The Chalcogen Bond in Crystalline Solids: A World Parallel to Halogen Bond

The origin of synthons and supramolecular motifs: beyond atoms and functional groups

A four-membered R22(4) supramolecular motif formed by S...S and S...I chalcogen-bonding interactions in the crystal structure of 4-iodo-1,3-dithiol-2-one (C3HIOS2, IDT) is analysed and compared with a similar R22(4) motif (stabilized by Se...Se and Se...O chalcogen bonds) observed in the previously reported crystal structure of selenaphthalic anhydride (C8H4O2Se, SePA) through detailed charge density analysis. Our investigation reveals that the chalcogen-bonding interactions participating in the R22(4) motifs observed in the two structures have the same characteristic orientation of local electrostatic electrophilic...nucleophilic interactions while involving different types of atoms. We carried out Cambridge Structural Database searches for synthons and supramolecular motifs involving chalcogen-, halogen- and hydrogen-bonding (ChB, XB and HB) interactions. Geometrical characterizations and topological analyses of the electron density ρ(r) and its negative Laplacian function [L(r) = -∇2ρ(r)] indicate that all the bonding interactions forming the motifs are driven by local electrophilic...nucleophilic interactions between complementary charge concentration (CC) and charge depletion (CD) sites present in the valence shells of the atoms, regardless of the atoms and functional groups involved. The graph-set assignment Gda(n) (G = C, R, D or S), formerly developed by Etter [Acc. Chem. Res. (1990), 23, 120-126] for HB interactions, is a convenient way to describe the connectivity in supramolecular motifs based on electrophilic...nucleophilic interactions (such as ChB, XB and HB interactions), exchanging the number of atomic acceptors (a) and donors (d) with the number of nucleophilic (n: CC) and electrophilic (e: CD) sites, and the number of atoms building the motif n by m, leading to the new graph-set assignment Gen(m) (G = C, R, D or S). Geometrical preferences in the molecular assembly of synthons and other supramolecular motifs are governed by the relative positions of CC and CD sites through CC...CD interactions that, in most cases, align with the internuclear directions within a <15° range despite low interaction energies. Accordingly, beyond atoms and functional groups, the origin of recurrent supramolecular structures embedded within different molecular environments is found in the local electrostatic complementarity of electrophilic and nucleophilic regions that are placed at particular geometries, driving the formation and the geometry of synthons and supramolecular motifs by directional and locally stabilizing electrostatic interactions.

Chalcogen bonded metal-organic frameworks: insights from X-ray analysis and theoretical calculations

The use of chalcogen bonding in the design of building blocks of metal-organic frameworks was demonstrated for the first time by experimental and theoretical methods. The supramolecular mode of the coordinated ligand as well as the chalcogen bond parameters (strengths and directionality) between the tectons are dependent on the metal centres.

Me2Se and Me2Te: Their Structures and Synergistic Effects of Halogen/Chalcogen Bonding with C6F5Br and C6F5I

This work combines halogen and chalcogen bonding. Short, polarity directed C-X⋅⋅⋅Ch (X=Br or I, Ch=Se or Te) contacts were prepared by in situ low-temperature cocrystallization of liquid mixtures of neutral pentafluorohalogenobenzenes C6F5X and dimethyl chalcogenides Me2Ch. Solid-state structures of Me2Se and Me2Te were determined 150 and 125 years after their first description. Significant C-Ch⋅⋅⋅Ch contacts make Me2Se dimeric and Me2Te polymeric. The cocrystals comprise C6F5X⋅⋅⋅Me2Ch⋅⋅⋅XC6F5 aggregates, except the combination X/Ch=I/Te which shows polymeric C6F5I⋅⋅⋅Me2Te⋅⋅⋅TeMe2⋅⋅⋅IC6F5 aggregation. The observed C-X⋅⋅⋅Te interactions are the shortest of this type, and the C-I⋅⋅⋅Ch contacts are shorter than the corresponding C-Br⋅⋅⋅Ch interactions. Heteromolecular C-X⋅⋅⋅Ch contacts are accompanied by F⋅⋅⋅H/F and X⋅⋅⋅H contacts in the cocrystals. The analysis of packing and contacts in all (co)crystals was complemented by computational studies. They both show that short interactions can be designed and engineered with reasonable predictability.

Amphoteric chalcogen-bonding and halogen-bonding rotaxanes for anion or cation recognition

The ever-increasing demand in the development of host molecules for the recognition of charged species is stimulated by their fundamental roles in numerous biological and environmental processes. Here, capitalizing on the inherent amphoteric nature of anisotropically polarized tellurium or iodine atoms, we demonstrate a proof of concept in charged guest recognition, where the same neutral host structure binds both cations or anions solely through its chalcogen or halogen donor atoms. Through extensive 1H nuclear magnetic resonance titration experiments and computational density functional theory studies, a library of chalcogen-bonding (ChB) and halogen-bonding (XB) mechanically interlocked [2]rotaxane molecules, including seminal examples of all-ChB and mixed ChB/XB [2]rotaxanes, are shown to function as either Lewis-acidic or Lewis-basic multidentate hosts for selective halide anion and metal cation binding. Notably, the exploitation of the inherent amphoteric character of an atom for the strategic purpose of either cation or anion recognition constitutes the inception of a previously unexplored area of supramolecular host-guest chemistry.

Computational Study of Hypervalent Chalcogen Bond Catalysis on the Hydroarylation of Styrene with Phenol: O-Activation vs π-Activation

Chalcogen bond catalysis is gaining recognition in organocatalysis due to its environmental benignity and relatively low cost. The hypervalent selenium salts can drive the hydroarylation of styrene and phenol, and hypervalent chalcogen···π catalysis has been proposed [Zhang, Q. Angew. Chem., Int. Ed. 2022, 61, e202208009]. In this work, the hydroarylation of styrene and phenol catalyzed by cyclic hypervalent selenium-based catalysts is investigated by density functional theory (DFT) calculations, and two activation modes are observed: one is on the styrene (π-activation mode), and the other is on the phenol (O-activation mode). The energy barriers via the O-activation mode are lower than those of the π-activation mode, and our proposed O-activation mode in this work may be more favorable. For the O-activation mode, energy barriers for the ortho-hydroarylation are lower than those for the para-hydroarylation, which is consistent with the experimental observation that the ortho-hydroarylation product is the major product and supports our proposed O-activation mode. Further investigation revealed that the stronger electrostatic interaction is the main factor leading to the ortho-hydroarylation in the O-activation mode compared to the para-hydroarylation. Moreover, the substituent effect of cyclic hypervalent selenium-based catalysts on the reactivity was investigated. This work would provide a valuable perspective on expanding applications for chalcogen bond catalysis.

Light-Induced Increase in Bond Strength─from Chalcogen Bond to Three-Electron σ Bond upon Excitation

Chalcogen bonds are σ hole interactions between a chalcogen center and a Lewis base center and have been applied in recent years as an alternative to hydrogen bonds in supramolecular chemistry and catalysis. While the electronic interactions of chalcogen bonds in the ground state have been intensively analyzed, there is barely any knowledge about the electron structure in the excited state. This is despite the fact that in some cases photoswitches containing chalcogen bonds exhibit exceptional switching behavior. Here, we investigate the effect of light absorption on chalcogen bonds containing divalent chalcogen centers. Quantum chemical calculations reveal that in the excited S1 state the noncovalent chalcogen bond converts to a covalent three-electron σ bond. The bond between the chalcogen center and the Lewis base center is thus significantly reinforced by light excitation. This change in bond type explains the previously experimentally observed nonswitchability of some tellurium-containing azo compounds. Furthermore, we were able to demonstrate that the switchability of certain selenium-containing compounds is temperature-dependent, whereby the ratio of the less stable cis compound is higher for higher temperatures. These results highlight the potential for designing responsive materials and dynamic molecular systems based on light-induced chalcogen bond modulation.

Heavy Chalcogen Properties of Sulfur and Selenium Enhance Nucleic Acid-Based Therapeutics

The Group 16 elements of the periodic table have a characteristic valence shell configuration instrumental to their chemical properties and reactivities. The electrostatic potentials of these so-called chalcogens have been exploited in the design of materials that require the efficient passage of electrons including supermagnets, photocatalytic dyes, and solar panels. Likewise, the incorporation of the heavy chalcogen selenium into organic frameworks has been shown to increase the reactivities of double bonds and heterocyclic rings, while its interactions with aromatic side chains in the hydrophobic core of proteins via selenomethionine impart a stabilizing effect. Typically present in the active site, the hypervalence of selenocysteine enables it to further stabilize the folded protein and mediate electron transfer. Selenium's native occurrence in bacterial tRNA maintains base pair fidelity, most notably during oxidative stress, through its electronic and steric effects. Such native modifications at the positions 2 and 5 of uridine render these sites relevant in the design of RNA-based therapeutics. Innocuous selenium substitution for oxygen in the former and the standard methods of selenium-derivatized oligonucleotide synthesis and detection have led to the establishment of a novel class of therapeutics. In this review, we summarize some progress in this area.

Crystal structure, Hirshfeld surface analysis and crystal voids of 4-nitro-benzo[c][1,2,5]selena-diazole

The title mol-ecule, C6H3N3O2Se, is almost planar. In the crystal, inter-molecular C-H⋯O hydrogen bonds link the mol-ecules into a network structure, enclosing R 2 2(7) and R 3 3(8) ring motifs, parallel to the bc plane. There are π-π inter-actions present with centroid-to-centroid distances of 3.746 (3) and 3.697 (3) Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (19.6%), H⋯N/N⋯H (11.0%), H⋯Se/Se⋯H (8.5%), O⋯Se/Se⋯O (8.2%), H⋯H (7.4%), C⋯N/N⋯C (7.3%) and N⋯Se/Se⋯N (7.2%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 25.60 Å3 and 3.73%, showing that there is no large cavity in the crystal.

Polarization Upends Convention: Halogen Bonding Propensities of Main Group Halides

The propensities for sigma hole bonding by halogen atoms bonded to central atoms below period 2 in the periodic table remain to be systematically examined. Using iodine as our reference halogen atom, a comprehensive analysis of the tendencies for halogen and other forms of significant sigma hole bonding by simple compounds of main group atoms from H to At is accomplished. An examination of the structure and bonding of complexes formed by those iodine-substituted main group compounds and sigma donating bases (ammonia and trimethylamine) is performed to probe the viability of halogen bonding by heavy main group RnM-I compounds in particular, given the historic focus on period 2. We show that propensities for halogen bonding by FnM-I systems for certain columns of the main group vary anomalously as M gets heavier due to a polarization-induced escalation of the electrostatic potential on I. In certain cases, the positive potential at the sigma hole on I is weaker than that at sigma holes on the central M or geminal R atoms. Previously unexplored cases of strong halogen bonding by the fluoroiodides of heavy group 13 atoms are identified, and prospects for other sigma hole type interactions to polarized (main group) central atoms are elucidated.

Chalcogen Bond-Driven Alkylations: Selenoxide-Pillar[5]arene as a Recyclable Catalyst for Displacement Reactions in Water

A novel strategy to catalyze alkylation reactions through chalcogen bond interaction using a supramolecular structure is presented herein. Utilizing just 1.0 mol % of selenoxide-pillar[5]arene (P[5]SeO) as the catalyst we achieved efficient catalysis in the cyanation of benzyl bromide in water. Our approach demonstrated high efficiency and effectiveness, with the results supported by designed control experiments and theoretical models, highlighting the catalytic effect of the pillar[5]arene through noncovalent interactions. Quantum-chemical calculations (ωB97X-D/def2-TZVP@SMD) pointed out that the catalyzed cyanation reaction followed an SN2-like mechanism, with energy barriers (ΔH≠) ranging from 16.7 to 18.2 kcal mol-1, exhibiting dissociative character depending on the para-substituent. 1H NMR analysis revealed that P[5]SeO acted as a catalyst through inclusion complex formation, facilitating the transfer of the electrophilic substrate to the aqueous solution for nucleophilic displacement. Our reaction protocol proved applicable to various substrates, including aromatic and alpha-carbonyl derivatives. The use of sodium azide as the nucleophile was also feasible. Importantly, our method allowed scalability, and the catalyst P[5]SeO could be recovered and reused effectively for multiple reaction cycles, showcasing sustainability.

Evolution of Peptidomimetics-Based Chiral Assemblies of β-Sheet, α-Helix, and Double Helix Involving Chalcogen Bonds

Developing chiral assemblies that mimic biological secondary structures, e.g., protein β-sheet, α-helix, and DNA double helix, is a captivating goal in supramolecular chemistry. Here, we create a family of biomimetic chiral assemblies from alanine-based peptidomimetics, wherein the incorporation of N-terminal 2,1,3-benzoselenadiazole groups enables the rarely utilized chalcogen bonding as the adhesive interaction. While the alanine-based acylhydrazine molecule 1L was designed as a building unit with an extended conformation, simple derivatization of 1L affords folded unilateral N-amidothiourea 2L with one β-turn and bilateral N-amidothiourea 3L with two β-turns. This derivatization leads to the evolution of molecular assemblies from β-sheet organization (1L) to single helix (α-helix mimic, 2L) and ultimately to double helix (3L), illustrating an evolutionary route relating the structures and superstructures. In the case of the double helix formed by 3L, an unexpected cis-form that brings the two β-turns into one side was observed, stabilized via the π···π interaction between two N-terminal 2,1,3-benzoselenadiazole groups. This conformation allows double-crossed N-Se···S═C chalcogen bonds to support a DNA-like P-double helix featuring intrastrand noncovalent interactions and interstrand covalent linkages, surviving in both the solid state and in dilute acetonitrile solution phase.

A Hexavalent Tellurium-Based Chalcogen Bonding Catalysis Platform: High Catalytic Activity and Controlling of Selectivity

Herein, we describe a hexavalent tellurium-based chalcogen bonding catalysis platform capable of addressing reactivity and selectivity issues. This research demonstrates that hexavalent tellurium salts can serve as a class of highly active chalcogen bonding catalysts for the first time. The tellurium centers in these hexavalent catalysts have only one exposed interaction site, thus providing a favorable condition for the controlling of reaction selectivity. The advantages of these hexavalent tellurium catalysts were demonstrated by their remarkable catalytic activity in the cyanidation of difluorocyclopropenes through C-F bond activation, which otherwise were low reactive under the catalysis of strong Lewis acids or inaccessible by representative divalent/tetravalent tellurium-based donors. The catalytic activity of the hexavalent tellurium catalyst was further highlighted by its capability to address a previously unresolved reactivity problem associated with the strong Lewis acid approach, upon using some less reactive silyl enol ethers as nucleophiles in the functionalization of difluorocyclopropenes. The generality of this catalysis platform was demonstrated by its versatile application in different reaction systems. The hexavalent tellurium catalyst can differentiate two similar free OH groups in glycosyl acceptors to achieve excellent regio- and stereoselectivity in the synthesis of disaccharides, in which the tetravalent tellurium catalyst gave low reactivity and selectivity. Mechanistic investigation suggests that a catalyst-glycosyl donor-acceptor ternary supramolecular complex is operative.

Methyl 2-amino-4-(morpholin-4-yl)benzo[d]thiazole-6-carboxyl-ate tetartohydrate

The title compound, C13H15N3O3S·0.25H2O, crystallizes in the triclinic space group P1 and features four organic mol-ecules in the asymmetric unit alongside one water mol-ecule. The extended structure exhibits both hydrogen bonds (O-H⋯O, N-H⋯O and N-H⋯N) and chalcogen (C-S⋯O) contacts, leading to a complex three-dimensional network.

Diverse Cyclization Pathways Between Nitriles with Active α-Methylene Group and Ambiphilic 2-Pyridylselenyl Reagents Enabled by Reversible Covalent Bonding

Herein, we describe a novel coupling between ambiphilic 2-pyridylselenyl reagents and nitriles featuring an active α-methylene group. Depending on the solvent employed, this reaction can yield two distinct types of cationic pyridinium-fused selenium-containing heterocycles, 1,3-selenazolium or 1,2,4-selenadiazolium salts, in high yields. This is in contrast to what we observed before for other nitriles. Notably, the formation of selenadiazolium is reversible, gradually converting into the more thermodynamically stable selenazolium product in solution. Our findings reveal, for the first time, the reversible nature of 1,3-dipolar cyclization between the CN triple bond and 2-pyridylselenyl reagents. Nitrile substitution experiments in the adducts confirmed the dynamic nature of this cyclization, indicating potential applications in dynamic covalent chemistry. DFT calculations revealed the mechanistic pathways for new cyclizations, suggesting a concerted [3 + 2] cycloaddition for the formation of selenadiazolium rings and a stepwise mechanism involving a ketenimine intermediate for the formation of selenazolium rings. Natural bond orbital analysis confirmed the involvement of σ-hole interactions and lone pair to σ* electron donation in these processes. Additionally, theoretical investigations of σ-hole interactions were performed, focusing on the selenium-centered contacts within the new compounds.

Constructing Molecular Networks on Metal Surfaces through Tellurium-Based Chalcogen-Organic Interaction

On-surface molecular self-assembly presents an important approach to the development of low-dimensional functional nanostructures and nanomaterials. Traditional strategies primarily exploit hydrogen bonding or metal coordination, yet the potential of chalcogen bonding (ChB) for on-surface self-assemblies remains underexplored. Here, we explore fabricating molecular networks via tellurium (Te)-directed chalcogen-organic interactions. Employing carbonitrile molecules as molecular building blocks, we have achieved extended 2D networks exhibiting a 4-fold binding motif on Au(111), marking a notable difference from the conventional coordinative interaction involving transition metals. Our findings, supported by density functional theory (DFT) and scanning tunneling spectroscopy (STS), show that the Te-carbonitrile interaction exhibits lower stability compared to the metal-organic coordination, and the construction of the Te-directed molecular networks does not alter the electronic properties of the involved molecules. Introducing chalcogen-directed interactions may expand the spectrum of strategies in supramolecular assembly, contributing to the design of advanced molecular architectures for nanotechnological applications.

Transition State Stabilizing Effects of Oxygen and Sulfur Chalcogen Bond Interactions

Non-covalent chalcogen bond (ChB) interactions have found utility in many fields, including catalysis, organic semiconductors, and crystal engineering. In this study, the transition stabilizing effects of ChB interactions of oxygen and sulfur were experimentally measured using a series of molecular rotors. The rotors were designed to form ChB interactions in their bond rotation transition states. This enabled the kinetic influences to be assessed by monitoring changes in the rotational barriers. Despite forming weaker ChB interactions, the smaller chalcogens were able to stabilize transition states and had measurable kinetic effects on the rotational barriers. Sulfur stabilized the bond rotation transition state by as much as -7.2 kcal/mol without electron-withdrawing groups. The key was to design a system where the sulfur σ ${\sigma }$ -hole was aligned with the lone pairs of the chalcogen bond acceptor. Oxygen rotors also could form transition state stabilizing ChB interactions but required electron-withdrawing groups. For both oxygen and sulfur ChB interactions, a strong correlation was observed between transition state stabilizing abilities and electrostatic potential (ESP) of the chalcogen, providing a useful predictive parameter for the rational design of future ChB systems.

Electrostatic Surface Potentials and Chalcogen-Bonding Motifs of Substituted 2,1,3-Benzoselenadiazoles Probed via 77Se Solid-State NMR Spectroscopy

Chalcogen bonds (ChB) are moderately strong, directional, and specific non-covalent interactions that have garnered substantial interest over the last decades. Specifically, the presence of two σ-holes offers great potential for crystal engineering, catalysis, biochemistry, and molecular sensing. However, ChB applications are currently hampered by a lack of methods to characterize and control chalcogen bonds. Here, we report on the influence of various substituents (halogens, cyano, and methyl groups) on the observed self-complementary ChB networks of 2,1,3-benzoselenadiazoles. From molecular electrostatic potential calculations, we show that the electrostatic surface potentials (ESP) of the σ-holes on selenium are largely influenced by the electron-withdrawing character of these substituents. Structural analyses via X-ray diffraction reveal a variety of ChB geometries and binding modes that are rationalized via the computed ESP maps, although the structure of 5,6-dimethyl-2,1,3-benzoselenadiazole also demonstrates the influence of steric interactions. 77Se solid-state magic-angle spinning NMR spectroscopy, in particular the analysis of the selenium chemical shift tensors, is found to be an effective probe able to characterize both structural and electrostatic features of these self-complementary ChB systems. We find a positive correlation between the value of the ESP maxima at the σ-holes and the experimentally measured 77Se isotropic chemical shift, while the skew of the chemical shift tensor is established as a metric which is reflective of the ChB binding motif.

An innovative deep eutectic solvent: chalcogen bonding as the primary driving force

Chalcogen bonding (ChB) interactions have drawn intensive attention in the last few decades as interesting alternatives to hydrogen bonding. The applications of ChB were mostly centered on the solid state and have rarely been explored in solution. In this work, a novel strategy for forming ChB-based deep eutectic solvents (DESs) was exploited. We set forth the formation, physicochemical properties, and interaction sites in detail. This work not only provides a new idea to design DES systems but also to exploit the potential application of ChB complexes.

Regulating Planarized Intramolecular Charge Transfer for Efficient Single-Phase White-Light Emission in Undoped Metal-Organic Framework Nanocrystals

The technology of combining multiple emission centers to exploit white-light-emitting (WLE) materials by taking advantage of porous metal-organic frameworks (MOFs) is mature, but preparing undoped WLE MOFs remains a challenge. Herein, a pressure-treated strategy is reported to achieve efficient white photoluminescence (PL) in undoped [Zn(Tdc)(py)]n nanocrystals (NCs) at ambient conditions, where the Commission International del'Eclairage coordinates and color temperature reach (0.31, 0.37) and 6560 K, respectively. The initial [Zn(Tdc)(py)]n NCs exhibit weak-blue PL consisting of localized excited (LE) and planarized intramolecular charge transfer (PLICT) states. After pressure treatment, the emission contributions of LE and PLICT states are balanced by increasing the planarization of subunits, thereby producing white PL. Meanwhile, the reduction of nonradiative decay triggered by the planarized structure results in 5-fold PL enhancement. Phosphor-converted light-emitting diodes based on pressure-treated samples show favorable white-light characteristics. The finding provides a new platform for the development of undoped WLE MOFs.

Synthesis, spectroscopic and crystallographic characterization of various cymantrenyl thioethers [Mn{C5HxBry(SMe)z}(PPh3)(CO)2]

Starting from [Mn(C5H4Br)(PPh3)(CO)2] (1a), the cymantrenyl thioethers [Mn(C5H4SMe)(PPh3)(CO)2] (1b) and [Mn{C5H4-nBr(SMe)n}(PPh3)(CO)2] (n = 1 for compound 2, n = 2 for 3 and n = 3 for 4) were obtained, using either n-butyllithium (n-BuLi), lithium diisopropylamide (LDA) or lithium tetramethylpiperidide (LiTMP) as base, followed by electrophilic quenching with MeSSMe. Stepwise consecutive reaction of [Mn(C5Br5)(PPh3)(CO)2] with n-BuLi and MeSSMe led finally to [Mn{C5(SMe)5}(PPh3)(CO)2] (11), only the fifth complex to be reported containing a perthiolated cyclopentadienyl ring. The molecular and crystal structures of 1b, 3, 4 and 11 were determined and were studied for the occurrence of S...S and S...Br interactions. It turned out that although some interactions of this type occurred, they were of minor importance for the arrangement of the molecules in the crystal.

Polydentate chalcogen bonding: anion trapping with a water-stable host compound carrying Se-CF3 functions

Bidentate and tetradentate chalcogen bonding host systems with SeCF3 functions as σ-hole donors in close proximity at the alkyne functions of 1,8-diethynylanthracene and its syn-dimer were prepared in quantitative yield by tin-selenium exchange reactions of the corresponding trimethylstannyl precursors with ClSeCF3. The bidentate system shows chalcogen bonding interactions with THF, but does not bind halide ions. The tetradentate system cooperatively chelates chloride, bromide and iodide ions with its four CC-SeCF3 units by rotating the four σ-holes towards the halide ion. The structures of these halide ion adducts were determined by X-ray diffraction. The hydrobromide and -iodide salts of the ethyl derivative of Schwesinger's phosphazene superbase served as halide salts with very weakly coordinating cations.

Insight into the Metal-Involving Chalcogen Bond in the PdII/PtII-Based Complexes: Comparison with the Conventional Chalcogen Bond

The metal-involving Ch···M chalcogen bond and the conventional Ch···O chalcogen bond between ChX2 (Ch = Se, Te; X = CCH, CN) acting as a Lewis acid and M(acac)2 (M = Pd, Pt; Hacac = acetylacetone) acting as a Lewis base were studied by density functional theory calculations. It has been observed that the nucleophilicity of the PtII complexes is higher than that of the corresponding PdII complexes. As a result, the PtII complexes tend to exhibit a more negative interaction energy and larger orbital interaction. The strength of the chalcogen bond increases with the increase of the chalcogen atom and the electronegativity of the substituent on the Lewis acid and vice versa. The metal-involving chalcogen bond shows a typical weak closed-shell noncovalent interaction in the (HCC)2Ch···M(acac)2 complexes, while it exhibits a partially covalent nature in the (NC)2Ch···M(acac)2 complexes. The conventional Ch···O chalcogen bond displays the character of a weak noncovalent interaction, and its strength is generally weaker than that of metal-involving Ch···M interactions. It could be argued that the metal-involving chalcogen bond is primarily determined by the correlation term, whereas the conventional chalcogen bond is mainly governed by the electrostatic interaction.

Anion⋯anion self-assembly under the control of σ- and π-hole bonds

The electrostatic attraction between charges of opposite signs and the repulsion between charges of the same sign are ubiquitous and influential phenomena in recognition and self-assembly processes. However, it has been recently revealed that specific attractive forces between ions with the same sign are relatively common. These forces can be strong enough to overcome the Coulomb repulsion between ions with the same sign, leading to the formation of stable anion⋯anion and cation⋯cation adducts. Hydroden bonds (HBs) are probably the best-known interaction that can effectively direct these counterintuitive assembly processes. In this review we discuss how σ-hole and π-hole bonds can break the paradigm of electrostatic repulsion between like-charges and effectively drive the self-assembly of anions into discrete as well as one-, two-, or three-dimensional adducts. σ-Hole and π-hole bonds are the attractive forces between regions of excess electron density in molecular entities (e.g., lone pairs or π bond orbitals) and regions of depleted electron density that are localized at the outer surface of bonded atoms opposite to the σ covalent bonds formed by atoms (σ-holes) and above and below the planar portions of molecular entities (π-holes). σ- and π-holes can be present on many different elements of the p and d block of the periodic table and the self-assembly processes driven by their presence can thus involve a wide diversity of mono- and di-anions. The formed homomeric and heteromeric adducts are typically stable in the solid phase and in polar solvents but metastable or unstable in the gas phase. The pivotal role of σ- and π-hole bonds in controlling anion⋯anion self-assembly is described in key biopharmacological systems and in molecular materials endowed with useful functional properties.

Synthesis, characterization, and biological activity of cationic ruthenium-arene complexes with sulfur ligands

Five cationic ruthenium-arene complexes with the generic formula [Ru(SAc)(S2C·NHC)(p-cymene)](PF6) (5a-e) were prepared in almost quantitative yields using a straightforward one-pot, two-step experimental procedure starting from [RuCl2(p-cymene)]2, an imidazol(in)ium-2-dithiocarboxylate (NHC·CS2) zwitterion, KSAc, and KPF6. These half-sandwich compounds were fully characterized by various analytical techniques and the molecular structures of two of them were solved by X-ray diffraction analysis, which revealed the existence of an intramolecular chalcogen bond between the oxygen atom of the thioacetate ligand and a proximal sulfur atom of the dithiocarboxylate unit. DFT calculations showed that the C=S…O charge transfer amounted to 2.4 kcal mol-1. The dissolution of [Ru(SAc)(S2C·IMes)(p-cymene)](PF6) (5a) in moist DMSO-d6 at room temperature did not cause the dissociation of its sulfur ligands. Instead, p-cymene was slowly released to afford the 12-electron [Ru(SAc)(S2C·IMes)]+ cation that could be detected by mass spectrometry. Monitoring the solvolysis process by 1H NMR spectroscopy showed that more than 22 days were needed to fully decompose the starting ruthenium-arene complex. Compounds 5a-e exhibited a high antiproliferative activity against human glioma Hs683 and human lung carcinoma A549 cancer cells. In particular, the IMes derivative (5a) was the most potent compound of the series, achieving toxicities similar to those displayed by marketed platinum drugs.

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations

Among various non-covalent interactions, selenium-centered chalcogen bonds (SeChBs) have garnered considerable attention in recent years as a result of their important contributions to crystal engineering, organocatalysis, molecular recognition, materials science, and biological systems. Herein, we systematically investigated π-hole-type Se∙∙∙O/S ChBs in the binary complexes of SeO2 with a series of O-/S-containing Lewis bases by means of high-level ab initio computations. The results demonstrate that there exists an attractive interaction between the Se atom of SeO2 and the O/S atom of Lewis bases. The interaction energies computed at the MP2/aug-cc-pVTZ level range from -4.68 kcal/mol to -10.83 kcal/mol for the Se∙∙∙O chalcogen-bonded complexes and vary between -3.53 kcal/mol and -13.77 kcal/mol for the Se∙∙∙S chalcogen-bonded complexes. The Se∙∙∙O/S ChBs exhibit a relatively short binding distance in comparison to the sum of the van der Waals radii of two chalcogen atoms. The Se∙∙∙O/S ChBs in all of the studied complexes show significant strength and a closed-shell nature, with a partially covalent character in most cases. Furthermore, the strength of these Se∙∙∙O/S ChBs generally surpasses that of the C/O-H∙∙∙O hydrogen bonds within the same complex. It should be noted that additional C/O-H∙∙∙O interactions have a large effect on the geometric structures and strength of Se∙∙∙O/S ChBs. Two subunits are connected together mainly via the orbital interaction between the lone pair of O/S atoms in the Lewis bases and the BD*(OSe) anti-bonding orbital of SeO2, except for the SeO2∙∙∙HCSOH complex. The electrostatic component emerges as the largest attractive contributor for stabilizing the examined complexes, with significant contributions from induction and dispersion components as well.

Neighboring Effects of Sulfur Oxidation State on Dynamic Covalent Bonds and Assemblies

The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.

Benzoyl Valine Quasiracemates: Pairing CF3 Quasienantiomers with H to t-Butyl

Understanding the interplay of structural features responsible for molecular assembly is essential for molecular crystal engineering. When assembling molecules with encoded motifs, first choice supramolecular strategies almost always include robust directional nonbonded contacts. Quasiracemic materials, considered near racemates since cocrystallization occurs with chemically unique components, lack a molecular framework or functional group restrictions, highlighting the importance of molecular shape to molecular assembly. Recently, our group reported quasiracemates derived from benzoyl leucine/phenylalanine derivatives with two points of chemical difference. In this study, we modified the chemical framework with valine and increased the scope of the work by imposing a larger variance in the side chain substituents. Pairing a CF3 component with quasienantiomers that differ iteratively from hydrogen to t-butyl offers an important view into the supramolecular landscape of these materials. Single-crystal X-ray crystallography and lattice energy assessments, coupled with conformational and crystal structure similarity searches, show an elevated degree of isomorphism for many of the targeted 17 racemates and quasiracemates. These benzoyl amino acid molecular architectures create extended hydrogen-bond patterns in the crystal that provide enhanced opportunities to study the shape space and molecular recognition profiles for a diverse family of quasienantiomeric components.

Investigating Recurrent Matere Bonds in Pertechnetate Compounds

In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H2O)4(TcO4)2], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H2O)4(ReO4)2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H2O)4(TcO4)2], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H2O)4(ReO4)2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds.

Location of S-nitrosylated cysteines in protein three-dimensional structures

Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially. (2) S-nitrosylation may be a protection against irreversible thiol oxidation; because the NO group of Snc is relatively accessible to the solvent, it may act as a cork to protect the sulfur atoms of cysteines from oxidation by molecular oxygen to sulfenic, sulfinic, and sulfonic acid; moreover, Snc are frequently found at the start or end of helices and strands and this might shield secondary structural elements from unfolding.

Spodium bonding with noble gas atoms

The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.

The Missing Chalcogen Bonding Donor: Strongly Polarized Oxygen of Water

A biscyclen molecular cabin, synthesized by connecting two cyclen macrocycles with four linkages, entraps a Li+···H2O···Li+ trimer with a water molecule clamped by two Li+ ions. This configuration results in strongly polarized water, characterized by a water proton resonance shift of up to 10.00 ppm. The arrangement facilitates unprecedented O-centered chalcogen bonds between the lone pairs of pyridinyl nitrogen atoms and polarized water oxygen, as confirmed by X-ray crystallography, NMR spectroscopy, and theoretical calculations. Further observation of O-centered chalcogen bonding in a H2O·(LiCl)2 cluster suggests its widespread presence in hydrated salt systems.

Chalcogen and Hydrogen Bond Team up in Driving Anion⋅⋅⋅Anion Self-Assembly

H-selenite anions (HSeO3 - ) form in the solid unprecedented anionic supramolecular chains wherein single units are assembled via alternating short Se⋅⋅⋅O and H⋅⋅⋅O contacts. Crystallographic analyses and computational studies (the quantum theory of "atoms-in-molecules", QTAIM, and the noncovalent interaction plot, NCIPlot) consistently prove the attractive nature of these chalcogen bonds (ChBs) and hydrogen honds (HBs), the Janus-type character of HSeO3 - anions which act as both donors and acceptors of ChB and HB, and the possible stability of anion dimers in solution. The effectiveness of the ChBs herein described may lead to consider the HSeO3 - moiety as a new entry in the toolbox of crystal engineering based on ChB.

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.

Affinity of Telluronium Chalcogen Bond Donors for Lewis Bases in Solution: A Critical Experimental-Theoretical Joint Study

Telluronium salts [Ar2 MeTe]X were synthesized, and their Lewis acidic properties towards a number of Lewis bases were addressed in solution by physical and theoretical means. Structural X-ray diffraction analysis of 21 different salts revealed the electrophilicity of the Te centers in their interactions with anions. Telluroniums' propensity to form Lewis pairs was investigated with OPPh3 . Diffusion-ordered NMR spectroscopy suggested that telluroniums can bind up to three OPPh3 molecules. Isotherm titration calorimetry showed that the related heats of association in 1,2-dichloroethane depend on the electronic properties of the substituents of the aryl moiety and on the nature of the counterion. The enthalpies of first association of OPPh3 span -0.5 to -5 kcal mol-1 . Study of the affinity of telluroniums for OPPh3 by state-of-the-art DFT and ab-initio methods revealed the dominant Coulombic and dispersion interactions as well as an entropic effect favoring association in solution. Intermolecular orbital interactions between [Ar2 MeTe]+ cations and OPPh3 are deemed insufficient on their own to ensure the cohesion of [Ar2 MeTe ⋅ Bn ]+ complexes in solution (B=Lewis base). Comparison of Grimme's and Tkatchenko's DFT-D4/MBD-vdW thermodynamics of formation of higher [Ar2 MeTe ⋅ Bn ]+ complexes revealed significant molecular size-dependent divergence of the two methodologies, with MBD yielding better agreement with experiment.

Influence of donor point modifications on the assembly of chalcogen-bonded organic frameworks

Incremental, single-atom substitutions of Se-based chalcogen bond (Ch-bond) donors with stronger donating Te centers were implemented in two new triptycene tris(1,2,5-chalcogenadiazole) tectons. The appreciably more favorable Ch-bonding ability of the Te-based donors promotes assembly of low-density networks and more stable Ch-bonded organic frameworks (ChOFs).

Bidentate Ligand Driven Intramolecularly Te…O Bonded Organotellurium Cations from Synthesis, Stability to Catalysis

A new series of unsymmetrical phenyl tellurides derived from 2-N-(quinolin-8-yl) benzamide ligand has been synthesized in a practical manner by the copper-catalyzed method by using diaryl ditelluride and Mg as a reductant at room temperature. In order to augment the Lewis acidity of these newly formed unsymmetrical monotellurides, these have been transformed into corresponding unsymmetrical 2-N-(quinolin-8-yl)benzamide tellurium cations. Subsequently, these Lewis acidic tellurium cations were used as chalcogen bonding catalysts, enabling the synthesis of various substituted 1,2-dihydroquinolines by activating ketones with anilines under mild conditions. Moreover, the synthesized 2-N-(quinolin-8-yl)benzamide phenyl tellurium cation has also catalyzed the formation of β-amino alcohols in high regioselectivity by effectively activating epoxides at room temperature. Mechanistic insight by 1 H and 19 F NMR study, electrostatic surface potential (ESP map), control reaction in which tellurium cation reacted explosively with epoxide, suggested that the enhanced Lewis acidity of tellurium center seems responsible for efficient catalytic activities under mild conditions enabling β-amino alcohols with excellent regioselectivity and 1,2-dihydroquinolines with trifluoromethyl, nitro, and pyridylsubstitution, which were difficult to access.

Crystal structure and anti-mycobacterial evaluation of 2-(cyclo-hexyl-meth-yl)-7-nitro-5-(tri-fluoro-meth-yl)benzo[d]iso-thia-zol-3(2H)-one

The title compound, C15H15F3N2O3S, crystallizes in the monoclinic system, space group I2/a, with Z = 8. As expected, the nine-membered heterobicyclic system is virtually planar and the cyclo-hexyl group adopts a chair conformation. There is structural evidence for intra-molecular N-S⋯O chalcogen bonding between the benziso-thia-zolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N-S bond [N-S⋯O = 162.7 (1)°]. In the crystal, the mol-ecules form centrosymmetric dimers through C-H⋯O weak hydrogen bonding between a C-H group of the electron-deficient benzene ring and the benzo-thia-zolinone carbonyl O atom with an R 2 2(10) motif. In contrast to the previously described N-acyl 7-nitro-5-(tri-fluoro-meth-yl)benzo[d]iso-thia-zol-3(2H)-ones, the title N-cyclo-hexyl-methyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro.

Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)

In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported in the literature. Herein, the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes formed between XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) were systematically studied by using quantum chemical computations. The model complexes are stabilized via one primary X∙∙∙Y chalcogen bond (ChB) and the secondary C-H∙∙∙O hydrogen bonds. The binding energies of the studied complexes are in the range of -21.6~-60.4 kJ/mol. The X∙∙∙Y distances are significantly smaller than the sum of the van der Waals radii of the corresponding two atoms. The X∙∙∙Y ChBs in all the studied complexes except for the SO2∙∙∙CH3OCH3 complex are strong in strength and display a partial covalent character revealed by conducting the quantum theory of atoms in molecules (QTAIM), a non-covalent interaction plot (NCIplot), and natural bond orbital (NBO) analyses. The symmetry-adapted perturbation theory (SAPT) analysis discloses that the X∙∙∙Y ChBs are primarily dominated by the electrostatic component.

Hydrogen Bonds Stabilize Chloroselenite Anions: Crystal Structure of a New Salt and Donor-Acceptor Bonding to SeO2

The single-crystal X-ray diffraction structure characterizing a new 4-methylbenzamidinium salt of chloroselenite [C8H11N2][ClSeO2] is reported. This is only the second crystal structure report on a ClSeO2- salt. The structure contains an extended planar hydrogen bond net, including a double interaction with both O atoms of the anion (an R228 ring in Etter notation). The anion has the shortest Se-Cl distances on record for any chloroselenite ion, 2.3202(9) Å. However, the two Se-O distances are distinct at 1.629(2) and 1.645(2) Å, attributed to weak anion-anion bridging involving the oxygen with the longer bond. DFT computations at the RB3PW91-D3/aug-CC-pVTZ level of theory reproduce the short Se-Cl distance in a gas-phase optimized ion pair, but free optimization of ClSeO2- leads to an elongation of this bond. A good match to a known value for [Me4N][ClSeO2] is found, which fits to the Raman spectroscopic evidence for this long-known salt and to data measured on solutions of the anion in CH3CN. The assignment of the experimental Raman spectrum was corrected by means of the DFT-computed vibrational spectrum, confirming the strong mixing of the symmetry coordinate of the Se-Cl stretch with both ν2 and ν4 modes.

Synthesis, X-ray characterization and DFT analysis of dicyanidoaurate telluronium salts: on the importance of charge assisted chalcogen bonds

In this manuscript we report the synthesis and X-ray characterization of two cyanidoaurate telluronium salts, namely (3-fluorophenyl)(methyl)(phenyl)telluronium dicyanidoaurate [(3-F-Ph)(Me)(Ph)Te][Au(CN)2] (1) and methyldiphenyltelluronium dicyanidoaurate [(Me)(Ph)2Te][Au(CN)2] (2). In the solid state, the tellurium atom establishes three concurrent and directional chalcogen bonds (ChBs) with the adjacent anions, in both compounds. These charge-assisted ChBs (CAChBs) have been analyzed using DFT calculations and several computational tools. The MEP surface analysis discloses the existence of three σ-holes at the Te-atoms capable of establishing strong CAChBs with the counter-ions. In addition, significant charge transfer from the lone pair orbital at the N-atom of the anion to the antibonding σ*(Te-C) orbital of the cation is observed in some cases.

The Ambiguous Origin of Thermochromism in Molecular Crystals of Dichalcogenides: Chalcogen Bonds versus Dynamic Se-Se/Te-Te Bonds

We report thermochromism in crystals of diphenyl diselenide (dpdSe) and diphenyl ditelluride (dpdTe), which is at variance with the commonly known mechanisms of thermochromism in molecular crystals. Variable temperature neutron diffraction studies indicated no conformational change, tautomerization or phase transition between 100 K and 295 K. High-pressure crystallography studies indicated no associated piezochromism in dpdSe and dpdTe crystals. The evolution of the crystal structures and their electronic band structure with pressure and temperature reveal the contributions of intramolecular and intermolecular factors towards the origin of thermochromism-especially the intermolecular Se⋅⋅⋅Se and Te⋅⋅⋅Te chalcogen bonds and torsional modes of vibrations around the dynamic Se-Se and Te-Te bonds. Further, a co-crystal of dpdSe with iodine (dpdSe-I2 ) and an alloy crystal of dpdSe and dpdTe implied a predominantly intramolecular origin of the observed thermochromism associated with vibronic coupling.

Elucidating mechanochemical reactivity of a ternary halogen-bonded cocrystal system by computational and calorimetric studies

Discovery of a halogen-bonded ternary cocrystal of 1,3,5-trifluoro-2,4,6-triiodobenzene with pyrazine and triphenylphosphine sulfide has revealed a complex landscape of multicomponent phases, all achievable by mechanochemical interconversion. The observed solid-state reaction pathways were explained by periodic density-functional calculations and comprehensive intermolecular interaction analysis, supported by dissolution calorimetry measurements.

Halide Complexes of 5,6-Dicyano-2,1,3-Benzoselenadiazole with 1 : 4 Stoichiometry: Cooperativity between Chalcogen and Hydrogen Bonding

The [M4 -Hal]- (M=the title compound; Hal=Cl, Br, and I) complexes were isolated in the form of salts of [Et4 N]+ cation and characterized by XRD, NMR, UV-Vis, DFT, QTAIM, EDD, and EDA. Their stoichiometry is caused by a cooperative interplay of σ-hole-driven chalcogen (ChB) and hydrogen (HB) bondings. In the crystal, [M4 -Hal]- are connected by the π-hole-driven ChB; overall, each [Hal]- is six-coordinated. In the ChB, the electrostatic interaction dominates over orbital and dispersion interactions. In UV-Vis spectra of the M+[Hal]- solutions, ChB-typical and [Hal]- -dependent charge-transfer bands are present; they reflect orbital interactions and allow identification of the individual [Hal]- . However, the structural situation in the solutions is not entirely clear. Particularly, the UV-Vis spectra of the solutions are different from the solid-state spectra of the [Et4 N]+ [M4 -Hal]- ; very tentatively, species in the solutions are assigned [M-Hal]- . It is supposed that the formation of the [M4 -Hal]- proceeds during the crystallization of the [Et4 N]+ [M4 -Hal]- . Overall, M can be considered as a chromogenic receptor and prototype sensor of [Hal]- . The findings are also useful for crystal engineering and supramolecular chemistry.

Gold(III) derivatives as the noncovalent interaction donors: theoretical study of the π-hole regium bonds

Except for the well-known σ-hole regium bonds formed by metal nanoparticles and M(I) (M = Cu, Ag, and Au) derivatives, the existence of π-hole regions located above and below the Au atom in gold(III) derivatives suggests that gold(III) also functions as an efficient electrophilic site. In this study, a comprehensive analysis was conducted on the electrophilicity of trichloro-(p-toluonitrilo-N)-gold(III) derivatives AuL3(NCC6H4X) (L = Cl, Br, CN; X = NH2, CH3, CF3, NC, and CN) and the nature of π-hole regium bonds in the AuL3(NCC6H4X)⋯LB (LB = NH3, N(NH3)3, CH2O, C2H2, C2H4, C6H6) and (AuCl3(NCC6H4Y))n (Y = Cl, CN, NC, NO2; n = 2, 3)) complexes. The characteristics of the π-hole regium bonds were studied with respect to the influence of ligands and substituents, the strength of intermolecular interactions between Au(III) derivatives and Lewis bases, and those in the polymers. In the case of the AuL3(NCC6H4X)⋯NH3 complexes, the strength of the regium bonds increases gradually in the order of L = Cl < Br < CN and X = NH2 < CH3 < CF3 ≈ NC < CN. The ligands (L) attached to the Au atom exert a significant effect on the strength of the π-hole regium bonds in comparison to the substituents (X) on the benzene ring. The regium bonds are primarily dominated by electrostatic interaction, accompanied by moderate contribution from polarization. Linear relationships were identified between the electrostatic energies and the local most positive potentials over the Au atom, as well as between the polarization energies and the amount of charge transfer. Most of the π-hole regium bonds in the AuL3(NCC6H4X)⋯LB complexes exhibit the characters of closed shell noncovalent interactions. In the polymers (AuCl3(NCC6H4Y))n, weak face-to-face π-π stacking interactions are also present, in addition to regium bonds. The trimers displayed a slightly negative cooperativity in comparison to the dimers.

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.

Chalcogen Bonding Catalysis: Tellurium, the Last Frontier?

Chalcogen bonding (ChB) is the non-covalent interaction occurring between chalcogen atoms as Lewis acid sites and atoms or groups of atoms able to behave as Lewis bases through their lone pair or π electrons. Analogously to its sister halogen bonding, the high directionality of this interaction was implemented for precise structural organizations in the solid state and in solution. Regarding catalysis, ChB is now accepted as a new mode of activation as demonstrated by the increased number of examples in the last five years. In the family of ChB catalysts, those based on tellurium rapidly appeared to overcome their lighter sulfur and selenium counterparts. In this review, we highlight the Lewis acid properties of tellurium-based derivatives in solution and summarize the start-of-the-art of their applications in catalysis.

Fluorogenic In Situ Thioacetalization: Expanding the Chemical Space of Fluorescent Probes, Including Unorthodox, Bifurcated, and Mechanosensitive Chalcogen Bonds

Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ. Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds.

Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding

Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.

Ligand and Substituent Effect on Regium-π Bonding in Cu and Ag π-Conjugated Complexes: A Density Functional Study

Density functional theory investigation of regium (Rg)-π bonding using the RgL-X model system, where Rg = Cu and Ag; L = CN, NO2, and OH; X = π-conjugated system (benzene, cyanobenzene, benzoic acid, pyridine, 2-methoxy aniline, 1,4-dimethoxy benzene, and cyclophane), has been performed. Conclusive evidence of the Rg-π bond has been provided by analysis of molecular electrostatic potential surfaces, Rg-π bond length, interaction energy (ΔE), second-order perturbation energy (E2), charge transfer (Δq), quantum theory of atom in molecules, and noncovalent interaction plots for 42 structural arrangements with varying ligands and the substituted aromatic ring. The Rg-π bond length in the optimized model systems varies from 2.03 to 2.12 Å in Cu complexes (1-21) and from 2.26 to 2.38 Å in Ag complexes (22-42) at the PBE0-D3 functional. While the ligand (L) attached to the Rg metal has a bargaining effect on the strength of the Rg-π bond (in the order of -OH > -CN = -NO2), the π-conjugated systems have a diminutive effect. Two X-ray crystal structures (CUCSOI and AHIDQU) having the Rg-π bond, accessed from Cambridge Crystallographic Data Centre (CCDC), are discussed here to signify the influence of Rg-π bonding on the crystal structure.

Automated identification of chalcogen bonds in AlphaFold protein structure database files: is it possible?

Protein structure prediction and structural biology have entered a new era with an artificial intelligence-based approach encoded in the AlphaFold2 and the analogous RoseTTAfold methods. More than 200 million structures have been predicted by AlphaFold2 from their primary sequences and the models as well as the approach itself have naturally been examined from different points of view by experimentalists and bioinformaticians. Here, we assessed the degree to which these computational models can provide information on subtle structural details with potential implications for diverse applications in protein engineering and chemical biology and focused the attention on chalcogen bonds formed by disulphide bridges. We found that only 43% of the chalcogen bonds observed in the experimental structures are present in the computational models, suggesting that the accuracy of the computational models is, in the majority of the cases, insufficient to allow the detection of chalcogen bonds, according to the usual stereochemical criteria. High-resolution experimentally derived structures are therefore still necessary when the structure must be investigated in depth based on fine structural aspects.