Tetrel Bond Interactions Research Articles

Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions.

The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX3 (MA = CH3NH3+; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH3NH3+) and an inorganic anion (TtX3-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX3 in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX3-) together. We have demonstrated that each Tt in each [CH3NH3+•TtX3-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX3- units, thus causing the emergence of an infinite array of 3D TtX64- octahedra in the crystalline phase. The TtX44- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.

Tetrel-bond interactions involving boron-substituted carbenes

Tetrel-bond interactions involving boron-substituted carbenes

Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work.

Understanding the molecular interactions that drive peptide folding is crucial to chemistry and biology. In this study, we analyzed the role of CO···CO tetrel bonding (TtB) interactions in the folding mechanism of three different peptides (ATSP, pDIQ, and p53), which exhibit a different propensity to fold in an α helix motif. To achieve this goal, we used both a recently developed Bayesian inference approach (MELDxMD) and Quantum Mechanics (QM) calculations at the RI-MP2/def2-TZVP level of theory. These techniques allowed us to study the folding process and to evaluate the strength of the CO···CO TtBs as well as the synergies between TtBs and hydrogen-bonding (HB) interactions. We believe that the results derived from our study will be helpful for those scientists working in computational biology, peptide chemistry, and structural biology.

Tetrel-Bond Interactions Involving Metallylenes TH2 (T = Si, Ge, Sn, Pb): Dual Binding Behavior.

The dual binding behavior of the metallylenes TH2 (T = Si, Ge, Sn, Pb) with some selected Lewis acids (T'H3F, T' = Si, Ge, Sn, Pb) and bases (N2, HCN, CO, and C6H6) has been investigated by using the high-level quantum chemical method. Two types (type-A and type-B) of tetrel-bonded complexes can be formed for TH2 due to their ambiphilic character. TH2 act as Lewis bases in type-A complexes, and they act as Lewis acids in type-B ones. CO exhibits two binding modes in the type-B complexes, one of which is TH2···CO and the other is TH2···OC. The TH2···OC complexes possess a weaker binding strength than the other type-B complexes. The TH2···OC complexes are referred to as the type-B2 complexes, and the other type-B complexes are referred to as the type-B1 complexes. The type-A complexes exhibit a relatively weak binding strength with Eint (interaction energy) values ranging from -7.11 to -15.55 kJ/mol, and the type-B complexes have a broad range of Eint values ranging from -9.45 to -98.44 kJ/mol. The Eint values of the type-A and type-B1 complexes go in the order SiH2 > GeH2 > SnH2 > PbH2. The AIM (atoms in molecules) analysis suggests that the tetrel bonds in type-A complexes are purely closed-shell interactions, and those in most type-B1 complexes have a partially covalent character. The EDA (Energy decomposition analysis) results indicate that the contribution values of the three energy terms go in the order electrostatic > dispersion > induction for the type-A and type-B2 complexes, and this order is electrostatic > induction > dispersion for the type-B1 complexes.

Experimental and Theoretical Study of Tetrel Bonding and Noncovalent Interactions in Hemidirected Lead(II) Phosphorodithioates: An Implication on Crystal Engineering

The importance of tetrel bonds (TtBs) in spontaneous self-assembly has been highlighted in two new lead(II) complexes: i.e. Pb[S2P{OC6H4(4-C(CH3)3)}2]2 (1) and Pb[S2P{OC6H4(4-C2H5)}2]2 (2), which were successfully isolated and characterized by FT-IR, UV–vis and multinuclear NMR (31P, 1H and 13C) spectroscopy. The structures of both complexes have been confirmed by single-crystal X-ray diffraction analyses. Interestingly, lead is coordinated by three sulfur atoms in 1 but by four sulfur atoms in 2, due to stereochemically active lone pair electrons, thus leading to trigonal-pyramidal and tetragonal-pyramidal geometries, respectively. Complex 1 is the first example of a lead(II) dithiophosphate wherein the lead(II) center is coordinated to three S atoms. These complexes are stabilized at a lower coordination number and display hemidirected structures that allow forming σ-hole bonds. The lead(II) center establishes short contacts with sulfur atoms to form Pb···S TtBs that contribute to the construction of a self-assembled dimer in 1 but to a supramolecular polymer in 2. The supramolecular assemblies are further stabilized by Pb···π TtB interactions. The attractive nature of TtBs has been studied by DFT calculations and characterized using a combination of Bader’s quantum theory of atoms-in-molecules (QTAIM) and noncovalent interaction plot (NCI plot) index based on a reduced density gradient (NCI-RDG) analysis. A systematic Hirshfeld surface analysis facilitates a comparison of intermolecular interactions such as C–H···π, π···π, Pb···S, and Pb···π in both complexes, which play a crucial role in the crystal engineering.

Syntheses, and Structural and Physical Properties of Axially Chiral Biaryl Dicarboxylic Acids Bearing Chalcogen Atoms

The preparation, optical resolution, and structural investigations of a series of axially chiral biaryl dicarboxylic acids bearing oxygen, sulfur, and selenium atoms were carried out. The crystal structures of sulfur- and selenium-containing derivatives revealed that the carboxy groups of these compounds are located in a co-planar geometry with the fused aromatic rings including the chalcogen atoms. These conformational controls were found to be achieved by chalcogen-bonding interactions between chalcogen atoms in the aromatic rings and oxygen atoms in the carboxy groups. Even in the case of a binaphthofuran derivative, in which the formation of chalcogen-bonding interactions was expected to be negligible, the carboxy groups were also found to be located in a co-planar geometry toward its fused cyclic rings. Natural bond orbital (NBO) analyses of these dicarboxylic acids indicated the formation not only for the chalcogen-bonding interactions for S and Se derivatives, but also the tetrel-bonding interactions between the oxygen atoms in the carboxy groups and the carbon atoms in the fused cyclic rings for all biaryl dicarboxylic acids. These tetrel-bonding interactions were thought to contribute to conformational control in the binaphthofuran derivative. Physical and chiroptical properties such as the racemization barriers and circular dichroism (CD) spectra of these biaryl dicarboxylic acids were also revealed.

Unexplored σ-hole and π-hole interactions in (X2CY)2 complexes (X = F, Cl; Y = O, S)

The potentiality of the X2CY molecules (X = F, Cl; Y = O, S) to engage in σ-hole···σ-hole, di-σ-hole, σ-hole···π-hole, and π-hole···π-hole interactions was assessed. In that spirit, potential energy surface (PES) scan was devoted to thoroughly characterize the features of the (X2CY)2 complexes within a series of configurations, including halogen···halogen, halogen···chalcogen, chalcogen···chalcogen, halogen···tetrel, chalcogen···tetrel, and tetrel···tetrel. In most instances, the strength of the inspected interactions declined according to the order: tetrel···tetrel (staggered) > tetrel···tetrel (eclipsed) > chalcogen···tetrel > halogen···tetrel > chalcogen···chalcogen > halogen···chalcogen > halogen···halogen configurations. The strength of the explored complexes within tetrel···tetrel configurations was found to be dominated further by the contributions of the three planar substituents rather than those of the π-hole center. Benchmarking of the binding energies emphasized an approximate similarity between the resulted energetic features that were evaluated at the MP2/aug-cc-pVTZ and CCSD/CBS levels of theory. Quantum theory of atoms in molecules (QTAIM) critically unveiled the closed-shell nature of the halogen-, chalcogen-, and tetrel-bonding interactions within the adopted configurations. Symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) demonstrated the domination of the σ-hole interactions by the dispersion forces (Edisp). In addition to the dominant Edisp, preferential contributions of the electrostatic (Eelst) and induction (Eind) forces were detected for the π-hole bonded complexes within all the scouted configurations. The emerging findings from the current work would be a fruitful underpinning for the forthcoming studies in materials science and crystal engineering.

Effect of External Electric Field on Tetrel Bonding Interactions in (FTF3···FH) Complexes (T = C, Si, Ge, and Sn).

A quantum chemical study was accomplished on the σ-hole interactions of the barely explored group IV elements, for the first time, in the absence and presence of the positively and negatively directed external electric field (EEF). The analyses of molecular electrostatic potential addressed the occurrence of the σ-hole on all the inspected tetrel atoms, confirming their salient versatility to engage in σ-hole interactions. MP2 energetic findings disclosed the occurrence of favorable σ-hole interactions within the tetrel bonding complexes. The tetrel bonding interactions became stronger in the order of C < Si < Ge < Sn for F–T–F3···FH complexes with the largest interaction energy amounting to −19.43 kcal/mol for the optimized F–Sn–F3···FH complex under the influence of +0.020 au EEF. The interaction energy conspicuously evolved by boosting the magnitude of the positively directed EEF value and declining the negatively directed EEF one. The decomposition analysis for the interaction energies was also executed in terms of symmetry-adapted perturbation theory, illuminating the dominant electrostatic contribution to all the studied complexes’ interactions except carbon-based interactions controlled by dispersion forces. The outcomes that emerged from the current work reported significantly how the direction and strength of the EEF affect the tetrel-bonding interactions, leading to further improvements in the forthcoming studies of supramolecular chemistry and materials science.

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.

Competition and cooperativity of hydrogen-bonding and tetrel-bonding interactions involving triethylene diamine (DABCO), H2O and CO2in air

Triethylene diamine (DABCO) can interact with H2O and CO2in air to form dimeric and trimeric complexesviahydrogen bond, tetrel bond as well as van der Waals interactions.

Synergistic and antagonistic interplay between tetrel bond and pnicogen bond in complexes involving ring compounds.

The binary and ternary complexes composed of GeH3F, AsH2F and ring compounds (benzene, borazine and cyclopentadienyl anion) have been studied by theoretical calculations to understand the interplay between the tetrel bond and pnicogen bond interactions. The bonding strength of intermolecular interactions in these complexes is analyzed by means of atoms in molecules (AIM), natural bond orbital (NBO) and noncovalent interaction (NCI) index methods. The binary tetrel-bonded and pnicogen-bonded complexes can be classified as an n-type or π-type complex according to the orbital interactions involved in the complexes. Three binding modes can be distinguished according to the interplay between interactions for the ternary complexes. The binding mode A is characterized by the interplay between π-type tetrel bond and n-type pnicogen bond; binding mode B is characterized by the interplay between π-type pnicogen bond and n-type tetrel bond, and binding mode C is characterized by the interplay between π-type tetrel bond and π-type pnicogen bond. The binding modes A and B exhibit the synergistic interplay effect, while the antagonistic effect is reflected in mode C. The synergistic effect in binding modes A and B is stronger than antagonistic effect in mode C, and the synergistic effect in binding mode B is stronger than that in mode A.

Theoretical and Crystallographic Study of Lead(IV) Tetrel Bonding Interactions.

The ability of tetrahedral lead(IV) to establish noncovalent σ-hole tetrel bonding interactions with electron-rich atoms (ElRs; anions and Lewis bases) has been studied at the PBE0-D3/def2-TZVPD level of theory. An analysis of the Cambridge Crystallographic Database (CSD), which is a convenient storehouse of geometric information, has been performed to investigate the existence of tetrel bonding interactions involving tetrahedral lead(IV) derivatives. Several examples of tetrel bonding interactions that are crucial in crystal packing, ranging from 0D to 2D assemblies, have been found. In addition to the energetic and theoretical study of several XPb(CH3 )3 ⋅⋅⋅ElR complexes (X=F, CN, CF3 , and CH3 ), Bader's theory of atoms in molecules has also been used to further analyze and characterize the noncovalent interactions described herein.

H&lt;sub&gt;3&lt;/sub&gt;XF (X = Ge, Si)与芳香环化合物间硅键作用的理论研究

H&lt;sub&gt;3&lt;/sub&gt;XF (X = Ge, Si)与芳香环化合物间硅键作用的理论研究

S⋅⋅⋅Sn Tetrel Bonds in the Activation of Peroxisome Proliferator-Activated Receptors (PPARs) by Organotin Molecules.

In this study, a PDB (Protein Data Bank) analysis and theoretical calculations (PBE0-D3/def2-TZVP level of theory) were combined to analyze the impact of S⋅⋅⋅Sn tetrel-bonding interactions in the activation mechanism of peroxisome proliferator-activated receptors (PPARs) by two organotin derivatives, triphenyltin (TPT) and tributyltin (TBT). The presence of a covalently bonded CYS285 to the organotin molecule was found to be key to enhance the σ-hole-donor ability of the tin atom, thus strengthening the tetrel-bonding interaction with a sulfur atom belonging to a vicinal methionine residue (MET364).

Strong Tetrel Bonds: Theoretical Aspects and Experimental Evidence.

In recent years, noncovalent interactions involving group-14 elements of the periodic table acting as a Lewis acid center (or tetrel-bonding interactions) have attracted considerable attention due to their potential applications in supramolecular chemistry, material science and so on. The aim of the present study is to characterize the geometry, strength and bonding properties of strong tetrel-bond interactions in some charge-assisted tetrel-bonded complexes. Ab initio calculations are performed, and the results are supported by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches. The interaction energies of the anionic tetrel-bonded complexes formed between XF3M molecule (X=F, CN; M=Si, Ge and Sn) and A− anions (A−=F−, Cl−, Br−, CN−, NC− and N3−) vary between −16.35 and −96.30 kcal/mol. The M atom in these complexes is generally characterized by pentavalency, i.e., is hypervalent. Moreover, the QTAIM analysis confirms that the anionic tetrel-bonding interaction in these systems could be classified as a strong interaction with some covalent character. On the other hand, it is found that the tetrel-bond interactions in cationic tetrel-bonded [p-NH3(C6H4)MH3]+···Z and [p-NH3(C6F4)MH3]+···Z complexes (M=Si, Ge, Sn and Z=NH3, NH2CH3, NH2OH and NH2NH2) are characterized by a strong orbital interaction between the filled lone-pair orbital of the Lewis base and empty BD*M-C orbital of the Lewis base. The substitution of the F atoms in the benzene ring provides a strong orbital interaction, and hence improved tetrel-bond interaction. For all charge-assisted tetrel-bonded complexes, it is seen that the formation of tetrel-bond interaction is accompanied bysignificant electron density redistribution over the interacting subunits. Finally, we provide some experimental evidence for the existence of such charge-assisted tetrel-bond interactions in crystalline phase.

Tetrel Bonding Interactions in Perchlorinated Cyclopenta- and Cyclohexatetrelanes: A Combined DFT and CSD Study.

In this manuscript, we combined DFT calculations (PBE0-D3/def2-TZVP level of theory) and a Cambridge Structural Database (CSD) survey to evaluate the ability of perchlorinated cyclopenta- and cyclohexatetrelanes in establishing tetrel bonding interactions. For this purpose, we used Tr5Cl10 and Tr6Cl12 (Tr = Si and Ge) and HCN, HF, OH− and Cl− as electron donor entities. Furthermore, we performed an Atoms in Molecules (AIM) analysis to further describe and characterize the interactions studied herein. A survey of crystal structures in the CSD reveals that close contacts between Si and lone-pair-possessing atoms are quite common and oriented along the extension of the covalent bond formed by the silicon with the halogen atom.

Comparison of σ-Hole and π-Hole Tetrel Bonds Formed by Pyrazine and 1,4-Dicyanobenzene: The Interplay between Anion-π and Tetrel Bonds.

The σ-hole tetrel bond in pyrazine/1,4-dicyanobenzene⋅⋅⋅TH3 F (T=C and Si) and the π-hole tetrel bond in pyrazine/1,4-dicyanobenzene⋅⋅⋅F2 TO have been compared. The π-hole tetrel bond is stronger than the corresponding σ-hole tetrel bond, with a larger interaction energy, shorter binding contact, greater electron density, and bigger charge transfer. Pyrazine forms a more stable tetrel-bonded complex than 1,4-dicyanobenzene even though the nitrogen atom in the former has a smaller negative electrostatic potential than the latter. An interesting cooperative effect was found when anion-π and tetrel-bond interactions coexisted in the same multicomponent complex of X- ⋅⋅⋅pyrazine/1,4-dicyanobenzene⋅⋅⋅TH3 F/F2 TO (X=F, Cl, and Br). Both interactions displayed a positive cooperative effect, as shown by the larger interaction energies, shorter binding separations, and greater electron densities. The enhancement in the tetrel bond is dependent on the strength of the anion-π interaction and it becomes larger in the order Br- <Cl- <F- . The enhancement in the tetrel bond changes its nature from a purely closed-shell interaction to a partially covalent interaction. Conversely, the anion-π interaction shows a prominent strengthening of up to -38 kcal mol-1 . This effect has been analyzed in terms of electrostatic potentials and charge transfer.

Importance of R-CF3···O Tetrel Bonding Interactions in Biological Systems.

In this article, ab initio calculations have been combined with a search in the Protein Data Bank (PDB) to demonstrate the importance of σ-hole tetrel bonding interactions in biological systems. In particular, we focus our attention on the ability of the -CF3 group to participate in noncovalent interactions as Lewis acids, and we show the importance of this interaction in the inhibition mechanism of a NADP+-dependent isocitrate dehydrogenase (IDH) enzyme that converts isocitrate to α-ketoglutarate. IDH mutations are found in multiple hematologic and solid tumors, inducing premalignant disorders. A potent triazine-based inhibitor of the mutant IDH (enasidenib) presents two -CF3 groups in the structure. One establishes a tetrel bonding interaction with an aspartate residue that contributes to the binding and selectivity of the inhibitor to the active site.

Tetrel Bonding Interactions.

Tetrel (Tr) bonding is first placed into perspective as a σ-hole bonding interaction with atoms of the Tr family. An sp(3) R4Tr unit has four σ-holes with which a Lewis base can form a complex. We then highlight some inspiring crystal structures where Tr bonding is obvious, followed by an account of our own work. We have shown that Tr bonding is ubiquitous in the solid state and we have highlighted that Tr bonding with carbon is possible when C is placed in the appropriate chemical context. We hope that this account serves as an initial guide and source of inspiration for others wishing to exploit this vastly underexplored interaction.

Interplay between hydrogen bond and single-electron tetrel bond: H3C⋯COX2⋯HY and H3C⋯CSX2⋯HY (X = F, Cl; Y = CN, NC) complexes as a working model

UMP2 calculations with aug-cc-pVTZ basis set were performed to analyze intermolecular interactions in a series of ring-shaped molecular complexes formed by CH3, CO(S)X2 (X=F, Cl) and HCN(NC) which are connected via two hydrogen bonds and a single-electron tetrel bond interactions. Molecular geometries and interaction energies of triads are investigated at the UMP2/aug-cc-pVTZ computational level. Particular attention is paid to many-body interaction energies. The impacts of the hydrogen bonds on the single-electron tetrel bond in each complex are systematically investigated. The electronic properties of the complexes are analyzed using parameters derived from the atoms in molecules (AIM) methodology.