C(sp3) atoms as tetrel bond donors: A crystallographic survey

Metal-Induced Enhancement of Tetrel Bonding. The Case of C⋅⋅⋅X-IrIII (X=Cl, Br) Tetrel Bond Involving a Methyl Group

In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X=Cl 1, Br 2; THT=tetrahydrothiophene; Xyl=2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe⋅⋅⋅X-IrIII (X=Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe⋅⋅⋅X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe⋅⋅⋅X-IrIII (X=Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.

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.

The Tetrel Bonds of Hypervalent Halogen Compounds

The tetrel bond between PhXF2Y(TF3) (T = C and Si; X = Cl, Br, and I; Y = F and Cl) and the electron donor MCN (M = Li and Na) was investigated at the M06-2X/aug-cc-pVDZ level of theory. As the electronegativity of the halogen atom X increases, the strength of the tetrel bond also increases, but as the electronegativity of the halogen atom Y increases, the strength of the tetrel bond decreases. The magnitude of the interaction energy in most -CF3 complexes was found to be less than 10 kcal/mol, but to exceed 11 kcal/mol for PhClF2Cl(CF3)⋯NCNa. The tetrel bond is greatly enhanced when the -SiF3 group interacts with LiCN or NaCN, with the largest interaction energy approaching 100 kcal/mol and displaying a covalent Si⋯N interaction. Along with this enhancement, the Si⋯N distance was found to be less than the X-Si bond length, the -SiF3 group to be closer to the N atom, and in most -SiF3 systems, the X-Si-F angle to be less than 90°; the -SiF3 group therefore undergoes inversion and complete transfer in some systems.

C∙∙∙O and Si∙∙∙O Tetrel Bonds: Substituent Effects and Transfer of the SiF3 Group

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF3-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO2, CN, F, CH3, OH, OCH3, NH2, and Li) is examined by quantum chemical means. The Si∙∙∙O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C∙∙∙O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite effect. The SiF3 group transfers roughly halfway between the N of the acid and the O of the base without the aid of cooperative effects from a third entity.

Halogen bonds, chalcogen bonds, pnictogen bonds, tetrel bonds and other σ-hole interactions: a snapshot of current progress

We report here on the status of research on halogen bonds and other σ-hole interactions involving p-block elements in Lewis acidic roles, such as chalcogen bonds, pnictogen bonds and tetrel bonds. A brief overview of the available literature in this area is provided via a survey of the many review articles that address this field. Our focus has been to collect together most review articles published since 2013 to provide an easy entry into the extensive literature in this area. A snapshot of current research in the area is provided by an introduction to the virtual special issue compiled in this journal, comprising 11 articles and entitled `Halogen, chalcogen, pnictogen and tetrel bonds: structural chemistry and beyond.'

DFT potentials from a chemical perspective: Anatomy of electron (de)localization in molecules and crystals

We introduce a fermionic potential, v f $$ {v}_f $$ , as a comprehensive measure of electron (de)localization in atomic-molecular systems. Unlike other common descriptors as ELF, LOL, etc., it characterizes all physical effects responsible for (de)localization of electrons, namely: an exchange hole depth, its tendency to change, a sensitivity of an exchange correlation hidden in a pair density and kinetic potential to local variations in electron density. Wells in the v f $$ {v}_f $$ distribution correspond to the domains of maximum electron localization, while the potential's barriers prevent delocalization of electrons through them. It also estimates bond orders and successfully reveals the impact of chemical modifications or environmental effects on the delocalization of electrons in molecules and crystals. The v f $$ {v}_f $$ components provide a unique opportunity to compare the influence of the mentioned physical effects on electron (de)localization. This merges physical and chemical views of electron delocalization using functions appearing in density functional theory.

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.

Geminal Charge-Assisted Tetrel Bonds in Bis-Pyridinium Methylene Salts

C(sp³) atoms are known to act as electrophilic sites in self-assembly processes, and in all cases reported till now, they form only one interaction with nucleophiles; that is, they function as monodentate tetrel bond donors. This manuscript reports experimental (X-ray structural analysis) and theoretical evidence (DFT calculations), proving that the methylene carbon in bis-pyridinium methylene salts establishes two short and directional C(sp³)···anion interactions; that is, they function as bidentate tetrel bond donors.

Square Planar Pt(II) Ion as Electron Donor in Pnictogen Bonding Interactions

It has been proposed that late transition metals with low coordination numbers (square planar or linear) can act as nucleophiles and participate in σ-hole interactions as electron donors. This is due to the existence, in this type of metal complexes, of a pair of electrons located at high energy d-orbitals (dz2 or dx2-y2), which are adequate for interacting with antibonding σ-orbitals [σ*(X–Y)] where Y is usually an electron withdrawing element and X an element of the p-block. This type of d[M]→σ*(X–Y) interaction has been reported for metals of groups 9–11 in oxidation states +1 and +2 (d8 and d10) as electron donors and σ-holes located in halogen and chalcogen atoms as electron acceptors. To our knowledge, it has not been described for σ-holes located in pnictogen atoms. In this manuscript, evidence for the existence of pnictogen bonding involving the square planar Pt(II) metal as the electron donor and Sb as the electron acceptor is provided by using an X-ray structure retrieved from the Cambridge Structural Database (CSD) and theoretical calculations. In particular, the quantum theory of atoms in molecules (QTAIM), the noncovalent interaction plot (NCIPlot) and molecular electrostatic potential (MEP) methods were used. Moreover, to further confirm the nature of the Sb···Pt(II) contact, a recently developed method was used where the electron density (ED) and electrostatic potential (ESP) distribution were compared along the Sb···Pt(II) bond path.

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.

C-F Bonds as "Frozen" Nucleophiles: Unconsummated SN2 Reactions

In this note, we present a series of rigid molecules that show close enforced interactions between Ar-F moieties and -CH₂X groups in a "tetrel bond" configuration similar to a nascent S_N2 attack. We explore the spectroscopic, crystallographic, and chemical reactivity consequences of these unusual interactions, including significant through-space spin-spin couplings, short C-F···CH₂X distances, and differential S_N1 and S_N2 reaction pathways. We also reveal experimental evidence of carbon-based tetrel bonds influencing chemical reactivity in solution. Finally, density functional theory (DFT) calculations are employed throughout this study to confirm and illuminate our experimental data.

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.

Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions

Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.

Theoretical study on L-H+-L with identical donors: short strong hydrogen bond or not?

Short strong hydrogen bonds (SSHBs) play crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16 and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. We found that both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. Besides, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.

Periodate anions as a halogen bond donor: formation of anion⋯anion dimers and other adducts

Single crystal X-ray analyses show that iodine in pyridinium periodates acts as a halogen bond (HaB) donor forming short and almost linear contacts with neutral and anionic electron donors. A combination of QTAIM and NCIplot computational tools proves the attractive nature of these contacts.

Experimental and Theoretical Evidence of a Pb⋅⋅⋅Pb Ditetrel Bond Without a σ-Hole

The crystal structure of a newly synthesized compound, [PbL(Ac)]₂ , (where L=2 (amino(pyrazin-2-yl) methylene) hydrazinecarbothioamide, Ac=acetate anion) exhibits a close contact between pairs of Pb atoms, suggesting a ditetrel bond, in addition to two Pb⋅⋅⋅O tetrel bonds, and two C-H⋅⋅⋅O H-bonds. The presence of this ditetrel bond as an attractive component is confirmed by various quantum chemical methods. This novelty of this particular bond is its existence even in the absence of a σ-hole on the Pb atom, which is typically considered a prerequisite for a bond of this type. From a wider perspective, a survey of the Cambridge Structural Database suggests this bond may be more common than was hitherto thought, with 44 examples of Pb⋅⋅⋅Pb contacts amongst a total number of 219 examples of T⋅⋅⋅T interactions in general (T=Si, Ge, Sn, Pb).

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.

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.

Expanding the toolbox of coinage bond: Adducts involving new gold(III) derivatives and bioactive molecules

X-ray analyses of a small library of adducts between AuX3 (X=Cl, Br) and several pyridine derivatives indicate the systematic presence of quite short π -holes coinage bonds; computational studies reveal...

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.

Syntheses, crystal structures and supramolecular assemblies of two Cu(ii) complexes based on a new heterocyclic ligand: insights into C–H⋯Cl and π⋯π interactions

A new heterocyclic ligand, N3L [4-(1-methylimidazole)-2,6-di(pyrazinyl)pyridine] and two Cu(ii) complexes have been synthesized and characterized by several spectroscopic and DFT methods.

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...

Enhancement of tetrel bond involving tetrazole-TtR3 (Tt = C, Si; R = H, F). Promotion of SiR3 transfer by a triel bond

The combination of a CR3 (R = H, F) with a tetrazole can result in a moderate carbon bond, which can be further strengthened by a triel bond. On the other hand, SiR3 group is half transferred between the two N atoms in these conditions.

Frustrated Lewis Pairs Based on Carbon⋅⋅⋅Carbon+ Tetrel Bonds: A DFT Study

The ability of Triangulenium (TA⁺ ) compounds to form Frustrated Lewis Pairs (FLPs) with N-HeteroCycle Carbenes (NHCs) is analysed in this manuscript at the PBE0-D3/def2-TZVP level of theory. We have used six TA⁺ -based moieties, three presenting similar bridging groups (O (trioxo), -CH₂ (triaryl) and -NH (triaza)) and another three mixing, O, -CH₂ and NH moieties. In addition, several aryl-substituted NHCs have been used as electron donor moieties to undergo carbon⋅⋅⋅carbon⁺ tetrel bonds with the TA⁺ derivatives. More precisely, -Me,-iPr, -tBu and -Ph groups were used. Finally, we have used Bader's quantum theory of "atoms in molecules" (QTAIM) and Natural Bonding Analysis (NBO) to characterize the carbon⋅⋅⋅carbon⁺ tetrel bonds described herein. We expect the results gathered herein will be useful for further exploitation of carbon⋅⋅⋅carbon⁺ bonds in the formation of FLPs as well as to expand the current knowledge of tetrel bonds to the fields of synthetic chemistry and catalysis.

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.

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.

Molecular Electrostatic Potential and Noncovalent Interactions in Derivatives of Group 8 Elements

This communication reports experimental and theoretical evidences of σ‐hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements. Cocrystals between pyridine or pyridine N‐oxide derivatives and osmium tetroxide are characterized through various techniques and rationalized as σ‐hole interactions using DFT calculations and several other computational tools. We propose the term “osme bond” (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile. The word osme is the transcription of ὀσμή, the ancient Greek word for smell that was used to name the heaviest group 8 element in relation to the smoky odor of its tetroxide.

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.

Methyl groups as widespread Lewis bases in noncovalent interactions

It is well known that, under certain conditions, C(sp³) atoms behave, via their σ-hole, as Lewis acids in tetrel bonding. Here, we show that methyl groups, when bound to atoms less electronegative than carbon, can counterintuitively participate in noncovalent interactions as electron density donors. Thousands of experimental structures are found in which methyl groups behave as Lewis bases to establish alkaline, alkaline earth, triel, tetrel, pnictogen, chalcogen and halogen bonds. Theoretical calculations confirm the high directionality and significant strength of the interactions that arise from a common pattern based on the electron density holes model. Moreover, despite the absence of lone pairs, methyl groups are able to transfer charge from σ bonding orbitals into empty orbitals of the electrophile to reinforce the attractive interaction.

Chalcogen Bonds in Selenocysteine Seleninic Acid, a Functional GPx Constituent, and in Other Seleninic or Sulfinic Acid Derivatives

The controlled oxidation reaction of L-selenocystine under neutral pH conditions affords selenocysteine seleninic acid (3-selenino-L-alanine) which is characterized also by means of single-crystal X-ray diffraction. This technique shows that selenium forms three chalcogen bonds (ChBs), one of them being outstandingly short. A survey of seleninic acid derivatives in the Cambridge Structural Database (CSD) confirms that the C-Se(=O)O- functionality tends to act as a ChB donor robust enough to systematically influence the interactional landscape in the solid. Quantum Theory of Atom in Molecules (QTAIM) analysis proves the attractive nature of the short contacts observed in crystals containing the seleninic functionality and calculation of surface molecular electrostatic potential (MEP) reveals that remarkably positive σ-holes can frequently be found opposite to the covalent bonds at selenium. Both CSD searches and QTAIM and MEP approaches show that also the sulfinic acid moiety can function as a ChB donor, albeit less frequently than the seleninic acid one. These findings may contribute to a better understanding, at the atomic level, of the mechanism of action of the enzymes that control oxidative stress and ROS deactivation and that contain selenocysteine seleninic acid and cysteine sulfinic acid in the active site.

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.

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN^- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.

Relative Strengths of a Pnicogen and a Tetrel Bond and Their Mutual Effects upon One Another

The ability of the T and Z atoms of TR₃ZR₂ to engage in a noncovalent interaction with NH₃ is assessed by DFT calculations, where the T atom refers to C, Si, and Ge; Z = As, Sb, and P; and substituents R = H and F. In most instances, the tetrel bond (TB) is both stronger and shorter than the pnicogen bond (ZB). These two bond strengths can be equalized, or preference shifted to the ZB, if F substituents are placed on the Z and H on the T atoms. Employing C as the T atom results in a very weak TB, with the ZB clearly favored energetically. The simultaneous formation of both TB and ZB weakens both, particularly the latter, but both bonds survive intact. Geometric and spectroscopic perturbations of the subunits reflect the two types of noncovalent bonds.

Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond

The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl₄, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.

Origins and properties of the tetrel bond

The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.

Carbon (sp3) tetrel bonding mediated BODIPY supramolecular assembly via unprecedented synergy of Csp3⋯N and Csp3⋯F pair interactions

Here, we present the first example of sp³ hybridized carbon centered (C_sp3) tetrel bonding mediated 3D BODIPY assembly via the exceptional synergy of C_sp3⋯N and C_sp3⋯F pair interactions.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Tetrel Bonding Interactions Involving Carbon at Work: Recent Advances in Crystal Engineering and Catalysis

The σ- and π-hole interactions are used to define attractive forces involving elements of groups 12–18 of the periodic table acting as Lewis acids and any electron rich site (Lewis base, anion, and π-system). When the electrophilic atom belongs to group 14, the resulting interaction is termed a tetrel bond. In the first part of this feature paper, tetrel bonds formed in crystalline solids involving sp3-hybridized carbon atom are described and discussed by using selected structures retrieved from the Cambridge Structural Database. The interaction is characterized by a strong directionality (close to linearity) due to the small size of the σ-hole in the C-atom opposite the covalently bonded electron withdrawing group. The second part describes the utilization of two allotropic forms of carbon (C60 and carbon nanotubes) as supramolecular catalysts based on anion–π interactions (π-hole tetrel bonding). This part emphasizes that the π-hole, which is considerably more accessible by nucleophiles than the σ-hole, can be conveniently used in supramolecular catalysis.

Engineering Crystals Using sp3 -C Centred Tetrel Bonding Interactions

1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.

Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides

Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

Intermolecular interactions in antipyrine-like derivatives 2-halo-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)benzamides: X-ray structure, Hirshfeld surface analysis and DFT calculations

Based on experimental and computational data, a complex network of intermolecular interactions has been rationalized for antipyrine compounds.

The ditetrel bond: noncovalent bond between neutral tetrel atoms

The ability of a tetrel atom to serve in the capacity of electron donor in a σ-hole noncovalent bond is tested by quantum calculations.