Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent

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.

Solid-State Assembly by Chelating Chalcogen Bonding in Quinodimethane Tetraesters Fused with a Chalcogenadiazole

In contrast to p-quinodimethane tetraesters, which undergo facile polymerization due to their diradical character, newly synthesized 1 and 2 consisting of a chalcogenadiazole fused to a p-naphthoquinodimethane tetraester are thermodynamically stable due to butterfly-shaped deformation. Such a folded molecular structure is also favorable for chalcogen bond (ChB) formation through intermolecular close contacts between a chalcogen atom (E: Se or S) and the oxygen atoms of ester groups in a crystal. The less-explored chelating-ChB through a C=O⋅⋅⋅E⋅⋅⋅O=C contact [Se⋅⋅⋅O: 2.94-3.37 Å] is the key supramolecular synthon for the formation of a one-dimensional rod-like assembly in a crystal, which is commonly observed in selenadiazole-tetraesters (1) with OMe, OEt, and OiPr groups. The formation of inclusion cavities between the rods shows that 1 could serve as solid-state host molecules for clathrate formation, as found in a hexane-solvated crystal. In contrast, thiadiazole-tetraesters (2) are less suitable for the formation of a rod-like assembly since the ChB involving S is less effective, and thus is overwhelmed by weak hydrogen bonds through C-H⋅⋅⋅O contacts.

Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond

The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl₄, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

On the strength of hydrogen bonding within water clusters on the coordination limit

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18, 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice I_h ). The strongest HBs within H₂ O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H₂ O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H₂ O clusters.

Advances in anion transport and supramolecular medicinal chemistry

Advances in anion transport by synthetic supramolecular systems are discussed in this article. Developments in the design of discrete molecular carriers for anions and supramolecular anion channels are reviewed followed by an overview of the use of these systems in biological systems as putative treatments for diseases such as cystic fibrosis and cancer.

How Many Pnicogen Bonds can be Formed to a Central Atom Simultaneously?

A central ZF₃ molecule (Z = P, As, Sb, Bi) is allowed to interact with a number of nucleophiles exemplified by NCH, NH₃, and NC^– anion. The Z···N pnicogen bond (ZB) to a single base grows stronger for heavier Z atom: P < A < Sb < Bi and follows the NCH < NH₃ < NC^– order for the three bases. The maximum number of ZBs depends on both the nature of the base and pnicogen atom. PF₃ and AsF₃ can pnicogen bond with only a single CN^–; SbF₃ and BiF₃ can interact with two anions but only weakly. The weak NCH nucleophile can engage in a maximum of two ZBs, while three ZBs occur for NH₃. The latter NH₃ maximum can be extended to four ZBs but only for BiF₃. The fourth ZB is somewhat longer and weaker than the others, and the entire (H₃N)₄···BiF₃ complex relies partially on secondary interactions for its stability.

Anion Recognition by Neutral Chalcogen Bonding Receptors: Experimental and Theoretical Investigations

The utilization of neutral receptors for the molecular recognition of anions based on chalcogen bonding (ChB) is an undeveloped area of host-guest chemistry. In this manuscript, the synthesis of two new families of sulfur, selenium, and tellurium-based ChB binding motifs are reported. The stability of the thiophene, selenophene, and tellurophene binding motifs has enabled the determination of the association constants for ChB halide anion binding in the polar aprotic solvent THF by ¹ H, ⁷⁷ Se, and ¹²⁵ Te NMR experiments. Two different aromatic cores are used and one or two Ch-binding motifs are incorporated with the purpose of encapsulating the anion, offering up to two concurrent chalcogen bonds. Theoretical calculations and NMR experiments reveal that, for S and Se receptors, hydrogen-bonding interactions involving the acidic H atom adjacent to the chalcogen atom are energetically favored over the ChB interaction. However, for the tellurophene binding motif, the σ-hole interaction is competitive and more favored than the hydrogen bond.

Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X···I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

Theoretical Insights Into the Depolymerization Mechanism of Lignin to Methyl p-hydroxycinnamate by [Bmim][FeCl4] Ionic Liquid

Depolymerization of lignin into valuable aromatic compounds is an important starting point for its valorization strategies, which requires the cleavage of C-O and C-C bonds between lignin monomer units. The catalytic cleavage of these bonds is still difficult and challenging. Our previous experimental investigation (Green Chem., 2018, 20: 3743) has shown that methyl p-hydroxycinnamate (MPC) can be produced from molecular tailoring of H unit in lignin by the cleavage of the γ-O ester bond. In this study, the mechanism of [Bmim][FeCl4]-catalyzed depolymerization of lignin was investigated by using the density functional theory (DFT) method. The results reveal that [FeCl4]- anion of the catalyst plays a decisive role in the whole catalytic process, where two possible activation modes including three different potential reaction pathways can realize the depolymerization of lignin model compound. The calculated overall barriers of the catalytic conversion along these potential routes show that the third potential pathway, i.e., methanol firstly activated by [Bmim][FeCl4], has the most probability with the lowest energy barrier, while the second pathway is excluded because the energy barrier is too high. Also, the results illustrate that the solvent effect is beneficial to the reduction of the relative energy for the reaction to form the transition states. Hence, the obtained molecular level information can identify the favorable conversion process catalyzed by metallic ionic liquids to a certain extent, and it is desirable to enhance the utilization of biomass as a ubiquitous feedstock.

Cyclohexane-Based Scaffold Molecules Acting as Anion Transport, Anionophores, via Noncovalent Interactions

A theoretical study of a variety of cyclohexane-based anion transporters interacting with the chloride anion has been conducted using density functional theory. The calculations have been performed in the gas phase but also, in order to describe the solvation effects on the interaction, two different solvents-chloroform and dimethylsulfoxide-have been taken into account. Gas-phase interaction energies within the complexes are found to be up to 400 kJ/mol, while, when solvent effects are considered, the interaction energy values decreased drastically concomitantly with an elongation in the interatomic distances. Atoms in molecules and natural bond analysis corroborate the trends found for the intermolecular energies and Cl···H distances, suggesting strong donations from the Cl^- anion into the σ*H-N antibonding orbitals, as well as with noncovalent interaction plots showing large areas of electron density overlap within the chloride anion surroundings.

Co-crystals of an organic triselenocyanate with ditopic Lewis bases: recurrent chalcogen bond interactions motifs

Organic selenocyanates R–Se–CN can act as an amphoteric chalcogen bond (ChB) donor (through the Se atom) and acceptor (through the N atom lone pair). Co-crystallization of tri-substituted 1,3,5-tris(selenocyanatomethyl)-2,4,6-trimethylbenzene (1) is investigated with different ditopic Lewis bases acting as chalcogen bond (ChB) acceptors to investigate the outcome of the competition, as ChB acceptor, between the nitrogen lone pair of the SeCN group and other Lewis bases involving pyridinyl or carbonyl functions. In the presence of tetramethylpyrazine (TMP), benzoquinone (BQ) and para-dinitrobenzene (pDNB) as ditopic Lewis bases, a recurrent oligomeric motif stabilized by six ChB interactions is observed, involving six SeCN groups and the ChB acceptor sites of TMP, BQ and pDNB in the 2:1 adducts (1)2·TMP, (1)2·BQ and (1)2·pDNB.

Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bonds

A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.

Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions

Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl⁻ was thus compared to that of HCOO⁻, HSO₄⁻, and H₂PO₄⁻ with a wide variety of bidentate receptors. A pair of SnFH₂ groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)_n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO₂⁻ > Cl⁻ > H₂PO₄⁻ > HSO₄⁻ general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor.

On the capability of metal–halogen groups to participate in halogen bonds

Halogens in a M–X bond are inhibited from forming a halogen bond but can do so in certain circumstances, with or without a σ-hole.

Solvent and Substituent Effects on the Phosphine + CO2 Reaction

A theoretical study of the substituent and solvent effects on the reaction of phosphines with CO2 has been carried out by means of Møller-Plesset (MP2) computational level calculations and continuum polarizable method (PCM) solvent models. Three stationary points along the reaction coordinate have been characterized, a pre-transition state (TS) assembly in which a pnicogen bond or tetrel bond is established between the phosphine and the CO2 molecule, followed by a transition state, and leading finally to the adduct in which the P–C bond has been formed. The solvent effects on the stability and geometry of the stationary points are different. Thus, the pnicogen bonded complexes are destabilized as the dielectric constant of the solvent increases while the opposite happens within the adducts with the P–C bond and the TSs trend. A combination of the substituents and solvents can be used to control the most stable minimum.

Tetrel Bonding as a Vehicle for Strong and Selective Anion Binding

Tetrel atoms T (T = Si, Ge, Sn, and Pb) can engage in very strong noncovalent interactions with nucleophiles, which are commonly referred to as tetrel bonds. The ability of such bonds to bind various anions is assessed with a goal of designing an optimal receptor. The Sn atom seems to form the strongest bonds within the tetrel family. It is most effective in the context of a -SnF₃ group and a further enhancement is observed when a positive charge is placed on the receptor. Connection of the -SnF₃ group to either an imidazolium or triazolium provides a strong halide receptor, which can be improved if its point of attachment is changed from the C to an N atom of either ring. Aromaticity of the ring offers no advantage nor is a cyclic system superior to a simple alkyl amine of any chain length. Placing a pair of -SnF₃ groups on a single molecule to form a bipodal dicationic receptor with two tetrel bonds enhances the binding, but falls short of a simple doubling. These two tetrel groups can be placed on opposite ends of an alkyl diamine chain of any length although SnF₃⁺NH₂(CH₂)nNH₂SnF₃⁺ with n between 2 and 4 seems to offer the strongest halide binding. Of the various anions tested, OH− binds most strongly: OH− > F− > Cl− > Br− > I−. The binding energy of the larger NO₃− and HCO₃− anions is more dependent upon the charge of the receptor. This pattern translates into very strong selectivity of binding one anion over another. The tetrel-bonding receptors bind far more strongly to each anion than an equivalent number of K⁺ counterions, which leads to equilibrium ratios in favor of the former of many orders of magnitude.

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.