Unusually Short Chalcogen Bonds Involving Organoselenium: Insights into the Se–N Bond Cleavage Mechanism of the Antioxidant Ebselen and Analogues

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se???O chalcogen bonds that lead to conserved supramolecular recognition units. Se???O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se???O chalcogen bonds were explored using high‐resolution X‐ray charge density analysis and atons‐in‐molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se???O chalcogen bonding and soft‐metal‐like behavior of organoselenium. An analysis of the charge density around Se?N and Se?C covalent bonds in conjunction with the Se???O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se???O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS).     

Enantio‐ and Diastereoselective Formal Hetero‐Diels–Alder Reactions of Trifluoromethylated Enones Catalyzed by Chiral Primary Amines

Enantioselective formal hetero‐Diels‐Alder reactions of trifluoromethylated enones and 2‐amino‐1,3‐butadienes generated in situ from aliphatic acyclic enones and chiral primary amines are reported. The corresponding tetrahydropyran‐4‐ones are formed in up to 94 % yield and with up to 94 % ee. The reaction was carried out through a stepwise mechanism, including initial aminocatalytic aldol condensation of 2‐amino‐1,3‐butadiene to the trifluoromethylated carbonyl group followed by an intramolecular oxa‐Michael addition. Both NMR investigation and theoretical calculations on the transition state indicate that the protonated tertiary amine could effectively activate the carbonyl group of the trifluoromethyl ketone to promote the addition process through hydrogen‐bonding interaction of N?H???F and N?H???O simultaneously, and thus provide a chiral environment for the approach of amino‐1,3‐butadienes to the activated trifluoromethyl ketone, resulting in high enantioselectivity.     

Synthetic and Structural Studies of 1,8‐Chalcogen Naphthalene Derivatives

Four novel 1,8‐disubstituted naphthalene derivatives 4 – 7 that contain chalcogen atoms occupying the peri positions have been prepared and fully characterised by using X‐ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular distortion due to noncovalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X‐ray data for 4 – 7 was compared to the series of known 1,8‐bis(phenylchalcogeno)naphthalenes 1 – 3 , which were themselves prepared from novel synthetic routes. A general increase in the E???E′ distance was observed for molecules containing bulkier atoms at the peri positions. The decreased S???S distance from phenyl‐ 1 and ethyl‐ 4 analogues is ascribed to a weaker chalcogen lone pair–lone pair repulsion acting in the ethyl analogue due to the presence of two equatorial S(naphthyl) ring conformations. Two novel peri‐substituted naphthalene sulfoxides of 1 , Nap(O?SPh)(SPh) 8 and Nap(O?SPh)₂ 9 , which contain different valence states of sulfur, were prepared and fully characterised by using X‐ray crystallography and multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular structures were analysed by using naphthalene ring torsions, peri‐atom displacement, splay angle magnitude, S???S interactions, aromatic ring orientations and quasi‐linear O?S???S arrangements. The axial S(naphthyl) rings in 8 and 9 are unfavourable for S???S contacts due to stronger chalcogen lone pair–lone pair repulsion. Although quasi‐linear O?S???S alignments suggest attractive interaction is conceivable, analysis of the B3LYP wavefunctions affords no evidence for direct bonding interactions between the S atoms.     

The Importance of 1,5‐Oxygen⋅⋅⋅Chalcogen Interactions in Enantioselective Isochalcogenourea Catalysis

The importance of 1,5‐O???chalcogen (Ch) interactions in isochalcogenourea catalysis (Ch=O, S, Se) is investigated. Conformational analyses of N‐acyl isochalcogenouronium species and comparison with kinetic data demonstrate the significance of 1,5‐O???Ch interactions in enantioselective catalysis. Importantly, the selenium analogue demonstrates enhanced rate and selectivity profiles across a range of reaction processes including nitronate conjugate addition and formal [4+2] cycloadditions. A gram‐scale synthesis of the most active selenium analogue was developed using a previously unreported seleno‐Hugerschoff reaction, allowing the challenging kinetic resolutions of tertiary alcohols to be performed at 500 ppm catalyst loading. Density functional theory (DFT) and natural bond orbital (NBO) calculations support the role of orbital delocalization (occurring by intramolecular chalcogen bonding) in determining the conformation, equilibrium population, and reactivity of N‐acylated intermediates.     

Structural Diversity of Copper(I)–N‐Heterocyclic Carbene Complexes; Ligand Tuning Facilitates Isolation of the First Structurally Characterised Copper(I)–NHC Containing a Copper(I)–Alkene Interaction

The preparation of a series of imidazolium salts bearing N‐allyl substituents, and a range of substituents on the second nitrogen atom that have varying electronic and steric properties, is reported. The ligands have been coordinated to a copper(I) centre and the resulting copper(I)–NHC (NHC=N‐heterocyclic carbene) complexes have been thoroughly examined, both in solution and in the solid‐state. The solid‐state structures are highly diverse and exhibit a range of unusual geometries and cuprophilic interactions. The first structurally characterised copper(I)–NHC complex containing a copper(I)–alkene interaction is reported. An N‐pyridyl substituent, which forms a dative bond with the copper(I) centre, stabilises an interaction between the metal centre and the allyl substituent of a neighbouring ligand, to form a 1D coordination polymer. The stabilisation is attributed to the pyridyl substituent increasing the electron density at the copper(I) centre, and thus enhancing the metal(d)‐to‐alkene(π*) back‐bonding. In addition, components other than charge transfer appear to have a role in copper(I)–alkene stabilisation because further increases in the Lewis basicity of the ligand disfavours copper(I)–alkene binding.     

α‐Halogenoacetanilides as Hydrogen‐Bonding Organocatalysts that Activate Carbonyl Bonds: Fluorine versus Chlorine and Bromine

α‐Halogenoacetanilides (X=F, Cl, Br) were examined as H‐bonding organocatalysts designed for the double activation of C?O bonds through NH and CH donor groups. Depending on the halide substituents, the double H‐bond involved a nonconventional C?H???O interaction with either a H?CX_n (n=1–2, X=Cl, Br) or a H?C_Ar bond (X=F), as shown in the solid‐state crystal structures and by molecular modeling. In addition, the catalytic properties of α‐halogenoacetanilides were evaluated in the ring‐opening polymerization of lactide, in the presence of a tertiary amine as cocatalyst. The α‐dichloro‐ and α‐dibromoacetanilides containing electron‐deficient aromatic groups afforded the most attractive double H‐bonding properties towards C?O bonds, with a N?H???O???H?CX₂ interaction.     

Sterically Crowded peri‐Substituted Naphthalene Phosphines and their PV Derivatives

Three sterically crowded peri‐substituted naphthalene phosphines, Nap[PPh₂][ER] (Nap=naphthalene‐1,8‐diyl; ER=SEt, SPh, SePh) 1–3 , which contain phosphorus and chalcogen functional groups at the peri positions have been prepared. Each phosphine reacts to form a complete series of P^V chalcogenides Nap[P(E′)(Ph₂)(ER)] (E′=O, S, Se). The novel compounds were fully characterised by using X‐ray crystallography and multinuclear NMR spectroscopy, IR spectroscopy and MS. X‐ray data for 1 , 2 , n O , n S , n Se (n=1–3) are compared. Eleven molecular structures have been analysed by naphthalene ring torsions, peri‐atom displacement, splay angle magnitude, X???E interactions, aromatic ring orientations and quasi‐linear arrangements. An increase in the congestion of the peri region following the introduction of heavy chalcogen atoms is accompanied by a general increase in naphthalene distortion. P???E distances increase for molecules that contain bulkier atoms at the peri positions and also when larger chalcogen atoms are bound to phosphorus. The chalcogenides adopt similar conformations that contain a quasi‐linear E???P? C fragment, except for 3 O , which displays a twist‐axial‐twist conformation resulting in the formation of a linear O???Se? C alignment. Ab initio MO calculations performed on 2 O , 3 O , 3 S and 3 Se reveal Wiberg bond index values of 0.02 to 0.04, which indicates only minor non‐bonded interactions; however, calculations on radical cations of 3 O , 3 S and 3 Se reveal increased values (0.14–0.19).     

Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S,Se; X = H,Cl, Br,CCH, NC,OH, OCH3): Influence of substitution and cooperativity

MP2/aug‐cc‐pVTZ calculations are performed on complexes of YO₃ (Y = S, Se) with a series of electron‐donating chalcogen bases YHX (X = H, Cl, Br, CCH, NC, OH, OCH₃). These complexes are formed through the interaction of a positive electrostatic potential region (π‐hole) on the YO₃ molecule with the negative region in YHX. Interaction energies of the binary O₃Y???YHX complexes are in the range of ?4.37 to ?12.09 kcal/mol. The quantum theory of atoms in molecules and the natural bond orbital analysis were applied to characterize the nature of interactions. It was found that the formation and stability of these binary complexes are ruled mainly by electrostatic effects, although the electron charge transfer from YHX to YO₃ unit also seems to play an important role. In addition, mutual influence between the Y???N and Y???Y interactions is studied in the ternary HCN???O₃Y???YHX complexes. The results indicate that the formation of a Y???N interaction tends to weaken Y???Y bond in the ternary systems. Although the Y???Y interaction is weaker than the Y???N one, however, both types of interactions seem to compete with each other in the HCN???O₃Y???YHX complexes. © 2016 Wiley Periodicals, Inc.     

Micro‐ and Nanometer‐Scale Porous,Fibrous, and Sheet Architectures Constructed by Supramolecular Assemblies of Dipyrrolyldiketones

X‐ray analysis of some 1,3‐dipyrrolyl‐1,3‐propanediones synthesized from pyrroles and malonyl chloride derivatives revealed 1D supramolecular networks formed by N? H???O?C interactions in the solid state. Micro‐ and nanometer‐scale morphologies of porous, fibrous, and sheet structures were fabricated by hydrogen‐bonding interactions and determined by fine‐tuning the substituents and the solvents used. Of the unique polymorphs, ordered 2D lamellar sheet structures of the derivatives with long alkyl chains (C₁₆H₃₃, C₁₄H₂₉, and so on) were constructed by van der Waals hydrophobic effects between aliphatic chains as well as hydrogen bonding.     

The Carbonyl⋅⋅⋅Tellurazole Chalcogen Bond as a Molecular Recognition Unit: From Model Studies to Supramolecular Organic Frameworks

In the last years, chalcogen bonding, the noncovalent interaction involving chalcogen centers, has emerged as interesting alternative to the ubiquitous hydrogen bonding in many research areas. Here, we could show by means of high‐level quantum chemical calculations that the carbonyl???tellurazole chalcogen bond is at least as strong as conventional hydrogen bonds. Using the carbonyl???tellurazole binding motif, we were able to design complex supramolecular networks in solid phase starting from tellurazole‐substituted cyclic peptides. X‐ray analyses reveal that the rigid structure of the cyclic peptides is caused by hydrogen bonds, whereas the supramolecular network is held together by chalcogen bonding. The type of the supramolecular network depends on peptide used; both linear wires and a honeycomb‐like supramolecular organic framework (SOF) were observed. The unique structure of the SOF shows two channels filled with different types of solvent mixtures that are either locked or freely movable.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.     

Synthetic and Structural Studies of 1‐Halo‐8‐(alkylchalcogeno)naphthalene Derivatives

A series of eight 1‐halo‐8‐(alkylchalcogeno)naphthalene derivatives ( 1 – 8 ; halogen=Br, I; alkylchalcogen=SEt, SPh, SePh, TePh) containing a halogen and a chalcogen atom occupying the peri positions have been prepared and fully characterised by using X‐ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Naphthalene distortion due to non‐covalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X‐ray data for 1 , 2 , 4 and 5 – 8 were compared. Molecular structures were analysed in terms of naphthalene ring torsions, peri‐atom displacement, splay angle magnitude, X???E interactions, aromatic ring orientations and quasi‐linear X???E? C arrangements. A general increase in the X???E distance was observed for molecules that contain bulkier atoms at the peri positions. The I???S distance of 4 is comparable with the I???Te distance of 8 , and is ascribed to a stronger lone pair–lone pair repulsion due to the presence of an axial S(naphthyl) ring conformation. Density functional theory (B3LYP) calculations performed on 5 – 8 revealed Wiberg bond index values of 0.05–0.08, which indicate minor interactions taking place between the non‐bonded atoms in these compounds.     

Color Polymorphism: Understanding the Diverse Solid‐State Packing and Color in Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate

Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular O?H???O and O?H???Cl hydrogen bonds. Time‐dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid‐state dispersion‐corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum‐energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two ?OH groups through a hybrid intermediate having one intramolecular O?H???O and one O?H???Cl bond. The LY form is shown to exist on the higher‐energy pathway involving a concerted Y→W transformation.     

Copper‐Mediated C6‐Selective Dehydrogenative Heteroarylation of 2‐Pyridones with 1,3‐Azoles

A copper‐mediated C6‐selective dehydrogenative heteroarylation of 2‐pyridones with 1,3‐azoles has been developed. The reaction proceeded smoothly by twofold C? H cleavage even in the absence of noble‐metal catalysts. The observed site selectivity was directed by a pyridyl substituent on the nitrogen atom of the pyridone ring. This directing group was readily removed after the coupling event, thus leading to 2‐pyridone derivatives with a free N? H group. Moreover, in some cases, catalytic turnover of the Cu salt was also possible with the ideal terminal oxidant: molecular oxygen in air.     

Chloride‐Anion‐Templated Synthesis of a Strapped‐Porphyrin‐Containing Catenane Host System

The synthesis, structure and anion‐recognition properties of a new strapped‐porphyrin‐containing [2]catenane anion host system are described. The assembly of the catenane is directed by discrete chloride anion templation acting in synergy with secondary aromatic donor–acceptor and coordinative pyridine–zinc interactions. The [2]catenane incorporates a three‐dimensional, hydrogen‐bond‐donating anion‐binding pocket; solid‐state structural analysis of the catenane?chloride complex reveals that the chloride anion is encapsulated within the catenane’s interlocked binding cavity through six convergent CH????Cl and NH???Cl hydrogen‐bonding interactions and solution‐phase ¹H NMR titration experiments demonstrate that this complementary hydrogen‐bonding arrangement facilitates the selective recognition of chloride over larger halide anions in DMSO solution.     

Chalcogenide Derivatives of the seco‐Cubane [Sn3(μ2‐NHtBu)2(μ2‐NtBu)(μ3‐NtBu)]

A series of monochalcogenide derivatives of the seco‐cubane [Sn₃(μ₂‐NHtBu)₂(μ₂‐NtBu)(μ₃‐NtBu)] has been prepared and characterized by NMR and X‐ray crystallographic studies. These complexes exhibit different tin‐chalcogen bonding modes. In the case of the monotelluride, a terminal Sn=Te bond was observed in solution and in the solid state, whereas for the monosulfide, a μ₂ bridging mode was adopted by the sulfur atoms. The monoselenide was found to employ both bonding modes in solution, although only the terminal Sn=Se bonding mode was structurally characterized. The complexes undergo chalcogen exchange between tin atoms in solution, and this process was studied by variable temperature NMR.     

Chalcogen Bond Mediated Enhancement of Cooperative Ion‐Pair Recognition

A series of heteroditopic receptors containing halogen bond (XB) and unprecedented chalcogen bond (ChB) donors integrated into a 3,5‐bis‐triazole pyridine structure covalently linked to benzo‐15‐crown‐5 ether motifs exhibit remarkable cooperative recognition of halide anions. Multi‐nuclear ¹H, ¹³C, ¹²⁵Te and ¹⁹F NMR, ion pair binding investigations reveal sodium cation–benzo‐crown ether binding dramatically enhances the recognition of bromide and iodide halide anions, with the chalcogen bonding heteroditopic receptor notably displaying the largest enhancement of halide binding strength of over two hundred‐fold, in comparison to the halogen bonding and hydrogen bonding heteroditopic receptor analogues. DFT calculations suggest crown ether sodium cation complexation induces a polarisation of the sigma hole of ChB and XB heteroditopic receptor donors as a significant contribution to the origin of the unique cooperativity exhibited by these systems.     

Walking Down the Chalcogenic Group of the Periodic Table: From Singlet to Triplet Organic Emitters

The synthesis, X‐ray crystal structures, ground‐ and excited‐state UV/Vis absorption spectra, and luminescence properties of chalcogen‐doped organic emitters equipped on both extremities with benzoxa‐, benzothia‐, benzoselena‐ and benzotellurazole ( 1_X and 2_X ) moieties have been reported for the first time. The insertion of the four different chalcogen atoms within the same molecular skeleton enables the investigation of only the chalcogenic effect on the organisation and photophysical properties of the material. Detailed crystal‐structure analyses provide evidence of similar packing for 2_O – 2_Se , in which the benzoazoles are engaged in π–π stacking and, for the heavier atoms, in secondary X???X and X???N bonding interactions. Detailed computational analysis shows that the arrangement is essentially governed by the interplay of van der Waals and secondary bonding interactions. Progressive quenching of the fluorescence and concomitant onset of phosphorescence features with gradually shorter lifetimes are detected as the atomic weight of the chalcogen heteroatom increases, with the tellurium‐doped derivatives exhibiting only emission from the lowest triplet excited state. Notably, the phosphorescence spectra of the selenium and tellurium derivatives can be recorded even at room temperature; this is a very rare finding for fully organic emitters.     

N‐Heterocyclic Carbene (NHC)‐Stabilized Silanechalcogenones: NHC→Si(R2)E (E=O,S, Se,Te)

A series of N‐heterocyclic carbene‐stabilized silanechalcogenones 2 a , b (Si?O), 3 a , b (Si?S), 4 a , b (Si?Se), and 5 a , b (Si?Te) are described. The silanone complexes 2 a , b were prepared by facile oxygenation of the carbene–silylene adducts 1 a , b with N₂O, whereas their heavier congeners were synthesized by gentle chalcogenation of 1 a , b with equimolar amounts of elemental sulfur, selenium, and tellurium, respectively. These novel compounds have been isolated in a crystalline form in high yields and have been fully characterized by a variety of techniques including IR spectroscopy, ESIMS, and multinuclear NMR spectroscopy. The structures of 2 b , 3 a , 4 a , 4 b , and 5 b have been confirmed by single‐crystal X‐ray crystallography. Due to the NHC→Si donor–acceptor electronic interaction, the Si?E (E=O, S, Se, Te) moieties within these compounds are well stabilized and thus the compounds possess several ylide‐like resonance structures. Nevertheless, these species also exhibit considerable Si?E double‐bond character, presumably through a nonclassical Si?E π‐bonding interaction between the chalcogen lone‐pair electrons and two antibonding Si? N σ* orbitals, as evidenced by their high stretching vibration modes and the shortening of the Si–E distances (between 5.4 and 6.3 %) compared with the corresponding Si? E single‐bond lengths.     

Solid‐State Form Screen of Cardiosulfa and Its Analogues

Cardiosulfa is a biologically active sulfonamide molecule that was recently shown to induce abnormal heart development in zebrafish embryos through activation of the aryl hydrocarbon receptor (AhR). The present report is a systematic study of solid‐state forms of cardiosulfa and its biologically active analogues that belong to the N‐(9‐ethyl‐9H‐carbazol‐3‐yl)benzene sulfonamide skeleton. Cardiosulfa (molecule 1 ; R¹=NO₂, R²=H, R³=CF₃), molecule 2 (H, H, CF₃), molecule 3 (CF₃, H, H), molecule 4 (NO₂, H, H), molecule 5 (H, CF₃, H), and molecule 6 (H, H, H) were synthesized and subjected to a polymorph search and solid‐state form characterization by X‐ray diffraction, differential scanning calorimetry (DSC), variable‐temperature powder X‐ray diffraction (VT‐PXRD), FTIR, and solid‐state (ss) NMR spectroscopy. Molecule 1 was obtained in a single‐crystalline modification that is sustained by N? H???π and C? H???O interactions but devoid of strong intermolecular N? H???O hydrogen bonds. Molecule 2 displayed a N? H???O catemer C(4) chain in form I, whereas a second polymorph was characterized by PXRD. The dimorphs of molecule 3 contain N? H???π and C? H???O interactions but no N? H???O bonds. Molecule 4 is trimorphic with N? H???O catemer in form I, and N? H???π and C? H???O interactions in form II, and a third polymorph was characterized by PXRD. Both polymorphs of molecule 5 contain the N? H???O catemer C(4) chain, whereas the sulfonamide N? H???O dimer synthon R₂²(8) was observed in polymorphs of 6 . Differences in the strong and weak hydrogen‐bond motifs were correlated with the substituent groups, and the solubility and dissolution rates were correlated with the conformation in the crystal structure of 1 , 2 , 3 , 4 , 5 , 6 . Higher solubility compounds, such as 2 (10.5 mg mL^?1) and 5 (4.4 mg mL^?1), adopt a twisted confirmation, whereas less‐soluble 1 (0.9 mg mL^?1) is nearly planar. This study provides practical guides for functional‐group modification of drug lead compounds for solubility optimization.