Tetrel Bonds Research Articles

The ability of a tetrel bond to transition a neutral amino acid into a zwitterion

The interaction between glycine and F2CO/F2SiO occurs through the formation of a π-tetrel bond between the C/Si atom and a carboxyl O atom. The interaction energy is some 20 kJ/mol for the C⋯O tetrel bond, but exceeds 300 kJ/mol for Si⋯O. As part of the latter complexation process, the proton engaged in the intramolecular OH··N H-bond is transferred across to the N, forming a zwitterion. This Si⋯O tetrel bond is more effective in inducing this proton transfer than is placement of the glycine in an aqueous medium, complexation with an anionic BH4−, or adding an electron to the glycine.

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 () 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 , 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 (). Finally, a good linear correlation is found between and , the exchange correlation (xc) or covalent contribution to .

Forty years of progress in the study of the hydrogen bond

The author looks back at developments over the last few decades concerning the H–bond. The list of atoms involved as proton donor and acceptor has broadened dramatically, including most electronegative atoms and even metals. The factors that control the transfer of the proton across the H–bond have been elucidated and show the importance of even minor changes in its geometry. Small stretches can shut down the transfer entirely, and certain bends can force a proton to transfer against a pK gradient. Along with the recognition that a CH..O interaction can represent a true H–bond, and one with strength comparable to more traditional H–bonds, has come an understanding of its contributions to protein structure and function. The replacement of the bridging of H by any of a litany of electronegative atoms leads to similarly strong interactions, with many features virtually indistinguishable from a true H–bond. These noncovalent interactions are typically referred to as halogen, chalcogen, pnicogen, and tetrel bonds, depending upon the identity of the substitute bridging atom.

Tetrel Bonding along the Pathways of Transsilylation and Alkylation of N-Trimethylsilyl- N-methylacetamide with Bifunctional (Chloromethyl)fluorosilanes.

A quantum chemical study has been carried out on the complexes formed in the first stage of the reaction of (chloromethyl)trifluorosilane with an ambident nucleophile, N-trimethylsilyl- N-methylacetamide, existing in the amide and imidate tautomeric forms. The analysis of molecular electrostatic potential maps of the electrophile molecule revealed the presence of two σ-holes belonging to the Si and C atoms. Each of the two tautomers of the nucleophile form complexes having O···Si, O···C, N···Si, and N···C bonds of different characters. The natural bond orbital and quantum theory of atoms in molecules analyses showed the presence of the O···Si and O···C tetrel bonds or of electrostatic interaction in the complexes with the amide tautomer, depending on the orientation of the components. The imidate tautomer forms a complex with covalent N-Si bond, whereas the N···C bond is very weak. The effect of silicon atom arrangement on the structure of complexes between N-trimethylsilyl- N-methylacetamide and bifunctional silanes ClCH2SiX nF3- n (X = Me, OMe, Cl, n = 1, 2) and the effect of σ-hole tetrel bonding interactions on the reaction pathways are discussed.

Exploring N…C tetrel and O…S chalcogen bonds in HN(CH)SX:OCS systems, for X = F, NC, Cl, CN, CCH, and H

Ab initio MP2/aug’-cc-pVTZ calculations were carried out to investigate HN(CH)SX:OCS potential energy surfaces. Bound equilibrium complexes stabilized by N…C tetrel bonds and O…S chalcogen bonds have been found on all HN(CH)SX:OCS surfaces, but HN(CH)SF:OCS is the only bound molecule. Charge-transfer interactions are consistent with the nature of the intermolecular bonds in these complexes. Spin-spin coupling constants 1tJ(NC) for HN(CH)SF:OCS are consistent with the changing nature of the N…C bond as the complex passes through the transition state to become a molecule. 1cJ(OS) describes an intermolecular chalcogen bond in the complex, transition structure, and molecule.

Pnicogen and tetrel bonds—tetrahedral Lewis acid centres

It is obvious and well known that the hydrogen bond plays a crucial role in numerous physical, chemical and biochemical processes. However, the significance of other interactions is also analysed in numerous studies. They are often compared with the hydrogen bond. The halogen bond is an example of such interaction that reveals characteristics occurring also for the hydrogen bond. The other interactions which are often classified as the σ-hole bonds or π-hole bonds possess characteristics typical for the hydrogen bond. The interactions of tetrahedral pnicogen and tetrel centres with Lewis bases are analysed here. The former ones may be labelled as the charge-assisted pnicogen bonds and classified as the σ-hole bonds. The latter ones labelled as the tetrel bonds are also classified as interactions between the σ-hole and the electron-rich region. Both these interactions are compared with the hydrogen bond. In the case of the hydrogen bond, the A–H...B, A–H...π and A–H...σ types of interactions are discussed in different studies where A–H is the proton-donating bond while B, π and σ label the kind of the proton acceptor: the mono-atomic Lewis base centre B, the π-electrons and the σ-electrons, respectively. The pnicogen centre, Z, in the charge-assisted pnicogen bonds may also interact with these electron-rich regions thus the Z...B, Z...π and Z...σ pnicogen bonds are known.

On the interaction of propynal with HNO, HF, HCl, H2O, CH3OH, and NH3: Red- and blue-shifting hydrogen bonds and tetrel bonds

The potential energy surfaces of the complexes of propynal, (propiolaldehyde, propargyl aldehyde, HCCCOH), with a series of small molecules (HNO, HF, HCl, H2O, CH3OH, and NH3) have been investigated theoretically at the MP2 and CCSD(T) levels using several extended basis sets. Thirty low-lying minima have been detected, eight for HCCCOH-HNO, four for each of the dimers HCCCOH-HF, HCCCOH-HCl, and HCCCOH-H2O, seven for the HCCCOH-CH3OH complex, and three for HCCCOH-NH3. The most stable HCCCOH-HNO complex has a non-planar, orthogonal structure with a tetrel bond and a hydrogen bond. In most cases the calculated intramolecular bond length changes as induced by complex formation are allegeable on the basis of the intramolecular harmonic force fields of propynal and the partner molecules. The vibrational frequency shifts, typical for formyl groups engaged in hydrogen bonding, red shifts of CO stretches and blue shifts of CH stretches, occur in most of the dimers, whereas the acetylenic CH and CC stretches are red-shifted when this CH bond is involved in hydrogen bonding. In almost all HCCCOH-HNO complexes, the NH stretching frequency is also blue-shifted. However, in case of the most stable HCCCOH-HNO complex a red-shift of the harmonic NH stretch is calculated. Inclusion of anharmonic contributions reduces this red shift substantially and even converts it to a blue shift. Conventional red shifts of X-H (X = F, Cl, O) stretching frequencies and blue shifts for formyl CH stretches are calculated for most of the complexes with HF, HCl, H2O, CH3OH, and NH3.

Strategy To Form Eutectic Molecular Liquids Based on Noncovalent Interactions.

The concept of eutectic molecular liquids (EMLs) was defined, and a strategy to form EMLs based on noncovalent interactions was proposed. We verified the formation and investigated the properties, interaction sites, and interaction energies of the obtained 16 EMLs. Moreover, two new forms of noncovalent interactions, κ-hole and μ-hole bonding interactions, were proposed, which broaden the understanding of intermolecular interactions. Numerous EMLs can be strategically designed and prepared by simply mixing two parent molecule components based on noncovalent interactions, including hydrogen bonding interactions; π-π stacking; and σ-hole (halogen, chalcogen, pnicogen, and tetrel bonds), π-hole, κ-hole, and μ-hole bonding interactions. The properties of EMLs can be finely tailored by selecting or even designing appropriate parent compounds for task-specific applications. Our work presents a substantial step toward the innovative development of liquid systems.

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.

Identification of the Tetrel Bonds between Halide Anions and Carbon Atom of Methyl Groups Using Electronic Criterion.

The consideration of the disposition of minima of electron density and electrostatic potential along the line between non-covalently bound atoms in systems with Hal−···CH3–Y (Hal− = Cl, Br; Y = N, O) fragments allowed to prove that the carbon atom in methyl group serves as an electrophilic site provider. These interactions between halide anion and carbon in methyl group can be categorized as the typical tetrel bonds. Statistics of geometrical parameters for such tetrel bonds in CSD is analyzed. It is established that the binding energy in molecular complexes with tetrel bonds correlate with the potential acting on an electron in molecule (PAEM). The PAEM barriers for tetrel bonds show a similar behavior for both sets of complexes with Br− and Cl− electron donors.

Non-Covalent Interactions Involving Alkaline-Earth Atoms and Lewis Bases B: An ab Initio Investigation of Beryllium and Magnesium Bonds, B···MR2 (M = Be or Mg, and R = H, F or CH3)

Geometries, equilibrium dissociation energies (De), intermolecular stretching, and quadratic force constants (kσ) determined by ab initio calculations conducted at the CCSD(T)/aug-cc-pVTZ level of theory, with De obtained by using the complete basis set (CBS) extrapolation [CCSD(T)/CBS energy], are presented for the B···BeR2 and B···MgR2 complexes, where B is one of the following Lewis bases: CO, H2S, PH3, HCN, H2O or NH3, and R is H, F or CH3. The BeR2 and MgR2 precursor molecules were shown to be linear and non-dipolar. The non-covalent intermolecular bond in the B···BeR2 complexes is shown to result from the interaction of the electrophilic band around the Be atom of BeR2 (as indicated by the molecular electrostatic potential surface) with non-bonding electron pairs of the base, B, and may be described as a beryllium bond by analogy with complexes such as B···CO2, which contain a tetrel bond. The conclusions for the B···MgR2 series are similar and a magnesium bond can be correspondingly invoked. The geometries established for B···BeR2 and B···MgR2 can be rationalized by a simple rule previously enunciated for tetrel-bonded complexes of the type B···CO2. It is also shown that the dissociation energy, De, is directly proportional to the force constant, kσ, in each B···MR2 series, but with a constant of proportionality different from that established for many hydrogen-bonded B···HX complexes and halogen-bonded B···XY complexes. The values of the electrophilicity, EA, determined from the De for B···BeR2 complexes for the individual Lewis acids, A, reveal the order A = BeF2 > BeH2 > Be(CH3)2—a result that is consistent with the −I and +I effects of F and CH3 relative to H. The conclusions for the MgR2 series are similar but, for a given R, they have smaller electrophilicities than those of the BeR2 series. A definition of alkaline-earth non-covalent bonds is presented.

Comparison of σ‐hole and π‐hole tetrel bonds in complexes of borazine with TH3F and F2TO/H2TO (T = C, Si, Ge)

AbstractThe complexes between borazine and TH3F/F2TO/H2TO (T = C, Si, Ge) are investigated with high‐level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom of the BH bond, whereas TH3F and F2TO/H2TO provide the σ‐hole and π‐hole, respectively, for the tetrel bond. The N atom of borazine is the favored site for both the σ and π‐hole tetrel bonds. Less‐stable dimers include a σ‐tetrel bond to the borazine ring center and to the BH proton. The π‐hole tetrel‐bonded complexes are more strongly bound than are their σ‐hole counterparts. Due to the coexistence of both T···N tetrel and B···O triel bonding, the complexes of borazine with F2TO/H2TO (T = Si and Ge) are very stable, with interaction energies up to −108 kcal/mol. The strongly bonded complexes are accompanied by substantial net charge transfer from F2TO/H2TO to borazine.

Comparison of σ-/π-Hole Tetrel Bonds between TH3 F/F2 TO and H2 CX (X=O, S, Se).

Several σ-hole and π-hole tetrel-bonded complexes with a base H2 CX (X=O, S, Se) have been studied, in which TH3 F (T=C-Pb) and F2 TO (T=C and Si) act as the σ-hole and π-hole donors, respectively. Generally, these complexes are combined with a primary tetrel bond and a weak H-bond. Only one minimum tetrel-bonded structure is found for TH3 F, whereas two minima tetrel-bonded complexes for some F2 TO. H2 CX is favorable to engage in the π-hole complex with F2 TO relative to TH3 F in most cases, and this preference further expands for the Si complex. Particularly, the double π-hole complex between F2 SiO and H2 CX (X=S and Se) has an interaction energy exceeding 500 kJ/mol, corresponding to a covalent-bonded complex with the huge orbital interaction and polarization energy. Both the σ-hole interaction and the π-hole interaction are weaker for the heavier chalcogen atom, while the π-hole interaction involving F2 TO (T=Ge, Sn, and Pb) has an opposite change. Both types of interactions are electrostatic in nature although comparable contributions from dispersion and polarization are respectively important for the weaker and stronger interactions.

Insight from electron density and energy framework analysis on the structural features of Fx-TCNQ (x = 0, 2, 4) family of molecules.

In this study, the nature and characteristics of the intramolecular and intermolecular interactions in crystal structures of the fluoro-substituted 7,7,8,8-tetracyanoquinodimethane (TCNQ) family of molecules, i.e. Fx-TCNQ (x = 0, 2, 4), are explored. The molecular geometry of the reported crystal structures is directly dependent on the degree of fluorination in the molecule, which consequently also results in the presence of an intramolecular N[triple-bond]C...F-C π-hole tetrel bond. Apart from this, the energy framework analysis performed along the respective transport planes provides new insights into the energetic distribution in this class of molecules.

Enhancing effects of π-hole tetrel bonds on the σ-hole interactions in complexes involving F2TO (T = Si, Ge, Sn)

The bimolecular and termolecular complexes involving F2TO (T = Si, Ge, Sn) and XCN/BrY (X = H, Br, CH3, and PH2; Y = F, CN, OH, and H) were designed to form the π-hole tetrel bonds and different sorts of σ-hole interactions, to investigate the influence of π-hole tetrel bonds on the σ-hole interactions. The effect of π-hole tetrel bonds on the σ-hole interactions in three series HCN···F2TO···HCN, HCN···F2SiO···XCN, and HCN···F2SiO···BrY is reflected by the changes in geometry, interaction energy, and charge transfer. With the formation of π-hole tetrel bond, the VS, min value outside the oxygen atom of F2TO becomes more negative, resulting in a stronger σ-hole interaction. Comparing with the bimolecular complex, the σ-hole binding distance and binding angle in the corresponding termolecular complex changes a lot, with the formation of another tetrel bond. The σ-hole interaction energy is enhanced more than 100% in most of the complexes with the exception of HCN···F2SiO···BrCN. The enhancing effect is related to the strength of π-hole tetrel bond, but has no relationship with the strength of σ-hole interactions. In particular, the σ-hole tetrel bond between F2SiO and CH3CN varies from a weak tetrel bond in the bimolecular complex F2SiO···CH3CN to a moderate hydrogen bond in the termolecular complex HCN···F2SiO···CH3CN.

Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives.

When an N-base approaches the tetrel atom of TF4 (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.

Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bonds.

A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.

Systematic study of the substitution effect on the tetrel bond between 1,4-diazabicyclo[2.2.2]octane and TH3X.

A tetrel bond was characterized in the complexes of 1,4-diazabicyclo[2.2.2]octane (DABCO) with TH3X (T = C, Si, Ge; X= –Me, –H, –OH, –NH2, –F, –Cl, –Br, –I, –CN, –NO2). DABCO engages in a weak tetrel bond with CH3X but a stronger one with SiH3X and GeH3X. SiH3X is favorable to bind with DABCO relative to GeH3X, inconsistent with the magnitude of the σ-hole on the tetrel atom. The methyl group in the tetrel donor weakens the tetrel bond but an enhancing effect is found for the other substituents, particularly –NO2. The substitution effect is also related to the nature of the tetrel atom. The halogen substitution from F to I has a weakening effect in the CH3X complex but an enhancing effect in the SiH3X complex and a negligible effect in the GeH3X complex. The above abnormal results found in these complexes can be partly attributed to the charge transfer from the lone pair on the nitrogen atom of DABCO into the anti-bonding orbital σ*(T–X) of TH3X. The stability of both SiH3X and GeH3X complexes is primarily controlled by electrostatic interactions and polarization.

Tetrel bonds and conformational equilibria in the formamide-CO2 complex: a rotational study.

The rotational spectra of the complex formamide-CO2 have been measured and assigned by pulsed jet Fourier transform microwave spectroscopy. Two isomers of the complex have been detected where a CO tetrel bond dominates the interactions, and either N-HO or C-HO forms a secondary linkage. Bader's quantum theory of atoms in molecules and Johnson's non-covalent interaction analyses were applied to unveil the intermolecular binding sites and energetic properties in the complex. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population of the observed two isomers as NI/NII ≈ 18/1.

Influence of monomer deformation on the competition between two types of σ-holes in tetrel bonds.

One of several tetrel (T) atoms was covalently attached to three F atoms and a substituted phenyl ring. A NH3 base can form a tetrel bond with TF3C6H2R3 (T = Si, Ge, Sn, Pb; R = H, F, CH3) in a position opposite either an F atom or the ring. The σ-hole opposite the highly electron-withdrawing F (T-F) is more intense than that opposite the ring (T-C). However, when the Lewis base deforms from a tetrahedral to a trigonal bipyramidal shape so as to accommodate the base, it is the T-C σ-hole that is more intense. Accordingly, it is the T-C tetrel-bonded complex for which there is a larger interaction energy with NH3, as high as 34 kcal mol-1. Countering this trend, it requires more energy for the TF3C6H2R3 to deform into the geometry it adopts within the T-C complex than within its T-F counterpart. There is consequently a balance between the overall binding energies of the two competing sites. The smaller tetrel atoms Si and Ge, with their larger deformation energies, show a preference for T-F tetrel binding, while the T-C site is preferred by Pb which suffers from a smaller degree of deformation energy. There is a near balance for T = Sn and the two sites show comparable binding energies.