Σ-hole Bond Research Articles

Osme Bond: Geometric and Energetic Features in the Adducts between OsO4 and Lewis Bases.

Adducts between OsO4 and Lewis bases exert a role in important oxidation processes such as epoxidation and dihydroxylation. It has been shown that the attractive interaction driving the formation of these adducts is a σ-hole bond involving the metal as the electrophilic species; the term Osme Bond (OmB) was proposed for designating it. Here some new adducts between OsO4 and various bases have been characterized through single crystal x-ray diffraction (XRD) and computational studies (density functional theory, DFT), confirming the existence of a robust correlation between σ-hole interaction energy and deformation of the tetrahedral geometry of OsO4. Also, some adducts formed by RuO4 with nucleophiles were investigated computationally.

The Formation of σ-Hole Bonds: A Physical Interpretation.

This paper discusses two quite different computational experiments relating to the formation of σ-hole bonds A···B. The first involves looking at the complex at equilibrium and finding the contour X of the electronic density which allows the iso-density envelopes of A and B to be nearly touching. This contour increases, becoming closer to the nuclei, as the strength of the interaction increases. The second experiment involves allowing A and B to approach each other, with the aim of finding the distance at which their 0.001 a.u. iso-density envelopes are nearly merging into one envelope. What is found in the second experiment may be somewhat surprising, in that the ratio of the distance between interacting atoms at this nearly merging point-divided by the sum of the van der Waals radii of these atoms-covers a narrow range, typically between 1.2 and 1.3. It is intriguing to note that for the dataset presented, approaching molecules attracted to each other appear to do so unknowing of the strength of their ultimate interaction. This second experiment also supports the notion that one should expect favorable interactions, in some instances, to have close contacts significantly greater than the sums of the van der Waals radii.

Chromium(VI) Oxyfluoride Dianions, [Cr2 O4 F6 ]2- and [CrO2 F4 ]2- ; Syntheses and Structures of [XeF5 ]2 [Cr2 O4 F6 ], [XeF5 ]2 [Cr2 O4 F6 ] ⋅ nX (X=HF, n=4; X=XeOF4 , n=2), and [XeF5 ][Xe2 F11 ][CrO2 F4

The fluorobasic character of the strong oxidative fluorinator, XeF6 , and the oxidative resistance of the [XeF5 ]+ and [Xe2 F11 ]+ cations have been exploited for the syntheses of several novel Cr(VI) dianion salts. The reactions of XeF6 and CrO2 F2 in anhydrous HF and by direct fusion of the reactants in melts have yielded the first dinuclear Cr(VI) oxyfluoro-dianion salts, [XeF5 ]2 [Cr2 O4 F6 ], [XeF5 ]2 [Cr2 O4 F6 ] ⋅ 4HF, [XeF5 ]2 [Cr2 O4 F6 ] ⋅ 2XeOF4 , and mononuclear Cr(VI) oxyfluoro-dianion salt, [XeF5 ][Xe2 F11 ][CrO2 F4 ]. The salts were structurally characterized by low-temperature (LT) single-crystal X-ray diffraction (SCXRD) and LT Raman spectroscopy. The [CrO2 F4 ]2- and [Cr2 O4 F6 ]2- dianions have distorted octahedral cis-dioxo Cr(VI) coordination spheres in which two F-atoms are trans to one another and two F-atoms are trans to O-atoms, where the [Cr2 O4 F6 ]2- dianion is the fluorine-bridged dimer of the [CrO2 F3 ]- anion. Quantum-chemical calculations were used to obtain the energy-minimized, gas-phase geometries, and the calculated vibrational spectra of the gas-phase dianions and their ion-pairs, which were used to aid in the vibrational frequency assignments of the crystalline salts. NBO and MEPS analyses and SCXRD show these salts are comprised of intimate ion-pairs in which their cations and anions interact through primarily electrostatic Xe- - -F σ-hole bonds.

Transition between the Noncovalency and Covalency of σ-Hole Bonds.

The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.

XeF2 Coordination Complexes of the [BrO2]+ Cation, [O2Br(FXeF)n][AsF6] (n = 1, 2) and [O2Br(FXeF)2][SbF6]; Their Syntheses and Structural Characterizations.

The syntheses and structural characterizations of the first XeF2 coordination complexes of the [BrO2]+ cation are described. The reactions of [BrO2][PnF6] (Pn = As, Sb) with XeF2 in anhydrous HF solvent yield the salts [O2Br(FXeF)n][AsF6] (n = 1, 2) and [O2Br(FXeF)2][SbF6], which were characterized by low-temperature (LT) Raman spectroscopy and single-crystal X-ray diffraction (SCXRD). The XeF2 ligands and [PnF6]- coordinate to the Lewis acidic [BrO2]+ cation through primarily electrostatic BrV---FXe σ-hole bonds that result from coordination of the F atoms into regions of high positive electrostatic potential on the Br(V) atom and have bond trajectories that avoid the stereoactive valence electron lone-pair of Br(V). The complexes and their structural characterizations by LT Raman spectroscopy and SCXRD significantly extend the coordination chemistry of Br(V) and provide rare examples of a noble-gas difluoride coordinated to a strong oxidant main-group Lewis acid center.

Structure and Bonding of Halonium Compounds.

The geometrical parameters and the bonding in [D···X···D]+ halonium compounds, where D is a Lewis base with N as the donor atom and X is Cl, Br, or I, have been investigated through a combined structural and computational study. Cambridge Structural Database (CSD) searches have revealed linear and symmetrical [D···X···D]+ frameworks with neutral donors. By means of density functional theory (DFT), molecular electrostatic potential (MEP), and energy decomposition analyses (EDA) calculations, we have studied the effect of various halogen atoms (X) on the [D···X···D]+ framework, the effect of different nitrogen-donor groups (D) attached to an iodonium cation (X = I), and the influence of the electron density alteration on the [D···I···D]+ halonium bond by variation of the R substituents at the N-donor upon the symmetry, strength, and nature of the interaction. The physical origin of the interaction arises from a subtle interplay between electrostatic and orbital contributions (σ-hole bond). Interaction energies as high as 45 kcal/mol suggest that halonium bonds can be exploited for the development of novel halonium transfer agents, in asymmetric halofunctionalization or as building blocks in supramolecular chemistry.

Experimental and Theoretical Study of Tetrel Bonding and Noncovalent Interactions in Hemidirected Lead(II) Phosphorodithioates: An Implication on Crystal Engineering

The importance of tetrel bonds (TtBs) in spontaneous self-assembly has been highlighted in two new lead(II) complexes: i.e. Pb[S2P{OC6H4(4-C(CH3)3)}2]2 (1) and Pb[S2P{OC6H4(4-C2H5)}2]2 (2), which were successfully isolated and characterized by FT-IR, UV–vis and multinuclear NMR (31P, 1H and 13C) spectroscopy. The structures of both complexes have been confirmed by single-crystal X-ray diffraction analyses. Interestingly, lead is coordinated by three sulfur atoms in 1 but by four sulfur atoms in 2, due to stereochemically active lone pair electrons, thus leading to trigonal-pyramidal and tetragonal-pyramidal geometries, respectively. Complex 1 is the first example of a lead(II) dithiophosphate wherein the lead(II) center is coordinated to three S atoms. These complexes are stabilized at a lower coordination number and display hemidirected structures that allow forming σ-hole bonds. The lead(II) center establishes short contacts with sulfur atoms to form Pb···S TtBs that contribute to the construction of a self-assembled dimer in 1 but to a supramolecular polymer in 2. The supramolecular assemblies are further stabilized by Pb···π TtB interactions. The attractive nature of TtBs has been studied by DFT calculations and characterized using a combination of Bader’s quantum theory of atoms-in-molecules (QTAIM) and noncovalent interaction plot (NCI plot) index based on a reduced density gradient (NCI-RDG) analysis. A systematic Hirshfeld surface analysis facilitates a comparison of intermolecular interactions such as C–H···π, π···π, Pb···S, and Pb···π in both complexes, which play a crucial role in the crystal engineering.

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.

Synthesis, Structure, and Bonding of a XeIV Transition-Metal Coordination Complex, F3 XeFb - - -WOF4.

The coordination complex, F3 XeFb - - -WOF4 , was synthesized in CFCl3 solvent by reaction of the weak fluoride-ion donor and strong oxidative fluorinating agent, XeF4 , with the moderate-strength fluoride-ion acceptor, WOF4 . The compound is the only transition-metal coordination complex of XeIV and was characterized at low temperatures by single-crystal X-ray diffraction and Raman spectroscopy. Xenon tetrafluoride and WOF4 coordinate trans to the W=O bond through a W- - -Fb bond. The XeF3 moiety of F3 XeFb - - -WOF4 acquires a degree of [XeF3 ]+ character upon coordination that is reflected by its Xe-F stretching frequencies which are intermediate with respect to those of XeF4 and [XeF3 ]+ . Calculations show W- - -Fb is predominantly an electrostatic, σ-hole bond with a significant orbital contribution that accounts for the bent Xe-Fb - - -W angle. The calculations show F3 XeFb - - -MOF4 (M=Cr, Mo) are less stable than their W analogue, consistent with failed attempts to synthesize F3 XeFb - - -MoOF4 .

σ-Hole Bonds and the VSEPR Model—From the Tetrahedral Structure to the Trigonal Bipyramid

Complexes linked by various interactions are analysed in this study. They are characterized by the tetrahedral configuration of the Lewis acid centre. Interactions, being a subject of this study, are classified as σ-hole bonds, such as the halogen, chalcogen, pnicogen, and tetrel bonds. In the case of strong interactions, the tetrahedral configuration of the Lewis acid centre changes into the trigonal bipyramid configuration. This change is in line with the Valence-Shell Electron-Pair Repulsion model, VSEPR, and this is supported here by the results of high-level ab initio calculations. The theoretical results concerning the geometries are supported mainly by the Natural Bond Orbital, NBO, method.

Anatomy of π-hole bonds: Linear systems.

The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weakerthan those of comparable planar systems.

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model.

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.

Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage.

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.

A “nucleophilic” iodine in a halogen-bonded iodonium complex manifests an unprecedented I+···Ag+ interaction

Summary When an electron is removed from a halogen atom, it forms a halenium ion X+ (X = I, Br, Cl). In halogen bonding (XB), X+ is considered as a strong XB donor, and when interacting with two XB acceptors (e.g., pyridine), it forms a halonium XB complex with a [N–I–N] three-center-four-electron bond with the two XB acceptors. An unprecedented I+···Ag+ interaction occurs between a [L1–I–L1]+ halogen-bonded complex and a [L2–Ag–L2]+ complex in which the iodonium ion acts like a nucleophile and donates electrons to the silver(I) cation. The X-ray diffraction analysis reveals a short contact [3.4608(3) A] between the I+ and Ag+ cations, and ITC measurements give a ΔG of −6.321 kcal/mol and Ka∼37,000 M−1 for the 1:1 complex. The DFT computational study on the nature of the I+···Ag+ interaction indicates that the I+ is nucleophilic in character, manifesting an unusual and strongly attractive interaction between the I+ and Ag+ cations.

The σ-hole⋯σ-hole stacking interaction: An unrecognized type of noncovalent interaction.

The σ-hole⋯σ-hole stacking interaction, an unrecognized type of noncovalent interaction, has been found to be present in large quantities in the Cambridge Structural Database. In the σ-hole⋯σ-hole stacking interaction, each of the two interacting σ-holes has the dual electron donor/electron acceptor character; when one σ-hole acts as an electron donor, the other σ-hole acts as an electron acceptor, and vice versa. The σ-hole⋯σ-hole stacking interaction is clearly different from the σ-hole bond in which the charge transfer occurs mainly from the electron donor to the σ-hole. Energy component analysis shows that the σ-hole⋯σ-hole stacking interaction is dominated by the dispersion energy, which is similar to the nature of the aromatic stacking interaction between unsaturated molecules or the σ⋯σ stacking interaction between saturated molecules.

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 architecture of hydrogen and sulfur σ-hole interactions explain differences in the inhibitory potency of C-β-d-glucopyranosyl thiazoles, imidazoles and an N-β-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design

C-Glucopyranosyl imidazoles, thiazoles, and an N-glucopyranosyl tetrazole were assessed in vitro and ex vivo for their inhibitory efficiency against isoforms of glycogen phosphorylase (GP; a validated pharmacological target for the development of anti-hyperglycaemic agents). Imidazoles proved to be more potent inhibitors than the corresponding thiazoles or the tetrazole. The most potent derivative has a 2-naphthyl substituent, a Ki value of 3.2 µM for hepatic glycogen phosphorylase, displaying also 60% inhibition of GP activity in HepG2 cells, compared to control vehicle treated cells, at 100 μM. X-Ray crystallography studies of the protein – inhibitor complexes revealed the importance of the architecture of inhibitor associated hydrogen bonds or sulfur σ-hole bond interactions to Asn284 OD1, offering new insights to structure-based design efforts. Moreover, while the 2-glucopyranosyl-tetrazole seems to bind differently from the corresponding 1,2,3-triazole compound, the two inhibitors are equipotent.

Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment.

Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X–H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.

Pnicogen and tetrel bonds—tetrahedral Lewis acid centres

It is obvious and well known that the hydrogen bond plays a crucial role in numerous physical, chemical and biochemical processes. However, the significance of other interactions is also analysed in numerous studies. They are often compared with the hydrogen bond. The halogen bond is an example of such interaction that reveals characteristics occurring also for the hydrogen bond. The other interactions which are often classified as the σ-hole bonds or π-hole bonds possess characteristics typical for the hydrogen bond. The interactions of tetrahedral pnicogen and tetrel centres with Lewis bases are analysed here. The former ones may be labelled as the charge-assisted pnicogen bonds and classified as the σ-hole bonds. The latter ones labelled as the tetrel bonds are also classified as interactions between the σ-hole and the electron-rich region. Both these interactions are compared with the hydrogen bond. In the case of the hydrogen bond, the A–H...B, A–H...π and A–H...σ types of interactions are discussed in different studies where A–H is the proton-donating bond while B, π and σ label the kind of the proton acceptor: the mono-atomic Lewis base centre B, the π-electrons and the σ-electrons, respectively. The pnicogen centre, Z, in the charge-assisted pnicogen bonds may also interact with these electron-rich regions thus the Z...B, Z...π and Z...σ pnicogen bonds are known.

Competition between σ-hole pnicogen bond and π-hole tetrel bond in complexes of CF2=CFZH2 (Z = P, As, and Sb)

ABSTRACTA computational study of the complexes formed by F2C=CFZH2 (Z = P, As, and Sb) and F2C=CFPF2 with two Lewis bases (NH3 and NMe3) has been carried out. In general, two minima complexes are found, one with a σ-hole pnicogen bond and the other one with a π-hole tetrel bond in most complexes but two σ-hole pnicogen bonded complexes are obtained for F2C=CFZH2 and NH3. They have similar stability though F2C=CFSbH2 engages in a much stronger σ-hole pnicogen bond with NMe3. The –PF2 substitution makes the π-hole on the terminal carbon form a tetrel bond with NH3. A heavier –ZH2 group engages in a stronger σ-hole pnicogen bond but results in a weaker π-hole tetrel bond. Other than electrostatic interaction, the stability of both complexes is attributed to the charge transfer from the N lone pair into the C–Z/H–Z anti-bonding orbital in the pnicogen bond and the C=C anti-bonding orbital in the tetrel bond.The σ-hole pnicogen bonded and π-hole tetrel bonded complexes between F2C=CFZH2 (Z = P, As, and Sb) and two Lewis bases (NH3 and NMe3) have been compared. The results indicate that both interactions can compete, dependent on the nature of the N base.