Chalcogen Bonds Research Articles

Charge-assisted chalcogen bonding in 2-(4-substituted benzoyl)thiazolo[3,2-a]pyridin-4-ium bromides

A series of 2-(4-substituted benzoyl)thiazolo[3,2-a]pyridin-4-ium bromides [−OCH3 (1), –H (2), –F (3), −Cl (4)] was obtained by the heterocyclization reaction of the corresponding 2-bromo-1-(4-substituted phenyl)-3,3-diethoxypropan-1-ones with pyridine-2-thiol in dry isopropyl alcohol under reflux for 2 h. The new compounds 1–4 were characterized by elemental analysis, 1H and 13C NMR spectroscopy and single crystal X-ray diffraction. Both the negative charge-assisted (S⋯Br−) and normal (S···π) chalcogen bonds were found in the crystal packing of 2−4, whereas one of the hydrogen atoms of an electron-donating –OCH3 group in 1, behaves as a bifurcated hydrogen bond donor centre towards a sulfur atom of the thiazolo ring and an oxygen atom of CO group of a neighboring molecule leading to the intermolecular hydrogen bonds. The optical properties of 1−4 in DMSO, DMF and MeOH were investigated by UV–vis absorption spectroscopy, with λmax being dependent on the solvent polarity and attached substituents (−OCH3, –H, –F, −Cl) at the para-position of the aromatic moiety.

Acid-Base and Anion Binding Properties of Tetrafluorinated 1,3-Benzodiazole, 1,2,3-Benzotriazole and 2,1,3-Benzoselenadiazole.

The influence of fluorination on the acid-base properties and the capacity of structurally related 6-5 bicyclic compounds - 1,3-benzodiazole 1, 1,2,3-benzotriazole 2 and 2,1,3-benzoselenadiazole 3 to σ-hole interactions, i. e. hydrogen (1 and 2) and chalcogen (3) bondings, is studied experimentally and computationally. The tetrafluorination increases the Brønsted acidity of the diazole and triazole scaffolds and the Lewis acidity of selenadiazole scaffold decreases the basicity. Increased Brønsted acidity facilitates anion binding via the formation of hydrogen bonds; particularly, tetrafluorinated derivative of 1 (compound 4) binds Cl- . Increased Lewis acidity of tetrafluorinated derivative of 3 (compound 10), however, is not enough for binding with Cl- and F- via chalcogen bonds in contrast to previously studied Te analog of 10. It is suggested that the maximum positive values of molecular electrostatic potential at the σ-holes, VS,max , can be a reasonable metric for design and synthesis of new anion receptors with selenadiazole-diazole/triazole hybrids as a special target. Related chlorinated compounds are also discussed.

A highly active and selective chalcogen bond-mediated perchlorate channel

Artificial membrane transporters that either use chalcogen bonds to facilitate transmembrane flux of anions or show high selectivity toward perchlorate anions are rare. In this work, we report on one such novel monopeptide-based transporter system, featuring both chalcogen bonds for highly efficient anion transport and high transport selectivity toward ClO4− anions. Structurally, these monopeptide molecules associate with each other via H-bonds to produce H-bonded 1D stack that not only one dimensionally but also directionally aligns the terminal bicyclic thiophene motifs to the same side. Functionally, these well-aligned thiophenes create a sulfur-rich transmembrane pathway, combinatorially fine-tunable to enable anions to efficiently cross the membrane in the increasing activity of Cl− < Br− < NO3− < ClO4−via chalcogen bonds, with EC50 values of 0.75, 0.40, 0.37 and 0.093 µmol/L (0.3 mol% relative to lipid molecules), respectively.

Bis-selenonium Cations as Bidentate Chalcogen Bond Donors in Catalysis

Bis-selenonium Cations as Bidentate Chalcogen Bond Donors in Catalysis

2Ch-2N Square Chalcogen Bonds between Pairs of Radicals: A Case Study of 1,2,3,5-Dichalcogenadiazolyl Derivatives.

Specific 2Ch-2N square interactions between pairs of heterocyclic rings have been the target of many recent crystallographic and computational studies. According to our search of the Cambridge Structural Database (CSD), a number of crystal structures of the derivatives of 1,2,3,5-dichalcogenadiazolyl (DChDA) radicals, which consist of 2Ch-2N square motifs in the dimer units, were extracted. On the basis of the CSD survey results, a set of dimeric complexes of DChDA-based radicals with diverse aryl substituents at the 4-position were selected to model such squares. Similar to that in conventional chalcogen bonds, 2Ch-2N square interactions become stronger as the atomic size of chalcogens increases. Both the orbital term and electrostatics contribute significantly to the attraction of these interactions, while the dispersion contribution is small but unneglectable. Some five-membered aryl substituents, such as imidazole, thiazole, and oxazole, produce markedly enhanced square interactions, leading to a pronounced influence on the distribution of spin populations on DChDA rings.

Metal-Involving Chalcogen Bond. The Case of Platinum(II) Interaction with Se/Te-Based σ-Hole Donors.

Platinum(II) complexes exhibiting an expressed dz2-nucleophilicity of the positively charged metal centers, namely, [Pt(ppy)(acac)] (1; acacH is acetylacetone; ppyH is 2-Ph-pyridine) and [Pt(ppy)(tmhd)] (2; tmhdH is 2,2,6,6-tetramethylheptanedione-3,5), were cocrystallized with the chalcogen bond donors (4-NC5F4)2Ch (Ch = Se, Te) to form two isostructural cocrystals 1·1/2(4-NC5F4)2Ch, and 2·2/3(4-NC5F4)2Se and 2·(4-NC5F4)2Te. The X-ray data for these cocrystals and appropriate theoretical DFT calculations (PBE0-D3BJ) allowed the recognition of the metal-involving chalcogen bond, namely, Ch···dz2-PtII (its energy spans from -7 to -12 kcal/mol). In 1·1/2(4-NC5F4)2Ch, Ch···dz2-PtII bonding is accompanied by the C···dz2-PtII interaction, representing a three-center bifurcate, whereas in 2·(4-NC5F4)2Te the chalcogen bond Te···dz2-PtII is purely two-centered and is stronger than that in 1·1/2(4-NC5F4)2Ch because of more efficient orbital overlap. The association of 2 with (4-NC5F4)2Te and the structure of the formed adduct in CDCl3 solutions was studied by using 1H, 13C, 19F, 195Pt, 125Te NMR, 19F-1H HOESY, and diffusion NMR methods. The 195Pt and 125Te NMR titration and the isothermal titration calorimetry results revealed a 1:1 association of 2 with (4-NC5F4)2Te.

Noncovalent Interactions at Lanthanide Complexes.

Lanthanide complexes have attracted a widespread attention due to their structural diversity, as well as multifunctional and tunable properties. The development of lanthanide based functional materials has often relied on the design of the secondary coordination sphere of the corresponding lanthanide complexes. For instance, usually simple lanthanide salts (solvento complexes) do not catalyze effectively organic reactions or provide low yield of the expected product, whereas the presence of a suitable organic ligand with a noncovalent bond donor or acceptor centre (secondary coordination sphere) modifies the symmetry around the metal centre in lanthanide complexes which then successfully can act as catalysts in both homogenous and heterogenous catalysis. In this minireview, we discuss several relevant examples, based on X-ray crystal structure analyses, in which the hydrogen, halogen, chalcogen, pnictogen, tetrel and rare-earth bonds, as well as cation-π, anion-π, lone pair-π, π-π and pancake interactions, are used as a synthon in the decoration of the secondary coordination sphere of lanthanide complexes.

Electronic structure, stability, and cooperativity of chalcogen bonding in sulfur dioxide and hydrated sulfur dioxide clusters: a DFT study and wave functional analysis

Density functional theory calculations and wave functional analysis are used to examine the (SO2)n and (SO2)n–H2O clusters with n = 1–7. The nature of interactions is explored by molecular electrostatic potentials, electron density distribution, atoms in molecules, noncovalent interaction, and energy decomposition analysis. The putative global minimum of SO2 molecules has a 3D growth pattern with tetrahedral. In the hydrated SO2 clusters, the pure hydrogen bond isomers are less stable than the O–S chalcogen bond isomers. The cluster absorption energy of SO2 on water increases with the size of sulfur dioxide, implying reactivity of sulfur dioxide with water increases with size. The presence of cooperativity was evident from the excellent linearity plot of binding energy/polarizability vs the number of SO2 molecules. Molecular electrostatic potential analysis elucidates the reason for the facile formation of S–O chalcogen than hydrogen bonding in hydrated sulfur dioxide. Atoms in molecule analysis characterize the bonds chalcogen and H bonds to be weak and electrostatic dominant. EDA analysis shows electrostatic interaction is dominated in complexes with more intermolecular chalcogen bonding and orbital interaction for systems with intermolecular H-bonding. The reduced density gradient (RDG) analysis of sulfur dioxide clusters has blue patches and green patches due to S–O chalcogen bonding O–O electrostatic interaction. The RDG analysis of hydrated sulfur dioxide clusters shows intensive blue patches and green patches for the existence of S–O chalcogen and hydrogen bonding respectively. Thus, the presence of strong electrostatic S–O chalcogen interaction and weak H bonds acts cooperatively and stabilize the hydrated sulfur dioxide clusters.

Chalcogen Bonds Involving Selenium in Protein Structures.

Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.

Study vibrational and structural properties of Cu3SeTe by raman spectroscopy and XRD

The compounds Cu3SeTe were synthesized, the crystal structure and atomic dynamics were studied. As a result of X-ray diffraction studies, it was determined that the crystal structure of this compound corresponds to the cubic symmetry of the space group P-43 m. The studies of atomic dynamics were carried out by the method of Raman spectroscopy in the frequency range [Formula: see text]–800 cm[Formula: see text]. It was found that the Raman modes obtained at frequencies [Formula: see text], 91.47, 119.83, 139.51, 208.18 and 266.41 cm[Formula: see text] correspond to vibrations of metal–chalcogen and chalcogen–chalcogen bonds.

Modulating Chalcogen Bonding and Halogen Bonding Sigma-Hole Donor Atom Potency and Selectivity for Halide Anion Recognition.

A series of acyclic anion receptors containing chalcogen bond (ChB) and halogen bond (XB) donors integrated into a neutral 3,5‐bis‐triazole pyridine scaffold are described, in which systematic variation of the electronic‐withdrawing nature of the aryl substituents reveal a dramatic modulation in sigma‐hole donor atom potency for anion recognition. Incorporation of strongly electron‐withdrawing perfluorophenyl units appended to the triazole heterocycle telluro‐ or iodo‐ donor atoms, or directly linked to the tellurium donor atom dramatically enhances the anion binding potency of the sigma‐hole receptors, most notably for the ChB and XB receptors displaying over thirty‐fold and eight‐fold increase in chloride anion affinity, respectively, relative to unfluorinated analogues. Linear free energy relationships for a series of ChB based receptors reveal the halide anion recognition behaviour of the tellurium donor is highly sensitive to local electronic environments. This is especially the case for those directly appended to the Te centre (3⋅ChB), where a remarkable enhancement of strength of binding and selectivity for the lighter halides is observed as the electron‐withdrawing ability of the Te‐bonded aryl group increases, highlighting the exciting opportunity to fine‐tune anion affinity and selectivity in ChB‐based receptor systems.

Modulating Chalcogen Bonding and Halogen Bonding Sigma‐Hole Donor Atom Potency and Selectivity for Halide Anion Recognition

AbstractA series of acyclic anion receptors containing chalcogen bond (ChB) and halogen bond (XB) donors integrated into a neutral 3,5‐bis‐triazole pyridine scaffold are described, in which systematic variation of the electronic‐withdrawing nature of the aryl substituents reveal a dramatic modulation in sigma‐hole donor atom potency for anion recognition. Incorporation of strongly electron‐withdrawing perfluorophenyl units appended to the triazole heterocycle telluro‐ or iodo‐ donor atoms, or directly linked to the tellurium donor atom dramatically enhances the anion binding potency of the sigma‐hole receptors, most notably for the ChB and XB receptors displaying over thirty‐fold and eight‐fold increase in chloride anion affinity, respectively, relative to unfluorinated analogues. Linear free energy relationships for a series of ChB based receptors reveal the halide anion recognition behaviour of the tellurium donor is highly sensitive to local electronic environments. This is especially the case for those directly appended to the Te centre (3⋅ChB), where a remarkable enhancement of strength of binding and selectivity for the lighter halides is observed as the electron‐withdrawing ability of the Te‐bonded aryl group increases, highlighting the exciting opportunity to fine‐tune anion affinity and selectivity in ChB‐based receptor systems.

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.

Methyl groups as widespread Lewis bases in noncovalent interactions

It is well known that, under certain conditions, C(sp3) atoms behave, via their σ-hole, as Lewis acids in tetrel bonding. Here, we show that methyl groups, when bound to atoms less electronegative than carbon, can counterintuitively participate in noncovalent interactions as electron density donors. Thousands of experimental structures are found in which methyl groups behave as Lewis bases to establish alkaline, alkaline earth, triel, tetrel, pnictogen, chalcogen and halogen bonds. Theoretical calculations confirm the high directionality and significant strength of the interactions that arise from a common pattern based on the electron density holes model. Moreover, despite the absence of lone pairs, methyl groups are able to transfer charge from σ bonding orbitals into empty orbitals of the electrophile to reinforce the attractive interaction.

Polymorphism, Halogen Bonding, and Chalcogen Bonding in the Diiodine Adducts of 1,3- and 1,4-Dithiane.

Through variations in reaction solvent and stoichiometry, a series of S-diiodine adducts of 1,3- and 1,4-dithiane were isolated by direct reaction of the dithianes with molecular diiodine in solution. In the case of 1,3-dithiane, variations in reaction solvent yielded both the equatorial and the axial isomers of S-diiodo-1,3-dithiane, and their solution thermodynamics were further studied via DFT. Additionally, S,S’-bis(diiodo)-1,3-dithiane was also isolated. The 1:1 cocrystal, (1,4-dithiane)·(I2) was further isolated, as well as a new polymorph of S,S’-bis(diiodo)-1,4-dithiane. Each structure showed significant S···I halogen and chalcogen bonding interactions. Further, the product of the diiodine-promoted oxidative addition of acetone to 1,4-dithiane, as well as two new cocrystals of 1,4-dithiane-1,4-dioxide involving hydronium, bromide, and tribromide ions, was isolated.

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model.

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.

Nature and Strength of the π‐Hole Chalcogen Bonded Complexes between Substituted Pyridines and SO3 Molecule

AbstractA theoretical study has been carried out on the π‐hole based chalcogen bonding interaction between SO3 and various pyridines (XC5H4N), at the MP2=full/aug‐cc‐pVTZ level, to obtain a better insight into the nature and strength of N…S bond. Our calculations predict two different types of chalcogen bonded complexes: (1) Type‐A complex is formed via lone pair‐ π‐hole (N…S) interaction, and (2) Type‐B complex is stabilized through π‐hole‐π‐electron interaction. The binding energy of the Type‐A complexes varies between −109.78 and ‐81.56 kJ/mol whereas it ranges between −28.93 and −17.82 kJ/mol for Type‐B complexes. The nature of the N…S bond and the changes in its properties on the influence of electron donating and electron withdrawing substituents have been discussed with the help of various computational tools like AIM, NCI, SAPT and NBO analysis. The binding energy of the Type‐A complexes are found to correlate with the basicity parameters such as PA and Vs,min of the substituted pyridines. The binding energies of the pyridine complexes with SF2, SO2, CS2 and OCS are also computed for finding the effect of variation of Vs,max value of the S‐atom on the binding energy. The 2nd order hyperconjugation interaction energy between LP(N) and σ*(S−O)/LP*(S) is well correlated to the binding energy as: −ΔE=0.11E(2) −20.08. The variation in the bond distances and their corresponding vibrational frequencies of both the interacting partners (XC5H4N and SO3) are discussed in detail.

Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage.

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.

Development of a Fluorophore with Enhanced Unorthodox Chalcogen Bonding for Highly Sensitive Detection of Trimethyl Arsine Vapor

In this work, we report the design of novel fluorophores that bear three benzothiadiazole and benzoselenadiazole groups, respectively, for sensitive detection of trimethyl arsine vapor. In particular, the fluorophore with the benzoselenadiazole groups can form stronger chalcogen bonding with trimethyl arsine than the fluorophore with the benzothiadiazole groups, which in turn triggers much faster and more sensitive fluorescence responses. On the basis of this novel mechanism, fluorescence detection of trimethyl arsine vapor with rapid response (∼3 s), high sensitivity (the theoretical LOD is 0.44 ppb), and high selectivity is achieved on bundled nanofibers from the fluorophore with the benzoselenadiazole groups. Here, the new fluorescence sensor may find wide applications in health and environmental monitoring, arsenic distribution recognition in soil, and arsenic mines exploration.

Bonding features in Appel's salt from the orbital-free quantum crystallographic perspective

Bonding properties in the crystal of 4,5-dichloro-l,2,3-dithiazolium chloride (Appel's salt) were studied using a combination of single-crystal high-resolution X-ray diffraction data and the orbital-free quantum crystallography approach. A QTAIM-based topological model shows the proximity of S—C and S—N bonds to the sesquialteral type and establishes the low S—S bond order in the l,2,3-dithiazolium heterocycle. It is found that the electrostatic potential carries the traces of a common positive area on the junction of interatomic zero-flux surfaces of S1 and S2 atomic basins; meanwhile the exchange energy density per particle shows perfectly here two separate minima through which the two bond paths run. Thus, the pair intermolecular interactions Cl−...S1 and Cl−...S2 formed by the common chloride anion placed near the center of the S—S bond are categorized as chalcogen bonds.