Tetrel Bonds Research Articles

Tetrel bonds, penta‐ and hexa‐coordinated tin and lead centres

A tetrel bond – an interaction between a Group 14 element acting as Lewis acid centre and an electron‐donating moiety – is analysed for ZF4 (Z = Sn, Pb) complexes with NH3 and HCN species. MP2/aug‐cc‐pVTZ calculations were performed and supported by results of the quantum theory of atoms in molecules. The results of calculations show that the tetrel centre may be considered as a pentavalent one if ZF4 interacts with one NH3 or HCN ligand or even as a hexavalent centre if it interacts with two ligands; thus the hypervalency phenomenon is discussed for the complexes analysed here. The theoretical analysis is supported by a discussion of the crystal structures containing the SnF4 fragment; these structures are characterized by a hexa‐coordinated tin centre.

Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods

The physical nature of charge-inverted hydrogen bonds in H3 XH ⋯YH3 (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: EintSAPT<EintSCS-MP2≤EintMP2C<EintMP2≈EintCCSD(T). It is confirmed that the aug-cc-pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole-ζ quality. Considerably large binding energies suggest potential usefulness of charge-inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ- and π-hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge-inverted hydrogen bond would become the first described case of a hydride-triel bond. © 2017 Wiley Periodicals, Inc.

Interplay between the σ-tetrel bond and σ-halogen bond in PhSiF3⋯4-iodopyridine⋯N-base

The ternary complexes of PhSiF3⋯4-iodopyridine⋯N-base (N-base = HCN, NH3, NHNH2, and NH2CH3), PhTF3⋯4-iodopyridine⋯NH3 (T = C and Ge), PhSiY3⋯4-iodopyridine⋯NH3 (Y = H and Cl), PhSiF3⋯4-bromopyridine⋯NH3 and the respective binary complexes have been investigated. 4-Halopyridine in these ternary complexes plays a dual role of both a Lewis acid with the σ-hole on the halogen atom in the halogen bond and a Lewis base with the nitrogen atom in the tetrel bond. The interplay between both interactions in the ternary complexes has been analyzed in terms of the binding distance, binding energy, charge transfer, electron density and electrostatic potentials. A synergistic effect is found for the tetrel and halogen bonds in most of the ternary complexes, while a diminutive effect is present for the hydrogen and halogen bonds in PhCF3⋯4-iodopyridine⋯NH3. The magnitude of cooperative energy depends on the strength of both interactions. Interestingly, PhSiCl3⋯4-iodopyridine has a stronger tetrel bond than PhSiH3⋯4-iodopyridine, inconsistent with the size of the σ-hole on the Si atom. In addition, the tetrel bond exhibits a partially covalent interaction nature.

Tetrel, pnictogen and chalcogen bonds identified in the gas phase before they had names: a systematic look at non-covalent interactions

The terms tetrel bond, pnictogen bond and chalcogen bond were coined recently to describe non-covalent interactions involving group 14, 15 and 16 atoms, respectively, acting as the electrophilic site that seeks a nucleophilic region of another molecule, for example a non-bonding electron pair or π-electron pair of a Lewis base. Many complexes containing these non-covalent bonds were identified and characterised in isolation in the gas phase by rotational and vibrational spectroscopy long before they were given these names. In this article, the geometries so determined for selected examples of complexes of each type are rationalised in terms of the molecular electrostatic surface potentials of the component molecules. Examples of chalcogen-bonded complexes considered are based mainly on sulfur dioxide, with the region near the sulfur atom as the electrophilic site that interacts with n-electron and π-electron pairs for a range of simple Lewis base molecules. For tetrel bonds, the examples discussed involve the carbon atom of carbon dioxide as the electrophilic centre, while for pnictogen bonds the central nitrogen of the closely related molecule nitrous oxide is chosen. Geometrical similarities within each series allow simple definitions of each type of non-covalent bond that are conformal with that recently advanced for the halogen bond, a related non-covalent interaction.

Comparison of halide receptors based on H, halogen, chalcogen, pnicogen, and tetrel bonds.

A series of halide receptors are constructed and the geometries and energetics of their binding to F-, Cl-, and Br- assessed by quantum calculations. The dicationic receptors are based on a pair of imidazolium units, connected via a benzene spacer. The imidazoliums each donate a proton to a halide in a pair of H-bonds. Replacement of the two bonding protons by Br leads to binding via a pair of halogen bonds. Likewise, chalcogen, pnicogen, and tetrel bonds occur when the protons are replaced, respectively, by Se, As, and Ge. Regardless of the binding group considered, F- is bound much more strongly than are Cl- and Br-. With respect to the latter two halides, the binding energy is not very sensitive to the nature of the binding atom, whether H or some other atom. But there is a great deal of differentiation with respect to F-, where the order varies as tetrel > H ∼ pnicogen > halogen > chalcogen. The replacement of the various binding atoms by their analogues in the next row of the periodic table enhances the fluoride binding energy by 22-56%. The strongest fluoride binding agents utilize the tetrel bonds of the Sn atom, whereas it is I-halogen bonds that are preferred for Cl- and Br-. After incorporation of thermal and entropic effects, the halogen, chalcogen, and pnicogen bonding receptors do not represent much of an improvement over H-bonds with regard to this selectivity for F-, even I which binds quite strongly. In stark contrast, the tetrel-bonding derivatives, both Ge and Sn, show by far the greatest selectivity for F- over the other halides, as much as 1013, an enhancement of six orders of magnitude when compared to the H-bonding receptor.

Comparison of tetrel bonds in neutral and protonated complexes of pyridineTF3 and furanTF3 (T = C, Si, and Ge) with NH3.

Ab initio calculations have been performed for the complexes H+-PyTX3NH3 and H+-furanTF3NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an FH hydrogen bond to a CN tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol-1. The tetrel bonding becomes stronger in the order H+-p-PySiF3NH3 < H+-m-PySiF3NH3 < H+-o-PySiF3NH3, showing a reverse trend from that of the neutral analogues. In addition, there is competition between the tetrel and hydrogen bonds in the protonated complexes, in which the hydrogen bond is favored in the complexes of H+-p-PyCF3 but the tetrel bond is preferred in the complexes of H+-p-PyTX3 (T = Si, Ge; X = F, Cl) and H+-o/m-PySiF3.

Intermolecular interactions in molecular crystals: what's in a name?

Structure-property relationships are the key to modern crystal engineering, and for molecular crystals this requires both a thorough understanding of intermolecular interactions, and the subsequent use of this to create solids with desired properties. There has been a rapid increase in publications aimed at furthering this understanding, especially the importance of non-canonical interactions such as halogen, chalcogen, pnicogen, and tetrel bonds. Here we show how all of these interactions - and hydrogen bonds - can be readily understood through their common origin in the redistribution of electron density that results from chemical bonding. This redistribution is directly linked to the molecular electrostatic potential, to qualitative concepts such as electrostatic complementarity, and to the calculation of quantitative intermolecular interaction energies. Visualization of these energies, along with their electrostatic and dispersion components, sheds light on the architecture of molecular crystals, in turn providing a link to actual crystal properties.

Prospects for 207Pb solid-state NMR studies of lead tetrel bonds.

The feasibility and value of 207Pb solid-state NMR experiments on compounds featuring lead tetrel bonds is explored. Although the definition remains to be formalized, lead tetrel bonds may be qualitatively described as existing when there is evidence of a net attractive interaction between an electrophilic region associated with lead in a molecular entity and a nucleophilic region in another, or the same, molecular entity. Unambiguous identification of lead tetrel bonds can be challenging due to the hypervalent tendency of lead. We report here a series of 207Pb solid-state NMR experiments on five metal-organic frameworks featuring lead coordinated to hydrazone-based ligands. Such frameworks may be held together in part by lead tetrel bonds. The acquisition of 207Pb solid-state NMR spectra for such materials is feasible and is readily accomplished using a combination of magic-angle spinning and Carr-Purcell-Meiboom-Gill methods in moderate to low applied magnetic fields. The lead centres are characterized by 207Pb isotropic chemical shifts ranging from -426 to -2591 ppm and chemical shift tensor spans ranging from 910 to 2681 ppm. Careful inspection of the structures of the compounds and the literature 207Pb NMR data may suggest that a tetrel bond to lead results in chemical shift parameters which are intermediate between those which are characteristic of holodirected and hemidirected lead coordination geometries. Challenges associated with DFT computations of the 207Pb NMR parameters are discussed. In summary, the 207Pb data for the compounds studied herein show a marked response to the presence of non-coordinating electron-rich moieties in close contact with the electrophilic surface of formally hemidirectionally coordinated lead compounds.

Regulation of coin metal substituents and cooperativity on the strength and nature of tetrel bonds

Ab initio calculations have been performed for the tetrel-bonded dyad MCN⋯TF4 (M = Cu, Ag, and Au; T = C, Si, Ge, and Sn) and C2H4…MCN…TF4 and C2(CN)4…MCN…TF4.

Tetrel bond of pseudohalide anions with XH3F (X = C, Si, Ge, and Sn) and its role in SN2 reaction.

The complexes of XH3F⋯N3-/OCN-/SCN- (X = C, Si, Ge, and Sn) have been investigated at the MP2/aug-cc-pVTZ(PP) level. The σ-hole of X atom in XH3F acts as a Lewis acid forming a tetrel bond with pseudohalide anions. Interaction energies of these complexes vary from -8 to -50 kcal/mol, mainly depending on the nature of X and pseudohalide anions. Charge transfer from N/O/S lone pair to X-F and X-H σ* orbitals results in the stabilization of these complexes, and the former orbital interaction is responsible for the large elongation of X-F bond length and the remarkable red shift of its stretch vibration. The tetrel bond in the complexes of XH3F (X = Si, Ge, and Sn) exhibits a significant degree of covalency with XH3F distorted significantly in these complexes. A breakdown of the individual forces involved attributes the stability of the interaction to mainly electrostatic energy, with a relatively large contribution from polarization. The transition state structures that connect the two minima for CH3Br⋯N3- complex have been localized and characterized. The energetic, geometrical, and topological parameters of the complexes were analyzed in the different stages of the SN2 reaction N3- + CH3Br → Br- + CH3N3.

Carbene tetrel-bonded complexes

An ab initio calculation has been carried for the carbene tetrel bonded complexes CH3Y∙∙∙CH2 (Y = F, CN, NC, and NO2), CH3F∙∙∙CZ2 (Z = Cl and CH3), XH3F∙∙∙CF2 (X = C, Si, Ge, and Sn), SiF4∙∙∙CF2, and XH3F∙∙∙NHC (N-heterocyclic carbene), where carbene is treated as a Lewis base and XH3Y is a Lewis acid. Formation of the tetrel bond is mainly attributed to charge transfer from the lone pair on the C atom in the carbene toward the σ* X–Y orbital and also the σ* X–H one in the strong tetrel bond. The carbene tetrel bond is strengthened/weakened by the electron-withdrawing group in the tetrel donor/acceptor and enhanced by the methyl group in C(CH3)2. NHC forms a stronger carbene tetrel bond in XH3F∙∙∙NHC (X = Si, Ge, and Sn) where it exceeds that of the majority of H-bonds. Interestingly, the tetrel bond becomes stronger in the order of X = C < Ge < Sn < Si in XH3F∙∙∙NHC and the largest interaction energy occurs in SiH3F∙∙∙NHC, amounting to −103 kJ/mol. The carbene tetrel bond can be strengthened by cooperative effect with the N∙∙∙M interaction in trimers H2C∙∙∙CH3CN∙∙∙M (M = CH3CN, HCN, ICN, SbH2F, LiCN, and BeH2) and has doubled in H2C∙∙∙CH3CN∙∙∙BeH2.

Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds.

The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.

Modulating the strength of tetrel bonding through beryllium bonding.

Quantum chemical calculations were performed to investigate the stability of the ternary complexes BeH2···XMH3···NH3 (X = F, Cl, and Br; M = C, Si, and Ge) and the corresponding binary complexes at the atomic level. Our results reveal that the stability of the XMH3···BeH2 complexes is mainly due to both a strong beryllium bond and a weak tetrel-hydride interaction, while the XMH3···NH3 complexes are stabilized by a tetrel bond. The beryllium bond with a halogen atom as the electron donor has many features in common with a beryllium bond with an O or N atom as the electron donor, although they do exhibit some different characteristics. The stability of the XMH3···NH3 complex is dominated by the electrostatic interaction, while the orbital interaction also makes an important contribution. Interestingly, as the identities of the X and M atoms are varied, the strength of the tetrel bond fluctuates in an irregular manner, which can explained by changes in electrostatic potentials and orbital interactions. In the ternary systems, both the beryllium bond and the tetrel bond are enhanced, which is mainly ascribed to increased electrostatic potentials on the corresponding atoms and charge transfer. In particular, when compared to the strengths of the tetrel and beryllium bonds in the binary systems, in the ternary systems the tetrel bond is enhanced to a greater degree than the beryllium bond. Graphical Abstract A tetrel bond can be strengthened greatly by a beryllium bond.

Cooperative Halogen Bond, Tetrel Bond and Van Der Waals Interaction Coexisting in the CO2, CO and XY (X=Cl, Br; Y=F, Cl, Br) Trimeric Complexes

AbstractA series of four‐membered ring‐shaped molecular complexes formed by CO2, CO and XY (X=Cl, Br; Y=F, Cl, Br) molecules have been investigated at the moderate M06‐2X/6‐311++G(2d,2p) level of theory, in which these molecules interact with each other via halogen bond, tetrel bond and van der Waals interaction. The optimized geometry, stretching mode and interaction energy have been obtained and discussed. Molecular electrostatic potential and the contour maps of Laplacian ∇2ρ were used to reveal the formation mechanisms of these complexes. The cooperativity was found in these complexes because their interaction energies are stronger than the sum of the pair interaction energies. The electrostatic force was believed to be the main net contribution to the stability of these complexes. The simultaneous interactions involving CO2, CO and dihalogen molecules in these complexes would provide insight into the CO2 and CO fixation via noncovalent interactions.

Anionic complexes of F− and Cl− with substituted methanes: Hydrogen, halogen, and tetrel bonds

Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the anionic complexes X−:CX(FnH3−n), for X=F, Cl, and n=0–3. These complexes are stabilized by tetrel, hydrogen, and halogen bonds. Hydrogen-bonded complexes are the most stable complexes and halogen-bonded complexes are the least stable, with one exception. Charge-transfer across intermolecular bonds stabilizes all complexes, and occurs from the anion lone-pair to a σ∗ orbital of the substituted methane. EOM-CCSD spin–spin coupling constants 1tJ(X–C) across intermolecular tetrel bonds, 2hJ(C–X) across hydrogen bonds, and 1xJ(Cl–Cl) and 2xJ(C–Cl) across halogen bonds correlate with intermolecular distances.

Analysis of Hydrogen Bonds in Crystals

The determination of crystal structures provides important information on the geometry of species constituting crystals and on the symmetry relations between them. Additionally, the analysis of crystal structures is so conclusive that it allows us to understand the nature of various interactions. The hydrogen bond interaction plays a crucial role in crystal engineering and, in general, its important role in numerous chemical, physical and bio-chemical processes was the subject of various studies. That is why numerous important findings on the nature of hydrogen bonds concern crystal structures. This special issue presents studies on hydrogen bonds in crystals, and specific compounds and specific H-bonded patterns existing in crystals are analyzed. However, the characteristics of the H-bond interactions are not only analyzed theoretically; this interaction is compared with other ones that steer the arrangement of molecules in crystals, for example halogen, tetrel or pnicogen bonds. More general findings concerning the influence of the hydrogen bond on the physicochemical properties of matter are also presented.

Tuning of tetrel bonds interactions by substitution and cooperative effects in XH3Si···NCH···HM (X = H, F, Cl, Br; M = Li, Na, BeH and MgH) complexes

ABSTRACTIn this work, the interplay between the tetrel bond and the dihydrogen bond is investigated in ternary XH3Si···NCH···HM complexes, where X = H, F, Cl, Br and M = Li, Na, BeH, MgH. The nature of Si···N and H···H interactions is studied by molecular electrostatic potential (MEP), noncovalent interaction and electron localisation function analyses. All binding distances in the ternary complexes are shorter than those of isolated XH3Si···NCH and NCH···HM systems. That is, the two types of interactions have a cooperative effect on each other. The results of the MEP analysis indicate that the enhancement of the Si···N and H···H bonds can mainly be attributed to the electrostatic interaction. The plot of the reduced density gradient versus sign (λ2)ρ indicates that the location of the spike associated with each interaction in the ternary systems moves slightly towards the negative (λ2)ρ values with respect to the binary systems. This confirms that both Si···N and H···H interactions in the ternary complexes are strengthened by the presence of other. Besides, cooperative effects lead to a considerable change in the 14N nuclear quadrupole coupling constant values of the ternary complexes relative to the XH3Si···NCH complexes.

RCH3···O Interactions in Biological Systems: Are They Trifurcated H-Bonds or Noncovalent Carbon Bonds?

In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH3···O complexes (X = any atom or group). Recently, it has been demonstrated both experimentally and theoretically the importance of noncovalent carbon bonds in the solid state. When an electron-rich atom interacts with a methyl group, the role of the methyl group is commonly viewed as a weak H-bond donor. However, if the electron-rich atom is located equidistant from the three H atoms, the directionality of each individual H-bond in the trifurcated binding mode is poor. Therefore, the XCH3···O interaction could be also defined as a tetrel bond (C···O interaction). In this manuscript, we shed light into this matter and demonstrate the importance of XCH3···O noncovalent carbon bonding interactions in two relevant protein-substrate complexes retrieved from the PDB.

Tetrel bonds between PySiX3 and some nitrogenated bases: Hybridization, substitution, and cooperativity

Ab initio calculations have been performed to study the influence of hybridization, substitution, and cooperativity on the tetrel bond in the complexes of PySiX3 (Py=pyridine and X=halogen). The tetrel bond becomes stronger in the order of p-PySiF3⋯NCH(sp)<p-PySiF3⋯NHCH2(sp2)<p-PySiF3⋯NH3(sp3). The electron-donating group in the electron donor strengthens the tetrel bond, and this effect is mainly achieved through electrostatic and polarization interactions. Tetrel bonding displays cooperative effects with triel bonding and chalcogen bonding, characterized by shorter binding distances and greater electron densities. The cooperative effects between triel/chalcogen bond and tetrel bond have been analyzed by molecular electrostatic potentials and charge transfer. Energy decomposition indicates that many-body effects are mainly caused by polarization energy. The geometries of Si⋯N interaction and its applications in crystal materials have been characterized and evidenced by a CSD research.

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.