Supramolecular rectangles through directional chalcogen bonding

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.

Shifting the Triangle-Square Equilibrium of Self-Assembled Metallocycles by Guest Binding with Enhanced Photosensitization

Shifting a triangle-square equilibrium in one direction is an important problem in supramolecular self-assembly. Reaction of a benzothiadiazole-based diimidazole donor with a cis-Pt(II) acceptor yielded an equilibrium mixture of a triangle ([C₁₈H₂₄N₁₀O₆S₁Pt₁]₃≡ PtMC^T) and a square ([C₁₈H₂₄N₁₀O₆S₁Pt₁]₄≡ PtMC^S). We report here the shifting of such equilibrium toward a triangle using a guest (pyrene aldehyde, G1). While both benzothiadiazole and pyrene aldehyde can form reactive oxygen species (ROS) in organic solvents, their therapeutic use in water is restricted due to aqueous insolubility. The enhanced water solubility of the benzothiadiazole unit and G1 by macrocycle formation and host-guest complexation, respectively, enabled enhanced ROS generation by the host-guest complex (G1' ⊂ PtMC^T) in water (G1' = hydrated form of G1). The guest-encapsulated metallacycle (G1' ⊂ PtMC^T) has shown synergistic antibacterial activity compared to the mixture of macrocycles upon white-light irradiation due to enhanced ROS generation. The mechanism for such enhanced activity was established by measuring the oxidative stress and relative internalization of PtMCs and G1' ⊂ PtMC^T.

77Se and 125Te solid-state NMR and X-ray diffraction structural study of chalcogen-bonded 3,4-dicyano-1,2,5-chalcogenodiazole cocrystals

Three novel chalcogen-bonded cocrystals featuring 3,4-dicyano-1,2,5-selenodiazole (C₄N₄Se) or 3,4-dicyano-1,2,5-tellurodiazole (C₄N₄Te) as chalcogen-bond donors and hydroquinone (C₆H₆O₂), tetraphenylphosphonium chloride (C₂₄H₂₀P⁺·Cl^-) or tetraethylphosphonium chloride (C₈H₂₀P⁺·Cl^-) as chalcogen-bond acceptors have been prepared and characterized by single-crystal X-ray diffraction (XRD), powder X-ray diffraction and ⁷⁷Se/¹²⁵Te magic-angle spinning solid-state NMR spectroscopy. The single-crystal XRD results show that the chalcogenodiazole molecules interact with the electron donors through two σ-holes on each of the chalcogen atoms, which results in highly directional and moderately strong chalcogen bonds. Powder XRD confirms that the crystalline phases are preserved upon moderate grinding of the samples for solid-state NMR experiments. Measurement of ⁷⁷Se and ¹²⁵Te chemical shift tensors via magic-angle spinning solid-state NMR spectroscopy confirms the number of magnetically unique chalcogen sites in each asymmetric unit and reveals the impact of chalcogen-bond formation on the local electronic structure. These NMR data are further assessed in the context of analogous data for a wider range of crystalline chalcogen-bonded systems.

Noncovalent interactions between benzochalcogenadiazoles and nitrogen bases

A theoretical study has been carried out on the intermolecular interactions between tetrafluoro-benzochalcogenadiazoles (chalcogen = S, Se, Te) and a series of nitrogen bases (FCN, ClCN, NP, trans-N₂H₂, pyridine, pyrazole, imidazole) at the B97-D3/def2-TZVP level, to obtain a better insight into the nature and strength of Ch···N chalcogen bond and secondary interaction in the binary and 1:2 ternary complexes. The dispersion force plays a prominent role on the stability of the sulfur complexes, and the electrostatic effect enhanced for the heavier chalcogen complexes. Most of intermolecular bonds display the characters of closed-shell and noncovalent interaction. For the complexes involving pyridine and imidazole, chalcogen bond is stronger than hydrogen bond, while the strength of chalcogen bond is equivalent to the secondary interaction for other complexes. With the addition of nitrogen base in the 1:2 complexes, chalcogen bond is weakened, while the secondary interaction remains unchanged. In the 1:2 complexes formed by pyridine and imidazole, stronger chalcogen bond results in larger negative cooperativity than that of other complexes.

Various Sorts of Chalcogen Bonds Formed by an Aromatic System

The chalcogen Y atom in the aromatic ring of thiophene and its derivatives YC₄H₄ (Y = S, Se, Te) can engage in a number of different interactions with another such unit within the homodimer. Quantum calculations show that the two rings can be oriented perpendicular to one another in a T-shaped dimer in which the Y atom accepts electron density from the π-system of the other unit in a Y···π chalcogen bond (ChB). This geometry best takes advantage of attractions between the electrostatic potentials surrounding the two monomers. There are two other geometries in which the two Y atoms engage in a ChB with one another. However, instead of a simple interaction between a σ-hole on one Y and the lone pair of its neighbor, the interaction is better described as a pair of symmetrically equivalent Y···Y interactions, in which charge is transferred in both directions simultaneously, thereby effectively doubling the strength of the bond. These geometries differ from what might be expected based simply on the juxtaposition of the electrostatic potentials of the two monomers.

Molecular Cavity for Catalysis and Formation of Metal Nanoparticles for Use in Catalysis

The employment of weak intermolecular interactions in supramolecular chemistry offers an alternative approach to project artificial chemical environments like the active sites of enzymes. Discrete molecular architectures with defined shapes and geometries have become a revolutionary field of research in recent years because of their intrinsic porosity and ease of synthesis using dynamic non-covalent/covalent interactions. Several porous molecular cages have been constructed from simple building blocks by self-assembly, which undergoes many self-correction processes to form the final architecture. These supramolecular systems have been developed to demonstrate numerous applications, such as guest stabilization, drug delivery, catalysis, smart materials, and many other related fields. In this respect, catalysis in confined nanospaces using such supramolecular cages has seen significant growth over the years. These porous discrete cages contain suitable apertures for easy intake of substrates and smooth release of products to exhibit exceptional catalytic efficacy. This review highlights recent advancements in catalytic activity influenced by the nanocavities of hydrogen-bonded cages, metal-ligand coordination cages, and dynamic or reversible covalently bonded organic cages in different solvent media. Synthetic strategies for these three types of supramolecular systems are discussed briefly and follow similar and simplistic approaches manifested by simple starting materials and benign conditions. These examples demonstrate the progress of various functionalized molecular cages for specific chemical transformations in aqueous and nonaqueous media. Finally, we discuss the enduring challenges related to porous cage compounds that need to be overcome for further developments in this field of work.

Topochemical Polymerization of a Diacetylene in a Chalcogen-Bonded (ChB) Assembly

The successful topochemical polymerization of bis(selenocyanatomethyl)butadyine 1 is achieved upon association in a 1 : 1 co-crystal with 1,2-bis(2-pyridyl)ethylene (2-bpen) through strong and linear (NC)-Se⋅⋅⋅N_Py chalcogen bonding (ChB) interactions, allowing for an appropriate parallel alignment of the diacetylene moieties toward the solid-state reaction. Co-crystal 1⋅(2-bpen) undergoes polymerization upon heating at 100 °C. The reaction progress was monitored by IR, DSC and PXRD. An enhancement of the polymer conductivity by 8 orders of magnitude is observed upon iodine doping. Strikingly, the course of polymerization is accompanied with sublimation of the ChB acceptor molecules 2-bpen, providing the polymer in a pure form with full recovery of the co-former, at variance with the usual hydrogen-bonded co-crystal strategies toward polydiacetylenes.

Principles Guiding the Square Bonding Motif Containing a Pair of Chalcogen Bonds between Chalcogenadiazoles

The bonding motif adopted by a dimer of chalcogenadiazole molecules is characterized by a pair of equivalent Ch···N chalcogen bonds. Quantum calculations show that the interaction energy is substantial, varying between 4 kcal/mol for Ch = S and 17 kcal/mol for Te. The interaction is cooperative in that the total bond strength is greater than either chalcogen bond individually. Neither the addition of a phenyl ring nor the addition of a pair of cyano substituents to the diazole ring has much influence on this binding. Removal of one N from the diazole weakens the binding, and addition of two nitrogens has little effect. The largest perturbation arises with three N atoms in each ring, for which the binding energy increases by some 25%. The ring size plays a minor role in most cases, although a near doubling of bond strength occurs if there are two N atoms present on a four-membered ring.

Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study

In this study, we provide experimental (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the involvement of charge assisted chalcogen bonding (ChB) interactions in the recognition and folding mechanisms of S-adenosylmethionine (SAM) riboswitches. Concretely, an initial PDB search revealed several examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine (EEM) molecules and uracil (U) bases belonging to RNA take place. While these interactions are usually described as a merely Coulombic attraction between the positively charged S/Se group and RNA, theoretical calculations indicated that the σ holes of S and Se are involved. Moreover, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader’s “Atoms in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot) visual index, and Natural Bonding Orbital (NBO) analyses. As far as our knowledge extends, this is the first time that ChBs in SAM–RNA complexes have been systematically analyzed, and we believe the results might be useful for scientists working in the field of RNA engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

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) Å at 150 K, i.e., a reduction ratio of 0.85 vs. the van der Waals contact distance.

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.