Selective Activation of Chalcogen Bonding: An Efficient Structuring Tool toward Crystal Engineering Strategies

ConspectusAmong the noncovalent interactions available in the toolbox of crystal engineering, chalcogen bonding (ChB) has recently entered the growing family of σ-hole interactions, following the strong developments based on the halogen bonding (XB) interaction over the last 30 years. The monovalent character of halogens provides halogen bonding directionality and strength. Combined with the extensive organic chemistry of Br and I derivatives, it has led to many applications of XB, in solution (organo-catalysis, anion recognition and transport), in the solid state (cocrystals, conducting materials, fluorescent materials, topochemical reactions, ...), in soft matter (liquid crystals, gels,···), and in biochemistry. The recognition of the presence of two σ-holes on divalent chalcogens and the ability to activate them, as in XB, with electron-withdrawing groups (EWG) has fueled more recent interest in chalcogen bonding. However, despite being identified for many years, ChB still struggles to make a mark due to (i) the underdeveloped synthetic chemistry of heavier Se and Te; (ii) the limited stability of organic chalcogenides, especially tellurides; and (iii) the poor predictability of ChB associated with the presence of two σ-holes. It therefore invites a great deal of attention of molecular chemists to design and develop selected ChB donors, for the scrutiny of fundamentals of ChB and their successful use in different applications. This Account aims to summarize our own contributions in this direction that extend from fundamental studies focused on addressing the lack of directionality/predictability in ChB to a systematic demonstration of its potential, specifically in crystal engineering, and particularly toward anionic networks on the one hand, topochemical reactions on the other hand.In this Account, we share our recent results aimed at recovering with ChB the same degree of strength and predictability found with XB, by focusing on divalent Se and Te systems with two different substituents, one of them with an EWG, to strongly unbalance both σ-holes. For that purpose, we explored this dissymmetrization concept within three chemical families, selenocyanates R-SeCN, alkynyl derivatives R-C≡C-(Se/Te)Me, and o-carborane derivatives. Such compounds were systematically engaged in cocrystals with either halides or neutral bipyridines as ChB acceptors, revealing their strong potential to chelate halides as well as their ability to organize reactive molecules such as alkenes and butadiynes toward [2+2] cycloadditions and polydiacetylene formation, respectively. This selective activation concept is not limited to ChB but can be effectively used on all other σ-hole interactions (pnictogen bond, tetrel bond, etc.) where one needs to control the directionality of the interaction.

Fluoride Anions: Unexploited but Effective Halogen Bond Acceptors

Due to their high electron density, fluoride anions can be considered the most effective halogen bond (HaB) acceptors among the halides. However, under common experimental conditions, F- uncommonly acts as HaB acceptor, expectedly as it is present in hydrated form. Herein we report that under specific crystallization conditions a hydrogen bond-free F- functioning as donor of electron density can be obtained, with the formed HaBs constituting the driving force of the observed crystal packings. Computations confirm the strength of these HaBs compared to analogous interactions involving other halides.

Solution Studies of a Water-Stable, Trivalent Antimony Pnictogen Bonding Anion Receptor with High Binding Affinities for CN-, OCN-, and OAc. Inorg Chem 2023. [PMID: 37499143 DOI: 10.1021/acs.inorgchem.3c01887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The solution phase anion binding behavior of a water-stable bidentate pnictogen bond donor was studied. A modest change in the visible absorption spectrum allowed for the determination of the binding constants. High binding constants were observed with cyanide, cyanate, and acetate, and these were corroborated with density functional theory (DFT) calculations. The receptor could be recovered free from the anion following treatment with methyl triflate, confirming that it remains intact. The tight binding of cyanide and water stability were exploited to use this system as a supramolecular catalyst in a phase-transfer Strecker reaction, further demonstrating the utility of pnictogen bonding as a tool in noncovalent catalysis.

Systematic Study of Podand Molecules for Synergistic Halogen and Hydrogen Bond-Driven Anion Recognition in the Solid State

The increasing demand of species for the efficient capture and sensing of anions benefits from a systematic study of anion binding capabilities in the solid state. This work reports a detailed crystallographic study of ten structurally related podands and shows that these charged receptors bind anions with a combination of charge-assisted halogen and hydrogen bonds. Computational tools helped in highlighting the role of the different involved interaction and afforded possible design principles for the design of improved podands.

Activation of perfluoroalkyl iodides by anions: extending the scope of halogen bond activation to C(sp3)-H amidation, C(sp2)-H iodination, and perfluoroalkylation reactions

A simple, efficient, and convenient activation of perfluoroalkyl iodides by tBuONa or KOH, without expensive photo- or transition metal catalysts, allows the promotion of versatile α-sp³ C-H amidation reactions of alkyl ethers and benzylic hydrocarbons, C-H iodination of heteroaryl compounds, and perfluoroalkylations of electron-rich π bonds. Mechanistic studies show that these novel protocols are based on the halogen bond interaction between perfluoroalkyl iodides and tBuONa or KOH, which promote homolysis of perfluoroalkyl iodides under mild conditions.

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E_int) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E_int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E_int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E_int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E_int values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

Halogen and Hydrogen Bond Motifs in Ionic Cocrystals Derived from 3-Halopyridinium Halogenides and Perfluorinated Iodobenzenes

Four halopyridinium salts, 3-chloro- and 3-bromopyridinium chlorides and bromides, have been successfully cocrystallized with two ditopic perfluorinated iodobenzenes, 1,4-diiodotetrafluorobenzene and 1,2-diiodotetrafluorobenzene. These halogen bond donor molecules were chosen because the different positionings of halogen bond donor atoms can lead to different supramolecular architectures. In this work, we present insight into the halogen bond acceptor potential of chloride and bromide ions, as well as the halogen bond donor potential of chlorine and bromine atoms substituted on the pyridinium ring when combined with the expectedly very strong hydrogen bonds between halopyridinium ions and free halogenide anions. A series of eight cocrystals were obtained in which three pairs of isostructural cocrystals were formed. Dominant interactions in the obtained cocrystals were charge-assisted hydrogen bonds between halopyridinium cations and halogenide ions as well as halogen bonds between halogen atoms on the pyridinium ring and halogenide ions.

Tuning of Ionic Liquid Crystal Properties by Combining Halogen Bonding and Fluorous Effect

We report halogen-bonded complexes between 1-polyfluoroalkyl-3-alkylimidazolium iodides and mono-iodoperfluoroalkanes of different chain lengths or di-iodoperfluorooctane. ¹⁹ F NMR analyses revealed that the preferred stoichiometry between the donors and acceptors is 1 : 1 in the cases of the mono-iodoperfluoroalkanes, and 2 : 1 with di-iodoperfluorooctane, as a result of the monodentate behavior of the iodide anion (halogen bond acceptor). Single crystal X-ray diffraction analyses showed the presence of a perfluorinated superanion, which interdigitates with the cation fluorinated chains, favoring the formation of lamellar structures. All of the obtained supramolecular complexes exhibit enantiotropic liquid crystalline phases over a broad range of temperatures. Most of the obtained complexes show melting points lower than 100 °C, two of them being liquid at room temperature, thus representing a new family of fluorinated ionic liquid crystals.

Theoretical, Solid-State, and Solution Quantification of the Hydrogen Bond-Enhanced Halogen Bond

Proximal noncovalent forces are commonplace in natural systems and understanding the consequences of their juxtaposition is critical. This paper experimentally quantifies for the first time a Hydrogen Bond-Enhanced Halogen Bond (HBeXB) without the complexities of protein structure or preorganization. An HBeXB is a halogen bond that has been strengthened when the halogen donor simultaneously accepts a hydrogen bond. Our theoretical studies suggest that electron-rich halogen bond donors are strengthened most by an adjacent hydrogen bond. Furthermore, stronger hydrogen bond donors enhance the halogen bond the most. X-ray crystal structures of halide complexes (X^- =Br^- , I^- ) reveal that HBeXBs produce shorter halogen bonds than non-hydrogen bond analogues. ¹⁹ F NMR titrations with chloride highlight that the HBeXB analogue exhibits stronger binding. Together, these results form the foundation for future studies concerning hydrogen bonds and halogen bonds in close proximity.

Peroxide-Templated Assembly of a Trimetal Neodymium Complex Single-Molecule Magnet

In this work, we present a trimetal neodymium complex with two notable qualities. First, the assembly of the complex is templated by peroxide derived from atmospheric oxygen. Second, the bulk material behaves as a superparamagnet, implying that the individual complexes are molecular magnets. Peroxide-templated assembly is possible because of the confluence of the high oxophilicity of neodymium along with the use of an azeotropic distillation synthesis method, which excludes water but admits oxygen. SQUID magnetometry measurements show an extremely high magnetic susceptibility as well as a lack of remanence.

Morpholino-Substituted BODIPY Species: Synthesis, Structure and Electrochemical Studies

Functionalization of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) chromophores at the 2,6-positions with iodo substituents and morpholino-substituted α-methyl groups affords molecules with strong absorbance in the visible spectrum. The effect of such substitution on the solid-state arrangements, absorption, fluorescence and electronic properties of these dye molecules is reported. The spectroscopic and spectroelectrochemical measurements display intense absorptions in the UV-visible spectrum with bathochromic shifts, in comparison to unfunctionalized BODIPY, and a positive shift in redox potentials due to functionalisation of the BODIPY core. Halogen bonds are observed in the solid-state structures of both halogenated BODIPY species, which in one case leads to the formation of an unusual halogen bonded framework.

Anion Influence on the Packing of 1,3-Bis(4-Ethynyl-3-Iodopyridinium)-Benzene Halogen Bond Receptors

Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focuses on receptor conformation, anion shape, solvation, and long range packing of these systems. Coupled with our previously reported structures, we conclude that anions can be classified as building units within this family of halogen bonding receptors. Two kinds of antiparallel dimers are observed for these dicationic receptors. An off-centered species is most frequent, present among geometrically diverse anions, and assorted receptor conformations. In contrast, the centered antiparallel dimers are observed with receptors adopting a bidentate conformation in the solid-state. While anions support the solid-state formation of dimers, the molecular geometry and characteristics (planarity, rigidity, and directionality) of arylethynyl systems increases the likelihood of dimer formation by limiting efficient packing arrangements. The significantly larger cation may have considerable influence on the solid-state packing, as similar cationic arylethynyl systems also display these dimers, suggesting.

Methanesulfonyl-polarized halogen bonding enables strong halide recognition in an arylethynyl anion receptor

A 3,5-bis((2-iodophenyl)ethynyl)pyridinium scaffold was synthesized which introduces the use of methanesulfonyl withdrawing groups to polarize iodine halogen bonding units for anion binding. We investigate the capability of this receptor to bind halides in polar media, while further probing the structure-property relationship of this well-polarized yet under-explored halogen bonding system.

Halogen bonding, chalcogen bonding, pnictogen bonding, tetrel bonding: origins, current status and discussion

The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen. This article is based upon my Closing Remarks Lecture at the 203^rd Faraday Discussion meeting on Halogen Bonding in Supramolecular and Solid State Chemistry, held in Ottawa, Canada, on 10-12^th July, 2017. The Discussion included papers on fundamentals and applications of halogen bonding in the solid state and solution phase. Analogous interactions involving main group elements outside group 17 were also examined. In the closing lecture and in this article these contributions have been grouped into the four themes: (a) fundamentals, (b) beyond the halogen bond, (c) characterisation, and (d) applications. The lecture and paper also include a short reflection on past work that has a bearing on the Discussion.

The intramolecular hydrogen bonded-halogen bond: a new strategy for preorganization and enhanced binding

Natural and synthetic molecules use weak noncovalent forces to preorganize structure and enable remarkable function. Herein, we introduce the intramolecular hydrogen bonded-halogen bond (HB-XB) as a novel method to preorganize halogen bonding (XBing) molecules, while generating a polarization-enhanced XB. Positioning a fluoroaniline between two iodopyridinium XB donors engendered intramolecular hydrogen bonding (HBing) to the electron-rich belt of both XB donors. NMR solution studies established the efficacy of the HB-XB. The receptor with HB-XBs (G2XB) displayed a nearly 9-fold increase in halide binding over control receptors. Gas-phase density functional theory conformational analysis indicated that the amine stabilizes the bidentate conformation. Furthermore, gas-phase interaction energies showed that the bidentate HB-XBs of G2XBme2+ are more than 3.2 kcal mol-1 stronger than the XBs in a control without the intramolecular HB. Additionally, crystal structures confirm that HB-XBs form tighter contacts with I- and Br- and produce receptors that are more planar. Collectively the results establish the intramolecular HB-XB as a tractable strategy to preorganize XB molecules and regulate XB strength.

Cation-cation and anion-anion complexes stabilized by halogen bonds

Stable minima showing halogen bonds between charged molecules with the same sign have been explored by means of theoretical calculations. The dissociation transition states and their corresponding barriers have also been characterized. In all cases, the results indicate that the complexes are thermodynamically unstable but kinetically stable with respect to the isolated monomers in gas phase. A corrected binding energy profile by removing the charge-charge repulsion of the monomers shows a profile similar to the one observed for the dissociation of analogous neutral systems. The nature of the interaction in the minima and TSs has been analyzed using the symmetry adapted perturbation theory (SAPT) method. The results indicate the presence of local favorable electrostatic interactions in the minima that vanish in the TSs. Natural bond orbital (NBO) and "atoms-in-molecules" (AIM) theories were used to analyze the complexes, obtaining good correlations between Laplacian and electron density values with both bond distances and charge-transfer energy contributions E(2). The largest E(2) orbital interaction energies for cation-cation and anion-anion complexes are 561.2 and 197.9 kJ mol^-1, respectively.

Halogen bonding and triiodide asymmetry in cocrystals of triphenylmethylphosphonium triiodide with organoiodines

Halogen bonding in triiodide–organoiodine cocrystals.

A pyrrole-containing cleft-type halogen bonding receptor for oxoanion recognition and sensing in aqueous solvent media

A halogen bonding pyrrole-bis(iodotriazolium) motif facilitates rarely observed augmented binding affinities and selective sensing of oxoanions (H₂PO₄⁻ and SO₄²⁻).

Connectivity and Topology Invariance in Self-Assembled and Halogen-Bonded Anionic (6,3)-Networks

We report here that the halogen bond driven self-assembly of 1,3,5-trifluorotriiodobenzene with tetraethylammonium and -phosphonium bromides affords 1:1 co-crystals, wherein the mutual induced fit of the triiodobenzene derivative and the bromide anions (halogen bond donor and acceptors, respectively) elicits the potential of these two tectons to function as tritopic modules (6,3). Supramolecular anionic networks are present in the two co-crystals wherein the donor and the acceptor alternate at the vertexes of the hexagonal frames and cations are accommodated in the potential empty space encircled by the frames. The change of one component in a self-assembled multi-component co-crystal often results in a change in its supramolecular connectivity and topology. Our systems have the same supramolecular features of corresponding iodide analogues as the metric aspects seem to prevail over other aspects in controlling the self-assembly process.

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.

Halogen bonded Borromean networks by design: topology invariance and metric tuning in a library of multi-component systems

A library of supramolecular anionic networks showing Borromean interpenetration has been prepared by self-assembly of crypt-222, several metal or ammonium halides, and five bis-homologous α,ω-diiodoperfluoroalkanes. Halogen bonding has driven the formation of these anionic networks. Borromean entanglement has been obtained starting from all the four used cations, all the three used anions, but only two of the five used diiodoperfluoroalkanes. As the change of the diiodoperfluoroalkane, the cation, or the anion has a different relative effect on the metrics and bondings of the self-assembled systems, it can be generalized that bonding, namely energetic, features play here a less influential role than metric features in determining the topology of the prepared tetra-component cocrystals. This conclusion may hold true for other multi-component systems and may function as a general heuristic principle when pursuing the preparation of multi-component systems having the same topology but different composition.

Co-crystallization of 1,3,5-trifluoro-2,4,6-triiodobenzene (1,3,5-TFTIB) with a variety of Lewis bases through halogen-bonding interactions

Co-crystallization of 1,3,5-trifluoro-2,4,6-triiodobenzene (1,3,5-TFTIB) with a variety of halogen-bonding acceptors.

Halogen-bonding contacts determining the crystal structure and fluorescence properties of organic salts

Different inorganic anions tuning halogen-bonding contacts to form different 3D networks with various absorption and emission properties.

Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.

Halogen bonding rotaxanes for nitrate recognition in aqueous media

Incorporating halogen bonding into an interlocked [2]rotaxane anion host system results in unprecedented nitrate recognition in 90% water.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

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.

Halogen bonding anion recognition

The development of solution-based anion receptor molecules which exploit halogen bonding interactions is an emerging area of research. This Feature Article reviews recent advances which have been made in this rapidly developing field, surveying the use of iodoperfluoroarene, haloimidazolium and halotriazole/triazolium halogen-bond-donor motifs in anion receptor design and describing the application of mechanically interlocked rotaxane and catenane frameworks as halogen bonding anion host systems.

Supramolecular interactions in the solid state

In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

A Halogen-Bonded Dimeric Resorcinarene Capsule

Iodine (I2) acts as a bifunctional halogen-bond donor connecting two macrocyclic molecules of the bowl-shaped halogen-bond acceptor, N-cyclohexyl ammonium resorcinarene chloride 1, to form the dimeric capsule [(1,4-dioxane)3@1(2)(I2)2]. The dimeric capsule is constructed solely through halogen bonds and has a single cavity (V=511 Å(3)) large enough to encapsulate three 1,4-dioxane guest molecules.