Σ-hole Bond Research Articles

XeO3 adducts of pyridine, 4-dimethylaminopyridine, and their pyridinium salts

Xenon trioxide (XeO3), a highly shock-sensitive detonator, forms adducts with the N-bases, pyridine and 4-dimethylaminopyridine (4-DMAP). The reactions of pyridine and 4-DMAP with XeO3 in rigorously dried CH3CN and in CH3CN that had not been dried yielded (C5H5N)3XeO3(1) and (4-(CH3)2NC5H5N)3 XeO3·H2O (3), respectively, whereas their reactions in HF-acidified CH3CN yielded [C5H5NH]4[HF2]2[F]2(XeO3)2(2) and [4-(CH3)2NC5H4NH][HF2]XeO3(4). Crystalline (1), (2), and (4) failed to detonate when subjected to mechanical shock; however, (3) was significantly more sensitive to mechanical or thermal shock than XeO3. The adducts and their pyridinium salts were structurally characterized by low-temperature, single-crystal X-ray diffraction, and Raman spectroscopy. The crystal structures of (1) and (3) consist of XeO3 molecules that are N-coordinated to three pyridine and 4-DMAP ligands, respectively. A water molecule is also H-bonded to two oxygen atoms of two adjacent XeO3 molecules of (3). The pyridinium cations of (2) and (4) are H-bonded to [F]− and/or [HF2]− ions which are, in turn, F-coordinated to XeO3. Both [F]− ions of (2) bridge two XeO3 molecules to form Xe2F2-rings. Each [HF2]− anion of (4) bridges two cations and two XeO3 molecules by means of Xe⋯F secondary bonds and N(H)⋯F H-bonds. Quantum-chemical calculations for (1) and (2) provided energy-minimized geometries and calculated vibrational frequencies and intensities which were used to aid in the assignments of their Raman spectra. The NBO analyses showed the Xe⋯N, Xe⋯O, and Xe⋯F secondary bonding interactions are electrostatic in nature and may be described as σ-hole bonds.

Exploration of Hypervalent Lewis Acid/Base Interactions in 2-(2'-Thiazolyl)-3-thienylphosphanes.

The synthesis of a series of conjugated organophosphorus materials with intramolecular Lewis acid/base interactions and the exploration of the electronic nature of the bonding around the resulting hypervalent phosphorus centers are reported. To further establish the influence of increasing the size of the π-conjugated backbone, two scaffolds, thiazolyl-thiophene and benzothiazolyl-thiophene, were included in this study. Single-crystal X-ray crystallography of several of the compounds supports the hypervalent nature of the phosphorus center in the new species. Surprisingly, altering the Lewis acidity of the phosphorus center via oxidation or methylation impacts the coordinating mode of the thiazolyl substituent, which also has considerable impact on the photophysical and electrochemical properties of the π-conjugated molecular scaffolds. Through theoretical calculations involving natural bond orbital (NBO) analysis and atom-in-molecules (AIM) correlation, the existence and electronic nature of weak hypervalent bonding interactions around the phosphorus center was solidified as weak 3c-4e and/or σ-hole bonds, depending on the coordination mode of the peripheral thiazolyl substituent as well as the Lewis acidity of the phosphorus center.

Hydrogen bonds and other interactions as a response to protect doublet/octet electron structure.

MP2/aug-cc-pVTZ calculations were performed for complexes linked by hydrogen bonds. Three types of proton donating species were taken into account: H2O, CCl3H, and H3O+. These calculations are supported by the natural bond orbital (NBO) method and the quantum theory of atoms in molecules (QTAIM) approach. Numerous correlations between parameters of H-bonded systems were found. The most important are those which show the response of the system on the H-bond formation; for example, the increase of polarization of the A-H bond correlates with the strength of the hydrogen bond. Similar relationships were found for the σ-hole bonds while the π-hole bonds do not follow the trends known for the hydrogen bonds. Graphical abstract Hydrogen bonds and other interactions as a response to protect doublet/octet electron structureᅟ.

Importance of Nonclassical σ-Hole Interactions for the Reactivity of λ3-Iodane Complexes.

Key for the observed reactivity of λ3-iodanes, powerful reagents for the selective transfer of functional groups to nucleophiles, are the properties of the 3-center-4-electron bond involving the iodine atom and the two linearly arranged ligands. This bond is also involved in the formation of the initial complex between the λ3-iodane and a nucleophile, which can be a solvent molecule or a reactant. The bonding in such complexes can be described by means of σ-hole interactions. In halogen compounds, σ-hole interaction was identified as a force in crystal packing or in the formation of supramolecular chains. More recently, σ-hole interactions were also shown to affect the reactivity of the iodine-based hypervalent reagents. Relative to their monovalent counterparts, where the σ-hole is located on the extension of the sigma-bond, in the hypervalent species our DFT calculations reveal the formation of a nonclassical σ-hole region with one or even two maxima. This observation is also made in fully relativistic calculations. The SAPT analysis shows that the σ-hole bond between the λ3-iodane and the nucleophile is not necessarily of purely electrostatic nature but may also contain a significant covalent component. This covalent component may facilitate chemical transformation of the compound by means of reductive elimination or other mechanisms and is therefore an indicator for its reactivity. Here, we also show that the shape, location, and strength of the σ-holes can be tuned by the choice of ligands and measures such as Brønsted activation of the iodane reagent. At the limit, the tuning transforms the nonclassical σ-hole regions into coordination sites, which allows us to control how a nucleophile will bind and react with the iodane.

Exploring hydride-π interactions and their tuning by σ-hole bonds: an ab initio study

ABSTRACT In the present work, ab initio calculations are performed to investigate the geometry, interaction energy and bonding properties of binary complexes formed between metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CH3) and a series of π-acidic heteroaromatic rings. In all the resulting complexes, the heteroaromatic ring acts as a Lewis acid (electron acceptor), while the H atom of the HMX molecule acts as a Lewis base (electron donor). The nature of this interaction, called ‘hydride-π’ interaction, is explored in terms of molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. The results show that the interaction energies of these hydride-π interactions are between −1.24 and −2.72 kcal/mol. Furthermore, mutual influence between the hydride-π and halogen- or pnicogen-bonding interactions is studied in complexes in which these interactions coexist. For a given π-acidic ring, the formation of the pnicogen-bonding induces a larger enhancing effect on the strength of hydride-π bond than the halogen-bonding.

Supramolecular Two-Dimensional Network Mediated via Sulfur’s σ-Holes in a Conducting Molecular Crystal: Effects of Its Rigidity on Physical Properties and Structural Transition

This study reveals that noncovalent intermolecular interactions mediated by σ-holes on sulfur atoms can function as an efficient tool to design and construct a novel supramolecular motif, and that these noncovalent bonds are rigid enough to regulate the displacement of molecules at the structural transition. A novel two-dimensional cation···anion supramolecular structure via sulfur’s σ-holes was constructed in a functional molecular crystal, (ethyl-4-bromothiazolium)2[Pt(mnt)2]3 (mnt = maleonitriledithiolato). The unit cell contained two crystallographically independent anions A and B. Electrostatic σ-hole bonds were detected between σ-holes on sulfur in the cation and lone pairs of −CN moieties in B, while A did not form such S···N σ-hole bonds. This salt exhibited a structural transition at ca. 150 K, in which B did not show apparent displacement, while A shifted along the anion’s stacking direction. This shift enhanced trimerization of the anion in the low-temperature phase, leading to the enhanced ant...

The effect of hydrogen-bonding cooperativity on the strength and properties of σ-hole interactions: an ab initio study

ABSTRACTAb initio calculations at the MP2/aug-cc-pVTZ level of theory are performed to investigate the effect of hydrogen-bonding cooperativity on the strength and bonding properties of σ-hole interaction in linear FCl⋅⋅⋅(NCH)n=2–5, FHS⋅⋅⋅(NCH)n=2–5, FH2P⋅⋅⋅(NCH)n=2–5 and FH3Si⋅⋅⋅(NCH)n=2–5 clusters. It is found that the cooperative effects in the hydrogen-bonding tend to strengthen the σ-hole interaction. However, these effects are almost saturated in the larger clusters (n > 5). For a given cluster, the amount of bond contraction in FCl⋅⋅⋅(NCH)n is more important than other systems. A nice linear relationship is found between the σ-hole bond energies and absolute 15N chemical shieldings or spin–spin coupling constants across the σ-hole bond.

How do halogen bonds (S–O⋯I, N–O⋯I and C–O⋯I) and halogen–halogen contacts (C–I⋯I–C, C–F⋯F–C) subsist in crystal structures? A quantum chemical insight

Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen-halogen contacts and hydrogen bonds (I⋯N, I⋯F, I⋯I, F⋯F, I⋯H and F⋯H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of -9.58kcalmol-1 and -7.10kcalmol-1 observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen-halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures. Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.

Tuning of carbon bonds by substituent effects: an ab initio study

ABSTRACTAn ab initio study, at the MP2/aug-cc-pVTZ level of theory, is performed to study σ-hole bond in binary XH3C···CNY complexes, where X = CN, F, NO2, CCH and Y = H, OH, NH2, CH3, C2H5, Li. This type of interaction is labelled as ‘carbon bond’, since a covalently bonded carbon atom acts as the Lewis acid in these systems. The geometrical and energetic parameters of the resulting complexes are analysed in details. The interaction energies of these complexes are between −4.97 kJ/mol in (HCC)H3C···CNH and −23.07 kJ/mol in (O2N)H3C···CNLi. It is found that the electrostatic interaction plays a key role in the overall stabilisation of these carbon-bonded complexes. To deepen the understanding of the nature of the carbon-bonding, the molecular electrostatic potential, natural bond orbital, quantum theory of atoms in molecules and non-covalent interaction index analyses are also used. Our results indicate that the carbon bond is favoured over the C-H···C hydrogen bond in the all complexes considered and may suggest the possible important roles of the C···C interactions in the crystal growth and design.

Exploring “aerogen–hydride” interactions between ZOF2 (Z = Kr, Xe) and metal hydrides: An ab initio study

In this work, a new σ-hole interaction formed between ZOF2 (Z=Kr and Xe) as the Lewis acid and a series of metal-hydrides HMX (M=Be, Mg, Zn and X=H, F, CN, CH3) is reported. The nature of this interaction, called “aerogen–hydride” interaction, is unveiled by molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. Our results indicate that the aerogen–hydride interactions are quite strong and can be comparable in strength to other σ-hole bonds. An important charge-transfer interaction is also associated with the formation of OF2Z⋯HMX complexes.

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond.

The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.

σ-Hole bond tunability in YO2X2:NH3 and YO2X2:H2O complexes (X = F, Cl, Br; Y = S, Se): trends and theoretical aspects

A σ-hole is defined as an electron-deficient region on the extension of a covalently bonded group IV–VII atoms. If the electronic density in the σ-hole is sufficiently low, then this region will have a positive electrostatic potential, which allows attractive noncovalent interactions with negative sites. SO2X2 and SeO2X2 (X = F, Cl and Br) have three Lewis acid sites of σ-hole located in the outermost of chalcogen atom and X end, participating in the chalcogen and halogen bonds with NH3 and H2O, respectively. MP2/aug-cc-pVTZ and M06-2X/aug-cc-pVTZ calculations reveal that for a given halogen atom, SeO2X2 forms stronger chalcogen bond interactions than SO2X2 counterpart. Almost a perfect linear relationship is evident between the interaction energies and the magnitudes of the product of most positive and negative electrostatic potentials. The interaction energies calculated by M06-2X and MP2 methods are almost consistent with each other.

Strength order and nature of the π-hole bond of cyanuric chloride and 1,3,5-triazine with halide.

The (13)C NMR chemical shift moving upfield indicates the main model of π-holeX(-) bond between cyanuric chloride/1,3,5-triazine (3ClN/3N), which possess both the π-hole and σ-hole, and X(-). (13)C NMR and UV absorption titration in acetonitrile confirmed that the bonding abilities of 3ClN/3N with X(-) follow the order I(-) > Br(-) > Cl(-), which is apparently the order of the charge transfer ability of halide to 3ClN/3N. Chemical calculations showed that the bonding abilities in solution were essentially consistent with those obtained by titration experiments. However, the results in the gas phase were the reverse, i.e., π-holeCl(-) > π-holeBr(-) > π-holeI(-) in bonding energy, which obeys the order of electrostatic interaction. In fact, the π-hole bond and σ-hole bond compete with solvation and possible anion-hydrogen bond between a solvent molecule and a halide in solution. An explanation is that the apparent charge transfer order of π-/σ-holeI(-) > π-/σ-holeBr(-) > π-/σ-holeCl(-) occurs for weak π-hole bonds and σ-hole bonds, whereas the order of electrostatic attraction of π-/σ-holeCl(-) > π-/σ-holeBr(-) > π-/σ-holeI(-) is valid for strong bonds. It can be concluded by combining energy decomposition analysis and natural bond orbital analysis that the π-holeX(-) bond and σ-holeX(-) bond are electrostatically attractive in nature regardless of whether the order is I(-) > Br(-) > Cl(-) or the reverse.

Experimental charge density evidence for pnicogen bonding in a crystal of ammonium chloride.

Chemical binding in crystalline ammonium chloride, a simple inorganic salt with an unexpectedly complex bonding pattern, was studied by using a topological analysis of electron density function derived from high-resolution X-ray diffraction. Supported by periodic quantum chemical calculations, it provided experimental evidence for weak σ-hole bonds (1.5 kcal mol(-1) ) that involve ammonium cations in a crystal. Our results show this type of supramolecular interaction to be more numerous than has been found to date by using gas-phase calculations or statistical analysis of CSD.

Lewis acid–Lewis base interactions: From NFH3+⋯NCH and NF4+⋯NCH complexes to NFH3+⋯(NCH)n and NF4+⋯(NCH)n clusters

The Lewis acid centers of NFH3+ and NF4+ were analyzed and the MP2/6-311++G(d,p) calculations were performed for complexes of these cations with HCN molecule. The HCN molecule may be linked through the N-atom with the H, F or N centre of cation, i.e. through the hydrogen bond or the σ-hole bond. The geometry optimizations were also performed for the NFH3+⋯(NCH)n and NF4+⋯(NCH)n clusters (n up to 8). The Quantum Theory of Atoms in Molecules and the Natural Bond Orbitals method were applied to analyze mechanisms of the formation of intermolecular links. The DFT/NEDA decomposition scheme was used and it was found that for the hydrogen bonded systems the charge transfer is the most important attractive interaction while for the N⋯N and N⋯F σ-hole bonds it is the electrostatic interaction followed by the polarization.

Clusters of Ammonium Cation—Hydrogen Bond versus σ‐Hole Bond

MP2/6-311++G(d,p) calculations were performed on the NH4 (+) ⋅⋅⋅(HCN)n and NH4 (+) ⋅⋅⋅(N2 )n clusters (n=1-8), and interactions within them were analyzed. It was found that for molecules of N2 and HCN, the N centers play the role of the Lewis bases, whereas the ammonium cation acts as the Lewis acid, as it is characterized by sites of positive electrostatic potential, that is, H atoms and the sites located at the N atom in the extension of the HN bonds. Hence, the coordination number for the ammonium cation is eight, and two types of interactions of this cation with the Lewis base centers are possible: NH⋅⋅⋅N hydrogen bonds and HN⋅⋅⋅N interactions that are classified as σ-hole bonds. Redistribution of the electronic charge resulting from complexation of the ammonium cation was analyzed. On the one hand, the interactions are similar, as they lead to electronic charge transfer from the Lewis base (HCN or N2 in this study) to NH4 (+) . On the other hand, the hydrogen bond results in the accumulation of electronic charge on the N atom of the NH4 (+) ion, whereas the σ-hole bond results in the depletion of the electronic charge on this atom. Quantum theory of "atoms in molecules" and the natural bond orbital method were applied to deepen the understanding of the nature of the interactions analyzed. Density functional theory/natural energy decomposition analysis was used to analyze the interactions of the ammonium ion with various types of Lewis bases. Different correlations between the geometrical, energetic, and topological parameters were found and discussed.

The Competition of σ-Hole···Cl– and π-Hole···Cl– Bonds between C6F5X (X = F, Cl, Br, I) and the Chloride Anion and Its Potential Application in Separation Science

On the basis of the varying amplitude and patterns of the (19)F NMR chemical shift of C6F5X (X = F, Cl, Br, I) in the presence of chloride anions, bonding models of C6F5X·Cl(-) complexes were tentatively established, and the relevant binding constants were obtained. Interaction models were also simulated using computational chemistry. The theoretical computations were found to be highly consistent with the results of the experiments. The results show that C6F5Br/C6F5I and Cl(-) were prone to forming C-I/Br···Cl(-) σ-hole bonding complexes with the (19)F NMR signal shifting to higher fields, and the interaction strength of the C6F5I···Cl(-) σ-hole bond was larger than that of C6F5Br···Cl(-); C6F6/C6F5Cl and Cl(-) formed π-hole···Cl(-) bonding complexes with the signal shifting to lower fields, and the interaction strength of C6F6 was larger than that of C6F5Cl. The binding constant of the C6F5I···Cl(-) σ-hole bonding complex is 38.0 M(-1), which is nearly 165- to 345-fold larger than that of the other C6F5X·Cl(-) complexes. On the basis of the above results, solid phase extraction experiments were designed, and the results demonstrated the potential applicability of the C-I···Cl(-) σ-hole bond in separation science.

Tetrel bond–σ-hole bond as a preliminary stage of the SN2 reaction

MP2/aug-cc-pVTZ calculations were carried out on complexes of ZH4, ZFH3 and ZF4 (Z = C, Si and Ge) molecules with HCN, LiCN and Cl(-) species acting as Lewis bases through nitrogen centre or chlorine ion. Z-Atoms in these complexes usually act as Lewis acid centres forming σ-hole bonds with Lewis bases. Such noncovalent interactions may adopt a name of tetrel bonds since they concern the elements of the group IV. There are exceptions for complexes of CH4 and CF4, as well as for the F4SiNCH complex where the tetrel bond is not formed. The energetic and geometrical parameters of the complexes were analyzed and numerous correlations between them were found. The Quantum Theory of 'Atoms in Molecules' and Natural Bonds Orbital (NBO) method used here should deepen the understanding of the nature of the tetrel bond. An analysis of the electrostatic potential surfaces of the interacting species is performed. The electron charge redistribution, being the result of the tetrel bond formation, is the same as that of the SN2 reaction. The energetic and geometrical parameters of the complexes analyzed here correspond to different stages of the SN2 process.

Could the lithium bond be classified as the σ-hole bond? – QTAIM and NBO analysis

The lithium bond is analyzed in complexes of ZH3Li and ZF3Li (ZC, Si and Ge) acting as the Lewis acids with HCN and N2 Lewis bases. There are the unique properties of the lithium bond if it is compared with the other non-covalent interactions. For the lithium bond the complexation leads to the decrease of the positive charge of the Li-atom and the increase of its volume while for the hydrogen bond usually the increase of the positive charge of H-atom and the decrease of its volume is observed. The lithium bond may be probably classified as the σ-hole bond. The other properties of the lithium bond are presented and analyzed based on MP2/aug-cc-pVTZ calculations, the quantum theory of atoms in molecules, natural bond orbitals method and the decomposition of the interaction energy.

Cover Picture: Cocrystal Assembled by 1,2‐Diiodotetrafluorobenzene and Acridine via CI···N Halogen Bond and π‐hole···F Bonds (Chin. J. Chem. 10/2013)

The cover picture shows a cocrystal with repeated 8-F-atom unit as basic structural motif, which is assembled based on combination of bifurcated CI···N···IC σ-hole bond and antiparallel double π-hole···F bonds by 1,2-diiodotetrafluorobenzene and acridine. The concepts on the σ-hole and π-hole bonds are suggested based on the physical framework, the molecular surface electrostatic potential, which can be considered as another nomenclative system of fashionable halogen/chalcogen/pnicogen/silicogen bonds and anion-π interaction, respectively. The combination of the two bonds or together with other weak interactions could play a key role in assembling function materials, molecular recognition and design of drugs and so on. More details are discussed in the article by Jin et al. on page 1279–1284.