Amrita Das

Anion induced formation of supramolecular associations involving lone pair-π and anion-π interactions in Co(II) malonate complexes: experimental observations, Hirshfeld surface analyses and DFT studies.

Three Co(II)-malonate complexes, namely, (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](NO(3))(2) (1), (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](ClO(4))(2) (2), and (C(5)H(7)N(2))(4)[Co(C(3)H(2)O(4))(2)(H(2)O)(2)](PF(6))(2) (3) [C(5)H(7)N(2) = protonated 2-aminopyridine, C(3)H(4)O(4) = malonic acid, NO(3)(-) = nitrate, ClO(4)(-) = perchlorate, PF(6)(-) = hexafluorophosphate], have been synthesized from purely aqueous media, and their crystal structures have been determined by single crystal X-ray diffraction. A thorough analysis of Hirshfeld surfaces and fingerprint plots facilitates a comparison of intermolecular interactions in 1-3, which are crucial in building supramolecular architectures. When these complexes are structurally compared with their previously reported analogous Ni(II) or Mg(II) compounds, a very interesting feature regarding the role of counteranions has emerged. This phenomenon can be best described as anion-induced formation of extended supramolecular networks of the type lone pair-π/π-π/π-anion-π/π-lone pair and lone pair-π/π-π/π-anion involving various weak forces like lone pair-π, π-π, and anion-π interactions. The strength of these π contacts has been estimated using DFT calculations (M06/6-31+G*), and the formation energy of the supramolecular networks has been also evaluated. The influence of the anion (NO(3)(-), ClO(4)(-), and PF(6)(-)) on the total interaction energy of the assembly is also studied.

Supramolecular Assembly of Mg(II) Complexes Directed by Associative Lone Pair−π/π−π/π−Anion−π/π−Lone Pair Interactions

Two Mg(II) malonate complexes with protonated 2-aminopyridine and protonated 2-amino-4-picoline as counterions, namely, (C(5)H(7)N(2))(4)[Mg(C(3)H(2)O(4))(2)(H(2)O)(2)](ClO(4))(2) (1) and (C(6)H(8)N(2)H)(2)[Mg(C(3)H(2)O(4))(2)(H(2)O)(2)] x 4 H(2)O (2) [C(5)H(7)N(2) = protonated 2-aminopyridine, C(3)H(4)O(4) = malonic acid, C(6)H(8)N(2)H = protonated 2-amino-4-picoline], have been synthesized from purely aqueous media, and their crystal structures have been determined by single-crystal X-ray diffraction. The role of lone pair...pi interactions in stabilizing the self-assembly process appears to be of great importance in both complexes. Additional weak forces like anion...pi and noncovalent O...O interactions are also found to be operating in 1. A rare combination of lone pair...pi and anion...pi interactions in 1, of the type lone pair...pi/pi...pi/pi...anion...pi/pi...lone pair, is observed, and this unusual supramolecular network is fully described here. An attempt to prepare an analogous complex with 2-amino-4-picoline resulted in 2, which is isomorphous with our recently reported transition-metal complexes of the type (C(6)H(8)N(2)H)(2)[M(C(3)H(2)O(4))(2)(H(2)O)(2)] x 4 H(2)O (M = Ni/Co/Mn). A high-level DFT-D study (RI-B97-D/TZVP) has been used to characterize the different noncovalent interactions present in the solid state. We have also analyzed some crystal fragments to examine energetically some important assemblies that drive the crystal packing. Finally, we have studied the influence of magnesium on some hydrogen-bonding interactions.

A successive layer-by-layer assembly of supramolecular frameworks driven by a novel type of face-to-face π+–π+ interactions

The solid-state complex [PTPH3](NO3)3·2(HNO3) (1) has been synthesized and characterized by X-ray studies, where PTPH3 is the triply protonated form of 4′-(4-pyridyl)-2,2′:6′,2′′-terpyridine (PTP). The solid-state structure of the complex reveals that the π+–π+ interactions are the major driving force in the crystal packing while π+–π, π–π and π–anion interactions assist the overall stabilization of self-assembly. Complex 1 exhibits two different π-stack layers, where layer 1 is generated through π+–π+ interactions and the mutual forces of π+–π+ and π+–π form layer 2. The interaction energies of the main driving forces (π+–π+, π+–π and π–anion interactions) observed in the crystal structure have been calculated using dispersion-corrected density functional theory (DFT-D). An analysis of the Hirshfeld surface of complex 1 shows the intermolecular interactions involved within the crystal structure and corresponding quantitative information are presented by fingerprint plots.

Supramolecular assemblies involving anion–π and lone pair–π interactions: experimental observation and theoretical analysis

Two nickel(II) malonate coordination compounds, namely (C5H7N2)4[Ni(C3H2O4)2(H2O)2](ClO4)2 (1) and (C5H7N2)4[Ni(C3H2O4)2(H2O)2](PF6)2 (2) [where C5H7N2 = protonated 2-aminopyridine, C3H4O4 = malonic acid, ClO4− = perchlorate, PF6− = hexafluoridophosphate], have been synthesized from purely aqueous media, and their single-crystal structures have been determined by X-ray diffraction. As anticipated, various weak forces, i.e. lone pair–π, π–π and anion–π interactions, play a key role in stabilizing the self-assembly process observed for both compounds. Intricate combinations of lone pair–π, π–π and anion–π interactions of the type lone pair–π/π–π/π–anion–π/π–lone pair and lone pair–π/π–π/π–anion are observed that are fully described, including by computational methods. The theoretical calculations allow estimating the strength of these π contacts.

Molecular architecture using novel types of non-covalent π-interactions involving aromatic neutrals, aromatic cations and π-anions

A solid-state complex utilizing non-covalent interactions between two aromatic cations is synthesized and characterized. The X-ray study of the structure shows that the anion templated π+–π+ interactions are the major driving force in the crystal packing, while π+–π, π–π, π–anion and π+–anion interactions assist the overall stabilization of self-assembly. In addition, we also identify the cation-mediated non-covalent interaction between two π anions (π−–π− interaction). The interaction energies of the important driving forces (π+–π+, π+–π, π–anion, π+–anion, and π−–π− interactions) observed in the crystal structure are calculated using dispersion-corrected density functional theory (DFT-D).

Salt-bridge–π (sb–π) interactions at work: associative interactions of sb–π, π–π and anion–π in Cu(II)-malonate–2-aminopyridine–hexafluoridophosphate ternary system

An essentially unexplored noncovalent interaction involving aromatic rings is re-defined and described: the salt-bridge–π interaction. It consists of the stacking interaction between an aromatic ring and a planar salt-bridge. If the aromatic ring is located under the cation of the salt-bridge, the interaction must be described as a cation–π interaction. Similarly, if the aromatic ring is located under the anion of the salt-bridge, the interaction must be described as an anion–π interaction. However, if the aromatic ring is just in the middle of both, a new definition of noncovalent bonding is required. Herein, we propose the term “salt-bridge–π (sb–π) interaction” to describe the stacking between an aromatic ring and a planar salt-bridge (for example, guanidinium and carboxylate ion pair). We also report the synthesis and X-ray characterization of one Cu(II) malonate complex with protonated 2-aminopyridine as the auxiliary ligand, which is acting as the counter cation, namely, {(C5H7N2)6[Cu(C3H2O4)2(H2O)2][Cu(C3H2O4)2](PF6)2}n (A) (C5H7N2 = protonated 2-aminopyridine, C3H4O4 = malonic acid) where this type of interaction is observed. Other weak forces like hydrogen bonding, π⋯π stacking and anion⋯π interactions were also found to be responsible for the overall stabilisation of the complex A. Interestingly, an extended supramolecular network of the type sb–π/π–π/π–π/π–anion has been observed in the solid state structure of complex A. This outstanding network of weak forces was observed for the first time in the crystalline structures of metal–organic hybrid complexes. From this perspective, the self-assembly process appears to be of great importance in this complex. The analysis of the crystalline structure of A with an emphasis on exploring this rare supramolecular network is presented here. The theoretical study combines the energetic analysis of the noncovalent forces that participate in the extended supramolecular network and the characterization of the different interactions by means of Baders theory of “atoms in molecules”. We also present here Hirshfeld surface analysis to investigate the close intermolecular contacts.

On the importance of unprecedented lone pair-salt bridge interactions in Cu(II)-malonate-2-amino-5-chloropyridine-perchlorate ternary system.

A Cu(II)-malonate complex with formula {(C5H6N2Cl)12[Cu(1)(C3H2O4)2][Cu(2)(C3H2O4)2(H2O)2][Cu(4)(C3H2O4)2][Cu(3)(C3H2O4)2(H2O)2](ClO4)4}n (1) [C5H6N2Cl = protonated 2-amino-5-chloropyridine, C3H4O4 = malonic acid, ClO4(-) = perchlorate] has been synthesized from purely aqueous media simple by mixing the reactants in their stoichiometric ratio, and its crystal structure has been determined by single-crystal X-ray diffraction. In 1, copper(II) malonate units form infinite 1D polymeric chains, which are interlinked by hydrogen bonds to generate 2D sheets. These 2D sheets are joined side by side primarily by various hydrogen bonds to form a 3D structure. A multitude of salt bridges are formed in this structure, connecting the protonated 2-amino-5-chloropyridines and the malonate ligands of the polymeric polyanion. Examining this characteristic of the solid-state architecture, we noticed several salt-bridge (sb)···π interactions and an unexplored interaction between the lone pair (lp) of one malonate oxygen atom and a planar salt bridge. The combination of this interaction with various other weak intermolecular forces results in a remarkably extended supramolecular network combining a wide variety of interactions involving π-systems (Cl···π, π···π) and salt bridges (sb···π and lp···sb). We describe the energetic and geometric features of this lone pair-salt-bridge interaction and explore its impact on the resultant supramolecular organization using theoretical DFT-D3 calculations.

DNA Binding Ability and Hydrogen Peroxide Induced Nuclease Activity of a Novel Cu(II) Complex with Malonate as the Primary Ligand and Protonated 2-Amino-4-picoline as the Counterion †

The DNA binding property of a Cu(II) complex, viz., [Cu(mal)(2)](picH)(2).2H(2)O, (mal)(2) = malonic acid, picH = protonated 2-amino-4-picoline, has been investigated in this study. The binding of this complex with plasmid and chromosomal DNA has been characterized by different biophysical techniques. From the absorption and fluorescence spectroscopic studies, it has been observed that the said copper complex binds strongly with pUC19 plasmid and CT DNA with a binding affinity of 2.368 x 10(3) and 4.0 x 10(3) M(-1), respectively, in 10 mM citrate-phosphate buffer, pH 7.4. Spectrofluorimetric studies reveal that the copper complex exhibits partial DNA intercalation as well as partial DNA minor groove binding properties. Consequently, in agarose gel electrophoresis study, it has been observed that the complex alone induces positive supercoiling in plasmid DNA while in the presence of H(2)O(2) it exhibits nuclease activity. The induction of the breakage in DNA backbone depends upon the relative concentrations of H(2)O(2) and copper complex followed by the time of incubation with DNA. Optical DNA melting study, isothermal titration calorimetry, and absorption spectroscopy have been used to characterize the nuclease activity of this complex in the presence of H(2)O(2). Further, (1)H NMR study indicates that Cu(II) in the complex is converted into the Cu(I) state by the reduction of H(2)O(2). Finally, agarose gel electrophoresis study with different radical scavengers concludes that the production of both hydroxyl radicals and reactive oxygen species is responsible for this nuclease activity.