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

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.

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.

Azido-mediated intermolecular interactions of transition metal complexes

The coordinated azido ligand has a variety of ways to establish intermolecular contacts whose nature is computationally analysed in this work on dimers of the [N3-Hg(CF3)] complex with different interactions involving only N⋯N contacts, or with an additional Hg⋯N contact. The applied tools include the molecular electrostatic map of the monomer, an energy decomposition analysis (EDA), a topological AIM analysis of the electron density and the study of NCI (non-covalent interactions) isosurfaces. The interactions between two azido ligands are found to be weakly stabilizing (by 0.2 to 2.7 kcal mol-1), topology-dependent and require dispersion forces to complement orbital and electrostatic stabilization. Those interactions are supplemented by the formation of simultaneous Hg⋯N secondary interactions by about -1 kcal mol-1, and by the ability of the monomer to simultaneously interact with several neighbours in the crystal structure.

Types of noncovalent bonds within complexes of thiazole with CF4 and SiF4

The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.

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.

Influence of Internal Noncovalent Bonds on Rotational Dynamics

While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.

Competition of hydrogen, tetrel, and halogen bonds in COCl2-HOX (X=F, Cl, Br, I) complexes

The present study investigates the competition between hydrogen, halogen, and tetrel bonds from the interaction of COCl₂ with HOX using quantum chemistry simulations at the MP2/aug-cc-pVTZ computational level, in which five configurations were optimized, including adducts I -V. Two hydrogen bonds, two halogen bonds, and two tetrel bonds were obtained for five forms of adducts. The compounds were investigated using spectroscopic, geometry, and energy properties. Adduct I complexes are more stable than others, and adduct V halogen bonded complexes are more stable than adduct II complexes. These results are in agreement with their NBO and AIM results. The stabilization energy of the XB complexes depends on the nature of both the Lewis acid and base. The stretching frequency of the O-H bond in adducts I, II, III, and IV displayed a redshift, and a blue shift was observed in adduct V. The results for the O-X bond showed a blue shift in adducts I and III and a red shift in adducts II, IV, and V. The nature and characteristics of three types of interactions are investigated via NBO analysis and atoms in molecules (AIM).

Simultaneous Hydrogen Bonds with Different Binding Modes: The Acceptor "Rules" but the Donor "Chooses"

This computational work studies the different hydrogen bond (HB) binding modes that can be established between neighbouring HB donors and acceptors in structures with relevance in catalysis and biology. To analyse the electronic effect on the σ-hole, unsubstituted HB donors and ones with two different substituents, an electron withdrawing (EWG), and an electron donating (EDG) group, were studied. Upon complexation, three different binding modes were observed: bifurcated, parallel, and zigzag. It was found that, as a general trend, HBs within a parallel pattern are the strongest followed by those within bifurcated and zigzag binding modes, leading to a "competition" between the last two. Similar patterns and trends have been found in experimental structures found in a search within the CSD. In conclusion, even though the HB acceptors "rule" the pattern and strength of the HB interactions within the dimers, when there is an option for different binding modes within a particular dimer, the HB donors "choose" the type of binding established.

Adjusting the balance between hydrogen and chalcogen bonds

A complex is assembled which pairs a carboxyl group of X₁COOH with a 1,2,5-chalcogenadiazole ring containing substituents on its C atoms. The OH of the carboxyl group donates a proton to a N atom of the ring to form a OH⋯N H-bond (HB), while its carbonyl O engages in a Y⋯O chalcogen bond (ChB) with the ring in which Y = S, Se, Te. The ChB is strengthened by enlarging the size of the Y atom from S to Se to Te. Placement of an electron-withdrawing group (EWG) X₁ on the acid strengthens the HB while weakening the ChB; the reverse occurs when EWGs are placed on the ring. By selection of the proper substituents on the two units, it is possible to achieve a near perfect balance between the strengths of these two bonds. These bond strengths are also reflected in the NMR spectroscopic properties of the chemical shielding of the various atoms and the coupling between the nuclei directly involved in each bond.

Disrupting bonding in azoles through beryllium bonds: Unexpected coordination patterns and acidity enhancement

Although triazoles and tetrazole are amphoteric and may behave as weak acids, the latter property can be hugely enhanced by beryllium bonds. To explain this phenomenon, the structure and bonding characteristics of the complexes between triazoles and tetrazoles with one and two molecules of BeF₂ have been investigated through the use of high-level G4 ab initio calculations. The formation of the complexes between the N basic sites of the azoles and the Be center of the BeF₂ molecule and the (BeF₂)₂ dimer leads to a significant bonding perturbation of both interacting subunits. The main consequence of these electron density rearrangements is the above-mentioned increase in the intrinsic acidity of the azole subunit, evolving from a typical nitrogen base to a very strong nitrogenous acid. This effect is particularly dramatic when the interaction involves the (BeF₂)₂ dimer, that is, a Lewis acid much stronger than the monomer. Although the azoles investigated have neighboring N-basic sites, their interaction with the (BeF₂)₂ dimer yields a monodentate complex. However, the deprotonated species becomes extra-stabilized because a second N-Be bond is formed, leading to a new five-membered ring, with the result that the azole-(BeF₂)₂ complexes investigated become stronger nitrogenous acids than oxyacids such as perchloric acid.

Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0-5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0-3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.

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.

Relative Strengths of a Pnicogen and a Tetrel Bond and Their Mutual Effects upon One Another

The ability of the T and Z atoms of TR₃ZR₂ to engage in a noncovalent interaction with NH₃ is assessed by DFT calculations, where the T atom refers to C, Si, and Ge; Z = As, Sb, and P; and substituents R = H and F. In most instances, the tetrel bond (TB) is both stronger and shorter than the pnicogen bond (ZB). These two bond strengths can be equalized, or preference shifted to the ZB, if F substituents are placed on the Z and H on the T atoms. Employing C as the T atom results in a very weak TB, with the ZB clearly favored energetically. The simultaneous formation of both TB and ZB weakens both, particularly the latter, but both bonds survive intact. Geometric and spectroscopic perturbations of the subunits reflect the two types of noncovalent bonds.

Interplay between Polymorphism and Isostructurality in the 2-Fur- and 2-Thenaldehyde Semi- and Thiosemicarbazones

The four compounds, namely: 5-nitro-2-furaldehyde thiosemicarbazone (1); 5-nitro-2-thiophene thiosemicarbazone (2); 5-nitro-2-furaldehyde semicarbazone (3); and 5-nitro-2-thiophene semicarbazone (4) were synthesized and crystallized. The three new crystal structures of 1, 2, and 4 were determined and compared to three already known crystal structures of 3. Additionally, two new polymorphic forms of 1 solvate were synthesized and studied. The influence of the exchange of 2-thiophene to 2-furaldehyde as well as thiosemicarbazone and semicarbazone on the self-assembly of supramolecular nets was elucidated and discussed in terms of the formed synthons and assemblies accompanied by Full Interaction Maps analysis. Changes in the strength of IR oscillators caused by the molecular and crystal packing effects are described and explained in terms of changes of electron density.

Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry

The halogen bond (XB) has become an important tool for molecular design in all areas of chemistry, including crystal and materials engineering and medicinal chemistry. Its similarity to the hydrogen bond (HB) makes the relationship between these interactions complex, at times competing against and other times orthogonal to each other. Recently, our two laboratories have independently reported and characterized a synergistic relationship, in which the XB is enhanced through direct intramolecular HBing to the electron-rich belt of the halogen. In one study, intramolecular HBing from an amine polarizes the iodopyridinium XB donors of a bidentate anion receptor. The resulting HB enhanced XB (or HBeXB) preorganizes and further augments the XB donors. Consequently, the affinity of the receptor for halogen anions was significantly increased. In a parallel study, a meta-chlorotyrosine was engineered into T4 lysozyme, resulting in a HBeXB that increased the thermal stability and activity of the enzyme at elevated temperatures. The crystal structure showed that the chlorine of the noncanonical amino acid formed a XB to the protein backbone, which augmented the HB of the wild-type enzyme. Calorimetric analysis resulted in an enthalpic contribution of this Cl-XB to the stability of the protein that was an order of magnitude greater than previously determined in biomolecules. Quantum mechanical (QM) calculations showed that rotating the hydroxyl group of the tyrosine to point toward rather than away from the halogen greatly increased its potential to serve as a XB donor, equivalent to what was observed experimentally. In sum, the two systems described here show that the HBeXB concept extends the range of interaction energies and geometries to be significantly greater than that of the XB alone. Additionally, surveys of structural databases indicate that the components for this interaction are already present in many existing molecular systems. The confluence of the independent studies from our two laboratories demonstrates the reach of the HBeXB across both chemistry and biochemistry and that intentional engineering of this enhanced interaction will extend the applications of XBs beyond these two initial examples.

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

Competition between two competing sites on a tetrel atom is explained by balance between structural deformation and σ-hole intensity.