σ/π-Hole noble gas bonding interactions: Insights from theory and experiment

Taming XeO3 with Aza-Crowns: Computational Studies into σ-Hole Mediated Host-Guest Interactions

Various aza-crowns with different sizes and substituents have been explored computationally as potential hosts for stabilizing the explosive guest xenon trioxide (XeO3) through σ-hole-mediated aerogen bonding interactions. Interestingly, aza-crowns demonstrate superior binding towards XeO3 compared to their oxygen and thio counterparts. However, unlike the latter cases, where the binding was found to be increasingly favorable with the increase in the size of the crowns, aza-crowns exhibit a variable size preference for XeO3, peaking with aza-15-crown-5, and reducing thereafter with increase in crown size.

Dynamic Gas-Bridged Bond: An Opportunity of Fabricating Dynamic Assembled Materials with Gas

Gas molecules, as a family of unique polyatomic building blocks, have long been considered hard to involve in molecular assembly or construct assembled materials due to their structural simplicity yet paucity of defined interacting sites. To solve this non-trivial challenge, a core idea is to break the limit of current ways of bonding gas molecules, endowing them with new modes of interactions that match the basic requirements of molecular assembly. In recent years, a new concept, named the dynamic gas-bridged bond (DGB), has emerged, which allows for gas molecules to constitute a dynamic bridging structure between other building blocks with the aid of frustrated Lewis pairs. This makes it possible to harness gas in a supramolecular or dynamic manner. Herein, this perspective discusses distinct dynamic natures of DGBs and manifests their particular functions in various fields, including the control of molecular/polymeric self-assembly nanostructures, creation of multidimensional assembled materials, and recyclable catalysts. The future research direction and challenges of dynamic gas-bridged chemistry toward gas-programmed self-assembly and gas-constructed adaptive materials are highlighted.

Unveiling the Inverse Sandwich Complexes of XeO3: A Computational Exploration

Our study introduces the design of inverse sandwich (iSw) complexes incorporating a noble gas compound: xenon trioxide (XeO3). Through comprehensive computational analyses, we have investigated the critical factors influencing their stability by employing a variety of state-of-the-art computational tools. We demonstrated that the coordination number of xenon in the iSw complex of XeO3 with 18-crown-6 is influenced by the presence of a rare, weakly stabilizing Xe···Xe interaction between the XeO3 molecules. Furthermore, we observed that the stability of iSw complexes of 1,3,5-triphenylbenzene (TPB) and its derivatives is not solely attributed to aerogen bonding, but also involves contributions from C-H···O interactions and back-donation from the lone pair of Xe to the antibonding C-C orbitals of TPB. Additionally, the significant contributions from orbital interactions and dispersion interactions in the TPB derivatives highlight the multifaceted amphoteric properties of XeO3 and reveal that the iSw complexes of TPB and derivatives are not predominantly governed by electrostatic interactions, contrary to conventional belief.

Noble Gas Anions: An Overview of Strategies and Bonding Motifs

This review article aims to provide an overview of the strategies employed to prepare noble gas anions under different environments and experimental conditions, and of the bonding motifs typically occurring in these species. Observed systems include anions fixed into synthesized salts, detected in the gas phase or in high-pressure devices. The major role of the theoretical calculations is also highlighted, not only in support of the experiments, but also as effective in predicting still unreported species. The chemistry of noble gas anions overall appears as a varied and rich paint, offering fascinating opportunities for both experimentalists and theoreticians.

Investigating Recurrent Matere Bonds in Pertechnetate Compounds

In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H2O)4(TcO4)2], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H2O)4(ReO4)2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H2O)4(TcO4)2], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H2O)4(ReO4)2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds.

Exploring Unconventional σ-Hole Interactions: Computational Insights into the Interaction of XeO3 with Non-Aromatic Coordinating Solvents

In order to control the explosiveness and shock sensitivity of XeO3 , we have investigated its plausible interaction with various non-aromatic coordinating solvents, serving as potential Lewis base donors, through density functional theory (DFT) calculations. Out of twenty six such solvents, the top ten were thus identified and then thoroughly examined by employing various computational tools such as the mapping of the electrostatic potential surface (MESP), Wiberg bond indices (WBIs), non-covalent interaction (NCI) plots, Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, and the energy decomposition analysis (EDA). The amphoteric nature of XeO3 was also explored by investigating the extent of back donation from the lone pair of Xe to the antibonding orbital of the donating atom/group of the solvent molecules. The C-H…O interactions were also found to be a contributing factor in the stabilization of these adducts. Although these aerogen-bonding interactions were found to be predominantly electrostatic, significant contributions from the orbital contributions, as well as dispersion interactions, were observed. The top three non-aromatic solvents (among the twenty six studied) which form the strongest adducts with XeO3 are proposed to be hexamethylphosphoramide (HMPA), N,N'-dimethylpropyleneurea (DMPU) and tetramethylethylenediamine (TMEDA).

Spodium bonding with noble gas atoms

The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.

Size Matters: Computational Insights into the Crowning of Noble Gas Trioxides

In pursuit of enhancing the stability of the highly explosive and shock-sensitive compound XeO3, we performed quantum chemical calculations to investigate its possible complexation with electron-rich crown ethers, including 9-crown-3, 12-crown-4, 15-crown-5, 18-crown-6, and 21-crown-7, as well as their thio analogues. Furthermore, we expanded our study to other noble gas trioxides (NgO3), namely, KrO3 and ArO3. The basis set superposition error (BSSE) corrected interaction energies for these adducts range from -13.0 kcal/mol to -48.2 kcal/mol, which is notably high for σ-hole-mediated noncovalent interactions. The formation of these adducts was observed to be more favorable with the increase in the ring size of the crowns and less favorable while going from XeO3 to ArO3. A comprehensive analysis by various computational tools such as the mapping of the electrostatic potential (ESP), Wiberg bond indices (WBIs), Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, noncovalent interaction (NCI) plots, and energy decomposition analysis (EDA) revealed that the C-H···O interactions, as well as dispersion interactions, play a pivotal role in stabilizing adducts involving larger crowns. A noteworthy outcome of our study is the revelation of a coordination number of 9 for xenon in the complex formed between XeO3 and the thio analogue of 18-crown-6, which is higher than the largest number reported to date.

The Cambridge Structural Database and structural dynamics

With the availability of the computer readable information in the Cambridge Structural Database (CSD), wide ranging, largely automated comparisons of fragment, molecular, and crystal structures have become possible. They show that the distributions of interatomic distances, angles, and torsion angles for a given structural fragment occurring in different environments are highly correlated among themselves and with other observables such as spectroscopic signals, reaction and activation energies. The correlations often extend continuously over large ranges of parameter values. They are reminiscent of bond breaking and forming reactions, polyhedral rearrangements, and conformational changes. They map-qualitatively-the regions of the structural parameter space in which molecular dynamics take place, namely, the low energy regions of the respective (free) energy surfaces. The extension and continuous nature of the correlations provides an organizing principle of large groups of structural data and suggests a reconsideration of traditional definitions and descriptions of bonds, "nonbonded" and "noncovalent" interactions in terms of Lewis acids interacting with Lewis bases. These aspects are illustrated with selected examples of historic importance and with some later developments. It seems that the amount of information in the CSD (and other structural databases) and the knowledge on the nature of, and the correlations within, this body of information should allow one-in the near future-to make credible interpolations and possibly predictions of structures and their properties with machine learning methods.

Types of noncovalent bonds within complexes of thiazole with CF4 and SiF4

The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.

Hole interactions of aerogen oxides with Lewis bases: an insight into σ-hole and lone-pair-hole interactions

σ-Hole and lone-pair (lp)-hole interactions of aerogen oxides with Lewis bases (LB) were comparatively inspected in terms of quantum mechanics calculations. The ZOn ⋯ LB complexes (where Z = Kr and Xe, n = 1, 2, 3 and 4, and LB = NH3 and NCH) showed favourable negative interaction energies. The complexation features were explained in light of σ-hole and lp-hole interactions within optimum distances lower than the sum of the respective van der Waals radii. The emerging findings outlined that σ-hole interaction energies generally enhanced according to the following order: KrO4 ⋯ < KrO⋯ < KrO3⋯ < KrO2⋯LB and XeO4⋯ < XeO⋯ < XeO2⋯ < XeO3⋯LB complexes with values ranging from -2.23 to -12.84 kcal mol-1. Lp-hole interactions with values up to -5.91 kcal mol-1 were shown. Symmetry-adapted perturbation theory findings revealed the significant contributions of electrostatic forces accounting for 50-65% of the total attractive forces within most of the ZOn⋯LB complexes. The obtained observations would be useful for the understanding of hole interactions, particularly for the aerogen oxides, with application in supramolecular chemistry and crystal engineering.

Erythronium Bonds: Noncovalent Interactions Involving Group 5 Elements as Electron-Density Acceptors

Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These kinds of bonding are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythronium bond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show that these interactions are present also in biological systems.

Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding

Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.

Tetrel bonds involving a CF3 group participate in protein-drug recognition: a combined crystallographic and computational study

In this study, the ability of CF₃ groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF₃ group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF₃⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications

In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as -NH₂, -OCH₃, -CH₃, -H, -CF₃ and -CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett's plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet's σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader's theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.

Xenon Derivatives as Aerogen Bond-Donating Catalysts for Organic Transformations: A Theoretical Study on the Metaphorical "Spherical Cow in a Vacuum" Provides Insights into Noncovalent Organocatalysis

Computations indicate that cationic and noncharged xenon derivatives should exhibit higher catalytic activity than their iodine-based noncovalent organocatalytic congeners. Perfluorophenyl xenonium(II) is expected to demonstrate the best balance between catalytic activity and chemical stability for use in organocatalysis. Comparing its catalytic activity with that of isoelectronic perfluoroiodobenzene indicates that the high catalytic activity of cationic noncovalent organocatalysts is predominantly attributed to the electrostatic interactions with the reaction substrates, which cause the polarization of ligated species during the reaction progress. In contrast, the electron transfer and covalent contributions to the bonding between the catalyst and substrate have negligible effects. The dominant effect of electrostatic interactions results in a strong negative correlation between the calculated Gibbs free energies of activation for the modeled reactions and the highest potentials of the σ-holes on the central atoms of the catalysts. No such correlation is observed for noncharged catalysts.

Beryllium bonding with noble gas atoms

Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be₃ ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be₃ complexes. The Be atoms in the Be₃ moiety are chemically bonded to one another, with the BeBe bond dissociation energy being ~125 kJ mol^-1 . The Be₃ ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be₃ ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.

Importance of Cu and Ag regium-π bonds in supramolecular chemistry and biology: a combined crystallographic and ab initio study

Identifying and characterizing new binding events between electron donor and acceptor counterparts represents a crucial step to complete the molecular recognition and aggregation picture, which is key to chemistry and biology. In this study we interrogated both the PDB (Protein Data Bank) and CSD (Cambridge Structural Database) for the presence of Cu and Ag regium-π (Rg-π) bonds (an attractive noncovalent force between elements from group 11 and π-systems). Concretely, we found evidence of the plausible biological role of the interaction in protein-DNA systems, bacterial Ag extrusion processes and Heme group redox functionality. Furthermore, we also highlighted the implications of Rg-π bonds in the crystal packing of two host-guest systems, where this interaction is key for the binding and recognition of small organic molecules as well as for the encapsulation of organometallic complexes. Theoretical models were used to analyse the strength of the interaction (RI-MP2/def2-TZVP level of theory) together with QTAIM (Quantum Theory of Atoms in Molecules), NBO (Natural Bonding Orbital) and NCIplot (Non Covalent Interactions plot) analyses, which further assisted in the characterization of the regium-π interactions described herein. We expect the results from this study will be useful to attract the attention of chemical biologists as well as to expand the potential of the interaction to the supramolecular chemistry and crystal engineering communities.

Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors

In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal-ligand interaction). We provide evidence of the existence of this interaction by inspecting the X-ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf-Ligand orbital involved) are also analyzed by means of ab initio calculations (RI-MP2/def2-TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.

Crystallographic and Theoretical Study of Osme Bonds in Nitrido-Osmium(VI) Complexes

Osme bonds have been recently defined as the attractive interaction between an element of group 8 acting as an electrophile and any atom or group of atoms acting as a nucleophile. To date, the known examples of osme bonds in X-ray structures involve mostly the highly reactive OsO4 and amines and amine oxides. In this work, evidence supporting the existence of osme bonds in osmium(VI) derivatives is reported. In particular, nitrido-osmium(VI) complexes that present square-pyramidal geometries are well disposed to participate in osme bonds opposite to the Os≡N bond. By using a combination of experimental and theoretical results, the existence and importance of this new class of σ-hole interactions is demonstrated in the solid state of several nitrido-osmium(VI) derivatives.

Metal Coordination Enhances Chalcogen Bonds: CSD Survey and Theoretical Calculations

In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein. Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole donor ability of Chs, we believe that the findings presented herein are of remarkable importance for supramolecular chemists as well as for those scientists working in the field of solid state chemistry.

Theoretical study on Xe⋯N non-covalent interactions: Three hybridization N with XeO3 and XeOF2

The interactions of complexes of XeOF2 and XeO3 with a series of different hybridization N-containing donors are studied by means of DFT and MP2 calculations. The aerogen bonding interaction energies range from 6.5 kcal/mol to 19.9 kcal/mol between XeO3 or XeOF2 and typical N-containing donors. The sequence of interaction for N-containing hybridization is sp3>sp2>sp, and XeO3 is higher than XeOF2. For some donors of sp2 and sp3 hybridization, the steric effect plays a minor role in the interaction with the evidence of reduced density gradient plots. The dominant stable part is the electrostatic interaction. In complex of XeO3, the weight of polarization is larger than dispersion, while the situation is opposite for XeOF2 complexes. Except for the sum of the maximum value of molecular electrostatic potential on Xe atom and minimum value of molecular electrostatic potential on N atom, the otherfive interaction parameters including the potential energy density at bond critical point, the equilibrium distances, interaction energies with the basis set superposition error correction, localized molecular orbital energy decomposition analysis interaction energies, and the electron charge density, show great linear correlation coefficients with each other.

An unprecedented interconversion between non-covalent and covalent interactions driven by halogen bonding

The spontaneous interconversion between covalent forces and noncovalent counterparts remains an unexplained mystery to date. Here we have discovered a marvelous transformation between them through halogen bonding using NI 3 as a prototype. Our results show that the interaction strength of the NI 3 dimer is 7.01 kcal mol -1 , demonstrating it is a quite strong halogen bond. Molecular orbital analyses indicate that the frontier MOs result from strong mixing of the fragment MOs, which may be the electronic structure basis of interconversion. Further studies on a series of NI 3 oligomers (5-, 10-, 15-, 20-, 26-, 30-mer) show that the interconversion occurs approximately at 26-mer on the basis on bond distance, ELF, etc.; the interconversion is a gradual transformation not a sudden one. This study provides more insights into the halogen bonding and the high explosivity of NI 3 containing species.

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.

Noble-gas compounds: A general procedure of bonding analysis

This paper accounts for a general procedure of bonding analysis that is, expectedly, adequate to describe any type of interaction involving the noble-gas (Ng) atoms. Building on our recently proposed classification of the Ng-X bonds (X = binding partner) [New J. Chem. 44, 15536 (2020)], these contacts are first distinguished into three types, namely, A, B, or C, based on the topology of the electron energy density H(r) and on the shape of its plotted form. Bonds of type B or C are, then, further assigned as B-loose (B^l) or B-tight (B^t) and C-loose (C^l) or C-tight (C^t) depending on the sign that H(r) takes along the Ng-X bond path located from the topological analysis of ρ(r), particularly at around the bond critical point (BCP). Any bond of type A, B^l/B^t, or C^l/C^t is, finally, assayed in terms of contribution of covalency. This is accomplished by studying the maximum, minimum, and average value of H(r) over the volume enclosed by the low-density reduced density gradient (RDG) isosurface associated with the bond (typically, the RDG isosurface including the BCP) and the average ρ(r) over the same volume. The bond assignment is also corroborated by calculating the values of quantitative indices specifically defined for the various types of interactions (A, B, or C). The generality of our taken approach should encourage its wide application to the study of Ng compounds.

Chalcogen-bonded donor–acceptor complexes of 5,6-dicyano[1,2,5]selenadiazolo[3,4-b]pyrazine with halide ions

With halides X− (X = Cl, Br, I) 5,6-dicyano-[1,2,5]selenadiazolo[3,4-b]pyrazine 1 forms chalcogen-bonded complexes [1–X]− structurally defined by XRD. UV/Vis spectra of [1–X]− feature red-shifted charge-transfer bands in the Vis part.

Large interaction energy for the homodimer and the heterodimer extracted from the supramolecular chain of a bent trinuclear zinc(ii) complex with a reduced Schiff base ligand

The coordinated amino groups in a trinuclear zinc complex participate in strong H-bonding interactions that have been analysed. The dimerization energy is very large for both the homodimer and the heterodimer in the 1D supramolecular chain.

A new krypton complex – Experimental and computational investigation of the krypton sulphur pentafluoride cation, [KrSF5]+, in the gas phase

The gas-phase reactions of noble gas (Ng) cations, namely Kr+ and Xe+, with SF6 were investigated experimentally by Fourier transform ion cyclotron resonance mass spectrometry and computationally using MP2 and...

Inorganic–Organic {dz2-MIIS4}···π-Hole Stacking in Reverse Sandwich Structures. The Case of Cocrystals of Group 10 Metal Dithiocarbamates with Electron-deficient Arenes

Cocrystallization of the dithiocarbamate complexes [M(S2CNEt2)2] (M = Ni 1, Pd 2, Pt 3) and X-substituted perfluoroarenes (X = I, Br; 1,2-dibromoperfluorobenzene FBrB and 1,2-diiodoperfluorobenzene FIB) gives isomorphous cocrystals of...

Maximal occupation by bases of π-hole bands surrounding linear molecules

Linear molecules such as CO₂ contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO₂ , where T = C, Si, Ge, Sn; bases are NCH and NH₃ . CO₂ engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH₃ . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH₃ . But like GeO₂ , SiO₂ can sustain only two bases in its equatorial ring. The π-hole ring of SnO₂ can engage in up to four tetrel bonds with either NCH or NH₃ , even though these bonds are weaker than those with GeO₂ or SiO₂ . As all of these complexes cast TO₂ in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.

On the Importance of Pnictogen and Chalcogen Bonding Interactions in Supramolecular Catalysis

In this review, several examples of the application of pnictogen (Pn) (group 15) and chalcogen (Ch) bonding (group 16) interactions in organocatalytic processes are gathered, backed up with Molecular Electrostatic Potential surfaces of model systems. Despite the fact that the use of catalysts based on pnictogen and chalcogen bonding interactions is taking its first steps, it should be considered and used by the scientific community as a novel, promising tool in the field of organocatalysis.

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.

Anatomy of π-hole bonds: Linear systems

The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.

On the Importance of σ–Hole Interactions in Crystal Structures

Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.

Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study

In this study, we provide experimental (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the involvement of charge assisted chalcogen bonding (ChB) interactions in the recognition and folding mechanisms of S-adenosylmethionine (SAM) riboswitches. Concretely, an initial PDB search revealed several examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine (EEM) molecules and uracil (U) bases belonging to RNA take place. While these interactions are usually described as a merely Coulombic attraction between the positively charged S/Se group and RNA, theoretical calculations indicated that the σ holes of S and Se are involved. Moreover, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader’s “Atoms in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot) visual index, and Natural Bonding Orbital (NBO) analyses. As far as our knowledge extends, this is the first time that ChBs in SAM–RNA complexes have been systematically analyzed, and we believe the results might be useful for scientists working in the field of RNA engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function

Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.

Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases

In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.

Noncovalent Interactions at Lanthanide Complexes

Lanthanide complexes have attracted a widespread attention due to their structural diversity, as well as multifunctional and tunable properties. The development of lanthanide based functional materials has often relied on the design of the secondary coordination sphere of the corresponding lanthanide complexes. For instance, usually simple lanthanide salts (solvento complexes) do not catalyze effectively organic reactions or provide low yield of the expected product, whereas the presence of a suitable organic ligand with a noncovalent bond donor or acceptor centre (secondary coordination sphere) modifies the symmetry around the metal centre in lanthanide complexes which then successfully can act as catalysts in both homogenous and heterogenous catalysis. In this minireview, we discuss several relevant examples, based on X-ray crystal structure analyses, in which the hydrogen, halogen, chalcogen, pnictogen, tetrel and rare-earth bonds, as well as cation-π, anion-π, lone pair-π, π-π and pancake interactions, are used as a synthon in the decoration of the secondary coordination sphere of lanthanide complexes.

Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.

Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes

The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX2 (M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (ωB97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX2 (X = H, F, Cl, Br, Me) and either a carbene ((NH2)2C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH3)2C, (NH3)2C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX2 one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered.

Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.

Ternary Cocrystals with Large Soft Cavities: A 1,4-diiodotetrafluorobenzene (DITFB)⋅4-Biphenylpyridine N-oxide (BPNO) Host Assembled by Inclusion of Planar Aromatic Guests

A large soft-cavity host composed of 1,4-diiodotetrafluorobenzene (DITFB) and 4-biphenylpyridine N-oxide (BPNO) is assembled under the mediation of a planar aromatic guest molecule (pyrene or perylene) through C-I⋅⋅⋅^- O-N⁺ halogen bonds and π-hole⋅⋅⋅π bonds. Single-crystal X-ray diffraction reveals that guest molecules can be completely encapsulated in the four-layer host cavity to assemble ternary host-guest cocrystals; namely, Pyr@DITFB ⋅ BPNO and Per@DITFB ⋅ BPNO. The luminescence of these ternary cocrystals originates from their discrete guest molecules, which exhibit pure-blue and yellow emissions, respectively, that are localized at 425 nm and in the range of 485 to 578 nm, respectively. In addition, the contribution of different fragments to the stabilization of the crystal structure is estimated by computational chemistry. These cocrystals have significant potential for use in optical applications or materials, such as photonics or organic light-emitting diodes, respectively, that require to avoid the aggregation between luminophores.

Comparison of ±σ-hole and ±R˙-hole interactions formed by tetrel-containing complexes: a computational study

For the first time, unconventional ±R˙-hole interactions were unveiled in tetrel-containing complexes. The nature and characteristics of ±R˙-hole interactions were explored relative to their ±σ-hole counterparts for ˙TF3⋯ and W-T-F3⋯B/R˙/A complexes (where T = C, Si, and Ge, W = H and F, B = Lewis bases, R˙ = free radicals, and A = Lewis acids). In an effort to thoroughly investigate such interactions, a plethora of quantum mechanical calculations, including molecular electrostatic potential (MEP), maximum positive electrostatic potential (V s,max), point-of-charge (PoC), interaction energy, symmetry adapted perturbation theory (SAPT), and reduced density gradient-noncovalent interaction (RDG-NCI) calculations, were applied. The most notable findings to emerge from this study are that (i) from the electrostatic perspective, the molecular stabilization energies of ˙TF3 and W-T-F3 monomers became more negative as the Lewis basicity increased, (ii) the most stable complexes were observed for the ones containing Lewis bases, forming -σ-hole and -R˙-hole interactions, and the interaction energies systematically increased in the order H-T-F3⋯B < ˙TF3⋯B < F-T-F3⋯B, (iii) contrariwise, the +σ-hole and +R˙-hole interactions with Lewis acids are more energetically favorable in the order F-T-F3⋯A < ˙TF3⋯A < H-T-F3⋯A, and (iv) generally, the dispersion force plays a key role in stabilizing the tetrel-containing complexes, jointly with the electrostatic and induction forces for the interactions with Lewis bases and acids, respectively. Concretely, the findings presented in this paper add to our understanding of the characteristics and nature of such intriguing interactions.

On the importance of RH3C⋯N tetrel bonding interactions in the solid state of a dinuclear zinc complex with a tetradentate Schiff base ligand

The tetrel bonding and π-stacking interactions in a new dinuclear zinc complex using a tetradentate N₂O₂ donor Schiff base have been analysed energetically using DFT calculations and several computational tools.