Tetrel Bonds Research Articles

Cover Feature: Tetrel Bond Affects the Self‐Assembly of Acetylcholine and its Analogues and is an Ancillary Interaction in Protein Binding (Chem. Eur. J. 59/2024)

Cover Feature: Tetrel Bond Affects the Self‐Assembly of Acetylcholine and its Analogues and is an Ancillary Interaction in Protein Binding (Chem. Eur. J. 59/2024)

Modulating the Amine-CO2 Interaction Strength: Toward Efficient Carbon Capture.

This study contributes to a comprehensive understanding of the interactions between CO2 and amines at the molecular level by exploring the rotational spectra of binary complexes between CO2 and eight different amines through pulsed-jet Fourier transform microwave spectroscopy and quantum chemical calculations. The findings reveal a consistent pattern in which CO2 is bonded to the amino group, primarily through a C···N tetrel bond, while being supported by C-H···O/C hydrogen bonds. Notably, the binding energies increase from primary through tertiary amines and with increasing chain length of the alkyl groups. These groups are found to enhance the electron density at the amino group significantly, thereby facilitating the formation of stronger C···N tetrel bonds. The insights provided into how the interaction strength is modulated by the geometries of amines are deemed essential for the design of more effective CO2 adsorption materials, thus advancing carbon capture technologies.

Synthesis, Structural Characterization, and Theoretical Analysis of Nonconventional Bonding in Dinuclear Zinc(II) Complexes with Tridentate Schiff Bases.

Two tridentate N,N,O-donor ligands, HL1 = 4-chloro-2-(((2-(methylamino)ethyl)amino)methyl)phenol and HL2 = 4-chloro-2-(((2-(dimethylamino)ethyl)amino)methyl)phenol, have been used to synthesize phenolate-bridged dinuclear complexes [Zn2(L1)2Cl2] (1) and [Zn2(L2)2(N3)2] (2). Single-crystal X-ray diffraction analysis confirmed their structures. Both complexes form assemblies in the solid state. Moreover, the existence of nonconventional spodium bonds in 1 and tetrel bonds in 2 has been explored using theoretical calculations, including MEP surface plots and QTAIM and NCIplot analyses.

Covalent Organic Frameworks in Computational Design of Second-Harmonic Generation Materials: Role of Tetrel Atoms and Their Interactions.

Modern approaches to the design of nonlinear optical materials often rely on computational techniques. Here, we discuss the effects of the variation in the center tetrel atoms, Tt = C, Si, or Ge, in a series of covalent organic frameworks of the COF-102 family. The effects of halogen substitution, Hal = Cl, Br, or I on intramolecular tetrel bonding are also discussed. The characteristics of the calculated electron density have been implemented to describe the features of the electron distribution around the central fragment involving a tetrahedral tetrel atom. The effect of the central Tt atom leads to a dramatic change in the character of electron delocalization on the Tt-Car bond with aromatic rings. The location of the halogen atom at the ortho-position of the aromatic ring leads to the formation of tetrel bonds, halogen bonds, or other noncovalent interactions. The changes in the second-order electric susceptibility χ(2) have been studied in order to describe the strength of nonlinear optical properties within the periodic couple-perturbed Kohn-Sham approach. A counterintuitive trend for the χ(2) decrease is observed upon substitution of H > Cl > Br > I at the ortho-position of the phenyl ring. This is due to the corresponding elongation of the Tt-Car bond.

Complex Dance of Molecules in the Sky: Choreography of Intermolecular Structure and Dynamics in the Cyclopentene-CO2-H2O Hetero Ternary Cluster.

This study delves into driving forces behind the formation of a hetero ternary cluster consisting of volatile organic compounds from industrial or combustion sources, specifically cyclopentene, alongside greenhouse gases like carbon dioxide, and water vapor. While substantial progress has been made in understanding binary complexes, the structural intricacies of hetero ternary clusters remain largely uncharted. Our research characterized the cyclopentene-CO2-H2O hetero ternary cluster utilizing Fourier transform microwave spectroscopy. The observed isomer in the pulsed jet has CO2 and H2O aligning above the cyclopentene ring, with water undergoing an internal rotation approximately about its C2 symmetry axis. Theoretical analyses support these observations, identifying an O-H···π hydrogen bond and a secondary C···O tetrel bond within this cluster. This study marks a critical step towards comprehending the molecular dynamics and interactions of VOCs, greenhouse gases, and water in the atmosphere, paving the way for further investigations into their roles in climate dynamics and air quality.

Supramolecular assembly governed by tetrel, CN⋅⋅⋅π and other weak noncovalent interactions in two acrylonitrile derivatives with D-π-A topology: Crystallography, optical properties and theoretical studies

Two D-π-A acrylonitriles, (Z)-3-(4-methoxyphenyl)-2-(pyridin-4-yl)acrylonitrile (1) and (Z)-3-(4-piperidin-1-yl)-2-(pyridin-4-yl)acrylonitrile (2), were synthesized to investigate how the varying donor moieties affect their structural and optical properties. Compound 1 crystallized with two crystallographically independent molecules, each showing different orientations of the methoxy group, and exhibited herringbone molecular arrangement in the solid-state. This structure is stabilized by CH···N/π interactions, π-stacking, cyano···π stacking (CN···π) and a σ-hole tetrel bond involving the C and O atoms of the methoxy group. Compound 2 crystallized with a single molecule in the asymmetric unit and displayed columnar packing mode. This structure is stabilized intermolecular CH···N interactions, where all nitrogen atoms serve as acceptors, as well as by intermolecular CH···π interactions and π-stacking between adjacent pyridyl rings. Hirshfeld surfaces and 2D-fingerprint plots revealed the effect of donor moieties on the intermolecular interactions. The energetics of the molecular dimers observed in these structures were characterized by both CLP-PIXEL energy and DFT calculations. The nature of the tetrel bond was characterized using molecular electrostatic surface potential and deformation electron density maps. Theoretical charge density analysis was performed to characterize the noncovalent interactions in various molecular dimers of 1 and 2. The absorption spectra of compounds 1 and 2 exhibit a 40 nm red-shift in solution, attributed to the presence of the piperidyl moiety in compound 2.

Exploring Uncharted Territory: Spectroscopic Evidence on a Novel Tetrel Bond with -C≡C- Triple Bond.

This study presents an investigation of the 2-butynyl alcohol···CO2 adduct, combining pulsed jet Fourier transform microwave spectroscopy with quantum chemical calculations. Two distinct isomers have been observed in the pulsed jet with a relative population ratio of 3/2. It marks the first instance of microwave spectroscopic evidence, to the best of our knowledge, suggesting the existence of a CCO2···π-C≡C- tetrel bond (π-C≡C-···π*CO2 interaction) in both observed isomers. This study highlights the importance of noncovalent interactions involving CO2 in reactant complexes, paving the way for more efficient applications of CO2 by understanding the physical basis of these noncovalent bonds.

Evolution of Electronic Properties along the Path from a Covalent to a Tetrel Bond in the Synthesis of Tetraphenyl Substituted Compounds

Evolution of Electronic Properties along the Path from a Covalent to a Tetrel Bond in the Synthesis of Tetraphenyl Substituted Compounds

Probing Self-Assembly of Ammeline in Chloroform and Aqueous Media: Interplay Between Hydrogen Bonding Diversity and Dimerization.

Ammeline (AM) is a molecule with a very low reputation in the field of supramolecular community, but with a recently proven potential both experimentally and theoretically. In this work, dispersion-corrected density functional theory (DFT-D) computations and molecular dynamics (MD) simulations were employed to understand the aggregation mechanism of AM in chloroform and water media. Our DFT-D and MD analyzes show that the most important interactions are those formed by the amine groups (-NH2) with both the pyridine-type nitrogen atoms and the carbonyl groups (C=O). In the more polar solvent, the interactions between water molecules and the C=O group prevent the AM from forming more interactions with itself. Nevertheless, four types of dimers involving N-H∙∙∙O interactions were found to exist in water solutions. The overlooked tetrel bond between endocyclic N and C atoms can also stabilize dimers in solution. Moreover, while most AM dimers are enthalpy-driven, our results indicate that the unique DD-AA dimer (D=donor, A=acceptor) that originates cyclic rosettes is entropy-driven.

Tetrel Bond Affects the Self-Assembly of Acetylcholine and its Analogues and is an Ancillary Interaction in Protein Binding.

The -N+(CH3)3 residue is present in acetylcholine (ACh) and in many of its analogues which are used as selective ACh agonist or antagonists for human therapy. The X-ray structures of four ACh derivatives show the presence of short and linear contacts between the C atoms of -N+(CH3)3 groups and lone pair possessing atoms. These contacts can be rationalized as tetrel bonds (TtBs) thanks to their geometric features. Interrogation of the Protein Data Bank suggests that similar -N+-C⋅⋅⋅nucleophile contacts affect the details of the binding of ACh and its derivatives to proteins. Quantum theory of atoms in molecules, noncovalent interaction plot, and natural bond orbital analyses consistently confirm that the -N+-C⋅⋅⋅nucleophile contacts observed in small molecule crystals and in substrate/protein complexes are attractive in nature and can be rationalized as TtBs. TtBs involving methyl groups of the -N+(CH3)3 moiety can be proposed as a new item in the palette of interactions allowing the compounds containing this pharmacophoric unit to bind to their target protein and/or to express their biological/pharmacological properties.

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.

Ab Initio Investigation of Tetrel Bonds in Isolated Complexes Formed Between a Lewis Acid H3MX, M-O or M-S (M = Si, Ge, or Sn) and the Lewis Bases B = N2, CO, HCCH, PH3, C2H4, HCN, CS, HNC, NP, H2O, and NH3.

Isolated complexes of the type B⋯A in which the noncovalent interaction is a tetrel bond have been characterized by ab initio calculations at the CCSD(T)(F12c)/cc-pVDZ-F12 level. The Lewis bases B involved were N2, CO, HCCH, PH3, C2H4, HCN, CS, HNC, NP, H2O and NH3. Two types of Lewis acid A were examined, each containing one of the tetrel atoms M = Si, Ge or Sn, The Lewis acids in the first series were the H3MX (X = F, Cl, CN, H), in each of which the most electrophilic region was found to lie on the C3 axis of the C3v molecules, near to the tetrel atom M. In the second series the Lewis acids were M-O and M-S. Graphs, consisting of calculated equilibrium dissociation energies De of each B⋯H3MX complex plotted against the nucleophilicities NB of the Lewis bases B, were used to obtain the electrophilicity EH3MX of each molecule H3MX (M = Si, Ge, Sn). The molecular electrostatic surface of potentials of the molecules M-S and M-O (M = Si, Ge, Sn) revealed that many of the B⋯M-S and B⋯M-O complexes should have a tetrel bond to M in which the axis of the M-S or M-O subunit should be approximately perpendicular to the axis of the nonbonding or π-bonding electron pair carried by B, a novel type of tetrel bond confirmed by geometry optimizations of the complexes.

The Rivalry between Intramolecular Tetrel Bonds and Intermolecular Hydrogen Bonds in (O-Si) Chelates of N-Silylmethylamides and -ureas. A Theoretical Study.

The comparison of the results of theoretical calculations of (O-Si) chelates of N-silylmethylated amides and ureas with the axial chlorine or fluorine atom at silicon to the data of X-ray analysis of related compounds revealed the formation of covalent O-Si tetrel bonds (TB) or noncovalent O⋅⋅⋅Si tetrel bonds (NTB). The nature of the formed tetrel bond depends on the substituents at silicon and the polarity of the medium. The competition between the intramolecular TB and intermolecular hydrogen bonds (HB) with proton donors depends on the center of basicity involved in the formation of HB, which could be either oxygen or halogen. The hydrogen bonding can result in changing the nature of the tetrel bonds from covalent to noncovalent and vice versa by varying their lengths and energies. The O-Si bond energies estimated by QTAIM analysis of N-[(chlorodimethylsilyl)methyl]-N-methylacetamide and its H-complexes vary within the range of 7.2 and 12 kcal/mol in gas and solution, respectively, and correlate with the O-Si bond lengths.

EVOLUTION OF ELECTRONIC PROPERTIES ALONG THE PATH FROM COVALENT TO TETREL BOND IN THE SYNTHESIS OF TETRAPHENYL SUBSTITUTED COMPOUNDS

The evolution of the electronic characteristics of chemical bonds formed and broken along the path of the bimolecular nucleophilic substitution reaction at a tetrahedral central atom, which is the Tt = C, Si, Ge atom, is analyzed. For this purpose, the reaction paths of the step-by-step replacement of the chlorine atom with the phenyl fragment have been modeled, and the energy characteristics of the equilibrium initial, transition and nal states were obtained within the framework of DFT. For different reaction centers, which are atoms of the carbon group (Tt), changes in electron density distributions, shifts in the positions of the extremes of the total static and electrostatic potential for the forming C-Tt and breaking Tt-Cl bonds along the reaction path are compared. Quantitative criteria have been re ned that determine the region of existence of a typical noncovalent tetrel bond Tt...Cl, allowing it to be distinguished from a covalent one. Establishment of the properties of the transition state stabilizing tetrel bond may be useful for monitoring the ef cient synthesis of covalent organic framework precursors.

Quantum study of the competition and interplay between complexes resulting from the interaction of methylamine and halogen cyanides

In this study, quantum calculations were conducted to investigate the nature, formation mechanism, and properties of complexes resulting from the interaction between methylamine (MA) and halogen cyanide molecules (XCN, X = F, Cl, Br, and I). Three types of complexes were formed from the interaction of MA with XCN, characterized as Tetrel bond-hydrogen bond (TB-HB), Tetrel bond (TB), and Halogen bond (XB), denoted by symbols A, B, and C, respectively. The data obtained from the interaction energy indicated that complexes with structure C are significantly more stable compared to the other two structures. Molecular electrostatic potential map (MEP) analysis revealed that the size of the σ-hole of the halogen atom ligand plays a crucial role in the stability of structure C complexes. To further evaluate the properties of the resulting complexes, various analyses were conducted, including Molecular electrostatic potential map (MEP), Geometry optimization, Spectroscopy, Interaction energy (SE), Natural bond orbital (NBO), Atoms in molecules (AIM), Non-covalent interaction index (NCI), and Energy decomposition analysis (EDA).

Decrypting the critical point of internal rotation of formaldehyde: A rotational study of the acrolein-formaldehyde complex.

The rotational spectrum of an acrolein-formaldehyde complex has been characterized using pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. One isomer has been observed in pulsed jets, which is stabilized by a dominant O=C⋯O tetrel bond (n → π* interaction) and a secondary C-H⋯O hydrogen bond. Splittings arising from the internal rotation of formaldehyde around its C2v axis were also observed, from which its V2 barrier was evaluated. It seems that when V2 equals or exceeds 4.61 kJ mol-1, no splitting of the spectral lines of the rotational spectrum was observed. The nature of the non-covalent interactions of the target complex is elucidated through natural bond orbital analysis. These findings contribute to a deeper understanding on the non-covalent interactions within the dimeric complex formed by two aldehydes.

Intermolecular interactions between metallylenes and carbonyl chalcogenides: Chalcogen bond and tetrel bond

The intermolecular interactions between the singlet metallylenes XH2 (X = Si, Ge, Sn, Pb) and carbonyl chalcogenides OCY (Y = S, Se, Te) have been studied by the high-level quantum chemical calculations. The chalcogen-bonded and tetrel-bonded complexes can be formed between XH2 and OCY due to their ambiphilic character. The structure and binding strength of the complexes have been explored on the basis of the MEP surfaces of the monomers, and geometrical parameters and interaction energies of the complexes. The nature of the complexes has been investigated by the NBO, AIM and SAPT analysis. The tetrel-bonded complexes exhibit a much stronger binding strength with larger interaction energies and shorter binding distances compared to the chalcogen-bonded complexes. The interaction energies of the complexes become larger with the increase of the Y atomic number, but become smaller with the increase of the X atomic number. NBO analysis reveals that the dominant orbital interactions in the chalcogen-bonded and tetrel-bonded complexes are LP(X) → σ*(C-Y) and LP(Y) → LP*(X), respectively. AIM analysis suggests that the chalcogen-bonded complexes are the purely noncovalent, but the tetrel-bonded complexes have partial covalent character. SAPT analysis indicates that the contribution of the energy component decreases in the order of Eele > Edisp > Eind for most chalcogen-bonded complexes, and this order is Eele > Eind > Edisp for most tetrel-bonded complexes.

A theoretical investigation of the competition between σ- and π-holes on the stability of the complexes resulting from the interaction between the COCl2 and OCY molecules (Y = S, Se, and Te)

Carbonyl dichloride (COCl2), also known as phosgene, is a highly toxic gas, whose exposure or acute inhalation causes severe respiratory complications, such as pulmonary edema, pulmonary emphysema, and even death. In this study, we theoretically investigated the complexes formed by the interaction between the COCl2 (phosgene) and OCY molecules (Y = S, Se, and Te). Complex geometry optimization yielded three distinct types of conformations. Conformation-I complexes were stabilized by two concurring chalcogen-bonding interactions (i.e. O⋯Y and Cl⋯Y) by forming a ring structure. However, only a single linear interaction (O⋯C) or (O⋯Cl) occurred in conformation-II and III complexes, forming complexes with the nature of tetrel and halogen bonds, respectively. According to the results of the molecular electrostatic potential (MEP), interaction energy (ΔET), natural bond orbital (NBO), and so on, the σ-hole of the Y atom in the OCY molecule exhibited higher acidic strength and formed more stable complexes than those resulting from the σ- and π-holes of the COCl2 molecule.

Tetrel Bonding of the Carbenium Ion Forms a Pentacoordinate Carbon Atom.

As a flat trigonal species, the CR3 + carbenium ion contains a pair of deep π-holes above and below its molecular plane. In the case of CH3 + a first base will form a covalent bond with the central C, making the combined species tetrahedral. Approach of a second base to the opposite side results in a longer but rather strong noncovalent tetrel bond (TB). While CMe3 + can also form a similar asymmetric complex with a pair of bases, it also has the capacity to form a pair of nearly equivalent TBs, such that the resulting symmetric trigonal bipyramid configuration is only slightly higher in energy. When the three substituents on the central C are phenyl rings, the symmetric configuration with two TBs predominates. These tetrel bonds are quite strong, reaching up to 20 kcal/mol. Adding OPH2 or OCH substituents to the phenyl rings permits the formation of intramolecular C⋅⋅O TBs to the central C, very similar in many respects to the case where these TBs are intermolecular.

Silatranes and germatranes as the systems with intramolecular tetrel bonds

Silatranes and germatranes as the systems with intramolecular tetrel bonds