Positive Σ-hole Research Articles

Halogen Bonding in Perfluoroalkyl Adsorption.

Adsorption is a promising technology to remove perfluoroalkyl substances (PFAS), including perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), from contaminated water. Although a large number of materials have been evaluated for PFAS adsorption, guidelines that can facilitate the rational design and selection of adsorbents have not been established due to the lack of a mechanistic understanding on the molecular level. Using a novel interpretation of the Freundlich isotherm, this study identifies halogen bonding as the main mechanism controlling perfluoroalkyl adsorption by using a materiomic approach that compares the electrostatic polarities of a variety of carbon, polymer, and mineral-based materials reported in the literature. Comparisons show that both PFOS and PFOA are favorably adsorbed by materials containing high densities of π electrons, lone electron pairs, and negative charges, consistent with the formation of halogen bonding between the positive σ-hole of fluorine as a Lewis acid and a nucleophilic solid as a Lewis base. The identification of this previously unappreciated noncovalent bonding mechanism offers fresh insight into the search of suitable materials for perfluoroalkyl adsorption.

Halogenation effects on the bridgehead position of the adamantane molecule

Halogen substitution effects on the bridgehead positioned carbon of adamantane molecule portraits many significant characteristics for the adamantane halides. As a result of the induction and electrostatic interaction caused by the substitution, large electron densities are formed around the halogens and a small positive electrostatic potential (σ-hole) is developed along the z-direction parallel to C-X bond axis. Computational study performed through EOM-CCSD method, B3LYP and WB97XD functionals of the density functional theory effectively supports this investigation in terms of molecular structure, vibrational properties, bonding behavior and electrostatic potential surfaces. Accordingly, substitution give rise to the change in the dipole moment and symmetry of the molecules. In addition, polarizabilities of the molecules along the C-X bond axis increases with respect to electron densities. HOMO-LUMO energy gap and positive σ-holes are found to decrease with the increase in the negative electron affinity. An anisotropic charge distribution developed upon substitution allows the adamantane halides to exhibit two different binding motifs like halogen and hydrogen bonding along the parallel and perpendicular directions of C-X bond. These characteristics feature of the halo adamantane finds applications in self-assembled monolayers, crystal engineering and biomedical applications.

Does a halogen bond require positive potential on the acid and negative potential on the base?

It is usually expected that formation of a halogen bond (XB) requires that a region of positive electrostatic potential associated with a σ or π-hole on the Lewis acid will interact with the negative potential of the base, either a lone pair or π-bond region. Quantum calculations of model systems suggest this not to be necessary. The placement of electron-withdrawing substituents on the base can reverse the sign of the potential in its lone pair or π-bond region to positive, and this base can nonetheless engage in a XB with the positive σ-hole of a Lewis acid. The reverse scenario is also possible in certain circumstances, as a negatively charged σ-hole can form a XB with the negative lone pair region of a base. Despite these classical Coulombic repulsions, the overall electrostatic interaction is attractive in these XBs, albeit only weakly so. The strengths of these bonds are surprisingly insensitive to changes in the partner molecule. For example, even a wide range in the depth of the σ-hole of the approaching acid yields only a minimal change in the strength of the XB to a base with a positive potential.

Origin of the unexpected attractive interactions between positive σ-holes and positive π-lumps

The unexpected attractive interactions between positive σ-holes and positive π-lumps in the complexes formed by 2,3,4,5-tetrafluorothiophene (C4F4S) and 2,3,4,5-tetrafluoroselenophene (C4F4Se) with Br2, BrCl, BrF, Cl2 and ClF, respectively, have been investigated by quantum chemical calculations. All the structures bound by these counter-intuitive noncovalent interactions (CI-NCIs) are real minima on the potential energy surfaces. The interaction energy of the complex C4F4Se···BrF reaches −5.49 kcal/mol. Energy component analysis reveals that, at the equilibrium intermolecular distances, these CI-NCIs are electrostatically attractive not electrostatically repulsive as expected. It is the short-range charge penetration that causes the electrostatically attractive interaction between positive σ-hole and positive π-lump. It is also found that, although the dispersion and electrostatics play a larger role in stabilizing these CI-NCIs, there is also a very large (up to 29%) contribution due to the induction.

Assessment of scalar relativistic effects on halogen bonding and σ‐hole properties

AbstractHalogen bond (X‐bond) is a noncovalent interaction between a halogen atom and an electron donor. It is often rationalized by a region of the positive electrostatic potential on the halogen atom, so‐called σ‐hole. The X‐bond strength increases with the atomic number of the halogen involved; thus, for heavier halogens, relativistic effects become of concern. This poses a challenge for the quantum chemical description of X‐bonded complexes. To quantify scalar relativistic effects (SREs) on the interaction energies and σ‐hole properties, we have performed highly accurate coupled‐cluster calculations at the complete basis set limit of several X‐bonded complexes and their halogenated monomers. We found that the SREs are comparable in magnitude to the effect of the basis set. The nonrelativistic calculations typically underestimate the attraction by up to 5% or 23% for brominated and iodinated complexes, respectively. Counterintuitively, the electron densities at the bond critical points are larger for SRE‐free calculations than for the relativistic ones. SREs yield smaller, flatter, and more positive σ‐holes. Finally, we highlight the importance of diffuse functions in the basis sets and provide quantitative arguments for using basis sets with pseudopotentials as an affordable alternative to a more rigorous Douglas‐Kroll‐Hess relativistic theory.

σ-Hole interactions in small-molecule compounds containing divalent sulfur groups R1-S-R2.

Hydrogen bonds, aromatic stacking contacts and σ-hole interactions are all noncovalent interactions commonly observed in biological systems. Structural data derived from the Protein Data Bank showed that methionine residues can interact with oxygen atoms through directional S...O contacts in the protein core. In the present work, the Cambridge Structural Database (CSD) was used in conjunction with ab initio calculations to explore the σ-hole interaction properties of small-molecule compounds containing divalent sulfur. CSD surveys showed that 7095 structures contained R1-S-R2 groups that interact with electronegative atoms like N, O, S and Cl. Frequencies of occurrence and geometries of the interaction were dependent on the nature of R1 and R2, and the hybridization of carbon atoms in C,C-S, and C,S-S fragments. The most common interactions in terms of frequency of occurrence were C,C-S...O, C,C-S...N and C,C-S...S with predominance of Csp2. The strength of the chalcogen interaction increased when enhancing the electron-withdrawing character of the substituents. The most positive electrostatic potentials (VS,max; illustrating positive σ-holes) calculated on R1-S-R2 groups were located on the S atom, in the S-R1 and S-R2 extensions, and increased with electron-withdrawing R1 and R2 substituents like the interaction strength did. As with geometric data derived from the CSD, interaction geometries calculated for some model systems and representative CSD compounds suggested that the interactions were directed in the extensions of S-R1 and S-R2 bonds. The values of complexation energies supported attractive interactions between σ-hole bond donors and acceptors, enhanced by dispersion. The interactions of R1-S-R2 with large VS,max and nucleophiles with large negative VS,min coherently provided more negative energies. According to NBO analysis, chalcogen interactions consisted of charge transfer from a nucleophile lone pair to an S-R1 or S-R2 antibonding orbital. The directional σ-hole interactions at R1-S-R2 can be useful in crystal engineering and the area of supramolecular biochemistry.

The Influence of Halogenated Hypercarbon on Crystal Packing in the Series of 1-Ph-2-X-1,2-dicarba-closo-dodecaboranes (X = F, Cl, Br, I).

Although 1-Ph-2-X-closo-1,2-C2B10H10 (X = F, Cl, Br, I) derivatives had been computed to have positive values of the heat of formation, it was possible to prepare them. The corresponding solid-state structures were computationally analyzed. Electrostatic potential computations indicated the presence of highly positive σ-holes in the case of heavy halogens. Surprisingly, the halogen•••π interaction formed by the Br atom was found to be more favorable than that of I.

Does Oxygen Feature Chalcogen Bonding?

Using the second-order Møller–Plesset perturbation theory (MP2), together with Dunning’s all-electron correlation consistent basis set aug-cc-pVTZ, we show that the covalently bound oxygen atom present in a series of 21 prototypical monomer molecules examined does conceive a positive (or a negative) σ-hole. A σ-hole, in general, is an electron density-deficient region on a bound atom M along the outer extension of the R–M covalent bond, where R is the reminder part of the molecule, and M is the main group atom covalently bonded to R. We have also examined some exemplar 1:1 binary complexes that are formed between five randomly chosen monomers of the above series and the nitrogen- and oxygen-containing Lewis bases in N2, PN, NH3, and OH2. We show that the O-centered positive σ-hole in the selected monomers has the ability to form the chalcogen bonding interaction, and this is when the σ-hole on O is placed in the close proximity of the negative site in the partner molecule. Although the interaction energy and the various other 12 characteristics revealed from this study indicate the presence of any weakly bound interaction between the monomers in the six complexes, our result is strongly inconsistent with the general view that oxygen does not form a chalcogen-bonded interaction.

σ-Holes and Si···N intramolecular interactions.

We report a computational study of two series of molecules, one having the Si-O-N linkage and the other with the Si-(CH2)n-N linkage, where n = 1-4. The silicons have various substituents-combinations of H, CH3, F, Cl and CF3. Many of these compounds have been prepared and characterized experimentally. The Si···N distances were found to be relatively short, which may denote a noncovalent interaction or may simply be dictated by the molecular structures. This and the nature of the interaction (if any) were the subjects of our study. We addressed these issues computationally, determining optimized geometries, energies and electrostatic potentials at the density functional M06-2X/6-31 + G(d,p) level. We conclude that there is an attractive Coulombic Si···N interaction in each case, although it is sometimes quite weak. It involves the lone pair of the nitrogen and the positive σ-hole potential produced on the silicon by the bonding from the substituent that is anti to the nitrogen. This accounts for the key features of these molecules, such as the dependence of the Si···N distances upon the electron-withdrawing power of the anti substituent and the effects of gauche chlorines in weakening the interactions. When the Si···N interactions are disrupted by rotation of the N(CH3)2 group or by conversion of the molecules to open-chain conformers, the Si···N distances lengthen and are essentially the same regardless of the substituent in the anti position. These observations confirm the presence of Si···N interactions in the original molecules.

A new insight for chalcogen bonding based on Point-of-Charge approach

This study investigated the chalcogen bond from an electrostatic perspective using Point-of-Charge (PoC) approach. Two molecular models –namely CX2 and H2X, where X = O, S, and Se– were studied. 2D stabilization energy surfaces were generated for all studied molecules. Moreover, Chal···PoC distance, A-Chal···PoC angle (θ) and solvent effects on chalcogen bond strength were investigated. Natural bond orbital (NBO) calculations were also performed for all studied molecules. Results found that chalcogen bond strength increased with increasing Lewis basicity (i.e., PoC negativity), with closing A-Chal···PoC angle (θ) to 180°, and with increasing chalcogen atomic size in the order O < S < Se. Polarization of the negative PoC on the σ-hole size was revealed. Aqueous medium contributions to molecular stabilization resulted from: (i) the favorable solvent contribution to the positive σ-hole, and (ii) the unfavorable solvent contribution to the negative electrostatic regions of the molecules. σ-node phenomenon was also investigated and explained in the chalcogen-containing molecules. It could thus be concluded that the chalcogen bond is electrostatic and a sum of (i) attractive electrostatic interaction between the σ-hole of chalcogen atom and the Lewis base, and (ii) repulsive electrostatic interaction between the negative belt of chalcogen atom and the Lewis base.

Halogen bonding in self-assembling systems: A comparison of intra- and interchain binding energies

Calculations using the M06-2X and ωB97-XD density functionals with a triple-zeta quality polarized basis sets have been used to investigate the binding energies in a series of halogen bonded complexes of C2F4I2 with NC(CH2)nCN (n = 0–2). Results for complexes with monomer ratios from 1:1 to 3:3 indicate a near constant binding energies per halogen bond of ∼8 kJ/mol, ∼13 kJ/mol, and ∼14 kJ/mol for n = 0–2, respectively, indicating no observable cooperative effects in the linear halogen bonding. Results from calculations on the stacking energy of the linear chains for systems up to 3:3 indicated that these binding energies were comparable to those for the linear halogen bonds. The strong stacking interaction is hypothesized to be due to favorable electrostatic forces between the F atoms on C2F4I2 with either adjacent H atoms on NC(CH2)2CN, or the CC π-hole on NCCN. The stacking interactions showed a significant cooperative effect, as well as a synergistic effect with the linear halogen bonds as demonstrated by a shortening of the I⋯N distances in the component chains. Binding energies for all 1:1 complexes of C2F4I2 and C4F8I2 with NC(CH2)nCN (n = 0–4) show a strong linear correlation with the ΔESP between the positive σ-hole on the I atom and the negative region around the N atom lone pair.

Pnictogen bonding in pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes.

This paper presents a study of pnictogen bonding in a series of pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. The whole series was studied computationally. Moreover, the pyrazine complexes with PCl5 and SbCl5 were prepared and characterized experimentally. It was found that the Pn-N distances are only slightly elongated when compared to the sum of covalent radii. The conformation of PnX5 changed considerably upon the complex formation, which resulted in a significant change of the dipole moment of the PnX5 fragment and a considerably more positive σ-hole on the pnictogen atom. Finally, interaction energies were decomposed in order to provide a deeper insight into the nature of the studied pnictogen-bonded complexes. Graphical abstract The conformation of PnX5 changed considerably upon the complex formation, which resulted in a considerably more positive σ-hole on the pnictogen atom.

Simultaneous Occurrence of Quadruple Lewis Acid-Base Interactions between Selenium Atoms in Selenocarbonyl Dimers.

High-level quantum chemical calculations are performed to investigate C=Se⋅⋅⋅Se=C interactions. Bounded structures are found with binding energies between -4 and -7 kJ mol-1 . An energy decomposition analysis shows that dispersion is the more attractive term, and in all cases save one, the electrostatic interaction is attractive despite each selenium atom having a positive σ-hole at the extension of the C=Se bond. The topological analysis of the molecular electrostatic potential and L(r)=-∇2 ρ(r) function, and natural bond orbital analysis reveal that these particular Se⋅⋅⋅Se contacts can be considered to be quadruple Lewis acid-base interactions.

Halogen bonding in hypervalent iodine and bromine derivatives: halonium salts.

Halogen bonds have been identified in a series of ionic compounds involving bromonium and iodonium cations and several different anions, some also containing hypervalent atoms. The hypervalent bromine and iodine atoms in the examined compounds are found to have positive σ-holes on the extensions of their covalent bonds, while the hypervalent atoms in the anions have negative σ-holes. The positive σ-holes on the halogens of the studied halonium salts determine the linearity of the short contacts between the halogen and neutral or anionic electron donors, as usual in halogen bonds.

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.

XeOXeOXe](2+), the Missing Oxide of Xenon(II); Synthesis, Raman Spectrum, and X-ray Crystal Structure of [XeOXeOXe][μ-F(ReO2F3)2]2.

The [XeOXeOXe](2+) cation provides an unprecedented example of a xenon(II) oxide and a noble-gas oxocation as well as a rare example of a noble-gas dication. The [XeOXeOXe](2+) cation was synthesized as its [μ-F(ReO2F3)2](-) salt by reaction of ReO3F with XeF2 in anhydrous HF at -30 °C. Red-orange [XeOXeOXe][μ-F(ReO2F3)2]2 rapidly decomposes to XeF2, ReO2F3, Xe, and O2 when the solid or its HF solutions are warmed above -20 °C. The crystal structure of [XeOXeOXe][μ-F(ReO2F3)2]2 consists of a planar, zigzag-shaped [XeOXeOXe](2+) cation (C2h symmetry) that is fluorine bridged through its terminal xenon atoms to two [μ-F(ReO2F3)2](-) anions. The Raman spectra of the natural abundance and (18)O-enriched [XeOXeOXe](2+) salts are consistent with a centrosymmetric (C2h) cation geometry. A proposed reaction pathway leading to [XeOXeOXe][μ-F(ReO2F3)2]2 consists of a series of oxygen/fluorine metathesis reactions that are presumably mediated by the transient HOXeF molecule. Quantum-chemical calculations were used to aid in the vibrational assignments of [Xe(16/18)OXe(16/18)OXe][μ-F(Re(16/18)O2F3)2]2 and to assess the bonding in [XeOXeOXe](2+) by NBO, QTAIM, ELF, and MEPS analyses. Ion pair interactions occur through Re-Fμ---Xe bridges, which are predominantly electrostatic in nature and result from polarization of the Fμ-atom electron densities by the exposed core charges of the terminal xenon atoms. Each xenon(II) atom is surrounded by a torus of xenon valence electron density comprised of the three valence electron lone pairs. The positive regions of the terminal xenon atoms and associated fluorine bridge bonds correspond to the positive σ-holes and donor interactions that are associated with "halogen bonding".

Modulation of the Interaction between a Peptide Ligand and a G Protein-Coupled Receptor by Halogen Atoms.

Systematic halogenation of two native opioid peptides has shown that halogen atoms can modulate peptide-receptor interactions in different manners. First, halogens may produce a steric hindrance that reduces the binding of the peptide to the receptor. Second, chlorine, bromine, or iodine may improve peptide binding if their positive σ-hole forms a halogen bond interaction with negatively charged atoms of the protein. Lastly, the negative electrostatic potential of fluorine can interact with positively charged atoms of the protein to improve peptide binding.

Chalcogen and pnicogen bonds in complexes of neutral icosahedral and bicapped square-antiprismatic heteroboranes.

A systematic quantum mechanical study of σ-hole (chalcogen, pnicogen, and halogen) bonding in neutral experimentally known closo-heteroboranes is performed. Chalcogens and pnicogens are incorporated in the borane cage, whereas halogens are considered as exo-substituents of dicarbaboranes. The chalcogen and pnicogen atoms in the heteroborane cages have partial positive charge and thus more positive σ-holes. Consequently, these heteroboranes form very strong chalcogen and pnicogen bonds. Halogen atoms in dicarbaboranes also have a highly positive σ-hole, but only in the case of C-bonded halogen atoms. In such cases, the halogen bond of heteroboranes is also strong and comparable to halogen bonds in organic compounds with several electron-withdrawing groups being close to the halogen atom involved in the halogen bond.

The dominant role of chalcogen bonding in the crystal packing of 2D/3D aromatics.

The chalcogen bond is a nonclassical σ-hole-based noncovalent interaction with emerging applications in medicinal chemistry and material science. It is found in organic compounds, including 2D aromatics, but has so far never been observed in 3D aromatic inorganic boron hydrides. Thiaboranes, harboring a sulfur heteroatom in the icosahedral cage, are candidates for the formation of chalcogen bonds. The phenyl-substituted thiaborane, synthesized and crystalized in this study, forms sulfur⋅⋅⋅π type chalcogen bonds. Quantum chemical analysis revealed that these interactions are considerably stronger than both in their organic counterparts and in the known halogen bond. The reason is the existence of a highly positive σ-hole on the positively charged sulfur atom. This discovery expands the possibilities of applying substituted boron clusters in crystal engineering and drug design.

σ-Hole Interactions of Covalently-Bonded Nitrogen, Phosphorus and Arsenic: A Survey of Crystal Structures

Covalently-bonded atoms of Groups IV–VII tend to have anisotropic charge distributions, the electronic densities being less on the extensions of the bonds (σ-holes) than in the intervening regions. These σ-holes often give rise to positive electrostatic potentials through which the atom can interact attractively and highly directionally with negative sites (e.g., lone pairs, π electrons and anions), forming noncovalent complexes. For Group VII this is called “halogen bonding” and has been widely studied both computationally and experimentally. For Groups IV–VI, it is only since 2007 that positive σ-holes have been recognized as explaining many noncovalent interactions that have in some instances long been known experimentally. There is considerable experimental evidence for such interactions involving groups IV and VI, particularly in the form of surveys of crystal structures. However we have found less extensive evidence for Group V. Accordingly we have now conducted a survey of the Cambridge Structural Database for crystalline close contacts of trivalent nitrogen, phosphorus and arsenic with six different types of electronegative atoms in neighboring molecules. We have found numerous close contacts that fit the criteria for σ-hole interactions. Some of these are discussed in detail; in two instances, computed molecular electrostatic potentials are presented.