Constructing Supramolecular Frameworks Based Imidazolate-Edge-Bridged Metallacalix[3]arenes via Hierarchical Self-Assemblies

Abstract

Hierarchical self-assembly of novel supramolecular structures has obtained increasing attention. Herein we design and synthesize the palladium(II)-based molecular basket-like structures, as structural analog of metallacalix[3]arene [M₃L₃]³⁺ (M = (dmbpy)Pd, (phen)Pd; dmbpy = 4,4’-dimethyl-bipyridine; phen = 1,10-phenanthroline), by coordination-driven self-assembly from imidazolate-containing ligand [4,5-bis(2,5-dimethylthiophen-3-yl)-1H-imidazole (HL) with palladium(II) nitrate precursors (dmbpy)Pd(NO₃)₂ and (phen)Pd(NO₃)₂. The difference of the palladium(II) nitrate precursors with π-surface in complex produces variations of the two-dimensional (2-D) and three-dimensional (3-D) high-ordered supramolecular architectures, constructed by π···π packing and hydrogen bonding interactions, with metallacalixarenes as building blocks. These results provide perceptions of further exploring the hierarchical assembly of supramolecular structures based on π···π packing and multiple hydrogen bonding.

1. Introduction

Supramolecular self-assembly is ubiquitous in nature, and builds up the high-ordered structures through spontaneous organization of building blocks driven by noncovalent interactions [1,2,3,4]. Recently, it has become more clearer that the nature often constructs complex structures by employing hierarchical self-assembly strategies that bring the compounds together step-by-step via multiple noncovalent interactions [5,6,7,8]. Inspired by the dedicated biological structures in nature, hierarchical self-assembly strategies have been increasingly used to create well-defined assemblies with high complexity [9,10,11].

Designing and constructing molecular architectures via metal-driven self-assembly has developed rapidly in the last few years [12,13]. These techniques come down to the design of multidentate ligands and choice of metal ions to afford self-assembled molecules under suitable reaction conditions [14,15,16]. Apart from the synthesis of new self-assemblers, the understanding and employing of non-covalent interactions, including hydrogen bond interactions and π-π packing, is fundamentally important to develop the field of crystal growing and designing [17,18,19,20,21,22,23,24,25]. These intermolecular interactions make great contributions to the supramolecular association [26,27,28,29,30].

The synthesis and structural studies of a variety of palladium(II) molecular structures as structural analogs of metallacalixarenes are well studied by changing different cis-protecting palladium(II) components or counter-anions or ligands in our previous work and others [31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47]. However, the hierarchical self-assembly of palladium(II)-based self-assembly molecules has been rarely studied [48,49]. Herein, we design nitrogen donor compounds with thiophene groups as ligands, and choose palladium(II) components with π-surface in the cis-protecting parts (Scheme 1) and nitrate/hexafluorophosphate as counter-anions, respectively. We study the difference of the palladium(II) components in the construction of configuration and the self-assembly step-by-step.

As an extension of our previous studies of metallacalixarene analogs via self-assembly approach, herein we present the design and synthesis of [M₃L₃]³⁺-type metallacalixarenes derived from imidazole-bridged bidentate ligand HL by reacting with coordinated palladium(II) precursors (phen)Pd(NO₃) and (dmbpy)Pd(NO₃)_{2 2} in aqueous media via self-assembly (Scheme 1). Single crystal X-ray diffraction and elemental analysis techniques were used to characterize the solid structures of two new complexes.

2. Experimental Section

2.1. Materials and Instrumentation

Chemicals purchased were of analytical grade and used without purification. The ¹H NMR spectra were recorded on a BRUKER AVANCE III HD 400 M Hz spectrometer (Bruker Corporation, Berlin, Germany). Elemental analyses (EA) for C, H and N were performed on a EA 1108 (Carlo Erba Instruments) elemental analyzer. Ligand HL was synthesized according to a reported literature [50,51].

2.1.1. Synthesis of Complex [(dmbpy)₃Pd₃L₃](NO₃)₃ (1•3NO₃)

Combination of (dmbpy)Pd(NO₃)₂ (14.10 mg, 0.034 mmol) with a suspension of HL (9.81 mg, 0.034 mmol) in H₂O (1 ml) and acetonitrile (1 ml), the mixture was stirred for 24 h at 25 °C. The desired product 1•3NO₃ was obtained as a light-yellow precipitate (yield: 65%).

The PF₆-salt [(dmbpy)₃Pd₃L₃](PF₆)₃ (1•3PF₆) was obtained with addition of excess of KPF₆ to solution, resulting in the deposition of 1•3PF₆ as yellow solids. The solids were filtered, washed with water and then dried (yield: 85%). Anal. Calc. for C₈₁H₈₁F₁₈N₁₂P₃Pd₃S₆: C 44.85, H 3.76, N 7.75; found: C 44.92, H 3.69, N 7.71.

2.1.2. Synthesis of Complex [(phen)₃Pd₃L₃](NO₃)₃ (2•3NO₃)

A combination of (phen)Pd(NO₃)₂ (13.96 mg, 0.034 mmol) with a suspension of HL (9.81 mg, 0.034 mmol) in H₂O (1 ml) and acetonitrile (1 ml) was stirred for 24 h at 25 °C The designed product 2•3NO₃·was obtained as yellow micro-crystals (yield: 55%). Anal. Calc. for C₈₁H₆₉N₁₅O₉Pd₃S₆: C 50.99, H 3.64, N 11.01; found: C 50.22, H 3.69, N 11.21.

2.2. X-ray Structure Determination and Structure Refinement

Single crystal X-ray diffraction data for compound HL and complexes 1•3PF₆ and 2•3NO₃ are collected on a Rigaku Super Nova CCD X-ray diffractometer equipped with low temperature device and a fine-focus sealed-tube X-ray source (graphite monochromated Cu-Kα radiation, λ = 1.54184 Å; Mo-Kα radiation, λ = 0.71073 Å; Ga-Kα radiation, λ = 1.34139 Å). Suitable single crystals were picked from the mother liquid, attached to a glass loop and transferred to a designed cold stream of liquid nitrogen (173 K) for data collections. Raw data collection and reduction were done using APEX2 software. The SHELXTL direct methods was used to solve all the crystal structures, which was again refined by employing full-matrix least-squares on F² by using the SHELXTL software program and expanded using Fourier techniques [52,53]. All non-H atoms of the complexes were refined with anisotropic thermal parameters. The hydrogen atoms were included in idealized positions. Final residuals, along with the unit cell, space group, date collection and refinement parameters, are presented in Table 1. Tables S1 and S2 give crystallographic details and selected bond distances and angles. Crystallographic data for structures reported in this paper have been deposited in the Cambridge Crystallographic Data Center under reference numbers CCDC 2126504, 2116570–2116571. These data can be downloaded via www.ccdc.cam.ac.uk/[email protected] (28 December 2021).

3. Results and Discussion

3.1. Ligand Synthesis and Structural Characterization

Compound 4,5-bis(2,5-dimethylthiophen-3-yl)-1H-imidazole (HL) as a ligand was prepared according to the literature, and charactered with spectroscopic data (Figure S1 in the Supplementary Materials) [50]. Single crystals of ligand HL were obtained by evaporating chloroform solution, and the X-ray crystallographic data further confirms the structure (Figure 1). The asymmetric unit of HL contains two independent molecules, and neighboring molecules are connected through [N-H···N] hydrogen bonds [r(N···N) = 2.819 Å and 2.844 Å; ∠N-H···N = 174.48° and 170.74°] to give a supramolecular chain. It is worth mentioning that the 1-D chain is also stabilized by another kind of weak interaction as [C-H···S] hydrogen bonds with C···S distances of 3.725 Å and 3.743 Å [54], which are shorter than the C···S distances reported in the literature [51], which is of important weak interaction in the hierarchical self-assembly for the construction of supramolecular frameworks, with imidazolate-edge-bridged metallacalixarenes as building blocks.

3.2. Synthesis and Structural Characterization of Metallacalix[3]arenes

Complexes [(dmbpy)₃Pd₃L₃](NO₃)₃ (1•3NO₃) and [(phen)₃Pd₃L₃](NO₃)₃ (2•3NO₃) were synthesized by metal-directed self-assembly. Reacting HL with one equivalent of cis-protected palladium(II) nitrate precursor (dmbpy)Pd-NO₃ and (phen)₃Pd-NO₃ in H₂O/acetonitrile (1:1, v/v) at room temperature gave a yellow reaction mixture (see Exp. Sect.). The conditions were fine-tuned to obtain appropriate crystals for single crystals XRD of 2•3NO₃ and 1•3PF₆, which was obtained by adding aqueous ammonium hexafluorophosphate to the solution of 1•3NO₃. In these structures, every ligand (HL) deprotonates spontaneously, and acts as a monovalent [(L)⁻] building unit. Complexes 1•3NO₃ and 2•3NO₃ were characterized by ¹H NMR spectrometry. The ¹H NMR spectra of both new complexes have been worked out in DMSO-d₆ (Figure S8). Unfortunately, the signals of all protons of the cis-protecting units and ligands are observed as broad signals, which could not be assigned exactly. Molecular structure of complexes 1•3PF₆ and 2•3NO₃ are further confirmed by satisfactory X-ray diffraction and elemental analysis.

Single crystals of 1•3PF₆ were collected by the vapor diffusion of diethylether into the acetonitrile solution, and single crystals of 2•3NO₃ were obtained from aqueous solutions. Part of the bond lengths and bond angles are listed in Tables S1 and S2. Complex 1•3PF₆ crystallizes in triclinic crystal system and P-1 space group, but complex 2•3NO₃ crystallizes in monoclinic crystal system and C2/c space group. Both contain three cationic {Pd(N^N)} units bound to three anionic ligands with three hexafluorophosphate or nitrate as counter-anions and the crystal structures of the complexed cation are displayed in Figure 2. One of the hexafluorophosphates or nitrates is present at the bottom of the basket-shaped structures, as shown in Figures S2 and S3.

Taking complex 1•3PF₆ as an example, the three dimethylthiophen-imidazolate ligands form the basket wall; all ligands are linked by [(dmbpy)Pd] units in a syn, syn, syn orientation. All palladium(II) atoms make up a triangle with Pd···Pd distances of 5.949 Å, 5.918 Å and 5.890 Å, as shown in Figure 2. The dimensions of the molecular basket are 5.974 Å, 5.985 Å, 6.202 Å, 5967 Å, 6.189 Å and 5.920 Å for the upper-rim lengths (e.g., the distances between two S atoms of thiophene groups); 2.374 Å, 2.228 Å and 2.133 Å for the lower-rim lengths between the protons of imidazolium units, and 6.63 Å in depth (Figure S4). The thiophene groups attached to the imidazole appear haphazard, due to the freely rotating nature of the single bond. In complex 1•3PF₆, the thiophene sulphur atoms of one ligand are H-bonded to methyl groups (S···H–C) from the ligand to form a dimer. 2-D growth is found resulting from π···π stacking and multiple [S···H–C] hydrogen bonding interactions in complex 1•3PF₆ (Figure 3).

The non-bonded distances of the triangle Pd₃ and the dimensions of the molecular basket 2•3NO₃ are listed in Figure 2. Interestingly, the imidazolate units are oriented same in the trimers relative to the Pd₃ plane. Three C atoms between two N atoms of the imidazole units are positioned to the same side and oriented in toward one another, which close off one side of the Pd₃ plane, including an anion of hydrogen bonded (Figure S3). On the opposite side, the thiophene groups attached to the ethylene units, designated as the all “up” configuration, rendering a basket-like open side. In complex 2•3NO₃, the thiophene sulphur atoms of the ligand are H-bonded to methyl groups (S···H–C) from the ligand to form a dimer. Nevertheless, 3-D growth is found resulting from π···π stacking and multiple [S···H–C] hydrogen bonding interactions in complex 2•3NO₃ (Figure 4).

3.3. Influence of cis-Protecting Groups on the Crystal Engineering

The more interesting points of the crystal structure are displayed by analyzing the packing model. One Hydrogen bonded dimer is observed to be associated with two more dimers via π-π packing of the planer ‘dmbpy’ or ‘phen’ moieties [55,56,57] in an interoverlaying manner, resulting in a 2-D layer and 3-D network, as shown in Figure 3 and Figure 4. All the crystal structures are stabilized via the π···π packing between planar ‘dmbpy’ or ‘phen’ components and hydrogen bonding weak interactions involving thiophene groups (C-H···S). Supramolecular frameworks with imidazolate-edge-bridged metallacalix[3]arenes are constructed by employing via coordination self-assembly, π···π packing and hydrogen-bonded interactions step-by-step. Further interactions seen in the packing are discussed in a later section.

The presence of π-surface in the cis-protecting units and thiophene groups is quite capable of influencing the crystal packing via hierarchical self-assembly. In the case of the complex 1•3PF₆, one molecular basket is linked by two other neighboring molecules via π···π packing, whereupon the ‘dmbpy’ units of 1•3PF₆ are stacked in a parallel manner with distances of ~3.640 Å and 3.850 Å. Then, they were arranged in a 1-D π-polymer as a chain, as already shown in Figure 3. The more interesting point is to note that a set of molecular chains is stacked to other sets via double [C-H···S] hydrogen bonding interactions in crystal packing of 1•3PF₆, resulting in a 2-D panel.

In the case of complex 2•3NO₃, molecules are stacked in the crystal engineering in a perfectly packing manner because of π···π packing. The π···π packing displays more favorable of ‘phen’ units due to its large aromatic ring. Thus, there is an almost face-to-face π···π stacking of ‘phen’ units in a triangle manner, where three ‘phen’ units of a molecular triangle overlap three other ‘phen’ units from three adjacent molecules to form a 2-D layer (Figure 3). Then, a set of molecular layers is linked to other sets via double [C-H···S] hydrogen bonding interactions, one above and one below, resulting in a 3-D supramolecular framework (Figure 4).

4. Conclusions

In this contribution, we have presented metal-driven self-assembling molecular basket-like nano-cavities as structural analogs of [M₃L₃]³⁺-type metallacalix[3]arene, using cis-protecting palladium(II) components with π-cloud and novel rigid imidazolate-bridging ligands that differ from previous ligands of this type by having thiophene as functionalized groups. The structures of these two metallacalixarenes have been confirmed by element analysis and single crystal X-ray diffraction methods. The crystallography shows that one anion (NO₃⁻ or PF₆⁻) binds at the lower rim of the basket via C–H∙∙∙anion weak interaction within basket-shaped metallacalixarenes. In particular, the design of ligands and choice of the π-cloud in the cis-protecting palladium(II) units could control the crystal growth, and guided us to study the hierarchical self-assembly in the crystalline state through π∙∙∙π packing and hydrogen bonding weak interaction. Further investigation will focus on their potentials as chemsensors for the multiple recognition of ions. These results bring new approaches for achieving 2-D and 3-D high-ordered supramolecular structure-based hierarchical self-assemblies and targeted functionalities.

Author Contributions

Conceptualization, J.T.; methodology and investigation, B.C.; formal analysis, L.Z.; writing—original draft preparation, review and editing, J.T.; supervision, X.W.; and supervision, S.Y. All authors have read and agreed to the published version of the manuscript.

Funding

We thank the National Natural Science Foundation of China (21906002), Beijing Natural Science Foundation of China (2212002), Beijing Municipal Science and Technology Project (KM202010005010) and Beijing Outstanding Young Scientist Program (BJJWZYJH01201910005017) for support with funding.

Data Availability Statement

Not applicable.

Conflicts of Interest

All authors declare no conflict of interest.

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures, Scheme and Table

Scheme 1. Scheme of the synthesis of molecular basket-like metallacalixarenes via bidentate imidazole-based ligands.

Figure 1. Crystal structure of (a) HL and (b) supramolecular chain structure in HL via[C-H···S] and [N-H···N] hydrogen bonds.

Figure 2. Crystal structures of complexed cations 13+ and 23+ via metal-ligand coordination: top views (a,c) and side views (b,d) (hydrogens, anions, and solvent molecules are excluded for clarity).

Figure 3. Supramolecular 1-D structural fragments in 1•3PF6 via π···π packing (a,b) and Supramolecular 2-D structure of 1•3PF6 via π···π packing and [C-H···S] hydrogen bonds (c,d) (the C-S distance of 3.589 Å and the CH-S angle of 132.81°).

Figure 4. Supramolecular 2-D structural fragments in 2•3NO3 via π···π packing (a–d) and Supramolecular 3-D structure of 2•3NO3 via π···π packing and [C-H···S] hydrogen bonds (e,f) (the C-S distance of 3.804 Å, the C-H···S angle of 147.48°).

Table 1

Crystal data and structure refinement for HL, 1•3PF₆ and 2•3NO₃.

	HL	1•3PF6	2•3NO3
Formula	C32H32N4S4	C81H81F18N12S6P3Pd3	C81H69N15O9S6Pd3
Formula weight	600.85	2169.04	1908.07
crystal system	triclinic	triclinic	monoclinic
space group	P-1	P-1	C2/c
a [Å]	9.6510(7)	16.8822(9)	33.3674(14)
b [Å]	12.1557(10)	18.9348(7)	20.8260(9)
c [Å]	13.4203(11)	18.9951(7)	35.088(3)
α [°]	98.101(3)	60.273(3)	90
β [°]	91.796(3)	74.678(3)	115.090(5)
γ [°]	101.972(2)	89.701(4)	90
V [Å3]	1521.8(2)	5027.8(4)	22082(2)
Z	2	2	8
ρcalcd, [g/cm−3]	1.311	1.433	1.148
μ [mm−1]	0.341	6.581	0.646
F(000)	632	2184	7728
2θmax [°]	56.764	69.999	27.000
no. unique data	7567	18,840	24,101
Parameters	5616	1126	1135
GOF [F2]	1.049	1.050	1.056
R[F2 > 2σ(F2)]	0.0568	0.0404	0.0508
wR[F2]	0.1755	0.0977	0.1035

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cryst12020212/s1, Figure S1: 1H NMR spectrum of HL. Tables S1 and S2: crystallographic data of complexes 1·3PF6 and 2·3NO₃. Figures S2 and S3: Top view and side view of the basket-shape structures with one anion of 1·3PF6 and 2·3NO₃. Figures S4 and S5: Top view and side view of the basket-shape structures with size of 1·3PF6 and 2·3NO₃. Figures S6 and S7: the packing model of the structures of 1·3PF₆ and 2·3NO₃.

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