Towards an unified chemical model of secondary 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.

Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding

The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.

The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative

A new Pb^II coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)₂·3H₂O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the Pb^II cation is N,N',S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N-H...O hydrogen bonds and π...π interactions. These chains are interlinked by C-H...py non-covalent interactions, realized between one of the acetate hydrogen atoms and the pyridine rings. According to the Hirshfeld surface analysis, the crystal packing is mainly characterized by intermolecular H...H, H...C and H...O contacts, followed by H...N, H...S, C...C, C...N, Pb...H, Pb...O and Pb...S contacts. The FTIR and ¹H NMR spectra of [PbL(OAc)] testify to the deprotonation of the parent ligand HL, while the acetate ligand exhibits an anisobidentate coordination mode as established by means of single-crystal X-ray diffraction and FTIR spectroscopy. Lastly, theoretical calculations at the PBE0-D3/def2-TZVP level of theory have been used to analyze and characterize the Pb...O and Pb...S tetrel bonds observed in the crystal of [PbL(OAc)], using a combination of QTAIM (Quantum Theory of Atoms in Molecules) and NCIPlot (Non-Covalent Interaction Plot) computational tools.

Exploring The Sequence of Electron Density Along The Chemical Reactions Between Carbonyl Oxides And Ammonia/Water Using Bond Evolution Theory

The molecular mechanism of the reactions between four carbonyl oxides and ammonia/water are investigated using the M06-2X functional together with 6-311++G(d,p) basis set. The analysis of activation and reaction enthalpy shows that the exothermicity of each process increased with the substitution of electron donating substituents (methyl and ethenyl). Along each reaction pathway, two new chemical bonds C-N/C-O and O-H are expected to form. A detailed analysis of the flow of the electron density during their formation have been characterized from the perspective of bonding evolution theory (BET). For all reaction pathways, BET revealed that the process of C-N and O-H bond formation takes place within four structural stability domains (SSD), which can be summarized as follows: the depopulation of V(N) basin with the formation of first C-N bond (appearance of V(C,N) basin), cleavage of N-H bond with the creation of V(N) and V(H) monosynaptic basin, and finally the V(H,O) disynaptic basin related to O-H bond. On the other hand, in the case of water, the cleavage of O-H bond with the formation of V(O) and V(H) basins is the first stage, followed by the formation of the O-H bond as a second stage, and finally the creation of C-O bond.

New insights in chemical reactivity from quantum chemical topology

Based on the quantum chemical topology of the modified electron localization function ELF_x , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH₃ NH₃ molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of E_dual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

Words in supramolecular chemistry: the ineffable advances of polyiodide chemistry

Polyiodide chemistry has a rich history deeply intertwined with the development of supramolecular chemistry. Technological and theoretical interest in polyiodides has not diminished in the last decade, quite the contrary; yet the advances this perspective intends to cover are muddled by the involution of supramolecular vocabulary, preventing their unbiased discussion. Herein we discuss the pressing necessity of ordering the current babel of novel - and less so - supramolecular terms. Shared decisions at the community level might be required to shape the field into a harmonious body of knowledge, dominated by concepts rather than words. Secondary, σ-hole and halogen bonding schools of thought are all addressed here, together with their respective impact on the field. Then, on the basis of a shared vocabulary, a discussion of polyiodide chemistry is presented, starting with a revisited view of triiodide. The contemporary fields of supramolecular caging and polyiodide networks are then discussed, with emphasis on how the terms we choose to use deeply affect scientific progress.

Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide

A new supramolecular Pb(II) complex [PbL(NO₂)]_n was synthesized from Pb(NO₃)₂, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO₂. [PbL(NO₂)]_n is constructed from discrete [PbL(NO₂)] units with an almost ideal N₂O₃ square pyramidal coordination environment around Pb(II). The ligand L⁻ is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ²-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N₄O₃ coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO₂)]_n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π⁺⋯π⁻ stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙8²). The Hirshfeld surface analysis of [PbL(NO₂)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO₂)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO₂)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO₂)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π⁺⋯π⁻ stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.

Beryllium bonding: insights from the σ- and π-hole analysis

Beryllium bonding is actually a subclass of secondary bonding. Similar to the case of halogen bonding, the σ- and π-holes on the Be atom of the monomers give in zeroth approximation the direction of electrophilic attack favorable to the formation of beryllium bonds. The nature of beryllium bonding is purely electrostatic so that the symmetry-adapted perturbation theory energy decomposition perfectly explains the relevance of the polarization and dispersion contribution on the formation of the beryllium bond.

A new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine

In this manuscript, the synthesis and X-ray characterization of a new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine are reported.