A carboxylic acid group connected directly to the 1,2,4-triazole ring could potentially play the same role as a 2-pyridyl moiety, forcing the formation of chelates. In addition, it should be noted that the presence of both carboxylic and 1,2,4-triazole groups as parts of one molecule provides interesting theoretical insights into the structural peculiarities of these molecules. This is mainly due to the possibility of 1,2,4-triazole existing in three tautomeric forms (Pagacz-Kostrzewa et al., 2019 , 2020 ). Generally, compounds containing a carboxylic function are probably the most important materials for high-throughput synthesis and 1,2,4-triazoles are not an exception. Recently, as part of our efforts to prepare new synthesis building blocks, we obtained a series of carboxylic acids and their derivatives (Khomenko et al., 2022 ). One of those compounds was used to synthesize a copper complex.

2. Structural commentary

The molecular structure of the title compound consists of a neutral complex unit [Cu(HL)₂(H₂O)₂] (Fig. 1), where HL is the deprotonated 5-methyl-1H-1,2,4-triazole-3-carboxylate ligand. The Cu^II atom occupies a special position (inversion centre), thus imposing crystallographic inversion symmetry on the complex. The central atom exhibits an N₂O₄ coordination environment in an elongated octahedral geometry provided by two bidentate L⁻ anions in the equatorial plane [Cu1—O1 = 1.9987 (12) Å, Cu1—N1 = 1.9603 (15) Å] and two water molecules in the axial positions [Cu1—O1W = 2.5405 (15) Å]. It is worth noting that the structure of the title compound closely resembles those of earlier published analogous compounds with unsubstituted 1H-1,2,4-triazole-3-carboxylate anions (Liu, 2007 ; Zhu et al., 2007 ).

Figure 1
The molecular structure of the title compound with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features

In the crystal, the complex molecules [Cu(HL)₂(H₂O)₂] interact via numerous intermolecular O—H⋯O and N—H⋯O hydrogen bonds (Table 1). Each NH group of the carboxylate ligands is involved as the donor of a proton in bifurcated hydrogen bonding towards atom N2 and the coordinated water molecule of the adjacent molecule, while each O1W molecule acts as donor in two hydrogen bonds with two O2 atoms of the symmetry-related complexes. Thus, all the potential hydrogen bonds are completely realized in the crystal, which results in the formation of a three-dimensional supramolecular network, as shown in Fig. 2.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯O1Wⁱ	0.86	2.06	2.822 (2)	147
N3—H3⋯N2ⁱⁱ	0.86	2.58	3.121 (2)	122
O1W—H1WB⋯O2ⁱⁱⁱ	0.85	1.93	2.781 (2)	175
O1W—H1WA⋯O2^iv	0.85	1.92	2.737 (2)	160
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

Figure 2
Partial view of the crystal packing showing the formation of the three-dimensional supramolecular architecture.

4. Hirshfeld surface analysis

A Hirshfeld surface analysis was performed and the associated two-dimensional fingerprint plots were generated using CrystalExplorer 17.5 software (Spackman et al., 2021 ), with a standard resolution of the three-dimensional d_norm surfaces. There are 20 red spots on the d_norm surface (Fig. 3). The dark-red spots arise as a result of short interatomic contacts and represent contacts shorter than the sum of van der Waals radii, while the other weaker intermolecular interactions appear as light-red spots. The Hirshfeld surfaces mapped over d_norm are shown for the H⋯O/O⋯H, H⋯H and H⋯N/N⋯H contacts, and the decomposed two-dimensional fingerprint plots of different types of interactions are given in Fig. 4. All short interatomic contacts are in the range of 1.797–2.505 Å. The shortest contacts are OH⋯O and the longest contacts are NH⋯N. The most abundant contributions to the overall crystal packing are from H⋯O/O⋯H (33.1%), H⋯H (29.5%) and H⋯N/N⋯H (19.3%). There is a small contribution by other weak intermolecular contacts: H⋯C/C⋯H (4.6%), O⋯N/N⋯O (4.2%), O⋯C/C⋯O (3.3%), C⋯C (2.2%), O⋯O (1.8%), N⋯C/C⋯N (1.4%) and N⋯N (0.5%). In addition, quantitative physical properties of the Hirshfeld surface for this compound were obtained, such as molecular volume (303.40 Å³), surface area (289.05 Å²), globularity (0.755), as well as asphericity (0.087).

Figure 3
Two projections of the Hirshfeld surfaces mapped over d_norm showing the intermolecular interactions within the molecule and the full two-dimensional fingerprint plot for the title compound.

Figure 4
Hirshfeld surface representations with the function d_norm plotted onto the surface and the decomposed two-dimensional fingerprint plots for selected interactions.

5. Database survey

A search of the Cambridge Structural Database (CSD version 5.43, November 2021; Groom et al., 2016 ) for the moiety including a transition metal coordinated by the N and O atoms of the 1H-1,2,4-triazole-3-carboxylate anion in a bidentate way revealed 22 hits. Most similar to the title compound are mononuclear complexes with two unsubstituted 1H-1,2,4-triazole-3-carboxylate anions and two water molecules in axial positions: Mn^II [GEVKAW (Yan et al., 2018 )]; Zn^II [RIRVIY (Liu, 2007)]; Cd^II [XIRZOO (Zhu et al., 2008 )]; Cu^II [YIQROG (Zhu et al., 2007) and YIQROG01 (Liu, 2007)]. Other compounds with a close relation to the title complex are mononuclear complexes with 5-substituted 1H-1,2,4-triazole-3-carboxylate anions. In all cases, the substituent was the NH₂ group: Mn^II [HEDWIZ (Yang et al., 2019 )], Mn^II dihydrate [OPOMAJ (Liu et al., 2015 )], Cd^II [ISACEL (Wang et al., 2011 )], Co^II dihydrate [ONILIJ (Li et al., 2021 )], Zn^II based on 5-amino-1H-1,2,4-triazole-3-carboxylate anion and with only one coordinated water molecule [OPOLUC (Liu et al., 2015)].

6. Synthesis and crystallization

H₂L: LiHL (Khomenko et al., 2022) (1.33 g, 10 mmol) was dissolved in H₂O (10 ml). The obtained solution was cooled and slowly acidified with concentrated HCl (1 ml), maintaining the temperature between 273 and 278 K. The precipitation of colourless crystals occurred after addition of all the HCl. The reaction mixture was additionally stirred for 15 min at low temperature. Then, the precipitate was filtered off, washed with cold water and dried in vacuo. Yield 0.76 g (60%). ¹H NMR (400 MHz, D₂O): δ 2.61 (s, 3H) ppm. IR data (in KBr, cm⁻¹): 3330, 1648, 1567, 1509, 1418, 1313, 1103, 835. Elemental analysis: analysis calculated for C₄H₅N₃O₂ (127.10): C, 37.80%; H, 3.97%; N, 33.06%. Found: C, 37.41%; H, 3.65%; N, 32.71%.

[Cu(HL)₂(H₂O)₂]: A solution of Cu(NO₃)₂·6H₂O (0.148 g, 0.5 mmol) in H₂O (5 ml) was added to an aqueous solution of H₂L (0.127 g, 13 ml, 1 mmol) to give a clear blue solution. The blue crystals obtained after 2 days were filtered off, washed with water and dried in air. Yield 0.140 g (80%). IR data (in KBr, cm⁻¹): 3330, 1648, 1557, 1509, 1418, 1304, 1113, 835. Elemental analysis: analysis calculated for C₈H₁₂CuN₆O₆ (351.77): C, 27.32%; H, 3.44%; N, 23.89%. Found: C, 27.30%; H, 3.45%; N, 23.82%.

IR and ¹H NMR spectra of 5-methyl-1H-1,2,4-triazole-3-carboxylic acid are given in the supporting information for this article.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were found in difference-Fourier maps, but subsequently included in the refinement using riding models, with constrained distances set to 0.96 Å (RCH₃), 0.86 Å (Nsp²—H), and 0.85 (OH₂). U_i_so(H) parameters were set to values of either 1.2U_eq or 1.5U_eq (RCH₃, OH₂) of the attached atom.

Table 2
Experimental details

Crystal data
Chemical formula	[Cu(C₄H₄N₃O₂)₂(H₂O)₂]
M_r	351.78
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	200
a, b, c (Å)	6.8465 (4), 7.1097 (7), 7.2090 (5)
α, β, γ (°)	79.267 (7), 83.193 (6), 64.076 (8)
V (Å³)	309.80 (5)
Z	1
Radiation type	Mo Kα
μ (mm⁻¹)	1.81
Crystal size (mm)	0.45 × 0.1 × 0.1

Data collection
Diffractometer	Xcalibur, Eos
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2012 )
T_min, T_max	0.774, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	2216, 1397, 1381
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.681

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.024, 0.062, 1.11
No. of reflections	1397
No. of parameters	101
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.38
Computer programs: CrysAlis PRO (Agilent, 2012), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2314480

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989023010770/pk2702sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023010770/pk2702Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989023010770/pk2702Isup3.cdx

IR spectrum of 5-methyl-1H-1,2,4-triazole-3-carboxylic acid. DOI: https://doi.org/10.1107/S2056989023010770/pk2702sup4.jpg

1H NMR spectrum of 5-methyl-1H-1,2,4-triazole-3-carboxylic acid. DOI: https://doi.org/10.1107/S2056989023010770/pk2702sup5.tif

checkCIF report

Computing details top

Diaquabis(5-methyl-1H-1,2,4-triazole-3-carboxylato)copper(II) top

Crystal data top

[Cu(C₄H₄N₃O₂)₂(H₂O)₂]	Z = 1
M_r = 351.78	F(000) = 179
Triclinic, P1	D_x = 1.886 Mg m⁻³
a = 6.8465 (4) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.1097 (7) Å	Cell parameters from 1444 reflections
c = 7.2090 (5) Å	θ = 2.9–28.9°
α = 79.267 (7)°	µ = 1.81 mm⁻¹
β = 83.193 (6)°	T = 200 K
γ = 64.076 (8)°	Prism, clear light blue
V = 309.80 (5) Å³	0.45 × 0.1 × 0.1 mm

Data collection top

Xcalibur, Eos diffractometer	1397 independent reflections
Radiation source: Enhance (Mo) X-ray Source	1381 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.016
Detector resolution: 16.1593 pixels mm^-1	θ_max = 29.0°, θ_min = 2.9°
ω scans	h = −8→9
Absorption correction: multi-scan (CrysAlisPro; Agilent, 2012)	k = −9→9
T_min = 0.774, T_max = 1.000	l = −9→9
2216 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.024	H-atom parameters constrained
wR(F²) = 0.062	w = 1/[σ²(F_o²) + (0.0239P)² + 0.1883P] where P = (F_o² + 2F_c²)/3
S = 1.11	(Δ/σ)_max < 0.001
1397 reflections	Δρ_max = 0.35 e Å⁻³
101 parameters	Δρ_min = −0.38 e Å⁻³
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cu1	0.500000	0.500000	0.500000	0.01665 (11)
O1	0.7195 (2)	0.6171 (2)	0.41929 (19)	0.0200 (3)
O1W	0.2171 (2)	0.8296 (2)	0.31785 (19)	0.0211 (3)
H1WA	0.100833	0.815339	0.353434	0.032*
H1WB	0.208435	0.929486	0.372183	0.032*
O2	0.8357 (2)	0.8422 (2)	0.49419 (19)	0.0216 (3)
N1	0.4392 (2)	0.6629 (2)	0.7081 (2)	0.0148 (3)
N2	0.5479 (2)	0.8664 (2)	0.8331 (2)	0.0184 (3)
N3	0.3859 (2)	0.8329 (2)	0.9412 (2)	0.0187 (3)
H3	0.332405	0.882766	1.045013	0.022*
C1	0.7246 (3)	0.7403 (3)	0.5225 (3)	0.0161 (3)
C2	0.5727 (3)	0.7621 (3)	0.6937 (2)	0.0151 (3)
C3	0.3199 (3)	0.7127 (3)	0.8661 (2)	0.0160 (3)
C4	0.1414 (3)	0.6522 (3)	0.9429 (3)	0.0223 (4)
H4A	0.011749	0.743962	0.876397	0.033*
H4B	0.115402	0.664910	1.074796	0.033*
H4C	0.181446	0.508565	0.927290	0.033*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.02239 (18)	0.01979 (18)	0.01580 (17)	−0.01517 (14)	0.00516 (11)	−0.00932 (12)
O1	0.0244 (7)	0.0226 (7)	0.0205 (7)	−0.0158 (6)	0.0067 (5)	−0.0108 (5)
O1W	0.0233 (7)	0.0253 (7)	0.0215 (7)	−0.0154 (6)	0.0071 (5)	−0.0113 (6)
O2	0.0219 (7)	0.0232 (7)	0.0275 (7)	−0.0161 (6)	0.0066 (5)	−0.0102 (6)
N1	0.0170 (7)	0.0143 (7)	0.0156 (7)	−0.0087 (6)	0.0009 (5)	−0.0038 (6)
N2	0.0198 (7)	0.0214 (8)	0.0188 (8)	−0.0121 (7)	0.0022 (6)	−0.0076 (6)
N3	0.0215 (8)	0.0221 (8)	0.0164 (8)	−0.0114 (7)	0.0041 (6)	−0.0098 (6)
C1	0.0168 (8)	0.0150 (8)	0.0165 (8)	−0.0067 (7)	−0.0001 (6)	−0.0034 (7)
C2	0.0162 (8)	0.0148 (8)	0.0166 (8)	−0.0085 (7)	−0.0006 (6)	−0.0033 (7)
C3	0.0180 (8)	0.0151 (8)	0.0147 (8)	−0.0063 (7)	−0.0002 (6)	−0.0041 (7)
C4	0.0216 (9)	0.0270 (10)	0.0216 (9)	−0.0140 (8)	0.0041 (7)	−0.0056 (8)

Geometric parameters (Å, º) top

Cu1—O1	1.9987 (12)	N1—C2	1.363 (2)
Cu1—O1ⁱ	1.9987 (12)	N1—C3	1.329 (2)
Cu1—O1W	2.5405 (15)	N2—N3	1.361 (2)
Cu1—N1	1.9603 (15)	N2—C2	1.310 (2)
Cu1—N1ⁱ	1.9603 (15)	N3—C3	1.340 (2)
O1—C1	1.264 (2)	C1—C2	1.501 (2)
O2—C1	1.239 (2)	C3—C4	1.481 (2)

O1ⁱ—Cu1—O1	180.0	C3—N1—C2	104.36 (14)
O1—Cu1—O1W	89.09 (5)	C2—N2—N3	101.94 (14)
O1ⁱ—Cu1—O1W	90.91 (5)	C3—N3—N2	111.67 (15)
N1ⁱ—Cu1—O1	97.00 (5)	O1—C1—C2	113.53 (15)
N1ⁱ—Cu1—O1ⁱ	83.00 (5)	O2—C1—O1	127.10 (17)
N1—Cu1—O1ⁱ	97.00 (5)	O2—C1—C2	119.35 (16)
N1—Cu1—O1	83.00 (5)	N1—C2—C1	116.79 (15)
N1ⁱ—Cu1—O1W	92.71 (5)	N2—C2—N1	114.35 (16)
N1—Cu1—O1W	87.29 (5)	N2—C2—C1	128.86 (16)
N1ⁱ—Cu1—N1	180.0	N1—C3—N3	107.67 (15)
C1—O1—Cu1	115.49 (11)	N1—C3—C4	126.36 (16)
C2—N1—Cu1	111.00 (11)	N3—C3—C4	125.95 (16)
C3—N1—Cu1	144.60 (12)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O1Wⁱⁱ	0.86	2.06	2.822 (2)	147
N3—H3···N2ⁱⁱⁱ	0.86	2.58	3.121 (2)	122
O1W—H1WB···O2^iv	0.85	1.93	2.781 (2)	175
O1W—H1WA···O2^v	0.85	1.92	2.737 (2)	160
C4—H4B···O1Wⁱⁱ	0.96	2.59	3.367 (2)	139

Symmetry codes: (ii) x, y, z+1; (iii) −x+1, −y+2, −z+2; (iv) −x+1, −y+2, −z+1; (v) x−1, y, z.

Funding information

This work was supported by grants 22BF037–06 obtained from the Ministry of Education and Science of Ukraine.

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