Close contacts involving germanium and tin in crystal structures: experimental evidence of tetrel bonds

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.

Tetrel bond in the triphenyltin(IV) chloride-cyclo-hexyl-diphenyl-phosphane oxide (1/1) cocrystal

The single-crystal X-ray diffraction structure of the title compound, [SnCl(C6H5)3]·C18H21OP, is reported. The 1:1 cocrystal features a short and directional tetrel bond between tin and oxygen. The tin-oxygen distance is 2.346 (4) Å, representing 62% of the sum of the van der Waals radii of Sn and O. The Cl-Sn⋯O angle is 174.0 (1)° and this nearly linear arrangement is consistent with a tetrel bond formed via a σ-hole opposite the tin-chlorine covalent bond. Some weak C-H⋯Cl inter-actions are noted between adjacent mol-ecules.

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.'

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.

Solid-state molecular structures of Se(IV) and Te(IV) dihalides X2Se(CH3)(C6F5) and the gas-phase structure of Se(CH3)(C6F5)

In a systematic study the Se(IV) and Te(IV) dihalides F2E(CH3)(C6F5), Cl2E(CH3)(C6F5) and Br2E(CH3)(C6F5) (E = Se, Te) have been synthesized and their crystal and molecular structures been investigated by X-ray diffraction and computational methods. The solid-state structures of all compounds show significant correlations between the lengths of the E–C1 bond and the intermolecular E···X (X = F, Cl and Br) contacts, indicating the presence of σ-hole interactions. For comparison, the crystal and gas phase (electron diffraction) structures of Se(CH3)(C6F5) are presented as well. They show very similar structural parameters in both phases. The structures of the single molecules X2E(CH3)(C6F5) have been analyzed by quantum-chemical methods in terms of their surface potentials. They show significant similarities of their molecular electrostatic-potential topologies (V s,max). The magnitude of V s,max correlates with the aggregation pattern.

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.

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.

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.

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.

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.

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.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.

Chalcogen-Bonding Interactions in Telluroether Heterocycles [Te(CH2 )m ]n (n=1-4; m=3-7)

The Te⋅⋅⋅Te secondary bonding interactions (SBIs) in solid cyclic telluroethers were explored by preparing and structurally characterizing a series of [Te(CH2 )m ]n (n=1-4; m=3-7) species. The SBIs in 1,7-Te2 (CH2 )10 , 1,8-Te2 (CH2 )12 , 1,5,9-Te3 (CH2 )9 , 1,8,15-Te3 (CH2 )18 , 1,7,13,19-Te4 (CH2 )20 , 1,8,15,22-Te4 (CH2 )24 and 1,9,17,25-Te4 (CH2 )28 lead to tubular packing of the molecules, as has been observed previously for related thio- and selenoether rings. The nature of the intermolecular interactions was explored by solid-state PBE0-D3/pob-TZVP calculations involving periodic boundary conditions. The molecular packing in 1,7,13,19-Te4 (CH2 )20 , 1,8,15,22-Te4 (CH2 )24 and 1,9,17,25-Te4 (CH2 )28 forms infinite shafts. The electron densities at bond critical points indicate a narrow range of Te⋅⋅⋅Te bond orders of 0.12-0.14. The formation of the shafts can be rationalized by frontier orbital overlap and charge transfer.

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.

Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms

The interactions in model ionic YTX₃···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F^-, Cl^-, Br^-, Li⁺) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX₃ molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li⁺···NCTCl₃···F^- (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li⁺ + NCTCl₃ + F^- fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.

Not Only Hydrogen Bonds: Other Noncovalent Interactions

In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Tetrel Interactions from an Interacting Quantum Atoms Perspective

Tetrel bonds, the purportedly non-covalent interaction between a molecule that contains an atom of group 14 and an anion or (more generally) an atom or molecule with lone electron pairs, are under intense scrutiny. In this work, we perform an interacting quantum atoms (IQA) analysis of several simple complexes formed between an electrophilic fragment (A) (CH₃F, CH₄, CO₂, CS₂, SiO₂, SiH₃F, SiH₄, GeH₃F, GeO₂, and GeH₄) and an electron-pair-rich system (B) (NCH, NCO-, OCN-, F-, Br-, CN-, CO, CS, Kr, NC-, NH₃, OC, OH₂, SH-, and N₃-) at the aug-cc-pvtz coupled cluster singles and doubles (CCSD) level of calculation. The binding energy ( E bind AB ) is separated into intrafragment and inter-fragment components, and the latter in turn split into classical and covalent contributions. It is shown that the three terms are important in determining E bind AB , with absolute values that increase in passing from electrophilic fragments containing C, Ge, and Si. The degree of covalency between A and B is measured through the real space bond order known as the delocalization index ( δ AB ). Finally, a good linear correlation is found between δ AB and E xc AB , the exchange correlation (xc) or covalent contribution to E bind AB .

The Chalcogen Bond in Crystalline Solids: A World Parallel to Halogen Bond

The distribution of the electron density around covalently bonded atoms is anisotropic, and this determines the presence, on atoms surface, of areas of higher and lower electron density where the electrostatic potential is frequently negative and positive, respectively. The ability of positive areas on atoms to form attractive interactions with electron rich sites became recently the subject of a flurry of papers. The halogen bond (HaB), the attractive interaction formed by halogens with nucleophiles, emerged as a quite common and dependable tool for controlling phenomena as diverse as the binding of small molecules to proteinaceous targets or the organization of molecular functional materials. The mindset developed in relation to the halogen bond prompted the interest in the tendency of elements of groups 13-16 of the periodic table to form analogous attractive interactions with nucleophiles. This Account addresses the chalcogen bond (ChB), the attractive interaction formed by group 16 elements with nucleophiles, by adopting a crystallographic point of view. Structures of organic derivatives are considered where chalcogen atoms form close contacts with nucleophiles in the geometry typical for chalcogen bonds. It is shown how sulfur, selenium, and tellurium can all form chalcogen bonds, the tendency to give rise to close contacts with nucleophiles increasing with the polarizability of the element. Also oxygen, when conveniently substituted, can form ChBs in crystalline solids. Chalcogen bonds can be strong enough to allow for the interaction to function as an effective and robust tool in crystal engineering. It is presented how chalcogen containing heteroaromatics, sulfides, disulfides, and selenium and tellurium analogues as well as some other molecular moieties can afford dependable chalcogen bond based supramolecular synthons. Particular attention is given to chalcogen containing azoles and their derivatives due to the relevance of these moieties in biosystems and molecular materials. It is shown how the interaction pattern around electrophilic chalcogen atoms frequently recalls the pattern around analogous halogen, pnictogen, and tetrel derivatives. For instance, directionalities of chalcogen bonds around sulfur and selenium in some thiazolium and selenazolium derivatives are similar to directionalities of halogen bonds around bromine and iodine in bromonium and iodonium compounds. This gives experimental evidence that similarities in the anisotropic distribution of the electron density in covalently bonded atoms translates in similarities in their recognition and self-assembly behavior. For instance, the analogies in interaction patterns of carbonitrile substituted elements of groups 17, 16, 15, and 14 will be presented. While the extensive experimental and theoretical data available in the literature prove that HaB and ChB form twin supramolecular synthons in the solid, more experimental information has to become available before such a statement can be safely extended to interactions wherein elements of groups 14 and 15 are the electrophiles. It will nevertheless be possible to develop some general heuristic principles for crystal engineering. Being based on the groups of the periodic table, these principles offer the advantage of being systematic.

Quantitative Assessment of Tetrel Bonding Utilizing Vibrational Spectroscopy

A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of -1.4 to -26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.

The halogen bond: a new avenue in recognition and self-assembly

Welcome to this themed issue of NJC entitled: ‘The halogen bond: a new avenue in recognition and self-assembly’.

Cyanine dyes: synergistic action of hydrogen, halogen and chalcogen bonds allows discrete I42− anions in crystals

Discrete tetraiodide dianions (I₄²⁻) are formed in crystals via halogen bond coordination of I₂ by iodide anions which are pinned in their positions by a network of hydrogen bonds involving a benzoselenazole cyanine dye.