Anisotropic Thermal Expansion of Structurally Related Lanthanide-Mercury(II) Cyanide Coordination Polymers

Three sets of related lanthanide-mercury(II) cyanide coordination polymers were synthesized by the reaction of LnCl3·xH2O (Ln = Ce, Nd, Eu, Gd, Tb, Dy, Ho, Tm, Yb, and Lu) with Hg(CN)2 and structurally characterized. [Ce(OH2)5][Hg(CN)2Cl]3·2H2O is a 3-D material with sheet-based architecture; its thermal expansion behavior shows uniaxial negative thermal expansion (-18.3(8), 39(2), and 68.3(16) ppm K-1 along the a, b, and c axes, respectively). This anisotropic thermal behavior is postulated to be driven elastically by weak Hg···Cl interactions: large area expansion of the sheets causes negative thermal expansion in the perpendicular direction. Using lanthanides heavier than Ce yielded 2-D sheet-based compounds with the formula [Ln(OH2)x]2[Hg(CN)2]5Cl6·2H2O (Ln = Nd and Eu, x = 7; Ln = Gd, Tb, Dy, Ho, Tm, Yb, and Lu, x = 6). Although there was also evidence for elastic behavior within these materials, both showed uniaxial zero thermal expansion (Ln = Nd: 27.9(17), 22.4(10), and 0.6(12) ppm K-1 along the I, II, and III principal axes, respectively; Ln = Tb: 39.6(12), 1.1(17), and 36.1(7) ppm K-1 along the a, b, and c axes, respectively). Despite their similar structural architecture, this zero thermal expansion was found to occur in different directions─within the plane of the 2-D sheets for [Nd(OH2)7]2[Hg(CN)2]5Cl6·2H2O but in the direction perpendicular to the 2-D sheets for [Tb(OH2)6]2[Hg(CN)2]5Cl6·2H2O. Overall, this system of compounds reveals the delicate relationship between coordination polymer structure and thermal expansion.

Spodium bonding in bis(alkynyl)mecurials

The new bis(alkynyl)mercurial Hg{CCSeCW(CO)2(Tp*)}2 (Tp* = tris(dimethylpyrazolyl)borate) forms adducts with fluoride and phenathroline, the structures of which are interpreted in the context of two-coordinate mercury presenting a σ-torroid for spodium bonding.

Ye Olde supramolecular chemistry, its modern rebranding and overarching trends in chemistry

We can describe current contingency of supramolecular chemistry as "post-halogen bonding", with clear reference to the success of the σ-hole model and the halogen bond concepts. This phase is characterized by a strong push towards a new nomenclature for non-covalent interactions, a group-by-group one focusing on the electrophile. As such nomenclature increasingly meets IUPAC endorsement, its proposers report resistances to such ideas, especially in the inorganic and coordination chemistry communities. The whole issue has been generating considerable debate in the last decade. Herein we fully embrace such discussion in the hope of involving a larger share of the relevant communities. Alternative descriptions are here reevaluated, novel views reconnected with older ones, and it is ultimately questioned whether the introduction of such a nomenclature and its subtending ideas would be beneficial. The themes of appreciation of general trends in chemistry, of counterintuitive interactions, of positioning of novel nomenclature with respect to existing ones, and of the extension of group-by-group naming from main block to d-block elements - as key and currently unresolved issues - are discussed. Equivalent, alternative and arguably more comprehensive descriptions are tentatively given, in the hope to overcome controversies together in the pursuit of higher rewards: a comprehensive shared view of supramolecular forces and a common language to express it.

Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN- Ions: A Holistic View in Crystal Engineering

In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).

Static and Dynamical Quantum Studies of CX3-AlX2 and CSiX3-BX2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center

The set of TX₃-TrX₂ (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX₃-AlX₂) and least (SiX₃-BX₂) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.

Matere Bonds vs. Multivalent Halogen and Chalcogen Bonds: Three Case Studies

The term matere bond has been recently used to refer to an attractive noncovalent interaction between any element of group 7 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. The utilization of metals such as σ-hole donors is starting to attract the attention of the scientific community. In this manuscript, a comparison between matere bonds and well-known σ-hole interactions (halogen and chalcogen bonds) is carried out using three X-ray structures, retrieved from the Cambridge structural database (CSD), and density functional theory calculations (DFT). The novelty of this work resides in the utilization of a neutral Re(VII) system as the matere bond donor and multivalent chalcogen and halogen donors. In fact, as far as our knowledge extends, the description of σ-hole interactions in Se(VI) is unprecedented in the literature. The σ-hole interactions in Re(VII), Se(VI) and Cl(VII) electron acceptors are analyzed and compared using several computational tools.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study

The spodium–π bonding between MX₂ (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C₂H₂/C₂H₄ acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX₂⋯C₂F₂ complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.

Substituent effects in π-hole regium bonding interactions between Au(p-X-Py)2 complexes and Lewis bases: an ab initio study

For the first time, long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated. The Au(I) atom is coordinated to two para -substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide some experimental support to the existence of regium π-hole bonding in [Au(Py) 2 ] + derivatives.

Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation

Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η¹-NCS)(η¹-SCN)] _n (1), using a compartmental Salen ligand (H₃L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P2₁/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N₂O₂ and heavier Pb(ii) in the outer O₄ compartments of the de-protonated form of the ligand [L]^2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.

Anion⋅⋅⋅Anion Interactions Involving σ-Holes of Perrhenate, Pertechnetate and Permanganate Anions

In this communication experimental and theoretical results are reported affording strong evidence that interactions between electron rich atoms and the metal of tetroxide anions of group 7 elements are a new case of attractive and σ‐hole interactions. Single crystal X‐ray analyses, molecular electrostatic potentials, quantum theory of atoms‐in‐molecules, and noncovalent interaction plot analyses show that in crystalline permanganate and perrhenate salts the metal in Mn/ReO₄⁻ anion can act as electron acceptors, the oxygen of another Mn/ReO₄⁻ anion can act as the donor and supramolecular anionic dimers or polymers are formed. The name matere bond (MaB) is proposed to categorize these noncovalent interactions and to differentiate them from the classical metal‐ligand coordination bond.

Unveiling the role of pyrylium frameworks on π-stacking interactions: a combined ab initio and experimental study

A multidisciplinary study is presented to shed light on how pyrylium frameworks, as π-hole donors, establish π-π interactions. The combination of CSD analysis, computational modelling (ab intitio, DFT and MD simulations) and experimental NMR spectroscopy data provides essential information on the key parameters that characterize these intereactions, opening new avenues for further applications of this versatile heterocycle.

Theoretical study of spodium bonding in the active site of three Zn-proteins and several model systems

In this manuscript, three examples retrieved from the PDB are selected to demonstrate the existence and relevance of spodium bonding (SpB) in biological systems. SpB is defined as an attractive noncovalent interaction between elements of group 12 of the periodic table acting as a Lewis acid and any atom or group of atoms acting as an electron donor. The utilization of this term (SpB) is convenient to differentiate classical coordination bonds from noncovalent interactions. In the latter, the distance between the electron rich and the spodium atoms is longer than the sum of the covalent radii but shorter than the sum of the van der Waals radii. In most Zn-dependent metalloenzymes, the spodium atom is bonded to three imidazole moieties belonging to the side chains of histidine amino-acids. Herein, in addition to the investigation of the SpB in the active site of three exemplifying enzymes, theoretical models where the Zn(ii) atom is bonded either to three imidazole or triazole ligands are used in order to investigate the strength of the SpB and its competition with hydrogen bonding. A series of Lewis bases and anions have been used as SpB acceptors combined with six SpB donors (receptors) of general formula [ZnY3X]+ (Y = imidazole and triazole and X = Cl, N3 and SCH3). In addition to the investigation of the energetic and geometric features of the complexes, the SpB interactions have been further characterized using the natural bond orbital (NBO) method, quantum theory of "atoms-in-molecules" and the noncovalent interaction plot (NCI plot).

π-Hole spodium bonding in tri-coordinated Hg(II) complexes

The important role of π-hole spodium bonding in tri-coordinated planar Hg(ii) complexes is highlighted in this feature article. Selected examples of Hg(ii)X3 structures (X = any atom) illustrate that this noncovalent interaction is relevant as a structural guiding force in crystal structures. For some examples, the interactions have been characterized using the quantum theory of "atoms in molecules" and the noncovalent interaction plot index. Finally, an analysis of the Cambridge structural database revealed that the HgX3 structures are predominantly T-shaped and that they are directional π-hole donors for electron rich atoms.

Change in molecular shapes of the trinuclear CuII2ZnII complexes on Schiff base reduction: structural and theoretical investigations

Structural analyses and theoretical studies of two new Cu₂Zn compounds and other analogous species established that subtle modification in a ligand system can stabilize various structures with versatile coordinating azide ion and flexible trinuclear core.

Coordination versus spodium bonds in dinuclear Zn(ii) and Cd(ii) complexes with a dithiophosphate ligand

Two new d10-metal dithiophosphate complexes have been synthesized in purely aqueous media and characterized by elemental and spectral analyses. DFT calculations, QTAIM and NCI Plot index methods are preformed to differentiate the coordination and spodium bonds in the complexes.