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Article

Diamond-like Cage Motifs in {Cu6(StBu)4} Complexes with Pyridines

by
Taisiya S. Sukhikh
,
Maxim N. Sokolov
and
Pavel A. Abramov
*
Nikolaev Institute of Inorganic Chemistry SB RAS, 3 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russian
*
Author to whom correspondence should be addressed.
Crystals 2025, 15(7), 607; https://doi.org/10.3390/cryst15070607
Submission received: 3 June 2025 / Revised: 25 June 2025 / Accepted: 26 June 2025 / Published: 28 June 2025
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Abstract

The reduction of Cu(NO3)2 by HStBu in CH3CN under Ar atmosphere produces a light-yellow solution containing numerous {Cux(StBu)y} species. The addition of different pyridines (py-R) into this solution results in the formation of {Cu6(StBu)4} hexanuclear complexes. The slow Et2O diffusion leads to crystals of [Cu6(StBu)4(2-Me-py)5(CH3CN)(NO3)](NO3) (1), [Cu6(StBu)4(Me3py)4(NO3)2]·3.5CH3CN (2a), [Cu6(StBu)4(Me3py)5(NO3)](NO3)·5CH3CN (2b), (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O (3), [Cu6(StBu)4(2-Br-py)4(NO3)2]·2-Br-Py (4), [Cu6(StBu)4(3-Br-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·9CH3CN (5), and [Cu6(StBu)4(3-Cl-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·5CH3CN (6). The titled compounds were characterized by single crystal X-ray diffraction (SCXRD). The Cu···Cu contacts were analyzed with quantum chemical methods.

Graphical Abstract

1. Introduction

Coinage metal nanoclusters are traditionally a focus of modern coordination chemistry. In recent years, studies of coinage metal clusters protected by ligands of various natures have become widespread due to their unique potential applications in catalysis, organic optoelectronics and the processing of “smart” luminescent materials [1,2,3,4,5]. The luminescent properties of such objects are a key driver in this research field aimed at the sensing of different substances [6,7,8,9,10,11,12], even in the case of water quality control [13].
There are several directions in the modern chemistry of copper nanoclusters which we are going to highlight here. Copper thiolate coordination polymers are also a focus of materials science. For example, [Cu(pot)]n (Hpot = 5-(3-pyridyl)-1,3,4-oxadiazole-2-thiol) has shown luminescent stability in different media [14]. [Cu(p-SPhCO2Me)]n reported as a temperature sensor, working in a temperature range from 100 to 500 K [15]. The MOF synthetic approach is useful for the preparation of [Cu9(pzt)7Cl2]n, [Cu2(pzt)Cl]n, [Cu4(pzt)3Br]n, [Cu(pzt)]n, [Cu4(pzt)3I]n, and [Cu7(pzt)6I]n (Hpzt = pyrazine-2-thiol) [16]. The unique 3d MOF [Cu12(StBu)9(CF3COO)3(bpy)4] was synthesized by reacting bpy with [CuStBu]n and trifluoroacetic acid under solvothermal conditions [17].
Commonly, thiolate ligands of different natures as well as various phosphines stabilize copper clusters. The synthesis and chemical properties of (Bu4N)6[Cu6(S,i-MNT)6] (i-MNT = [S2CC(CN)2]−) have been widely studied [18]. A series of trinuclear copper(I) thiolate complexes, [Cu3(μ-dppm)3(μ3-SR)2]BF4 (R = C6H4Cl-4, C6H4CH3-4, C6H4OCH3-4, C6H4(OCH3)2-3,4, C6H4-benzo-15-crown-5, or tBu), [Cu3(μ-dppm)3(μ3-StBu)](BF4)2, and [Cu3(μ-dppm)3(μ3-SR)(μ3-Cl)]BF4 (R = C6H4CH3-4, C6H4tBu-4, or C6H4(CH3)3-2,4,6) and two hexanuclear copper(I) selenolate complexes, [Cu6(μ-P∧P)4(μ3-SePh)4](BF4)2 (P∧P = dppm or (Ph2P)2NH), have been reported [19].
However, the synthesis and characterization of coinage metal nanoclusters with high nuclearity are still a challenging task and focus the attention of researchers. A general problem that must be solved for this type of object is reproducibility. For example, [Cu74S15(2-PET)45] (2-PET = 2-phenylethanethiol) reported in the literature [20] was not reproduced under our conditions, since the growth of crystals in the complex is uncontrollable and requires about two weeks of keeping the reaction mixture at a low temperature. The problem of [Cu74S15(2-PET)45] (2-PET = 2-phenylethanethiol) synthesis is a further reduction of {Cux(2-PET)y} species to aggregate into the nanoscale objects. This process cannot be controlled and needs a lot of time under the right conditions.
The next point to be addressed is cuprophilic interactions, which are often discussed only from geometric characteristics, while energy characteristics and the visualization of interactions are not studied. High-level quantum chemical calculations are needed to analyze and discuss these issues. At the moment the data are quite rare and exist, for example, for [Cu10O2(Mes)6]n [21].
The reduction of Cu2+ salts in the organic media by means of mercaptan (HSR) is a very complicated process including numerous species arising as a result of thiolate-to-copper(I) coordination. The association plays a key role in such solutions to produce highnuclear complexes. In this work we generated {Cux(StBu)y} species in CH3CN solution through the reduction of Cu2+ (as copper(II) nitrate) by HStBu as the first step. At the second stage, different pyridine derivatives (py-R) were added into this solution to functionalize the produced copper thiolates into {Cux(StBu)y(py-R)z}. Schematically, this process is depicted in Scheme 1. Slow Et2O diffusion helps in the isolation of crystalline materials from such reaction mixtures. We have isolated and structurally characterized six new complexes bearing a {Cu6(StBu)4}2+ structural unit.

2. Materials and Methods

2.1. General Information

Caution: All manipulations were carried out under Ar atmosphere to avoid CuI oxidation. All reported complexes are unstable without Ar atmosphere. All solvents used were freshly distilled according to the standard procedures. Triethyl amine (Merck Life Science LLC, Moscow, Russia) was distilled over KOH. Cu(NO3)2·3H2O (ECROS, Moscow, Russia) and tert-butyl mercaptan (Merck Life Science LLC, Moscow, Russia) were used as purchased. Elemental analysis on C, H, N, and S was performed with a CHNS analyzer vario MICRO cube (Elementar, Langenselbold, Germany) in the analytical laboratory of the Nikolaev Institute of Inorganic Chemistry SB RAS. IR spectra were recorded on a Bruker Vertex 60 FT-IR spectrometer (Bruker, Pike, Cottonwood, AZ, USA).

2.2. SCXRD

Single-crystal XRD data (Table S1, Supplementary Materials) for crystals of compounds 1–5 were collected with a Bruker D8 Venture diffractometer (Bruker AXS GmbH, Karlsruhe, Germany) (CMOS PHOTON III detector, Cu-IμS 3.0 microfocus source, focusing Montel mirrors, λ = 0.71073 Å MoKα radiation, N2-flow thermostat). The data for crystals of 6 were collected with an Xcalibur diffractometer (Xcalibur MPH Switzerland SA, Geneva, Switzerland) (AtlasS2 detector, graphite-monochromated microfocus source, MoKα radiation, N2-flow thermostat). Data reduction was performed routinely via APEX 3 or CrysAlisPro 1.171.40.74a suite. The crystal structures were solved using ShelXT [22] and were refined using ShelXL (2019/3) [23] programs assisted by Olex2 GUI (Olex2-1.5) [24]. Atomic displacements for non-hydrogen atoms were refined in harmonic anisotropic approximation, with the exception of disordered nitrate and solvate molecules in 1, 2a, and 3, which were refined in isotropic approximation. Hydrogen atoms were placed geometrically. For 2a, a solvent mask implemented in Olex2 was calculated and 137 electrons were found in a volume of 497 Å3 in three voids per unit cell. This is consistent with the presence of 2.5C2H3N per formula unit which accounts for 138 electrons per unit cell. For 2b, a solvent mask gave 566 electrons found in a volume of 1360 Å3 in one void per unit cell. This is consistent with the presence of 4C2H3N per formula unit which accounts for 580 electrons per unit cell. For 5, a solvent mask gave 1280 electrons found in a volume of 1964 Å3 in two voids per unit cell. This is consistent with the presence of 4 NO3, and 9C2H3N, per formula unit which accounts for 1284 electrons per unit cell. For 6, a solvent mask procedure gave 824 electrons in a volume of 2208 Å3 in two voids per unit cell. This is consistent with the presence of 4NO3, and 5C2H3N, per formula unit which accounts for 820 electrons per unit cell.
The structures of titled compounds were deposited to the Cambridge Crystallographic Data Centre (CCDC) as a supplementary publication, No. 2451538-2451544.

2.3. DFT Calculations

DFT calculations were performed using the ORCA 5.0.1 package [25]. Isolated complexes [Cu6(StBu)4(MePy)5(CH3CN)(NO3)]+ in 1, [Cu6(StBu)4(Me3Py)4(NO3)2] in 2a, [Cu6(StBu)4(Me3Py)5(NO3)]+ in 2b, (Et3NH)[Cu6(StBu)4(CH3CN)3(NO3)3] in 3, [Cu6(StBu)4(3-Cl-Py)6]2+ in 6, and [Cu6(StBu)4(CH3CN)6]2+ in 6 were derived from the SCXRD structures with lengthened C–H bond distances of 1.10 Å and used without further optimization. Disordered moieties were eliminated. The single-point ground-state calculations were carried at DFT PBE0/def2-TZVP level. The calculations were accelerated by means of the RIJCOSX algorithm and a def2/J auxiliary basis set was used for this. D3(BJ) dispersion corrections were included. For [Cu6(StBu)4(CH3CN)6]2+, the geometry was optimized at the same level of theory, revealing a slight geometrical difference compared with the experimental structure.
Cuprophilic interactions in the models were studied by means of two approaches, topological analysis based on Bader’s Atoms in Molecules (AIM) theory, and the Noncovalent Interaction (NCI) Index combined with the second derivative of the Reduced Density Gradient (RDG). The corresponding manipulations with the electron densities were performed using the Multiwfn program (version 3.8) [26]. For clarity, only inner-cage Cu6S4 surface maps were visualized, with RDG values where the value of sign(λ2) ρ is within the range of −0.5–0.01. In addition to PBE0/def2-TZVP, we also tested a higher level of theory, ωB97X/def2-TZVPP with scalar-relativistic ZORA corrections (with SARC/J and AutoAux auxiliary basis sets for acceleration via the RIJCOSX algorithm), based on the example of a geometry-optimized model [Cu6(StBu)4(CH3CN)6]2+, which gave comparable results.

2.4. Preparation of “{Cux(StBu)y}” Stock Solution

A total of 198 mg (0.819 mmol) of Cu(NO3)2 3H2O was dissolved in 12 mL of acetonitrile, after which 400 μL of tert-butyl mercaptan (3.54 mmol) and 400 μL of triethylamine (2.88 mmol) were added to the resulting solution [27]. The resulting yellow solution was stirred for one hour under argon atmosphere and then used in further syntheses (CCu+ c.a. 0.0586 M).

2.5. Synthesis of [Cu6(StBu)4(2-Me-py)5(CH3CN)(NO3)](NO3) (1)

A total of 30 mg (3·10−4 mol) of 2-methylpyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 5 days resulted in a crop of colorless crystals. The crystalline product was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The yield was 32%.
Calcd for C48Cu6H74N8O6S4 C, H, N, S (%): 42.12, 5.45, 8.19, 9.37. Found C, H, N, S (%): 42.30, 5.60, 8.50, 10.00.
FT-IR (ν, cm−1): 3010 (w), 2985 (w), 2964 (w), 2950 (w), 2934 (w), 2250 (w), 2237 (w), 2200 (w), 1970 (m), 1940 (w), 1866 (w), 1760 (w), 1754 (m), 1710 (m), 1630 (w), 1540 (w), 1440 (s), 1470 (w), 1430 (m), 1362 (m), 1290 (vs), 1240 (w), 1155 (s), 1044(w), 1028 (s), 1065 (w), 1000 (w), 950 (m), 870 (w), 810 (w), 650 (w), 633 (w), 553 (w), 468 (m), 372 (m).

2.6. Synthesis of [Cu6(StBu)4(Me3py)4(NO3)2]·3.5CH3CN (2a) and [Cu6(StBu)4(Me3py)5(NO3)](NO3)·5CH3CN (2b)

A total of 36 mg (3·10−4 mol) of 2,4,6-trimethylpyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 5 days resulted in a crop of colorless crystals of 2a and 2b. The mixture was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The total yield was 60%.

2.7. Synthesis of (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O (3)

A total of 45 mg (3·10−4 mol) of 2,6-dichloropyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 24 h resulted in a crop of colorless crystals. The crystalline product was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The yield was 56%.
Calcd for C28Cu6H63N7O10S4 C, H, N, S (%): 28.81, 5.44, 8.40, 10.99. Found C, H, N, S (%): 28.60, 5.60, 8.50, 10.40.
FT-IR (ν, cm−1): 3460 (w), 3012 (w), 2987 (m), 2979 (w), 2750 (w), 2630 (w), 2280 (w), 2238 (w), 2183 (m), 1773 (w), 1765 (w), 1705 (w), 1648 (m), 1620 (m), 1460 (w), 1370 (w), 1294 (vs), 1204 (s), 1059 (s), 1003 (m), 950 (w), 880 (w), 752 (w), 653 (w), 520 (w), 469 (m), 370 (w).

2.8. Synthesis of [Cu6(StBu)4(2-Br-py)4(NO3)2]·2-Br-py (4)

A total of 50 mg (3·10−4 mol) of 2-bromopyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 5 days resulted in a crop of colorless crystals. The crystalline product was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The yield was 50%.
Calcd for Br5C41Cu6H56N7O6S4 C, H, N, S (%): 29.81, 3.42, 5.94, 7.76. Found C, H, N, S (%): 30.10, 3.80, 6.0, 8.0.
FT-IR (ν, cm−1): 3008 (w), 2988 (w), 2964 (w), 1975 (m), 1940 (w), 1870 (w), 1762 (w), 1754 (m), 1711 (m), 1580 (w), 1562 (w), 1540 (w), 1468 (w), 1442 (s), 1463 (w), 1461 (w), 1420 (m), 1360 (m), 1295 (s), 1240 (w), 1155 (s), 1108 (w), 1044 (w), 1018 (s), 1005 (w), 990 (w), 950 (m), 870 (w), 790 (w), 782 (w), 692 (s), 653 (w), 550 (w), 468 (m), 372 (m).

2.9. Synthesis of [Cu6(StBu)4(3-Br-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·9CH3CN (5)

A total of 50 mg (3·10−4 mol) of 3-bromopyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 5 days resulted in a crop of colorless crystals. The crystalline product was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The yield was 60%.
Calcd for Br6C92Cu12H141N25O12S8 C, H, N, S (%): 33.61, 4.32, 10.65, 7.80. Found C, H, N, S (%): 33.30, 4.0, 10.4, 8.0.
FT-IR (ν, cm−1): 3008 (w), 2988 (w), 2964 (w), 2292 (w), 2248 (w), 2200 (w), 2191 (w), 1975 (m), 1940 (w), 1870 (w), 1762 (w), 1754 (m), 1711 (m), 1580 (w), 1562 (w), 1540 (w), 1468 (w), 1442 (s), 1472 (w), 1461 (w), 1443 (w), 1419 (m), 1356 (m), 1290 (vs), 1242 (w), 1178 (w), 1160 (s), 1108 (w), 1044 (w), 1018 (s), 1005 (w), 990 (w), 950 (m), 870 (w), 790 (w), 782 (w), 692 (s), 653 (w), 550 (w), 468 (m), 372 (m).

2.10. Synthesis of [Cu6(StBu)4(3-Cl-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·5CH3CN (6)

A total of 35 mg (3·10−4 mol) of 3-chloropyridine was added to 1.75 mL of the stock solution and stirred for one and a half hours. The final solution was placed in the first section of the two-section Schlenk tube. The second section was filled with Et2O. Keeping this tube at 5 °C for 5 days resulted in a crop of colorless crystals. The crystalline product was filtered on a glass frit under Ar, washed with ethyl ether, and then dried under vacuo. The yield was 65%.
Calcd for C84Cl6Cu12H129N21O12S8 C, H, N, S (%): 35.32, 4.55, 10.30, 8.98. Found C, H, N, S (%): 35.10, 4.80, 10.0, 8.3.
FT-IR (ν, cm−1): 3001 (w), 2985 (w), 2970 (w), 2290 (w), 2246 (w), 2205 (w), 2190 (w), 1978 (m), 1937 (w), 1872 (w), 1762 (w), 1754 (m), 1711 (m), 1580 (w), 1562 (w), 1540 (w), 1468 (w), 1442 (s), 1470 (w), 1461 (w), 1443 (w), 1421 (m), 1360 (m), 1295 (vs), 1242 (w), 1174 (w), 1155 (s), 1108 (w), 1044 (w), 1018 (s), 1005 (w), 990 (w), 950 (m), 870 (w), 790 (w), 782 (w), 752 (w), 730 (s), 650 (w), 550 (w), 456 (m), 388 (m).

3. Results and Discussion

3.1. Synthesis and Crystal Structure

The reduction of Cu2+ by HStBu in CH3CN with the addition of Et3N generates a light-yellow solution containing numerous {Cux(StBu)y} species. This solution exhibits a bright red luminescence upon excitation at 365 nm (Scheme 1), while it is hard to determine a complex responsible for this effect at the current stage. Recently we have published a procedure to obtain crystals of [Cu3(StBu)3]n in high yield just using Et2O diffusion into the solution containing generated {Cux(StBu)y} species [27]. In this research, we have studied the complexation of the generated {Cux(StBu)y} fragments with the following pyridine derivatives: 2-methylpyridine (2-Me-Py), 2,4,6-trimethylpyridine (Me3py), 2-bromopyridine (2-Br-py), 3-bromopyridine (3-Br-py), and 3-chloropyridine (3-Cl-py). After the addition of the corresponding pyridine, each reaction mixture was allowed to diffuse into Et2O. This provided an opportunity to collect crystals of the titled compounds in moderate yields. We have isolated and structurally characterized six new complexes, [Cu6(StBu)4(2-Me-py)5(CH3CN)(NO3)](NO3) (1), [Cu6(StBu)4(Me3py)4(NO3)2]·3.5CH3CN (2a), [Cu6(StBu)4(Me3py)5(NO3)](NO3)·5CH3CN (2b), (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O (3), [Cu6(StBu)4(2-Br-py)4(NO3)2]·2-Br-Py (4), [Cu6(StBu)4(3-Hal-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·9CH3CN (5), and [Cu6(StBu)4(3-Cl-py)6][Cu6(StBu)4(CH3CN)6](NO3)4·5CH3CN (6), schematically shown in Figure 1. According to SCXRD, the complexes feature a similar {Cu6(StBu)4} diamond-like cage motif across the series 1–6, with the Cu atoms further coordinating one of the substituted pyridine, acetonitrile, or nitrate ligands.
Therefore, the presence of py-R ligands shifted equilibria in the initial CH3CN solution to the {Cu6(StBu)4} unit dominance. We illustrated the comparison of the hexanuclear copper unit structure in the isolated complexes reported here and in the previously reported [Cu3(StBu)3]n coordination polymer in Figure 2. The main difference between the hexanuclear copper units is based on the number of thiolate ligands. This evidences the indirect transformation of {Cu6(StBu)4}2+ into the [Cu3(StBu)3]n coordination polymer and the presence of other {Cux(StBu)y} species in the solution.
The structural analysis of 1–6 reveals a number of interesting features. The Cu6 moiety adopts a distorted octahedron with the edge distances of 3.07–3.81 Å (Table S2). The shorter distances are observed between the Cu(N)–Cu(O) atoms, while the longer ones are between Cu(N)–Cu(N). This is a consequence of the higher polarization degree of the Cu(O) atom, so that neighboring StBu ligands bring the Cu atoms closer to each other: the corresponding Cu(O)–S distances are generally shorter by 0.01–0.04 Å than the Cu(N)–S ones. The coordination number of Cu+ in all presented complexes is typically three and copper has a triangular coordination environment (considering that nitrate tentatively occupies one coordination cite of Cu). The only exception is the structure of 1, where one Cu atom (the major position of the disordered structure, Figure S1a) coordinates both acetonitrile and methylpyridine ligands. Note that even in this case, we observe a minor position of the Cu atom with the acetonitrile further displaced (Figure S1b), suggesting an overall tendency of such clusters to form a triangular environment around Cu. From the solution chemistry point of view, such disordering reflects the leaching of this copper atom from the cluster to the solution. The same situation was previously reported in the case of silver thiolates [28].
In the case of the solution containing 2,4,6-trimethylpyridine (Me3py), we observed a mixture of two crystalline phases (named as 2a and 2b) as a diffusion result. According to the SCXRD results, the main difference between [Cu6(StBu)4(Me3py)4(NO3)2]·3.5CH3CN (2a) and [Cu6(StBu)4(Me3py)5(NO3)](NO3)·5CH3CN (2b) is in the ligand shell around the {Cu6(StBu)4}2+ cage. In the case of 2a, {Cu6(StBu)4}2+ coordinates two nitrates in a virtual trans-mode, while in the crystal structure of 2b there is only one nitrate ligand coordinated by {Cu6(StBu)4}2+ and another one is just a counter-anion (Figure S2). From the solution chemistry point of view, this reflects a close formation energy of [Cu6(StBu)4(Me3py)4(NO3)2] and [Cu6(StBu)4(Me3py)5(NO3)](NO3).
The crystal structure of (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O (3) is quite interesting because: (i) this addresses H2O and Et3NH+ utilization and (ii) the complex does not contain any coordinated 2,6-dichloropyridine (2,6-pyCl2) molecules. According to the collected data, H2O molecules and Et3NH+ form hydrogen bonds with the nitrate anions (Figure S3), which are strong H-bond acceptors in non-aqueous media. Thus, in the reaction mixture Et3NH+ forms close ionic pairs with NO3−, which can be introduced into the complex structure. The formation of (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O instead of [Cu6(StBu)4(2,6-pyCl2)4(NO3)2] or [Cu6(StBu)4(2,6-pyCl2)5(NO3)](NO3) can be caused by low donation of the N-atom in the 2,6-dichloropyridine that, however, dictates a specific media, giving {Cu6(StBu)4} species instead of {Cu3(StBu)3}n in the absence of 2,6-pyCl2.
[Cu6(StBu)4(2-Br-py)4(NO3)2]·2-Br-py (4) is only a complex containing an R-py molecule as a solvate molecule of crystallization (Figure S4). We did not detect any specific Br···Br interactions of 2-Br-py; only C-H···π and C-H···Br contacts were observed. The [Cu6(StBu)4(2-Br-py)4(NO3)2] complex has two coordinated nitrate anions located in a virtual trans-mode, the same as in [Cu6(StBu)4(Me3py)4(NO3)2].
Isostructural compounds 5 and 6 with halogenated pyridines comprise two different clusters, [Cu6(StBu)4(3-Hal-py)6]2+ and [Cu6(StBu)4(CH3CN)6]2+, i.e., in this case, pyridine and acetonitrile molecules allocate their ligand roles in favor of the “pure” pyridine and acetonitrile clusters. As a result, the clusters possess high symmetry of −43m for their geometry centers, while the pyridine moieties are disordered over four equivalent proximate positions (Figure 3a). Each cluster of one type is surrounded by four clusters of the other type, giving rise to the F-centered cubic crystal packing pattern (Figure 3b).
Strong disorder of py-X ligands in 5 and 6 prevents the analysis of halogen bonds in these structures, which can make sense in these structures’ formation.
Sarkar et al. reported a series of copper thiolate complexes containing {Cu4S6}, {Cu5S7}, and {Cu6S4} cores [29]. According to the reported data, the conversion between these structural units is straightforward. The hexanuclear copper(I)–thiolate complexes (Et4N)4[Cu6(SPh)4X6] (X = Cl− and Br−) are closely related to the complexes reported here. They were synthesized by treating [Cu(SPh)]n [30] with the respective Et4NX. The authors noticed that both complexes in CH3CN or any other protic solvent decompose with the precipitation of [Cu(SPh)]n. Even the solid-state crystals of (Et4N)4[Cu6(SPh)4X6] slowly decompose, which was detected by ESR. In our case, keeping the reaction mixtures containing py-R for a long time under Ar atmosphere did not result any orange or red coloration, nor were any solids formed. Thus, the further nucleation of copper thiolates into other nanoclusters did not proceed, as such processes need other conditions.
Gao et al. reported [Na(C3H6O)6][Cu6(SR)6] (C3H6O = acetone, SR = 2-mercaptobenzoxazolate) containing a Cu6 metal core as a slightly distorted octahedron bearing six copper atoms at 2.58–2.88 Å distances [31]. Each sulfur atom links a pair of copper atoms with two Cu–S bond lengths of 2.33 and 2.40 Å. Thus, Cu···Cu distances in this cluster are noticeably shorter than in ours. This can be a consequence of (i) partial cluster reduction, resulting in species with a Cu0/Cu+ formal charge; (ii) another Cu-to-thiolate ratio of 6:6 instead of 6:4. Unfortunately, the crystal structure of the compound was not deposited with any structural database, and we cannot perform further comparison with our structures.
We tried to measure the luminescent properties of 1–6 using different techniques but oxidation is still a problem to be solved.
The complexes reported here indeed shed light on the equilibrated species in solution. We found the following coordination modes of Cu(I) (Figure 4): (i) {Cu(NO3)} with asymmetric terminal bidentate type B01 coordination of the anion [32]; (ii) {Cu-NC-CH3}+; (iii) {Cu-py-R}; (iv) in the case of 5 and 6 there is a remarkable differentiation of the complex forms to {Cu6(StBu)4(CH3CN)6}2+ and {Cu6(StBu)4(py-X)6}2+ (X = Cl, Br).

3.2. Quantum Chemical Calculations

Whether Cu···Cu contacts exist in the complexes of 1–6 is an interesting question, as they exhibit rather long distances of 3.07–3.81 Å. For instance, in the work devoted to calculations of cuprophilic interactions in [Cu10O2(Mes)6]n, the corresponding distances are much shorter (2.776 Å) [21]. To shed light on this, we performed a topological analysis based on the Quantum Theory of Atoms in Molecules (QTAIM) and the Noncovalent Interaction (NCI) Index defined as the Reduced Density Gradient (RDG). We studied six types of complexes, rejecting examples with a similar constitution (Figure 5). For 3, the complex and the Et3NH+ counterion were tested to account for the hydrogen bond N–H···O between them. Along the Cu···Cu lines, no features were found; however, inside the Cu6 core, quadruple-bladed pyramidal surfaces of neutral character were observed (Figure 6), with the blades pointing toward four Cu3 faces not occupied by S atoms.
While the surface shapes are similar across the series, the blades exhibit a slight thickening for faces comprising Cu(O) atoms. The centers of the pyramids are characterized by cage critical points (CCP; 3, +3), while blade tips are characterized by ring critical points (RCP; 3, +1), both with neutral energetic characteristics (Table S3). The positions of the critical points are displaced relative to the geometrical centers of the Cu3 faces by 0.15–0.20 Å.
Geometry optimisation by the example of [Cu6(StBu)4(CH3CN)6]2+ gave a slightly different model (Table S4) with the Cu–S and Cu…Cu distances elongated by 0.02 and 0.05 Å, correspondingly. The RDG analysis for this model revealed the same quadruple-bladed surface (Figure S5); the characteristics of the critical points were also similar to those for the non-optimized model (Table S3). We further performed higher-level calculation, viz. with ωB97X/def2-TZVPP with ZORA corrections, based on the example of [Cu6(StBu)4(CH3CN)6]2+. The results agree with the lower-level ones. Thus, based on the example of [Cu6(StBu)4(CH3CN)6]2+ we have shown that a slight geometrical change and another level of theory negligibly affect the nature of the cuprophilic interactions. Given that the characteristics of the interactions are similar across the series, we speculate that this conclusion is acceptable for the other models. Thus, despite the rather long Cu···Cu distances, the complexes exhibit interesting cuprophilic interactions of neutral character, manifested by a quadruple-bladed pyramidal shape. Nevertheless, the interactions are rather a consequence of the cage geometry of {Cu6(StBu)4}, supported by the thiolate ligand, as well as acetonitrile, substituted pyridine, and nitrate.

4. Conclusions

This research focuses on the structural analysis of complexes isolated from the solutions containing {Cux(StBu)y} species and pyridine derivatives. Six new complexes have been characterized by SCXRD. All the structures reveal a diamond-like {Cu6(StBu)4}2+ cage as a main building unit, which shows the shift of equilibria between whole {Cux(StBu)y} species in solution to the {Cu6(StBu)4}2+ dominance by adding py-R. Analysis of the Cu(I) coordination modes shows the presence of {Cu6(StBu)4(CH3CN)6}2+ and {Cu6(StBu)4(py-X)6}2+ (X = Cl, Br) as the corner forms. Other complexes demonstrate the presence of {Cu(NO3)}, {Cu(NC-CH3)}+, and {Cu(py-R)}+ coordination sites. In the presence of 2,6-pyCl2, the complex (NHEt3)[Cu6(StBu)4(CH3CN)3(NO3)3]·H2O formed does not comprise the corresponding pyridine. However, it dictates a specific media for {Cu6(StBu)4}2+ species instead of {Cu3(StBu)3}n, formed in the absence of 2,6-pyCl2. The electronic structure of all complexes was studied by means of quantum chemical calculations. We found interesting cuprophilic interactions of neutral character combining copper atoms inside the Cu3 faces. Such interactions are a consequence of the geometry of {Cu6(StBu)4}2+ cages, which are stabilized by the thiolate ligand, as well as acetonitrile, substituted pyridine, and nitrate. The studies of equilibria between {Cux(StBu)y} species in different organic media are in progress.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cryst15070607/s1, Table S1: Crystal data and structure refinement for the compounds; Table S2: Cu–X (X = N, O, S, Cu) distances in the crystal structures of 1–6; Table S3: Characteristics of the critical points in Cu6 fragment in the complexes: values of the density of all electrons ρ(r) (a.u.), Laplacian of electron density ∇2ρ(r), potential energy density V(r), Lagrangian kinetic energy G(r), and estimated strength for the interactions Eint (kJ/mol); Table S4: Cartesian coordinates (Å) of the geometry-optimized [Cu6(StBu)4(CH3CN)6]2+ model (PBE0/def2-TZVP level) and the trajectory of atomic coordinates upon optimization, shown as spheres colored from blue through white to red. Figure S1: A fragment of the structure of 1, showing two positions of the disordered Cu atom, {CuS2N2} (a, site occupancy of 70%) and {CuS2N} (b, site occupancy of 30%). Nitrates and H atoms are omitted. The Cu–N(acetonitrile) distances are 2.119(13) Å for position (a) and 2.77(3) Å for (b); Figure S2: The comparison of 2a (a) and 2b (b) complexes. tBu fragments are omitted for clarity; Figure S3: H-bonding in the crystal structure of 3. tBu fragments are omitted for clarity; Figure S4: (a) The structure of [Cu6(StBu)4(2-Br-py)4(NO3)2] in the crystal structure of 4; (b) the position of 2-Br-py solvate molecule relatively to the cluster unit. tBu fragments are omitted for clarity. Figure S5: Comparison between fragments of plot of sign(λ2)·ρ mapped over the RDG inside the {Cu6S4} moieties (isovalue s = 0.6; –0.02 a.u.< sign(λ2)·ρ <0.02 a.u.) in different [Cu6(StBu)4(CH3CN)6]2+ models: (a) geometry derived from the XRD experiment, with the electron density calculated at PBE0/def2-TZVP level; (b) geometry-optimised model at the same level; (c) geometry-optimised model with the electron density calculated at ωB97X/ZORA-def2-TZVPP level. Cu atoms are shown as orange spheres, other atoms (S—yellow, O—red, N—blue, F—green, C—beige, H—white) are presented in stick model.

Author Contributions

Conceptualization, P.A.A. and T.S.S.; methodology, P.A.A.; investigation, P.A.A. and T.S.S.; writing—original draft preparation, P.A.A.; writing—review and editing, P.A.A., T.S.S. and M.N.S.; project administration, P.A.A.; funding acquisition, M.N.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Russian Science Foundation, grant number 24-13-00319.

Data Availability Statement

The structures of titled compounds were deposited to the Cambridge Crystallographic Data Centre (CCDC) as a supplementary publication, No. 2451538-2451544.

Acknowledgments

The authors thank the Ministry of Science and Higher Education for access to the NIIC XRD facilities. The authors thank N.K. Zaitsev for help with the experiments and V.S. Korenev for help with the color artworks.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
SCXRDSingle Crystal X-ray Diffraction
QTAIMQuantum Theory of Atoms in Molecules
NCINoncovalent Interactions
RDGReduced Density Gradient
RCPRing Critical Point
CCPCage Critical Point

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Crystals 15 00607 sch001
Scheme 1. The general route to [Cu6(StBu)4(py-R)x] complexes.
Scheme 1. The general route to [Cu6(StBu)4(py-R)x] complexes.
Crystals 15 00607 sch001
Crystals 15 00607 g001
Figure 1. Representation of {Cu6(StBu)4} fragment as an octahedron and structural formulae of compounds 1–6. Solvate molecules are not specified.
Figure 1. Representation of {Cu6(StBu)4} fragment as an octahedron and structural formulae of compounds 1–6. Solvate molecules are not specified.
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Crystals 15 00607 g002
Figure 2. The schematic transformation of {Cu6(StBu)4} units into [Cu3(StBu)3]n: (a) the diamond-like core of 1–6; (b) the main structural motif of [Cu3(StBu)3]n; and (c) the compressed {Cu6(StBu)6} unit in the crystal structure of [Cu3(StBu)3]n. Copper is cyan, StBu units are yellow.
Figure 2. The schematic transformation of {Cu6(StBu)4} units into [Cu3(StBu)3]n: (a) the diamond-like core of 1–6; (b) the main structural motif of [Cu3(StBu)3]n; and (c) the compressed {Cu6(StBu)6} unit in the crystal structure of [Cu3(StBu)3]n. Copper is cyan, StBu units are yellow.
Crystals 15 00607 g002
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Figure 3. (a) Relative arrangement of a pair of [Cu6(StBu)4(3-Hal-py)6]2+ (blue octahedron) and [Cu6(StBu)4(CH3CN)6]2+ (yellow octahedron) in the structures of 5–6. H atoms are omitted; disordered pyridine moieties are shown with van der Waals spheres. (b) The corresponding crystal packing, showing only the clusters.
Figure 3. (a) Relative arrangement of a pair of [Cu6(StBu)4(3-Hal-py)6]2+ (blue octahedron) and [Cu6(StBu)4(CH3CN)6]2+ (yellow octahedron) in the structures of 5–6. H atoms are omitted; disordered pyridine moieties are shown with van der Waals spheres. (b) The corresponding crystal packing, showing only the clusters.
Crystals 15 00607 g003
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Figure 4. Structural units found in the crystal structures of 1–6.
Figure 4. Structural units found in the crystal structures of 1–6.
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Figure 5. Fragments of plot of sign(λ2) ρ mapped over the RDG inside the {Cu6S4} moieties in the complexes (isovalue s = 0.6; −0.02 a.u.< sign(λ2)·ρ <0.02 a.u.). Cu atoms are shown as orange spheres, while other atoms (S—yellow, O—red, N—blue, F—green, C—beige, H—white) are presented in stick model form.
Figure 5. Fragments of plot of sign(λ2) ρ mapped over the RDG inside the {Cu6S4} moieties in the complexes (isovalue s = 0.6; −0.02 a.u.< sign(λ2)·ρ <0.02 a.u.). Cu atoms are shown as orange spheres, while other atoms (S—yellow, O—red, N—blue, F—green, C—beige, H—white) are presented in stick model form.
Crystals 15 00607 g005
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Figure 6. Cu6 octahedron and plot of sign(λ2)·ρ mapped over the RDG in the complexes of 1–6 by the example of 3. Copper is bronze, StBu units are yellow.
Figure 6. Cu6 octahedron and plot of sign(λ2)·ρ mapped over the RDG in the complexes of 1–6 by the example of 3. Copper is bronze, StBu units are yellow.
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Sukhikh, T.S.; Sokolov, M.N.; Abramov, P.A. Diamond-like Cage Motifs in {Cu6(StBu)4} Complexes with Pyridines. Crystals 2025, 15, 607. https://doi.org/10.3390/cryst15070607

AMA Style

Sukhikh TS, Sokolov MN, Abramov PA. Diamond-like Cage Motifs in {Cu6(StBu)4} Complexes with Pyridines. Crystals. 2025; 15(7):607. https://doi.org/10.3390/cryst15070607

Chicago/Turabian Style

Sukhikh, Taisiya S., Maxim N. Sokolov, and Pavel A. Abramov. 2025. "Diamond-like Cage Motifs in {Cu6(StBu)4} Complexes with Pyridines" Crystals 15, no. 7: 607. https://doi.org/10.3390/cryst15070607

APA Style

Sukhikh, T. S., Sokolov, M. N., & Abramov, P. A. (2025). Diamond-like Cage Motifs in {Cu6(StBu)4} Complexes with Pyridines. Crystals, 15(7), 607. https://doi.org/10.3390/cryst15070607

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