Coordination-Driven Self-Assembly of Discrete Molecular Nanotubular

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Cite This: Inorg. Chem. XXXX, XXX, XXX−XXX

Coordination-Driven Self-Assembly of Discrete Molecular Nanotubular Architectures Imtiyaz Ahmad Bhat,† Ennio Zangrando,‡ and Partha Sarathi Mukherjee*,† †

Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India Department of Chemical and Pharmaceutical Sciences, Universita degli Studi di Trieste, via Giorgieri 1, 34127 Trieste, Italy

‡

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ABSTRACT: Two new M8L4 tetrafacial nanotubes (T1 and T3) of different lengths have been synthesized in water using ligands L1 and L2, respectively, with acceptor cis-[(dch)Pt(NO3)2] (M) using coordination-driven self-assembly [where dch is 1,2-diaminocyclohexane, L1 is 1,4-di(pyrimidin-5-yl)benzene, and L2 is 4,4′di(pyrimidin-5-yl)-1,1′-biphenyl]. In addition to complex T1, a tetrahedral cage of composition [M12(L1)6] (T2) was also formed in the self-assembly reaction of ligand L1 with cis-[(dch)Pt(NO3)2]. The precise composition of the products (T1 and T2) in solution was confirmed by 1H NMR and ESI−MS. Pure tube T1 was separated out by a crystallization technique and fully characterized by 1H NMR and X-ray diffraction. Temperature- and concentration-dependent NMR studies indicated no equilibrium between T1 and T2 in the solution phase, and the proportion of T1 and T2 in the mixture depends on the temperature of the reaction. In contrast to ligand L1, the self-assembly of the longer ligand, L2, with cis-[(dch)Pt(NO3)2] gave only tetrafacial tube [M8(L2)4] (T3) without any tetrahedral cage.

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INTRODUCTION Supramolecular architectures synthesized through various selfassembly approaches have been found to be quite interesting in terms of both their diverse structural features and applications in recognition, catalysis, separation, drug delivery, and sensing. Among other synthetic self-assembly approaches, coordination-driven self-assembly based on the metal−ligand coordination bond as a driving force has emerged as a convincing tool for forming a plethora of coordination architectures with fascinating applications.1 This approach is endowed with numerous synthetic advantages which include the reversible nature of the bond, an inherent self-correction mechanism, a one-pot reaction, and high yields of the desired products. Highly ordered structures such as tetrahedrals,2 octahedrals,3 cubes,4 cuboctahedrals,5 dodecahedrals,6 and others7 have been produced through the judicious combination of donors with suitable acceptors that are held together by metal−ligand bonds. The formation of a single discrete metallocage as an exclusive product is generally observed in many cases. Nevertheless, in some cases, both equilibrium and nonequilibrium mixtures of products are also formed.8 The final outcome of the self-assembly is decided by many other external factors such as the nature of the solvent,9 pH,10 temperature,11 the coordination environment of the metal ions,12 and steric constraints.13 The ratio of the products in an equilibrium mixture is determined by a delicate balance between entropy and enthalpy. While smaller self-assembled structures are favored by entropy because a great number of such assemblies © XXXX American Chemical Society

are formed from the same number of building blocks, larger assemblies are enthalpy-favored with minimal possible conformational strain and other steric constrains. As a result of this balance, smaller assemblies having the ligand flexibility to reduce the possible strain end up as the major component in an equilibrium, while larger assemblies end up as minor products. However, with rigid ligands the larger assemblies are favored by a high enthalpy gain, and it overcompensates for the entropic loss to become the major component of the mixture. Mainly the pyridyl-based symmetric and rigid organic donors have been used to construct such molecular architectures owing to their well-behaved and easy prediction of product structure. Interestingly, pyrimidine-based donors remained less explored because of the weak coordinating ability of endocyclic N atoms. The parent pyrimidine molecule is a π-electron poor heteroaromatic and is weakly basic in nature. Because of the relatively low basicity, the nitrogen binding sites of the pyrimidine form weak coordination bond with the transitionmetal ions. However, few examples of metal complexes with pyrimidine-based ligands are reported in the literature.14 The relatively robust nature of the Pt(II)−N bond as compared to the Pd(II)−N bond encouraged us to explore the Pt(II) acceptors in combination with pyrimidine-based ligands, possibly to achieve stable molecular architectures. Molecular nanotubular structures are of particular importance with their Received: June 13, 2019

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DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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Inorganic Chemistry

Scheme 1. Schematic Representation of the Synthesis of the M8(L1)4 Tube (T1), M12(L1)6 tetrahedral Cage (T2), and M8(L2)4 Tube (T3)

purification. NMR spectra were recorded with a Bruker 400 MHz spectrometer, and the chemical shifts are reported in ppm with respect to tetramethylsilane (Me4Si, δ = 0.00 ppm) or the solvent peaks arising from their incomplete deuteration (δ = 7.26 for CDCl3; δ = 4.79 for D2O in the case of 1H NMR). ESI−MS spectra were recorded using an Agilent model 6538 ultra-high-definition (UHD) accurate mass Q-TOF spectrometer. Single-crystal X-ray diffraction data of tubes T1 and T3 were collected at the X-ray diffraction beamline (XRD1) of the Elettra Synchrotron of Trieste (Italy), with a Pilatus 2 M detector and a monochromatic wavelength of 0.700 Å. [CCDC 1922407 (T1) and 1922408 (T3) contain the supplementary crystallographic data for this paper. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre.] The complete data sets were collected at 100 K under a stream of nitrogen. The structures were solved by direct methods using the SIR program.20 The non-hydrogen atoms were refined with anisotropic displacement coefficients by the full-matrix least-squares method based on F2 implemented in SHELXL-201419 incorporated into WinGX.20 Hydrogen atoms were fixed at their geometrical positions with an isotropic displacement coefficient, U(H) = 1.2U(C) or 1.5U (C-methyl), and their coordinates were allowed to ride on their respective carbons. To further improve, the structure solution was performed by using the SQUEEZE tool of PLATON to take into account the void in the unit cell filled by disordered solvent molecules and counteranions. The geometry of the tetrahedral structure was optimized with the Hartree−Fock method by using the Gaussian 09 software package.21 Synthesis of Ligand (L1). A mixture of 1,4-dibromobenzene (400.0 mg, 1.69 mmol), pyrimidine-5-boronic acid (630.3 mg, 5.09 mmol), Pd(PPh3)4 (97.6 mg), and K2CO3 (1.38 g, 10.0 mmol) was taken in 50 mL of a THF and water (5:1) mixture and refluxed for 48 h under a nitrogen atmosphere. After 48 h, the reaction mixture was extracted with chloroform and the product was purified by column chromatography. Isolated yield: 75%. 1H NMR (400 MHz, CDCl3): δ = 9.24 (s, 2H), 9.01 (s, 4H), 7.75 (s, 4H). 13C NMR (100 MHz, CDCl3): δ = 158.38, 155.36, 135.45, 133.86, 128.49. HRMS (m/z): [M + H]+ calcd for C14H10N4, 235.0905; found, 235.0605. Synthesis of Ligand (L2). A mixture of 4,4′-dibromo-1,1′-biphenyl (500.0 mg, 1.602 mmol), pyrimidine-5-boronic acid (595.7 mg, 4.80 mmol), Pd(PPh3)4 (92.6 mg), and K2CO3 (1.38 g, 10.0 mmol) was taken in 50 mL of a THF and water (5:1) mixture and refluxed for 48 h under a nitrogen atmosphere. After 48 h, the reaction mixture was extracted with chloroform and the product was purified by column chromatography. Isolated yield: 80%. 1H NMR (400 MHz, CDCl3): δ = 9.23 (s, 2H), 9.02 (s, 4H), 7.76 (d, 4H), 7.71 (d, 4H). 13C NMR (100 MHz, CDCl3): δ = 158.11, 155.360, 141.21, 134.23, 134.14,

potential applications in selective ion inclusion and their transportation across the membranes.15 Several infinite tubular structures have been synthesized by utilizing noncovalent interactions such as hydrophobic interaction and hydrogen bonding,16 and yet very few discrete nanotubes synthesized through coordination-driven self-assembly have been reported.17 Herein, we report the self-assembly of two discrete nanotubes from linear pyrimidine-based ligands (L1 and L2) in combination with a cis-blocked Pt(II) acceptor. Two ligands of different lengths, viz., 1,4-di(pyrimidin-5-yl)benzene (L1) and 4,4′-di(pyrimidin-5-yl)-1,1′-biphenyl (L2) were synthesized, and their treatments with cis-[(dch)Pt(NO3)2] (M) (where dch is 1,2-diaminocyclohexane) in a 1:2 stoichiometric ratio led to the formation of self-assembled M8(L1,2)4 tubular structures. The treatment of ligand L1 with cis-[(dch)Pt(NO3)2] (M) formed a nonequilibrium mixture of the M8(L1)4 tube (T1) (major) and M12(L1)6 tetrahedral cage (T2) (minor), whereas a single product such as the M8(L2)4 tube (T3) was formed by treating ligand L2 with cis[(dch)Pt(NO3)2] (M) (Scheme 1). The nonequilibrium mixture of two assemblies T1 and T2 formed from ligand L1 was confirmed by the temperature- and concentration-dependent 1H NMR studies. Tube T1 was formed as the major product (90%) and tetrahedral cage T2 was formed as the minor species (10%) when the self-assembly reaction was carried out at 45 °C for 24 h in H2O (SI, Figure S2). However, self-assembly under reflux conditions for 24 h in water was found to enhance the formation of tetrahedral cage T2 to 35% and the remaining 65% as tube T1 (Figure S3). A single self-assembly product as tube T3 was obtained from ligand L2 under similar reaction conditions in water. Because of the higher Pt(II)−N bond strength as compared to that of the Pd(II)−N bond, the present self-assembly favors the smaller M8(L1)4 assembly product (T1) associated with less entropy loss rather than the larger M12(L1)6 assembly as reported by Fujita by treating the same ligand (L1) with a Pd(II) acceptor.18

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EXPERIMENTAL SECTION

Materials and Methods. Reagents and solvents were purchased from various commercial sources and were used without any further B

DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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Figure 1. (a) Partial 1H NMR and (b) 1H DOSY NMR of a mixture of tube T1 and tetrahedral cage T2 in D2O for the reaction carried out at 100 °C.

Figure 2. (a) Full ESI−MS spectra of T1 and T2 self-assembly solutions with isotopic distributions corresponding to (b) [M8(L1)4−3NO3−]3+, (c) [M8(L1)4−5NO3−]5+, (d) [M12(L1)6−4NO3−]4+, and (e) [M12(L1)6 −5NO3−]5+ charged fragments. The final product was isolated as a light-yellow powder by adding cold acetone to the aqueous solution. Yield: 32.0 mg (78%). 1H NMR (400 MHz, D2O): δ = 10.24 (s, 8H), 9.89 (s, 16H), 7.64 (d, 16H), 7.46 (d, 16H).

128.57, 128.02. HRMS (m/z): [M + H]+ calcd for C14H10N4, 311.1218; found, 311.1312. Synthesis of Tube T1 and Tetrahedral Cage T2. Ligand L1 (8.1 mg, 0.034 mmol) and cis-[(dch)Pt(NO3)2] (30.0 mg, 0.069 mmol) were taken in a 4 mL vial, and 1.5 mL of distilled water was added. The mixture was allowed to stir for 24 h at 45 °C. After 24 h, the reaction mixture was centrifuged to get a clear brownish solution. The final product was precipitated out as a solid powder by adding the cold acetone to the aqueous solution. Yield: 34.0 mg (89%). 1H NMR (400 MHz, D2O): δ = 10.71 (s, 12H), 10.25 (s, 8H), 9.76 (d, 16H), 9.63 (d, 24H), 7.79 (s, 24H), 7.05 (d, 16H). ESI−MS (m/z) = 1405.7610, 818.6600, 1589.3210, and 1259.1920 corresponding to [M 8 (L1) 4 −3NO 3 − ] 3+ , [M 8 (L1) 4 −5NO 3 − ] 5+ and [M 12 (L1) 6 −4NO3−]4+, [M12(L1)6 −5NO3−]5+ charged fragments, respectively. Synthesis of Tube T3. Ligand L2 (10.7 mg, 0.034 mmol) and cis[(dch)Pt(NO3)2] (30.0 mg, 0.069 mmol) were taken in 2 mL of distilled water. The white suspension was stirred for 24 h at 45 °C, and then the mixture was centrifuged to get a clear brownish solution.

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RESULTS AND DISCUSSION Synthesis and Characterization of Tubes T1 and T3. Ligands L1 and L2 were synthesized through the Suzuki coupling reaction of 1,4-dibromobenzene and 4,4′-dibromo1,1′-biphenyl with pyrimidin-5-ylboronic acid under a nitrogen atmosphere at 85 °C and were well characterized by 1H NMR and 13C NMR spectroscopy (Figures S1, S8, and S9). Ligand L1 upon treatment with cis-[(dch)Pt(NO3)2] (M) in water at 100 °C for 24 h gave a clear brownish solution. The clear solution was analyzed by 1H NMR, which showed a set of six peaks in the aromatic region of 7.03−10.69 ppm (Figure 1a). In comparison to the 1H NMR spectrum of a ligand which C

DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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Figure 3. Ball and stick view of the crystal structure of M8(L1)4 tube T1 (a) along a and (b) along c crystallographic axes. (c) Space-filling model representation of the crystal structure of T1. Solvent molecules are omitted for clarity (color codes: C, gray; Pt, red; N, blue; and H, white). (d) Partial 1H NMR of tube T1 recorded in D2O.

independent Pt(II) centers have square-planar coordination geometry with an inner (pyrimidine)N−Pt−N(pyrimidine) bite angle of 91.1° and an outer N−Pt−N bite angle of 91.9°. Tube T1 is featured with eight Pt(II) centers present at the corners and four ligands (L1) paneling the four faces of the tube held through Pt−N coordination bonds. The four metal centers each present at the top and bottom of the tube together form a perfect square with an adjacent Pt−Pt distance of 5.80 Å and a diagonal Pt−Pt distance of 8.20 Å. The length of the tube is 18.26 Å as measured between the two distant and opposite carbon atoms of the cyclohexane rings along the length of the tube (Figure S12). In the crystal structure, the central phenyl ring of each ligand (L1) is tilted by ca. 38° with respect to the side pyrimidine ring. 1H NMR of pure tube T1 showed only three peaks in the aromatic region that match well with one set of three peaks as observed for a mixture of assembly solutions (Figures 3d and S7). Considering the ESI−MS and NMR analyses, the proposed structure of the other assembly, M12(L1)6 (T2), is a tetrahedral cage because an analogous cage was reported by Fujita et al. employing the same donor with a cis-blocked ditopic Pd(II) acceptor. Moreover, the hydrodynamic radius (r = 14.19 Å) calculated for the M12(L1)6 composition based on the 1H DOSY NMR studies matches well with the optimized tetrahedral cage structure (T2) (r = 14.91). We were unable to get the crystal structure of the tetrahedral cage, but its structure was optimized using the Hartree−Fock (HF) method with STO-3G for C, H, N, and O atoms and LANL2DZ for Pt(II) ions as basis sets in the Gaussian 09 software package. The optimized structure displayed an edge-directed M12(L1)6

showed only three peaks, the six peaks displayed by the solution of the product were shifted quite far downfield, thus suggesting either the formation of a mixture of products or a nonsymmetric architecture with ligand present in different chemical environments. To confirm whether a single assembly or a mixture of assemblies was formed, 1H DOSY NMR was studied and showed two diffusion coefficient values with D = 1.69 × 10−10 m2/s (log D (m2/s) = −9.74) and D = 1.37 × 10−10 m2/s (log D (m2/s) = −9.84), thus indicating the formation of two assemblies (Figure 1b). The 1H NMR peaks at 10.23, 9.73, and 7.03 ppm correspond to one assembly (i.e., tube T1), while those at 10.59, 7.98, and 7.78 ppm correspond to another product (i.e., tetrahedral cage T2 (Figure 1b)). The ESI−MS analysis of the solution confirmed the exact composition of the assemblies formed as M8(L1)4 tube T1 and M12(L1)6 cage T2 with prominent peaks at m/z = 1405.8, 818.7, 1589.3, and 1259.2 corresponding to [M8(L1)4−3NO3−]3+, [M8(L1)4−5NO3−]5+ and [M12(L1)6−4NO3−]4+, [M12(L1)6−5NO3−]5+ charged fragments, respectively, with isotopic distribution patterns matching well with the theoretical patterns (Figures 2 and S4− S6). Though ESI−MS could reveal the exact composition of the assemblies formed in solution, the exact structures of the assemblies formed remained unknown. After many attempts, suitable single crystals were obtained by diffusing acetone into an aqueous solution of the assembly mixture. Single-crystal X-ray diffraction experiments using a synchrotron revealed the formation of tube T1 having the M8(L1)4 composition (Figure 3). Centrosymmetric tube T1 crystallizes in the triclinic system (space group P1̅). All four D

DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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Inorganic Chemistry tetrahedral cage with 6 ligands paneling the 6 edges of the tetrahedron and 12 square-planar Pt(II) centers present at the 4 corners of the tetrahedron. Each corner of the tetrahedron is made up of a triangular (Pt(II)-pym)3 cyclic moiety, with the formation of six coordination bonds between the three cisblocked Pt(II) acceptors and six nitrogen atoms from three donor ligands (Figure 4).

Figure 5. 1H NMR recorded in D2O for the (a) self-assembly reaction mixture obtained after the reaction carried out at 45 °C and (b) the reaction mixture after the reaction carried out at 100 °C. (c) 1H NMR of the pure tube obtained as crystals from the reaction mixture. The percentage ratio of the two products obtained at 45 and 100 °C is also indicated below the NMR spectra.

a set of four distinct peaks in the aromatic region from 7.03 to 10.69 ppm (Figure S10), reflecting the formation of a single symmetric and ordered structure. In comparison to 1H NMR of ligand L2, which also exhibited four distinct peaks, the peaks in the self-assembled product are shifted downfield because of the coordination of ligand L2 with the Pt(II) fragments (Figure 6). The 1H DOSY NMR study showed a single

Figure 4. Energy-optimized structure of M12(L2)6 tetrahedral cage T2 using the Hartree−Fock method with STO-3G and LANL2DZ basis sets (color codes: C, gray; Pt, red; N, blue; and H, white).

To confirm whether tube T1 and tetrahedral cage T2 are in equilibrium with each other or just exist as a physical mixture of the two ensembles, both temperature- and concentrationdependent NMR experiments were performed. At 25 °C, the reaction mixture containing both species was taken and 1H NMR was recorded, which showed six well-resolved peaks in the aromatic region. The 1H NMR spectrum of the same solution at 35 °C showed no change as compared to that recorded at 25 °C. Even up to 90 °C no remarkable change in 1 H NMR was detected, suggesting that the two species formed are not present in equilibrium but rather exist as a physical mixture with an independent existence. Similarly, upon changing the concentration of the solution no change was found in the 1H NMR spectra, a result again in favor of the nonexistence of equilibrium between species T1 and T2. However, when the self-assembly reaction of ligand L1 with cis-[(dch)Pt(NO3)2] (M) was carried out at 100 °C for 24 h, the fraction of the tetrahedral cage increased to 35% as compared to 10% obtained from the same self-assembly reaction performed at 45 °C for 24 h (Figures 5, S2, and S3). The above results suggested that the molecular tube formed as the major product (90% at 45 °C and 65% at 100 °C) is a kinetic product favored by entropy, while the tetrahedral cage obtained as the minor product (10% at 45 °C and 35% at 100 °C) is a thermodynamic product with no conformational strain in the structure. When ligand L2 was treated with cis-[(dch)Pt(NO3)2] (M) in water at 45 °C for 24 h, a clear brownish solution was obtained. The solution upon its analysis with 1H NMR showed

Figure 6. Stacked partial 1H NMR of ligand L2 and tube T3.

diffusion coefficient value with D = 10.1 × 10−11 m2/s [log D (m2/s) = −10.20], thus suggesting the formation of a single self-assembled product (Figure S11). Needle-shaped single crystals were obtained by diffusing acetone into a DMSO/H2O (1:1) solution of the mixture. The X-ray diffraction experiment using the synchrotron radiation source revealed the formation of an M8(L2)4 tubular structure of T3, displayed in Figure 7. Tube T3 crystallizes in monoclinic space group P21 with Pt−N bond lengths of ∼2.0 Å. All of the Pt(II) metal centers of the structure displayed square-planar geometry with an inner (pyrimidine)N−Pt−N(pyrimidine) bite angle of 90.54° and a chelating N− Pt−N bite angle of 91.33°. Tube T3 has eight Pt(II) centers located at the eight corners along with four ligands (L2) paneling the faces of the tube held together through 16 Pt− N(pyrimidine) coordination bonds. The length of the tube is 22.0 Å (Figure S12) as measured between the two distant carbon atoms of the opposite cyclohexane rings evaluated along the length of the tube. Tube T3 is longer than T1 by 3.7 Å, and the ligand panels present in the tube structure are not planar but rather bent outward, shaped to minimize the steric strain between the adjacent and opposite ligand faces of the structure. Because of the nonavailability of enough free space inside the cavity of both tubes T1 and T3, we could not explore them for cavity-directed applications. E

DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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Figure 7. Ball-and-stick view of the crystal structure of M8(L2)4 tube T3 (a) along a and (b) along c crystallographic axes. (c) Space-filling model representation of the crystal structure of T3. Solvent molecules are omitted for clarity (color codes: C, gray, Pt, red, N, blue; and H, white).

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ORCID

CONCLUSIONS We have reported the formation of two nanotubular architectures T1 and T3 of different lengths from the separate self-assembly of 1,4-di(pyrimidin-5-yl)benzene (L1) and 4,4′di(pyrimidin-5-yl)-1,1′-biphenyl] (L2) with a cis-[(dch)Pt(NO3)2] acceptor. The former self-assembly reaction with L1 led to a nonequilibrium mixture of the products with M8(L1)4 tube T1 as the major product and M12(L1)6 cage T2 as the minor species. The M8(L2)4 tube formed as the major product was successfully separated out through a crystallization technique, and the structure was fully elucidated through single-crystal X-ray crystallography. The tetrahedral structure of the M12(L1)6 assembly was optimized through computational modeling with the Gaussian 09 package, using the Hartree−Fock method with STO-3G/LANL2DZ basis sets. Temperature- and concentration-dependent NMR experiments of the mixture after the self-assembly reaction with L1 confirmed the formation of a nonequilibrium mixture of T1 and T2. A similar but extended ligand, 4,4′-di(pyrimidin-5-yl)1,1′-biphenyl (L2), with an extra phenyl ring in between the pyrimidine moieties upon self-assembly with the cis-[(dch)Pt(NO3)2] acceptor led to the formation of pure tube T3 as an exclusive product as confirmed by 1H NMR and single XRD techniques.

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Partha Sarathi Mukherjee: 0000-0001-6891-6697 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS P.S.M. is grateful to SERB-India for financial support (grant no. CRG/2018/000315). We are thankful to Dr. Prodip Howlader for his helpful suggestions in solving the crystal structures and Dr. Naiwrit Karmodak for fruitful discussions on theoretical calculations.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.inorgchem.9b01763. Additional 1D and 2D NMR and ESI−MS spectra (PDF) Accession Codes

CCDC 1922407−1922408 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K.; fax: +44 1223 336033.

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REFERENCES

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DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX

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DOI: 10.1021/acs.inorgchem.9b01763 Inorg. Chem. XXXX, XXX, XXX−XXX