Tetrel Bonds Research Articles

Unusual Changes of C−H Bond Lengths in Chiral Zinc Complexes Induced by Noncovalent Interactions

AbstractIn order to better understand the effect of non‐covalent weak interactions on molecules, we have explored a variety of weak interactions, such as improper H‐bonding (HB), tetrel bonds (TBs) and halogen bonds, in fluorinated chiral zinc complexes. High resolution neutron diffraction studies revealed a methylene carbon‐hydrogen bond elongation and shortening due to TB and improper HB interactions, respectively. To show the accumulative effects of multiple weak interactions on the C−H bond, three types of tetrel bonds have been carefully examined. We have also shown how C−H bond elongation can be easily offset by forming an improper HB with the H atom from this C−H bond. Non‐covalent interaction and electrostatic potential analysis investigations have been used to affirm the nature of the interactions based on density functional theory (DFT) and other related calculations.

Unusual Changes of C−H Bond Lengths in Chiral Zinc Complexes Induced by Noncovalent Interactions

AbstractIn order to better understand the effect of non‐covalent weak interactions on molecules, we have explored a variety of weak interactions, such as improper H‐bonding (HB), tetrel bonds (TBs) and halogen bonds, in fluorinated chiral zinc complexes. High resolution neutron diffraction studies revealed a methylene carbon‐hydrogen bond elongation and shortening due to TB and improper HB interactions, respectively. To show the accumulative effects of multiple weak interactions on the C−H bond, three types of tetrel bonds have been carefully examined. We have also shown how C−H bond elongation can be easily offset by forming an improper HB with the H atom from this C−H bond. Non‐covalent interaction and electrostatic potential analysis investigations have been used to affirm the nature of the interactions based on density functional theory (DFT) and other related calculations.

Cooperativity between H-bonds and tetrel bonds. Transformation of a noncovalent C⋯N tetrel bond to a covalent bond.

The dimers and trimers formed by imidazole (IM) and F2TO (T = C, Si, Ge) are studied by ab initio calculations. IM can engage in either a NH⋯O H-bond with F2TO or a T⋯N tetrel bond (TB) with the π-hole above the T atom. The latter is a true noncovalent TB for T = C but is a much shorter and stronger covalent bond with F2SiO or F2GeO. When a second IM is added, the cooperativity emerging from its H-bond with the first IM makes it a stronger nucleophile, leading to two minima with F2CO. The first structure contains a long noncovalent C⋯O TB and there is a much shorter covalent bond in the other, with a small energy barrier separating them. The same sort of double minimum occurs when the two IM units are situated parallel to one another in a stacked geometry.

Electron delocalization in defect-containing graphene and its influence on tetrel bond formation.

Using the advanced analyses of electron density and fermionic potential, we show how electron delocalization influences the ability of defect-containing graphene to form tetrel bonds. The Cg atoms of a vacancy defect can produce one nonpolar interaction, alongside a peculiar polar Cg⋯Cg bond. The latter stems from the presence of a localized electron pair on a vacancy defect Cg atom and the local depletion of electron localization on another Cg atom. This interaction is an example of intralayer tetrel bond. In the presence of an absorbed molecule of bisphenol A diglycidyl ether (DGEBA), graphene is able to form incipient tetrel Cg⋯O bonds with an ether group oxygen. In contrast to an epoxy group oxygen, the disposition of the ether oxygen often causes the orientation of electron-rich π-domains of graphene carbon on the weakly expressed electrophilic region of the oxygen. In the case of graphene with a point Si defect, the Si atom can form quite strong Si⋯C interactions with the DGEBA aryl carbons. In contrast to other noncovalent bonds, this interaction significantly alters the electron (de)localization on the Si atom and in the aryl ring. The reliability of the obtained results is enhanced by the use of multiple 2D periodic models with defects located at different positions along the DGEBA skeleton.

Tuneable tetrel bonds between tin and heavy pnictogens.

The first example of a binary cocrystal, comprised of SnPh3Cl and PPh3, whose components are organized via short and directional tetrel bonds (TtB) between tin and phosphorus, is described. DFT elucidates, for the first time, the factors influencing the strength of TtBs involving heavy pnictogens. A CSD survey reveals that such TtBs are also present and determinative in single component molecular systems, highlighting their significant potential as tuneable structure-directing elements.

Tetrel bonds involving a CF3 group participate in protein-drug recognition: a combined crystallographic and computational study.

In this study, the ability of CF3 groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF3 group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF3⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.

Definition of the tetrel bond

The definition of the term “tetrel bond” and instances of its occurance in chemical systems are proposed based on the evidence documented in the current literature.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond.

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

Heavy pnicogen atoms as electron donors in sigma-hole bonds.

DFT calculations evaluate the strength of σ-hole bonds formed by ZH3 and ZMe3 (Z = N, P, As, Sb) acting as electron donor. Bond types considered include H-bond, halogen, chalcogen, pnicogen, and tetrel bond to perfluorinated Lewis acids FH, FBr, F2Se F3As, F4Ge, respectively, as well as their monofluorinated analogues. All of the Z atoms can engage in bonds of at least moderate strength, varying from 3 to more than 40 kcal mol-1. In most cases, N forms the strongest bonds, but the falloff from P to Sb is quite mild. However, this pattern is not characteristic of all cases, as for example in the halogen bonds, where the heavier Z atoms are comparable to, or even stronger than N. Most of the bonds are strengthened by replacing the three H atoms of ZH3 by methyl groups, better simulating the situation that would be generally encountered. Structural and NMR shielding data ought to facilitate the identification of these bonds within crystals or in solution.

Fullerenes, carbon nanotubes and graphene as tetrel bond donors and acceptors of electrophiles

The signs of the extrema of the molecular electrostatic surface potential (MESP) are an effective means of probing the surface reactivity behavior of carbonaceous molecules.

Tetrel Bonding in Anion Recognition: A First Principles Investigation

Twenty-five molecule-anion complex systems [I4Tt···X-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I4Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I4C···X-] series and [I4Tt···X-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I4Tt···X-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.

Complexes of carbon dioxide with methanol and its monohalogen-substituted: Beyond the tetrel bond

This work aims to investigate a significant change in the bonding feature of CO2 complexes that turns from the C∙∙∙O tetrel bond to the OH∙∙∙O hydrogen one due to the effect of halogen-substitution into methanol. The behavior and bonding nature of noncovalent interactions are thoroughly analyzed and discussed. The binding energies were calculated at various methods and extrapolated to the CCSD(T)/CBS. Among DFT-based methods, the B3LYP-D3 is incredibly effective in calculating the binding energy of CH2XOH-CO2 (X = F, Cl, Br) complexes. This work would provide insight into the effect of halogen substituents on the bonding characteristics of noncovalent interactions.

Quantitative insights into noncovalent interactions involving halogen and tetrel bonds in 2,4,6-trimethylpyrylium tetrafluoroborate.

The crystal and molecular structure of an organic salt, in which a 2,4,6-trimethylpyrylium cation forms a salt with a tetrafluoroborate anion, namely, 2,4,6-trimethylpyrylium tetrafluoroborate, C8H11O+·BF4-, has been experimentally realized. The compound crystallizes in the orthorhombic centrosymmetric space group Pnma. The crystal packing is stabilized via a subtle interplay of [F3-B-F]-...O+-C fluorine/oxygen-centred halogen/chalcogen bonds and Cδ+...Fδ- tetrel-bonded contacts. Although the O centre has a formal charge of +1, the estimation of the partial negative charges on O is in accordance with electronegativity considerations. Hirshfeld surface analysis, which also includes an analysis of the three-dimensional deformation density, along with molecular electrostatic potential (MESP) calculations, provides quantitative insights into the nature of the intermolecular interactions. The topological analysis of the electron-density distribution has been performed using AIMAll and TOPOND, and unequivocally establishes the bonding character associated with the different noncovalent interactions. In addition, NBO analysis and polarizability calculations using PolaBer render deeper physical insights into the electronic characteristics of these noncovalent interactions.

Structure-Directing Interplay between Tetrel and Halogen Bonding in Co-Crystal of Lead(II) Diethyldithiocarbamate with Tetraiodoethylene.

The co-crystallization of the lead(II) complex [Pb(S2CNEt2)2] with tetraiodoethylene (C2I4) gave the co-crystal, [Pb(S2CNEt2)2]∙½C2I4, whose X-ray structure exhibits only a small change of the crystal parameters than those in the parent [Pb(S2CNEt2)2]. The supramolecular organization of the co-crystal is largely determined by an interplay between Pb⋯S tetrel bonding (TeB) and I⋯S halogen bonding (HaB) with comparable contributions from these non-covalent contacts; the TeBs observed in the parent complex, [Pb(S2CNEt2)2], remain unchanged in the co-crystal. An analysis of the theoretical calculation data, performed for the crystal and cluster models of [Pb(S2CNEt2)2]∙½C2I4, revealed the non-covalent nature of the Pb⋯S TeB (−5.41 and −7.78 kcal/mol) and I⋯S HaB (−7.26 and −11.37 kcal/mol) interactions and indicate that in the co-crystal these non-covalent forces are similar in energy.

C–F Bonds as “Frozen” Nucleophiles: Unconsummated SN2 Reactions

In this note, we present a series of rigid molecules that show close enforced interactions between Ar-F moieties and -CH2X groups in a "tetrel bond" configuration similar to a nascent SN2 attack. We explore the spectroscopic, crystallographic, and chemical reactivity consequences of these unusual interactions, including significant through-space spin-spin couplings, short C-F···CH2X distances, and differential SN1 and SN2 reaction pathways. We also reveal experimental evidence of carbon-based tetrel bonds influencing chemical reactivity in solution. Finally, density functional theory (DFT) calculations are employed throughout this study to confirm and illuminate our experimental data.

Unique Dispersion-Induced Tetrel Bond with Co-operative σ-hole-Induced Pnicogen Bond in the POCl3-Acetone Heterodimer: Experimental Confirmation at Low Temperatures.

Both tetrel and pnicogen bonds are known to be induced through σ-/π-holes. This work reports computational and experimental evidence of the carbonyl carbon of acetone hosting a tetrel bond by dispersion rather electrostatic forces, for the first time, while phosphorus of POCl3 sustains pnicogen bonding via the σ-hole. Heterodimers of POCl3 with acetone (CH3COCH3) have been isolated within inert gas matrixes of Ar and N2 at 12 K. Characteristic vibrational bands at P═O stretching of POCl3 and C═O stretching of CH3COCH3 have been obtained in support of the computations. The potential energy surface has been traced computationally using ab initio and density functional methods. CH3COCH3 harboring such a tetrel bond, in itself, is quite intriguing. The interplay of these interactions has been comprehended by the quantum theory of atoms in molecules, natural bond orbital, energy decomposition, electrostatic potential mapping, and noncovalent interaction analyses.

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.

Synthesis, crystal structure, and properties of three lead(II) complexes based on the 1,10-phenanthroline ligand

Abstract Three new lead(II) complexes containing the 1,10-phenanthroline ligand, [Pb(phen)2(3,5-DNB)2] (1), [Pb(phen)2(3,5-DNB)(NO3)]2·H2O (2), and [Pb(phen)(HCOO)(NO3)(H2O)] n (3) (phen = 1,10-phenanthroline, 3,5-DNB = 3,5-dinitrobenzoate anion) have been synthesized and characterized by elemental analyses, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analyses (TGA), and single-crystal X-ray diffraction. The complexes 1 and 2 are monomeric species, whereas complex 3 is a one-dimensional polymer. In the three complexes, the ligand phen creates a number of π···π stacking interactions and hydrogen bonds, which play an important role in extending complexes 1–3 to supramolecular architectures. The Pb(II) ion of complexes 1 and 2 shows hemidirected geometry with noncovalent Pb···O/C tetrel bonds formed which further stabilize the supramolecular structures.

Rotational spectrum of anisole-CO2: Cooperative C···O tetrel bond and C[sbnd]H···O hydrogen bond

Rotational spectrum of the 1:1 anisole-CO2 complex has been investigated using a pulsed jet Fourier transform microwave spectrometer supplemented with quantum chemical calculations. In the pulsed jet, only one isomer has been observed which is characterized by a dominant C···O tetrel bond and two CH···OCO2 weak hydrogen bonds. Different theoretical methods predict different orders of relative energies of plausible conformations. The experimental observation is most consistent with the theoretical estimation at the B3LYP-D3(BJ)/6–311++G(d,p) level of theory. Johnson’s non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses have been applied to better understand the nature of non-covalent interactions at play in the anisole-CO2 complex.

The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative.

A new PbII coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)2·3H2O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the PbII cation is N,N',S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N-H...O hydrogen bonds and π...π interactions. These chains are interlinked by C-H...py non-covalent interactions, realized between one of the acetate hydrogen atoms and the pyridine rings. According to the Hirshfeld surface analysis, the crystal packing is mainly characterized by intermolecular H...H, H...C and H...O contacts, followed by H...N, H...S, C...C, C...N, Pb...H, Pb...O and Pb...S contacts. The FTIR and 1H NMR spectra of [PbL(OAc)] testify to the deprotonation of the parent ligand HL, while the acetate ligand exhibits an anisobidentate coordination mode as established by means of single-crystal X-ray diffraction and FTIR spectroscopy. Lastly, theoretical calculations at the PBE0-D3/def2-TZVP level of theory have been used to analyze and characterize the Pb...O and Pb...S tetrel bonds observed in the crystal of [PbL(OAc)], using a combination of QTAIM (Quantum Theory of Atoms in Molecules) and NCIPlot (Non-Covalent Interaction Plot) computational tools.