The Impact of ortho-substituents on Bonding in Silver(I) and Halogen(I) Complexes of 2-Mono- and 2,6-Disubstituted Pyridines: An In-Depth Experimental and Theoretical Study.

The coordination nature of 2-mono- and 2,6-disubstituted pyridines with electron-withdrawing halogen and electron-donating methyl groups for [N-X-N]+ (X=I, Br) complexations have been studied using 15 N NMR, X-ray crystallography, and Density Functional Theory (DFT) calculations. The 15 N NMR chemical shifts reveal iodine(I) and bromine(I) prefer to form complexes with 2-substituted pyridines and only 2,6-dimethylpyridine. The crystalline halogen(I) complexes of 2-substituted pyridines were characterized by using X-ray diffraction analysis, but 2,6-dihalopyridines were unable to form stable crystalline halogen(I) complexes due to the lower nucleophilicity of the pyridinic nitrogen. In contrast, the halogen(I) complexes of 2,6-dimethylpyridine, which has a more basic nitrogen, are characterized by X-crystallography, which complements the 15 N NMR studies. DFT calculations reveal that the bond energies for iodine(I) complexes vary between -291 and -351 kJ mol-1 and for bromine between -370 and -427 kJ mol-1 . The bond energies of halogen(I) complexes of 2-halopyridines with more nucleophilic nitrogen are 66-76 kJ mol-1 larger than those of analogous 2,6-dihalopyridines with less nucleophilic nitrogen. The experimental and DFT results show that the electronic influence of ortho-halogen substituents on pyridinic nitrogen leads to a completely different preference for the coordination bonding of halogen(I) ions, providing new insights into bonding in halogen(I) chemistry.

Anions as Lewis Acids in Noncovalent Bonds.

The ability of an anion to serve as electron-accepting Lewis acid in a noncovalent bond is assessed via DFT calculations. NH3 is taken as the common base, and is paired with a host of ACln - anions, with central atom A=Ca, Sr, Mg, Te, Sb, Hg, Zn, Ag, Ga, Ti, Sn, I, and B. Each anion reacts through its σ or π-hole although the electrostatic potential of this hole is quite negative in most cases. Despite the contact between this negative hole and the negative region of the approaching nucleophile, the electrostatic component of the interaction energy of each bond is highly favorable, and accounts for more than half of the total attractive energy. The double negative charge of dianions precludes a stable complex with NH3.

Computational Design of Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis.

In recent years, halogen bond-based organocatalysis has garnered significant attention as an alternative to hydrogen-based catalysis, capturing considerable interest within the scientific community. This transition has witnessed the evolution of catalytic scaffolds from monodentate to bidentate architectures, and from monovalent to hypervalent species. In this DFT-based study, we explored a bidentate hypervalent iodine(III)-based system that has already undergone experimental validation. Additionally, we explore various functionalisations (-CF$_3$, -CH$_3$, -tBu, -OH, -OMe, -NO$_2$, -CN) and scaffold modifications, such as sulfur oxidation, theoretically proposed for an indole-based Michael addition. The investigated systems favour bidentate O-type binding, underlining the importance of ligand coordination in catalytic activity. Electron-deficient scaffolds exhibited stronger binding and lower activation energies, indicating the pivotal role of electronic properties for $\sigma$-hole-based catalysis. Of these groups, Lewis-base-like moieties formed stabilising intramolecular interactions with hypervalent iodines when in the ortho-position. Furthermore, inductive electron withdrawal was deemed more effective than mesomeric withdrawal in enhancing catalytic efficacy for these systems. Lastly, increasing sulfur oxidation was theoretically proven to improve catalytic activity significantly.

Exploring Unconventional σ-Hole Interactions: Computational Insights into the Interaction of XeO3 with Non-Aromatic Coordinating Solvents.

In order to control the explosiveness and shock sensitivity of XeO3 , we have investigated its plausible interaction with various non-aromatic coordinating solvents, serving as potential Lewis base donors, through density functional theory (DFT) calculations. Out of twenty six such solvents, the top ten were thus identified and then thoroughly examined by employing various computational tools such as the mapping of the electrostatic potential surface (MESP), Wiberg bond indices (WBIs), non-covalent interaction (NCI) plots, Bader's theory of atoms-in-molecules (AIM), natural bond orbital (NBO) analysis, and the energy decomposition analysis (EDA). The amphoteric nature of XeO3 was also explored by investigating the extent of back donation from the lone pair of Xe to the antibonding orbital of the donating atom/group of the solvent molecules. The C-H…O interactions were also found to be a contributing factor in the stabilization of these adducts. Although these aerogen-bonding interactions were found to be predominantly electrostatic, significant contributions from the orbital contributions, as well as dispersion interactions, were observed. The top three non-aromatic solvents (among the twenty six studied) which form the strongest adducts with XeO3 are proposed to be hexamethylphosphoramide (HMPA), N,N'-dimethylpropyleneurea (DMPU) and tetramethylethylenediamine (TMEDA).

Active Hydrogen Free, Z-Isomer Selective Isatin Derived "Turn on" Fluorescent Dual Anions Sensor.

An efficient and anions fluorescence "on-off" sensor of 1-(prop-2-yn-1-yl)-3-(quinolin-3-ylimino)indolin-2-one (PQI) has been developed for the selective sensing of dual anions of F- and NO3- ions in aqueous medium. Active hydrogen and Lewis acidic binding sites free, Z- isomer of isatin based π-conjugated quinoline exhibited excellent sensing activity against F- and NO3- ions in UV light. The fluorescence turns on the process accomplished via the PET "on-off" mechanism. The interaction between probe molecule and anions is thought to be a non-covalent interaction of the low electron density covalently bonded N-methylene moiety of propargyl isatin (-N-CH2-) of probe molecule with F- ion and the terminal acidic proton of propargyl group of isatin (-C≡C-H) with NO3- ions. The modes of anions binding with PQI and plausible mechanisms are proposed by 1H and 13C NMR titrations. The selectivity of anions sensing may be offered by the bucked structure of the Z-isomer. The calculated association constant values for PQI and F- and NO3- are ions 2.5 × 104 M-1 and 2.2 × 103 M-1, respectively, indicating strong binding interaction between the PQI and anions. The association nature of anions and probes was analyzed by a Jobs plot and the finding indicates both F- and NO3- ions are in 1:1 complexation with PQI. The limit of detection (LOD) of the probe with F- and NO3- ions is calculated and is to be 6.91 × 10-7 M and 9.93 × 10-7 M, respectively. The proposed PQI fluorophore possesses a low limit of detection (LOD) for both F- and NO3- ions which is within the WHO prescribed detection limit.

Erythronium Bonds: Noncovalent Interactions Involving Group†5 Elements as Electron-Density Acceptors.

Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These kinds of bonding are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythronium bond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show that these interactions are present also in biological systems.

Halogen Bonding Assembles Anion⋠⋠⋠Anion Architectures in Non-centrosymmetric Iodate and Bromate Crystals.

Single crystal X-ray diffraction of iodate and bromate salts shows that the I and Br atoms in IO3 - and BrO3 - anions form short and linear O-I/Br⋅⋅⋅O contacts with the O atoms of nearby anions. Non-centrosymmetric systems are formed wherein anions are orderly aligned into supramolecular 1D and 2D networks. Theoretical evidences, namely the outcome of QTAIM and NCIplot studies, prove the attractive nature of these contacts and the ability of iodate and bromate anions to act as robust halogen bond (HaB) donors. The HaB is proposed as a general and effective assisting tool to control the architecture of acentric iodate salts.

Se⋠⋠⋠O/S and S⋠⋠⋠O Chalcogen Bonds in Small Molecules and Proteins: A Combined CSD and PDB Study.

The importance of selenium-centered noncovalent chalcogen bonds represented as Se⋅⋅⋅A (A=O/S) has been explored for short directional contacts in small molecules and proteins. In addition, S⋅⋅⋅O centered contacts have been analyzed. Computational analyses involving the quantitative assessment of the associated energetics, the molecular electrostatic potentials (MEP), and electron density derived topological parameters, namely, quantum theory of atom in molecules (QTAIM) analyses, and NBO (natural bond orbital) based calculations, have been performed to unequivocally establish the strength, stability, and attractive role of chalcogen bonds in the solid-state. This investigation has been performed in molecules from both the Cambridge Structural Database (CSD) and Protein Data Bank (PDB). Thus futuristic materials may be designed keeping in mind the significance of these interactions, including their relevance in biology.

Anion Recognition with Antimony(III) and Bismuth(III) Triaryl-Based Pnictogen Bonding Receptors.

The synthesis and characterisation of a library of acyclic antimony(III) and bismuth(III) triaryl pnictogen bonding (PnB) receptor systems are reported. In the first-generation receptor series, quantitative 1 H NMR chloride titration experiments in THF solvent media reveal halide anion binding potency is intimately correlated with both the electronic-withdrawing nature of the aryl- substituent and the polarisability of the PnB donor. Further extensive anion binding investigations with the most potent Sb- and Bi-based PnB receptors: 1⋅Sb2CF3 and 1⋅Bi2CF3 , reveal novel selectivity profiles, both displaying Cl- selectivity relative to the heavier halides and, impressively, to a range of highly basic oxoanions. The synthesis and preliminary chloride anion binding studies of a series of novel tripodal tris-proto-triazole triaryl Sb(III) and Bi(III) mixed PnB-HB receptor systems are also described. Whereas parent triphenyl Sb(III) and Bi(III) compounds are incapable of binding Cl- in THF solvent media, the PnB-triazole HB host systems exhibit notable halide affinity.

Self-Assembly of Supramolecular Architectures Driven by σ-Hole Interactions: A Halogen-Bonded 2D Network Based on a Diiminedibromido Gold(III) Complex and Tribromide Building Blocks.

The reaction of the complex [Au(phen)Br2](PF6) (phen = 1,10-phenanthroline) with molecular dibromine afforded {[Au(phen)Br2](Br3)}∞ (1). Single crystal diffraction analysis showed that the [Au(phen)Br2]+ complex cations were bridged by asymmetric tribromide anions to form infinite zig-zag chains featuring the motif ···Au-Br···Br-Br-Br···Au-Br···Br-Br-Br···. The complex cation played an unprecedented halogen bonding (XB) donor role engaging type-I and type-II XB noncovalent interactions of comparable strength with symmetry related [Br3]- anions. A network of hydrogen bonds connects parallel chains in an infinite 2D network, contributing to the layered supramolecular architecture. DFT calculations allowed clarification of the nature of the XB interactions, showing the interplay between orbital mixing, analyzed at the NBO level, and electrostatic contribution, explored based on the molecular potential energy (MEP) maps of the interacting synthons.

Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics.

Intermolecular bonding attraction at π-bonded centers is often described as "electrostatically driven" and given quasi-classical rationalization in terms of a "pi hole" depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO-, CN-) with simple atomic anions (H-, F-) or with one another. Such "anti-electrostatic" anion-anion attractions are shown to lead to robust metastable binding wells (ranging up to 20-30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi-Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that "deletion" of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi-Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency ("charge transfer") rather than envisioned Coulombic properties of unperturbed monomers.

Halogen Bonding Heteroditopic Materials for Cooperative Sodium Iodide Binding and Extraction.

A series of novel heteroditopic halogen bonding (XB) receptor functionalised silica based materials, containing mono- and bis-iodotriazole benzo-15-crown-5 groups are investigated for the cooperative binding and extraction of sodium halide ion-pair species from aqueous solution. Characterisation of the XB materials by CHN elemental analysis, 13 C CP/MAS NMR and ATR-FTIR spectroscopies confirms and quantifies the successful incorporation of the ion-pair receptor frameworks to the silica material. ICP-MS solid-liquid extraction studies demonstrate the bidentate XB functionalised material is capable of NaI extraction from water. Importantly, cooperative XB-mediated sodium halide ion-pair binding is determined to be crucial to the material's extraction capabilities, impressively demonstrating a two-fold enhancement in sodium iodide extraction efficiency relative to a heteroditopic hydrogen bonding receptor functionalised silica material analogue.

Chalcogen Bonding in Co-Crystals: Activation through 1,4-Perfluorophenylene vs. 4,4'-Perfluorobiphenylene Cores.

The ability of alkylseleno/alkyltelluroacetylenes such as bis(selenomethylethynyl)-perfluorobenzene (4F-Se) to act as a ditopic chalcogen bond (ChB) donor in co-crystals with ditopic Lewis bases such as 4,4'-bipyridine is extended here to the octafluorobiphenylene analog, 4,4'-bis(selenomethylethynyl)-perfluorobiphenyl (8F-Se), with the more electron-rich 4,4'-bipyridylethane (bpe), showing in the 1:1 (8F-Se)•(bpe) co-crystal a shorter and more linear C-Se•••N ChB interaction than in (4F-Se)•(bpe), with Se•••N distances down to 2.958(2) Šat 150 K, i.e., a reduction ratio of 0.85 vs. the van der Waals contact distance.

Strong σ-Hole Activation on Icosahedral Carborane Derivatives for a Directional Halide Recognition.

Crystal engineering based on σ-hole interactions is an emerging approach for realization of new materials with higher complexity. Neutral inorganic clusters derived from 1,2-dicarba-closo-dodecaborane, substituted with -SeMe, -TeMe, and -I moieties on both skeletal carbon vertices are experimentally demonstrated herein as outstanding chalcogen- and halogen-bond donors. In particular, these new molecules strongly interact with halide anions in the solid-state. The halide ions are coordinated by one or two donor groups (µ1 - and µ2 -coordinations), to stabilize a discrete monomer or dimer motifs to 1D supramolecular zig-zag chains. Crucially, the observed chalcogen bond and halogen bond interactions feature remarkably short distances and high directionality. Electrostatic potential calculations further demonstrate the efficiency of the carborane derivatives, with Vs,max being similar or even superior to that of reference organic halogen-bond donors, such as iodopentafluorobenzene.

Molecular Electrostatic Potential and Noncovalent Interactions in Derivatives of Group 8 Elements.

This communication reports experimental and theoretical evidences of σ-hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements. Cocrystals between pyridine or pyridine N-oxide derivatives and osmium tetroxide are characterized through various techniques and rationalized as σ-hole interactions using DFT calculations and several other computational tools. We propose the term "osme bond" (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile. The word osme is the transcription of ὀσµÎ®, the ancient Greek word for smell that was used to name the heaviest group 8 element in relation to the smoky odor of its tetroxide.

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.

Theoretical Description of R-X⋯NH3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion.

In the present work, a number of R-X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme's type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R-Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback-Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R-X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br-CN]n system (n = 1-8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.

Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods.

This article analyzes the ability of semiempirical quantum-mechanical methods (PM6 and PM7) and self-consistent charge density-functional tight-binding (SCC-DFTB) method DFTB3 to describe halogen bonds. Calculations of the electrostatic potential on the surface of molecules containing halogens show that the σ-hole could be described well in modified neglect of diatomic overlap-based methods. The situation is more complex in the case of DFTB3 where a simpler model is used for the electrostatics, but short-ranged effects are covered in the Hamiltonian. All these methods can thus capture the effects that, for example, define the geometry of halogen bonds. The interaction energies are, however, affected by generally underestimated repulsion, which has been addressed earlier by standalone empirical corrections. Another approach to correcting this issue in DFTB3 is presented here-a modification of the energies of d-orbitals on halogens yields better results than the empirical correction in DFTB3-D3X, although it remains difficult to describe halogen and hydrogen bonds simultaneously. © 2019 Wiley Periodicals, Inc.

Chalcogen Bonding due to the Exo-Substitution of Icosahedral Dicarbaborane.

Chalcogen atoms are a class of substituents capable of generating inner and outer derivatives of boron clusters. It is well known that chalcogenated boron clusters can form strong σ-hole interactions when a chalcogen atom is a part of an icosahedron. This paper studies σ-hole interactions of dicarbaboranes with two exopolyhedral chalcogen atoms bonded to carbon vertices. Specifically, a computational investigation has been carried out on the co-crystal of (1,2-C2B10H10)2Se4•toluene and a single crystal of (1,2-C2B10H10)2Te4.

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.