Chalcogen Bonds Research Articles

Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds.

The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.

The intermolecular complexes of SSF2 with HF, H2O, NH3, HCN and CH3OH molecules

ABSTRACTIntermolecular complexes of thiothionyl-fluoride (SSF2) with HY molecules (HY = HF, H2O, NH3, HCN and CH3OH) have been studied theoretically at the MP2/aug-cc-pVTZ computational level. The SSF2 can have both hydrogen and chalcogen-bond (CB) interactions with HY molecules. The central S atom of SSF2 as a better electron acceptor gives stronger adducts with HY molecules. CB interactions for the central S atom correlate with red shift of the S═S band. The QTAIM and NBO analyses were carried out on SSF2 complexes.

Studies on the σ–hole bonds (halogen, chalcogen, pnicogen and carbon bonds) based on the orientation of crystal structure

ABSTRACTThe 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole (DDBT) crystal has two polymorphic forms [1], where the close contacts between two electronegative atoms are identified and studied through Hirshfeld surface analysis. Br---Br and O---O cut-off distances are addressed and analysed. The σ–hole of bromine, sulphur, oxygen atoms and π-hole of carbon and nitrogen atoms were subjected to study using molecular electrostatic potential map and 3D-deformation density map. Sixteen types of dimers from the two forms of crystal structure (6 for form I and 10 for form II) were studied using the charge transfer properties and interaction energies and made detailed analysis of halogen bond (Br---N), dihalogen bond (Br---Br), chalcogen bond (O---Br and S---Br), dichalcogen bond (S---O, O---S and O---O), pnicogen bond (N---O) and carbon bond (C---O and C---Br) interactions. The impact of orientations is discussed to define the type of interaction and its strength through charge transfer mechanism. The contribution of bond angle values for the σ-hole and π–hole bonds are discussed. Utilisation of σ–hole in smaller bond angle values (above 30°) of |θ1 − θ2| existing in type II halogen–halogen bond have been examined in the two forms.

Synthesis and Characterization of Adducts between SF4 and Oxygen Bases: Examples of O···S(IV) Chalcogen Bonding.

Lewis acid-base adducts between SF4 and the oxygen bases tetrahydrofuran, cyclopentanone, and 1,2-dimethoxyethane were synthesized and characterized by Raman spectroscopy and X-ray crystallography. Crystal structures of (SF4·OC4H8)2, SF4·(OC4H8)2, SF4·CH3OC2H4OCH3, and SF4·(O═C5H8)2 show weak S···O chalcogen bonding interactions ranging from 2.662(2) to 2.8692(9) Å. Caffeine, which has three Lewis basic sites, was reacted with SF4 and one aliquot of HF forming C8H10N4O2·2SF4·HF, which was also characterized by X-ray crystallography. Density functional theory calculations aided in the assignment of the vibrational spectra of (SF4·OC4H8)2, SF4·(OC4H8)2, SF4·CH3OC2H4OCH3, and SF4·(O═C5H8)2. Bonding was studied by natural bond order and the quantum theory of atoms in molecules analyses.

Difference in Energy between Two Distinct Types of Chalcogen Bonds Drives Regioisomerization of Binuclear (Diaminocarbene)PdII Complexes

The reaction of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with various 1,3-thiazol- and 1,3,4-thiadiazol-2-amines in chloroform gives a mixture of two regioisomeric binuclear diaminocarbene complexes. For 1,3-thiazol-2-amines the isomeric ratio depends on the reaction conditions and kinetically (KRs) or thermodynamically (TRs) controlled regioisomers were obtained at room temperature and on heating, respectively. In CHCl3 solutions, the isomers are subject to reversible isomerization accompanied by the cleavage of Pd-N and C-N bonds in the carbene fragment XylNCN(R)Xyl. Results of DFT calculations followed by the topological analysis of the electron density distribution within the formalism of Bader's theory (AIM method) reveal that in CHCl3 solution the relative stability of the regioisomers (ΔGexp = 1.2 kcal/mol; ΔGcalcd = 3.2 kcal/mol) is determined by the energy difference between two types of the intramolecular chalcogen bonds, viz. S···Cl in KRs (2.8-3.0 kcal/mol) and S···N in TRs (4.6-5.3 kcal/mol). In the case of the 1,3,4-thiadiazol-2-amines, the regioisomers are formed in approximately equal amounts and, accordingly, the energy difference between these species is only 0.1 kcal/mol in terms of ΔGexp (ΔGcalcd = 2.1 kcal/mol). The regioisomers were characterized by elemental analyses (C, H, N), HRESI+-MS and FTIR, 1D (1H, 13C{1H}) and 2D (1H,1H-COSY, 1H,1H-NOESY, 1H,13C-HSQC, 1H,13C-HMBC) NMR spectroscopies, and structures of six complexes (three KRs and three TRs) were elucidated by single-crystal X-ray diffraction.

An ab initio study on properties of cationic chalcogen bonds in XF2Y+⋯NCZ (X═H, CN, F; Y═S, Se; Z═H, Cl, Br) complexes

ABSTRACTThe geometries, interaction energies, and bonding properties of cationic chalcogen bonds are studied in binary complexes XF2Y+⋯NCZ (X═H, CN, F; Y═S, Se; Z═H, Cl, Br). The nature of these interactions is studied by a vast number of methods, including molecular electrostatic potential (MEP), Noncovalent Interaction Index (NCI), quantum theory of atoms in molecules (QTAIM), and natural bond orbital (NBO) analyses. The interaction energies of these complexes vary between −20.94 kcal/mol in HF2S+⋯NCH and −33.72 kcal/mol in F3Se+⋯NCBr. According to the QTAIM analysis, all these cationic chalcogen bonds are classified as a closed-shell interaction with a partial covalent character. Moreover, cooperative effects between cationic chalcogen bond and hydrogen or halogen bond interactions are studied in ternary XF2Y+⋯NCZ⋯NH3 complexes. These cooperative effects are analyzed in terms of the parameters derived from the QTAIM and NBO analyses, and electron density difference plots.

Understanding the effect of substitution on the formation of S. . .F chalcogen bond

In this study, we have investigated the effect of substitution on the formation of S …F non-covalent interactions in XHS …FCH 3 complexes (X =-H, -F, -Cl, -OH, -OCH 3, -NH 2, -NHCH 3, -NO 2, -CN) at MP2/aug-cc-pVDZ level of theory. The formation of S …F chalcogen bonds was observed in all the cases, except for X = -H. The binding energy of the S …F non-covalent interactions is strongly dependent on the nature of the substituent groups. The energy decomposition analysis revealed that electrostatic and exchange energy component are the dominant contributors towards the stability of these interactions. The topological analysis established the presence of the S …F chalcogen bond due to the presence of a bond critical point exclusively between sulphur and fluorine atoms representing a closed-shell interaction. The natural bond orbital analysis shows that the stability of the interaction comes from a charge transfer from F(lp) to s*(S-X) orbital transition.

Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S···O chalcogen bonds

The chalcogen bonds formed between carbonyl bases (H2C=O and CH3- and Cl-derivatives) and carbon disulfide have been studied by density functional BLYP-D3 and ab initio CCSD(T) methods. The CCSD(T)/CBS calculated interaction energies between these molecules are moderate, ranging from −1.45 to −2.29 kcal mol−1. The charge transfer occurs from the carbonyl base to CS2 and is small. According to the AIM analysis, the molecules are bonded by S···O chalcogen bonds. In addition, weak van der Waals S···Cl and S···H interactions stabilize most of the systems. The same results can be extracted from the NBO calculations which reveal the nature of the interacting bonding and antibonding orbitals. For some of the carbonyl derivatives, other stable structures characterized by S···Cl bonds or CH···C hydrogen bonds are also predicted. A SAPT decomposition of the interaction energies allows to conclude that the electrostatic energy is the predominant component in the stronger complexes and that the dispersion energy becomes more important in the weaker van der Waals complexes.

Anion Transport with Chalcogen Bonds

In this report, we introduce synthetic anion transporters that operate with chalcogen bonds. Electron-deficient dithieno[3,2-b;2',3'-d]thiophenes (DTTs) are identified as ideal to bind anions in the focal point of the σ holes on the cofacial endocyclic sulfur atoms. Anion binding in solution and anion transport across lipid bilayers are found to increase with the depth of the σ holes of the DTT anionophores. These results introduce DTTs and related architectures as a privileged motif to engineer chalcogen bonds into functional systems, complementary in scope to classics such as 2,2'-bipyrroles or 2,2'-bipyridines that operate with hydrogen bonds and lone pairs, respectively.

Hemi bonds and noncovalent interactions in the cational systems (XH2P: SHY)+

Quantum chemistry ab initio MP2 and CCSD calculations were performed to investigate the P⋯S hemi bonds and noncovalent interactions in the radical cational systems (H3P:SH2)+, (FH2P:SH2)+ and (H3P:SHF)+. The hydride dimer (H3P:SH2)+ has a P⋯S hemi bonding structure and a H-bonding structure, (FH2P:SH2)+ has two hemi bonding structures and a proton-transferred H-bonding structure, (H3P:SHF)+ has two hemi bonding structures and three noncovalent structures. It is remarkable that these hemi bonds also have characters of pnicogen and chalcogen bonds. The binding energy, stability and bonding nature of the hemi bonds were presented.

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

Structure, binding energy and chiral discrimination in oxathiirane homodimers

Oxathiirane (XHCSO) homodimers bonded by hydrogen bonds (HB) and chalcogen bonds (YB) were studied at the Møller-Plesset (MP2) computational level. Binding energies obtained at the Coupled-Cluster level up to the Complete Basis Set limit [CCSD(T)/CBS] indicate that HB complexes present stronger binding modes than the YB complexes. In terms of chiral discrimination energy, R,S complexes are favored over R,R complexes with the exceptions of SiCl3 and SiF3 derivatives. Natural Bond Orbital (NBO) results are in agreement with the interaction energies in the case of the HB complexes, but could not discriminate between R,R and R,S in the YB complexes. The lack of correlation between molecular electrostatic values on the 0.001a.u. and binding energies, in addition to the discrepancies between Atoms in Molecules (AIM) and NBO results may suggest that the electrostatics is not the dominant term in the interaction energy. This was corroborated by the Localized Molecular Orbital Energy Decomposition Analysis (LMOEDA) calculations which showed that the exchange and dispersion terms are the most important attractive components for all the complexes studied, contributing up to 50.6% and 42.5% to the total attractive forces respectively.

ChemInform Abstract: Unorthodox Interactions at Work

AbstractReview: [52 refs.

Efficient SO2 Capture through Multiple Chalcogen Bonds, Sulfur‐Centered Hydrogen Bonds and S•••π Interactions: A Computational Study

AbstractThe non‐toxic, environment friendly, biodegradable properties and cost effectiveness of active pharmaceutical ingredients (APIs) allow them to be used as green‐solvents for several applications. The presence of multiple binding sites in the APIs has an additional advantage for the flue gas capture. Herein we report a detailed analysis of efficient SO2 capture by the anions associated with APIs through several strong and weak non‐covalent interactions. The DFT studies and Langmuir adsorption model suggest that the APIs based anions are highly efficient alternatives for SO2 capture at low as well as high partial pressures (0.01 – 0.1 MPa) of SO2. The absorption capacity can be achieved as much as 5.8 mol SO2/mol APIs; the best absorption capacity till reported. Our computational results suggest that for the efficient SO2 capture, the enthalpy of absorption (ΔH) should be −65 to −50 kJ.mol−1; below this range absorption capacity reduces drastically. This study also emphasizes the importance of weak interactions (S•••π and C−H•••O and C−H•••S hydrogen bonds) together with the strong chalcogen bonds to be considered in designing new absorbing materials for SO2 capture.

The mutual influence of Y···N and H···H interactions in XHY···NCH···HM complexes (X = F, Cl, Br; Y = S, Se; M = Li, Na, BeH, MgH): tuning of the chalcogen bond by dihydrogen bond interaction

The equilibrium structures, interaction energies, and bonding properties of ternary XHY···NCH···HM complexes are studied by ab initio calculations, where X = F, Cl, Br, Y = S, Se, and M = Li, Na, BeH, MgH. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level. The results indicate that all optimized Y···N and H···H binding distances in the ternary complexes are smaller than the corresponding values in the binary systems. The calculated cooperative energies (Ecoop) are between −0.20 kcal/mol in BrHS···NCH···HBeH and −3.29 kcal/mol in FHSe···NCH···HNa. For a given Y and M, the estimated Ecoop values increase as X = F > Cl > Br. In addition, the selenium-bonded complexes exibit larger Ecoop values than those of the sulfur-bonded counterparts. The cooperativity between Y···N and H···H interactions is further analyzed by quantum theory of atoms in molecules and natural bond orbital methods. Cooperative effects make an increase in the J(Y–N) and J(H–H) spin–spin coupling constants of the ternary complexes with respect to the binary systems.

Double Pancake Versus Long Chalcogen-Chalcogen Bonds in Six-Membered C,N,S-Heterocycles.

The double "pancake" bonding in the dimers of the six-membered heterocycles 1,3-dithia-2,4,6-triazine (4) and 1,3-dithia-2,4-diazine (16) were investigated by means of high-level quantum chemical calculations (B3LYP and CCSD(T)). It was found that the S-S dimers, 20 a and 27, are not the most stable isomers, but the dimers showing short S-N (21 a) and S-C (25, 28) bonds. An investigation of the 5-phenyl-1,3-dithia-2,4,6-triazine (4 b) yields that the syn dimer with two S-S bonds (2.57 Å) is the most stable one. In this dimer, the phenyl groups are placed on top of each other. The additional dispersion energy of the phenyl rings causes a stabilization of the syn-S-S (C2v -like) isomer. As a result, two weak albeit relevant single S-S bonds (2.57 Å) are predicted. These findings contradict the recently published concept of double "pancake" bonding in the dimer 4 b2 .

Influence of acidic media on the supramolecular aggregation of iso-tellurazole N-oxides

Iso-tellurazole N-oxides are promising supramolecular building blocks. While in neutral solutions, they form tetra- and hexameric macrocyclic aggregates linked by Te···O secondary bonding (σ hole interactions or chalcogen bonds), protonation of the oxygen atom in acidic media disrupts such supramolecular association. The process is reversible and, consequently, can be used to switch on and off the self-assembly process. Hammett acidity measurements gave pKa values of –3.2 for the protonated molecules. Adducts with HCl and HBr were isolated and structurally characterized. Protonation in solution led to the crystallization of a new polymorph of 3-methyl-5-phenyl-1,2-tellurazole N-oxide, which features a unique polymeric arrangement.

Competition between chalcogen bond and halogen bond interactions in YOX4:NH3 (Y = S, Se; X = F, Cl, Br) complexes: An ab initio investigation

Using ab initio calculations, the geometries, interaction energies and bonding properties of chalcogen bond and halogen bond interactions between YOX4 (Y = S, Se; X = F, Cl, Br) and NH3 molecules are studied. These binary complexes are formed through the interaction of a positive electrostatic potential region (σ-hole) on the YOX4 with the negative region in the NH3. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level, through analysis of molecular electrostatic potentials, quantum theory of atoms in molecules and natural bond orbital methods. Our results indicate that even though the chalcogen and halogen bonds are mainly dominated by electrostatic effects, but the polarization and dispersion effects also make important contributions to the total interaction energy of these complexes. The examination of interaction energies suggests that the chalcogen bond is always favored over the halogen bond for all of the binary YOX4:NH3 complexes.

Unorthodox Interactions at Work.

This Perspective elaborates on the currently unfolding interest in integrating unorthodox non-covalent interactions into functional systems. Initial emphasis is on anion-π interactions at work, particularly in catalysis. Recent highlights are described in comparison to a coinciding renaissance of the more conventional, charge-inverted cation-π catalysis. Progress with these complementary aromatic systems is then compared to recent efforts to integrate halogen and chalcogen bonds, the unorthodox counterparts of hydrogen bonds, into functional systems. General focus is on catalysis, pertinent examples on self-assembly, transport, sensing, and templation are covered as well.

An ab initio study on competition between pnicogen and chalcogen bond interactions in binary XHS:PH2X complexes (X = F, Cl, CCH, COH, CH3, OH, OCH3 and NH2)

ABSTRACTChalcogen and pnicogen bond interactions are studied in the binary XHS:PH2X complexes (X = F, Cl, CCH, COH, CH3, OH, OCH3 and NH2) using quantum chemical calculations. These interactions can be explained in terms of electrostatic effects, considering the chalcogen or pnicogen as a Lewis acid due to the presence of an σ-hole. Almost a perfect linear relationship is found between the interaction energies and the magnitudes of the product of most positive and negative electrostatic potentials. This reveals that both the negative and positive regions of the interacting atoms can be used to predict the strength of the eventual interaction. The nature of chalcogen and pnicogen bond interactions is unveiled by means of the atoms in molecules and electron localisation function analyses.