Observations of tetrel bonding between sp3-carbon and THF

Covalent surface modification of single-layer graphene-like BC6N nanosheets with reactive nitrenes for selective ammonia sensing via DFT modeling

Novel graphene-like nanomaterials with a non-zero bandgap are important for the design of gas sensors. The selectivity toward specific targets can be tuned by introducing appropriate functional groups on their surfaces. In this study, we use first-principles simulations, in the form of density functional theory (DFT), to investigate the covalent functionalization of a single-layer graphitized BC6N with azides to yield aziridine-functionalized adducts and explore their possible use to realize ammonia sensors. First, we determine the most favorable sites for physical adsorption and chemical reaction of methylnitrene, arising from the decomposition of methylazide, onto a BC6N monolayer. Then, we examine the thermodynamics of the [1 + 2]-cycloaddition reaction of various phenylnitrenes and perfluorinated phenylnitrenes para-substituted with (R = CO2H, SO3H) groups, demonstrating favorable energetics. We also monitor the effect of the functionalization on the electronic properties of the nanosheets via density of states and band structure analyses. Finally, we test four dBC6N to gBC6N substrates in the sensing of ammonia. We show that, thanks to their hydrogen bonding capabilities, the functionalized BC6N can selectively detect ammonia, with interaction energies varying from -0.54 eV to -1.37 eV, even in presence of competing gas such as CO2and H2O, as also confirmed by analyzing the change in the electronic properties and the values of recovery times near ambient temperature. Importantly, we model the conductance of a selected substrate alone and in presence of NH3to determine its effect on the integrated current, showing that humidity and coverage conditions should be properly tuned to use HO2C-functionalized BC6N-based nanomaterials to develop selective gas sensors for ammonia.

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr)

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Spodium bonding with noble gas atoms

The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.

The Tetrel Bonds of Hypervalent Halogen Compounds

The tetrel bond between PhXF2Y(TF3) (T = C and Si; X = Cl, Br, and I; Y = F and Cl) and the electron donor MCN (M = Li and Na) was investigated at the M06-2X/aug-cc-pVDZ level of theory. As the electronegativity of the halogen atom X increases, the strength of the tetrel bond also increases, but as the electronegativity of the halogen atom Y increases, the strength of the tetrel bond decreases. The magnitude of the interaction energy in most -CF3 complexes was found to be less than 10 kcal/mol, but to exceed 11 kcal/mol for PhClF2Cl(CF3)⋯NCNa. The tetrel bond is greatly enhanced when the -SiF3 group interacts with LiCN or NaCN, with the largest interaction energy approaching 100 kcal/mol and displaying a covalent Si⋯N interaction. Along with this enhancement, the Si⋯N distance was found to be less than the X-Si bond length, the -SiF3 group to be closer to the N atom, and in most -SiF3 systems, the X-Si-F angle to be less than 90°; the -SiF3 group therefore undergoes inversion and complete transfer in some systems.

Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions

Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.

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.

Static and Dynamical Quantum Studies of CX3-AlX2 and CSiX3-BX2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center

The set of TX₃-TrX₂ (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX₃-AlX₂) and least (SiX₃-BX₂) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.

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.

Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as -NH₂, -OCH₃, -CH₃, -H, -CF₃ and -CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett's plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet's σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader's theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.

Beryllium bonding with noble gas atoms

Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be₃ ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be₃ complexes. The Be atoms in the Be₃ moiety are chemically bonded to one another, with the BeBe bond dissociation energy being ~125 kJ mol^-1 . The Be₃ ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be₃ ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.

Importance of Cu and Ag regium-π bonds in supramolecular chemistry and biology: a combined crystallographic and ab initio study

Identifying and characterizing new binding events between electron donor and acceptor counterparts represents a crucial step to complete the molecular recognition and aggregation picture, which is key to chemistry and biology. In this study we interrogated both the PDB (Protein Data Bank) and CSD (Cambridge Structural Database) for the presence of Cu and Ag regium-π (Rg-π) bonds (an attractive noncovalent force between elements from group 11 and π-systems). Concretely, we found evidence of the plausible biological role of the interaction in protein-DNA systems, bacterial Ag extrusion processes and Heme group redox functionality. Furthermore, we also highlighted the implications of Rg-π bonds in the crystal packing of two host-guest systems, where this interaction is key for the binding and recognition of small organic molecules as well as for the encapsulation of organometallic complexes. Theoretical models were used to analyse the strength of the interaction (RI-MP2/def2-TZVP level of theory) together with QTAIM (Quantum Theory of Atoms in Molecules), NBO (Natural Bonding Orbital) and NCIplot (Non Covalent Interactions plot) analyses, which further assisted in the characterization of the regium-π interactions described herein. We expect the results from this study will be useful to attract the attention of chemical biologists as well as to expand the potential of the interaction to the supramolecular chemistry and crystal engineering communities.

Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors

In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal-ligand interaction). We provide evidence of the existence of this interaction by inspecting the X-ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf-Ligand orbital involved) are also analyzed by means of ab initio calculations (RI-MP2/def2-TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.

Crystallographic and Theoretical Study of Osme Bonds in Nitrido-Osmium(VI) Complexes

Osme bonds have been recently defined as the attractive interaction between an element of group 8 acting as an electrophile and any atom or group of atoms acting as a nucleophile. To date, the known examples of osme bonds in X-ray structures involve mostly the highly reactive OsO4 and amines and amine oxides. In this work, evidence supporting the existence of osme bonds in osmium(VI) derivatives is reported. In particular, nitrido-osmium(VI) complexes that present square-pyramidal geometries are well disposed to participate in osme bonds opposite to the Os≡N bond. By using a combination of experimental and theoretical results, the existence and importance of this new class of σ-hole interactions is demonstrated in the solid state of several nitrido-osmium(VI) derivatives.

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Sp2- and sp3-C⋯O tetrel bonds in the 3-oxetanone homodimer

The structures and non-covalent interactions at play in the 3-oxetanone homodimer have been investigated using a pulsed jet Fourier transform microwave spectrometer supplemented with quantum chemical calculations. Two isomers were identified in the pulsed jet. With the analyses of non-covalent intermolecular interactions including the quantum theory of atoms, Johnson's non-covalent interactions and natural bond orbital, the observed global minimum is stabilized by a combination of one sp²-C⋯O tetrel bond and a network of multiple C-H⋯O weak hydrogen bonds. The second isomer is characterized by carbonyl-carbonyl interactions, with the formation of one sp²- and one sp³-C⋯O tetrel bond. The conformational population of the two observed isomers in the supersonic expansion was estimated to be N_CE1/N_CC1 ≈ 7/5.

Enhancement of tetrel bond involving tetrazole-TtR3 (Tt = C, Si; R = H, F). Promotion of SiR3 transfer by a triel bond

The combination of a CR3 (R = H, F) with a tetrazole can result in a moderate carbon bond, which can be further strengthened by a triel bond. On the other hand, SiR3 group is half transferred between the two N atoms in these conditions.

Frustrated Lewis Pairs Based on Carbon⋅⋅⋅Carbon+ Tetrel Bonds: A DFT Study

The ability of Triangulenium (TA⁺ ) compounds to form Frustrated Lewis Pairs (FLPs) with N-HeteroCycle Carbenes (NHCs) is analysed in this manuscript at the PBE0-D3/def2-TZVP level of theory. We have used six TA⁺ -based moieties, three presenting similar bridging groups (O (trioxo), -CH₂ (triaryl) and -NH (triaza)) and another three mixing, O, -CH₂ and NH moieties. In addition, several aryl-substituted NHCs have been used as electron donor moieties to undergo carbon⋅⋅⋅carbon⁺ tetrel bonds with the TA⁺ derivatives. More precisely, -Me,-iPr, -tBu and -Ph groups were used. Finally, we have used Bader's quantum theory of "atoms in molecules" (QTAIM) and Natural Bonding Analysis (NBO) to characterize the carbon⋅⋅⋅carbon⁺ tetrel bonds described herein. We expect the results gathered herein will be useful for further exploitation of carbon⋅⋅⋅carbon⁺ bonds in the formation of FLPs as well as to expand the current knowledge of tetrel bonds to the fields of synthetic chemistry and catalysis.

Enhancement of the Tetrel Bond by the Effects of Substituents, Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond

The T⋅⋅⋅N tetrel bond (TB) formed between TX₃ OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH₃ OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF₃ OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T-O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl₂ to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.

Computational Evaluation of Me2 TCCP as Lewis Acid

Supramolecular adducts between dimethyl-2,2,3,3-tetracyanocyclopropane (Me2 TCCP) with 21 small (polar) molecules and 10 anions were computed with DFT (B3LYP-D3/def2-TZVP). Their optimized geometries were used to obtain interaction energies, and perform energy decomposition and 'atoms-in-molecules' analyses. A set of 38 other adducts were also evaluated for comparison purposes. Selected examples were further scrutinized by inspection of the molecular electrostatic potential maps, Noncovalent Interaction index plots, the Laplacian, the orbital interactions, and by estimating the Gibbs free energy of complexation in hexane solution. These calculations divulge the thermodynamic feasibility of Me2 TCCP adducts and show that complexation is typically driven by dispersion with less polarized partners, but by orbital interactions when more polarized or anionic guests are deployed. Most Me2 TCCP adducts are more stable than simple hydrogen bonding with water, but less stable than traditional Lewis adducts involving Me3 B, or a strong halogen bond such as with Br2 . Several bonding analyses showed that the locus of interaction is found near the electron poor sp3 -hydridized (NC)2 C-C(CN)2 carbon atoms. An empty hybrid σ*/π* orbital on Me2 TCCP was identified that can be held responsible for the stability of the most stable adducts due to donor-acceptor interactions.

Selenium chalcogen bonds are involved in protein-carbohydrate recognition: a combined PDB and theoretical study

In this manuscript the ability of selenium carbohydrates to undergo chalcogen bonding (ChB) interactions with protein residues has been studied at the RI-MP2/def2-TZVP level of theory. An inspection of the Protein Data Bank (PDB) revealed SeA (A = O, C and S) intermolecular contacts involving Se-pyranose ligands and ASP, TYR, SER and MET residues. Theoretical models were built to analyse the strength and directionality of the interaction together with "Atoms in Molecules" (AIM), Natural Bonding Orbital (NBO) and Non Covalent Interactions plot (NCIplot) analyses, which further assisted in the characterization of the ChBs described herein. We expect that the results from this study will be useful to expand the current knowledge regarding biological ChBs as well as to increase the visibility of the interaction among the carbohydrate chemistry community.

The Effects of Electronegativity of X and Hybridization of C on the X-C⋅⋅⋅O Interactions: A Statistical Analysis on Tetrel Bonding

Cone and distance-cone corrected statistical analyses have been performed on X-C⋅⋅⋅O (X=H, B, C, N, O and F; the C atom is sp² and sp³ hybridized) tetrel bonds. The sp³ -C and sp² -C prefer to form the interactions through σ-hole (∠XCO≈180°) and π-hole (∠XCO≈90°), respectively. With the increase in electronegativity of X, the preference for the particular angles of the respective geometries increases and the C⋅⋅⋅O distance becomes shorter. The angular preference is found to be more prominent in the cases of π-hole interactions than that in the σ-hole interactions. A similar distance-cone corrected statistical analysis on O=C⋅⋅⋅O interaction also suggests that the preferred ∠OCO angle is ∼90° and the preferred C⋅⋅⋅O distance is around the sum of van der Waals radii (3.22 Å) of the C and O atoms. However, a cone-corrected statistical analysis on X-Si⋅⋅⋅O interactions suggests that the preference for linearity in this case is much higher than that for the X-C⋅⋅⋅O σ-hole interactions.

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN^- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.

Chlorine "Equatorial Belt" Activation of CF3Cl by CO2: The C···Cl Tetrel Bond Dominance in CF3Cl-CO2

Besides its typical halogen donor behavior (exhibiting a Cl σ-hole) in forming Cl···B halogen bonds (B is an electron-rich region), CF₃Cl reveals a new interaction site in its complex with CO₂ when explored by rotational spectroscopy. Experimental evidence and theoretical analyses point out irrefutably that CF₃Cl prefers to link to CO₂ through its Cl "equatorial belt" consisting of the lone pairs of the Cl atom, resulting in a C···Cl tetrel bond. In addition, a secondary plausible C···O tetrel bond and a F···O halogen bond might contribute to the relative orientation of the moieties forming the complex. The effects of the Cl "equatorial belt" present in perhalogenated molecules, such as CF₃Cl, have been hitherto overlooked in describing the origin of noncovalent interactions. That left a significant void that the present study tries to fill by outlining its importance.

Competitive and cooperative n →π* and n →σ* interactions in benzaldehyde-formaldehyde: rotational characterization

The rotational spectrum of the 1 : 1 benzaldehyde-formaldehyde complex has been investigated by pulsed jet Fourier transform microwave spectroscopy combined with ab initio calculations. The two most stable isomers were observed, with the relative abundance ratio N_I/N_II≈ 3/1 estimated with intensity measurements. Both observed isomers are stabilized by one dominating O[double bond, length as m-dash]CO tetrel bond (n →π* interaction) and one secondary C-HO hydrogen bond. Natural bond orbital analysis and electron localization function analysis were applied to characterize the nature of the noncovalent interactions in the target complex.

Intermolecular π-π Stacking Interactions Made Visible

Mixing the liquids hexafluorobenzene (1) and 1,3,5-trimethylbenzene (mesitylene, 2) results in a crystalline solid with a melting point of 34 °C. The solid consists of alternating π-π stacked pillars of both aromatics. This simple experiment can be used to visually demonstrate the existence and the effect of noncovalent intermolecular π-π stacking interactions. Both benzene derivatives are relatively benign and widely available, and the experiment can be performed within minutes for less than $15 when done on a 22 mL scale (total volume). The demonstration is very robust, as 1:2 mixtures in volume ratios between 2/3 and 3/2 all give a visually similar result (molar ratios of 1.8-0.8). Substituting 2 with the liquid aromatics o-xylene, p-xylene, and aniline also resulted in the formation of a crystalline solid, while using many other liquid aromatics did not.

Synthesis and characterization of N-heterocyclic carbene-MOEt2 complexes (M = Cu, Ag, Au). Analysis of solvated auxiliary-ligand free [(NHC)M]+ species

We report the synthesis, characterization and computational analysis of coinage metal-ether complexes supported by N-heterocyclic carbenes (NHC), SIPr and Et2CAAC. The related water adducts are also included. The [(NHC)M]+(M = Cu, Ag, Au) species show the noteworthy ability to bind Et2O and H2O. This interaction towards Et2O and H2O is partly ascribed to a σ-hole bonding with an almost linear disposition, taking advantage of the enhanced σ-hole potential evaluated for such [(NHC)M]+ species. This enhanced ability is larger than those found for non-covalent interactions involving main group species.

DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering

The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.

Carbon (sp3) tetrel bonding mediated BODIPY supramolecular assembly via unprecedented synergy of Csp3⋯N and Csp3⋯F pair interactions

Here, we present the first example of sp³ hybridized carbon centered (C_sp3) tetrel bonding mediated 3D BODIPY assembly via the exceptional synergy of C_sp3⋯N and C_sp3⋯F pair interactions.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Versatility of the Cyano Group in Intermolecular Interactions

Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.

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.

Engineering Crystals Using sp3 -C Centred Tetrel Bonding Interactions

1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

A Survey of Supramolecular Aggregation Based on Main Group Element⋯Selenium Secondary Bonding Interactions—A Survey of the Crystallographic Literature

The results of a survey of the crystal structures of main group element compounds (M = tin, lead, arsenic, antimony, bismuth, and tellurium) for intermolecular M⋯Se secondary bonding interactions is presented. The identified M⋯Se interactions in 58 crystals can operate independent of conventional supramolecular synthons and can sustain zero-, one-, two, and, rarely, three-dimensional supramolecular architectures, which are shown to adopt a wide variety of topologies. The most popular architecture found in the crystals stabilized by M⋯Se interactions are one-dimensional chains, found in 50% of the structures, followed by zero-dimensional (38%). In the majority of structures, the metal center forms a single M⋯Se contact; however, examples having up to three M⋯Se contacts are evident. Up to about 25% of lead(II)-/selenium-containing crystals exhibit Pb⋯Se tetrel bonding, a percentage falling off to about 15% in bismuth analogs (that is, pnictogen bonding) and 10% or lower for the other cited elements.