Enantioseparation of 5,5′-Dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography

The chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4′-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantioseparation of three 5,5′-dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van’t Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed.     

Competition Between the Two σ-Holes in the Formation of a Chalcogen Bond

A chalcogen atom Y contains two separate σ-holes when in a R₁YR₂ molecular bonding pattern. Quantum chemical calculations consider competition between these two σ-holes to engage in a chalcogen bond (ChB) with a NH₃ base. R groups considered include F, Br, I, and tert-butyl (tBu). Also examined is the situation where the Y lies within a chalcogenazole ring, where its neighbors are C and N. Both electron-withdrawing substituents R₁ and R₂ act cooperatively to deepen the two σ-holes, but the deeper of the two holes consistently lies opposite to the more electron-withdrawing group, and is also favored to form a stronger ChB. The formation of two simultaneous ChBs in a triad requires the Y atom to act as double electron acceptor, and so anti-cooperativity weakens each bond relative to the simple dyad. This effect is such that some of the shallower σ-holes are unable to form a ChB at all when a base occupies the other site.     

Chalcogen Bonds in Selenocysteine Seleninic Acid,a Functional GPx Constituent,and in Other Seleninic or Sulfinic Acid Derivatives

The controlled oxidation reaction of L-selenocystine under neutral pH conditions affords selenocysteine seleninic acid (3-selenino-L-alanine) which is characterized also by means of single-crystal X-ray diffraction. This technique shows that selenium forms three chalcogen bonds (ChBs), one of them being outstandingly short. A survey of seleninic acid derivatives in the Cambridge Structural Database (CSD) confirms that the C−Se(=O)O− functionality tends to act as a ChB donor robust enough to systematically influence the interactional landscape in the solid. Quantum Theory of Atom in Molecules (QTAIM) analysis proves the attractive nature of the short contacts observed in crystals containing the seleninic functionality and calculation of surface molecular electrostatic potential (MEP) reveals that remarkably positive σ-holes can frequently be found opposite to the covalent bonds at selenium. Both CSD searches and QTAIM and MEP approaches show that also the sulfinic acid moiety can function as a ChB donor, albeit less frequently than the seleninic acid one. These findings may contribute to a better understanding, at the atomic level, of the mechanism of action of the enzymes that control oxidative stress and ROS deactivation and that contain selenocysteine seleninic acid and cysteine sulfinic acid in the active site.     

Double Chalcogen Bonds: Crystal Engineering Stratagems via Diffraction and Multinuclear Solid-State Magnetic Resonance Spectroscopy

Group 16 chalcogens potentially provide Lewis-acidic σ-holes, which are able to form attractive supramolecular interactions with electron rich partners through chalcogen bonds. Here, a multifaceted experimental and computational study of a large series of novel chalcogen-bonded cocrystals, prepared using the principles of crystal engineering, is presented. Single-crystal X-ray diffraction studies reveal that dicyanoselenadiazole and dicyanotelluradiazole derivatives work as promising supramolecular synthons with the ability to form double chalcogen bonds with a wide range of electron donors including halides and oxygen- and nitrogen-containing heterocycles. Extensive ⁷⁷Se and ¹²⁵Te solid-state nuclear magnetic resonance spectroscopic investigations of cocrystals establish correlations between the NMR parameters of selenium and tellurium and the local chalcogen bonding geometry. The relationships between the electronic environment of the chalcogen bond and the ⁷⁷Se and ¹²⁵Te chemical shift tensors were elucidated through a natural localized molecular orbital density functional theory analysis. This systematic study of chalcogen-bond-based crystal engineering lays the foundations for the preparation of the various multicomponent systems and establishes solid-state NMR protocols to detect these interactions in powdered materials.     

Theoretical Density Functional Theory insights into the nature of chalcogen bonding between CX2 (X = S,Se, Te) and diazine from monomer to supramolecular complexes

Chalcogen bonding is a noncovalent interaction, highly similar to halogen and hydrogen bonding, occurring between a chalcogen atom and a nucleophilic region. Two density functional theory (DFT) approaches B3LY-D3 and B97-D3 were performed on a series of complexes formed between CX₂ (X = S, Se, Te) and diazine (pyridazine, pyrimidine and pyrazine). Chalcogen atoms prefer interacting with the lone pair of a nitrogen atom rather than with the π-cloud of an aromatic ring. CTe₂ and CSe₂ form a stronger chalcogen bond than CS₂. The electrostatic potential of CX₂ (X = S, Se and Te) reveals the presence of two equivalent σ-holes, one on each chalcogen atom. These CX₂ molecules interact with diazine giving rise to supramolecular interactions. Wiberg bond index and second-order perturbation theory analysis in NBO were performed to better understand the nature of the chalcogen bond interaction.     

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).     

Intramolecular S···O chalcogen bond in thioindirubin

Results of X-ray diffraction study and quantum-chemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C–H···O and S···O interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (σ-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C–S bonds. One of these σ-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of σ-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using “Atoms in Molecules” (AIM) theory. Energies of the C–H···O hydrogen bond and the S···O σ-hole bond derived from AIM and NBO theories are very close.     

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, V_S,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.     

The Bright Future of Unconventional σ/π‐Hole Interactions

Non‐covalent interactions play a crucial role in (supramolecular) chemistry and much of biology. Supramolecular forces can indeed determine the structure and function of a host–guest system. Many sensors, for example, rely on reversible bonding with the analyte. Natural machineries also often have a significant non‐covalent component (e.g. protein folding, recognition) and rational interference in such ‘living’ devices can have pharmacological implications. For the rational design/tweaking of supramolecular systems it is helpful to know what supramolecular synthons are available and to understand the forces that make these synthons stick to one another. In this review we focus on σ‐hole and π‐hole interactions. A σ‐ or π‐hole can be seen as positive electrostatic potential on unpopulated σ* or π⁽*⁾ orbitals, which are thus capable of interacting with some electron dense region. A σ‐hole is typically located along the vector of a covalent bond such as X?H or X?Hlg (X=any atom, Hlg=halogen), which are respectively known as hydrogen and halogen bond donors. Only recently it has become clear that σ‐holes can also be found along a covalent bond with chalcogen (X?Ch), pnictogen (X?Pn) and tetrel (X?Tr) atoms. Interactions with these synthons are named chalcogen, pnigtogen and tetrel interactions. A π‐hole is typically located perpendicular to the molecular framework of diatomic π‐systems such as carbonyls, or conjugated π‐systems such as hexafluorobenzene. Anion–π and lone‐pair–π interactions are examples of named π‐hole interactions between conjugated π‐systems and anions or lone‐pair electrons respectively. While the above nomenclature indicates the distinct chemical identity of the supramolecular synthon acting as Lewis acid, it is worth stressing that the underlying physics is very similar. This implies that interactions that are now not so well‐established might turn out to be equally useful as conventional hydrogen and halogen bonds. In summary, we describe the physical nature of σ‐ and π‐hole interactions, present a selection of inquiries that utilise σ‐ and π‐holes, and give an overview of analyses of structural databases (CSD/PDB) that demonstrate how prevalent these interactions already are in solid‐state structures.     

σ-Hole bond tunability in YO<Subscript>2</Subscript>X<Subscript>2</Subscript>:NH<Subscript>3</Subscript> and YO<Subscript>2</Subscript>X<Subscript>2</Subscript>:H<Subscript>2</Subscript>O complexes (X = F,Cl, Br; Y = S,Se): trends and theoretical aspects

A σ-hole is defined as an electron-deficient region on the extension of a covalently bonded group IV–VII atoms. If the electronic density in the σ-hole is sufficiently low, then this region will have a positive electrostatic potential, which allows attractive noncovalent interactions with negative sites. SO₂X₂ and SeO₂X₂ (X = F, Cl and Br) have three Lewis acid sites of σ-hole located in the outermost of chalcogen atom and X end, participating in the chalcogen and halogen bonds with NH₃ and H₂O, respectively. MP2/aug-cc-pVTZ and M06-2X/aug-cc-pVTZ calculations reveal that for a given halogen atom, SeO₂X₂ forms stronger chalcogen bond interactions than SO₂X₂ counterpart. Almost a perfect linear relationship is evident between the interaction energies and the magnitudes of the product of most positive and negative electrostatic potentials. The interaction energies calculated by M06-2X and MP2 methods are almost consistent with each other.     

New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems

Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.     

Detailed comparison of the pnicogen bond with chalcogen,halogen, and hydrogen bonds

The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H‐bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron‐acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction and charge transfer, along with a smaller dispersion component. The charge transfer arises from the overlap between the lone pair of the electron donor and a σ* antibond of the acceptor. The angular characteristics of the equilibrium geometry result primarily from a compromise between electrostatic and induction forces. Angular distortions of the H‐bond are typically less energetically demanding than comparable bends of the other noncovalent bonds. © 2012 Wiley Periodicals, Inc.     

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.     

Interaction of coinage metal clusters with chalcogen dihydrides

The interaction of chalcogen dihydrides (H 2E; E = O, S, and Se) with small coinage metal clusters (M n ; M = Cu, Ag, and Au, n = 3 and 4) is studied based on density functional theory, with a focus on the nature of chalcogen-metal bonds. A newly developed pseudopotential-based correlation-consistent basis set is used for metal clusters together with the 6-311++G** basis set for the remaining atoms. Geometrical data identified that no significant deviation has been observed for molecules before and after complexation. For these three metals, binding energy calculations indicate that gold has the highest and silver has the lowest affinities for interaction with H 2E. In comparison with gold and copper, complexation between silver and chalcogen dihydrides is significantly weaker. It is found that interaction of H 2E molecules with the coinage metals have the order of H 2Se > H 2S > H 2O. Therefore, in agreement with experimental works, our calculations confirm that the gold-selenium bond is the most stable. The nature of M-E bonds is also interpreted by means of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the QTAIM results, the bonds are found to be partially ionic and partially covalent. Natural resonance theory (NRT) is used to calculate natural bond order and bond polarity. The NRT result indicates that the percentage of polarity of M-E bonds is affected by coinage metals.     

H2XP…SHY复合物中磷键与硫键的理论研究

用从头算量子化学方法MP2 与CCSD(T)研究了H₂XP和SHY (X, Y=H, F, Cl, Br)分子的P与S之间形成的磷键X―P…S与硫键Y―S…P的本质与规律以及取代基X与Y对成键的影响. 计算结果表明, 硫键比磷键强, 连接在Lewis 酸上的取代基的电负性增大导致形成的磷键或硫键增强, 键能增大, 对单体的结构和性质的影响也增大; 而连接在Lewis 碱上的取代基效应则相反. 硫键键能为8.37-23.45 kJ·mol^-1, 最强的硫键结构是Y 电负性最大而X 电负性最小的HFS…PH₃, CCSD(T)计算的键能是16.04 kJ·mol^-1; 磷键键能为7.54-14.65 kJ·mol^-1, 最强的磷键结构是X 电负性最大而Y 电负性最小的H₂FP…SH₂, CCSD(T)计算的键能是12.52 kJ·mol^-1. 对磷键与硫键能量贡献较大的是交换与静电作用. 分子间超共轭lp(S)-σ^*(PX)与lp(P)-σ^*(SY)对磷键与硫键的形成起着重要作用, 它导致单体的极化, 其中硫键的极化效应较大, 从而有一定的共价特征.     

A Crystallographic Charge Density Study of the Partial Covalent Nature of Strong N⋅⋅⋅Br Halogen Bonds

The covalent nature of strong N?Br???N halogen bonds in a cocrystal ( 2 ) of N‐bromosuccinimide ( NBS ) with 3,5‐dimethylpyridine ( lut ) was determined from X‐ray charge density studies and compared to a weak N?Br???O halogen bond in pure crystalline NBS ( 1 ) and a covalent bond in bis(3‐methylpyridine)bromonium cation (in its perchlorate salt ( 3 ). In 2 , the donor N?Br bond is elongated by 0.0954 Å, while the Br???acceptor distance of 2.3194(4) is 1.08 Å shorter than the sum of the van der Waals radii. A maximum electron density of 0.38 e Å^?3 along the Br???N halogen bond indicates a considerable covalent contribution to the total interaction. This value is intermediate to 0.067 e Å^?3 for the Br???O contact in 1 , and approximately 0.7 e Å^?3 in both N?Br bonds of the bromonium cation in 3 . A calculation of the natural bond order charges of the contact atoms, and the σ*(N1?Br) population of NBS as a function of distance between NBS and lut , have shown that charge transfer becomes significant at a Br???N distance below about 3 Å.     

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D₂Ch⋅⋅⋅A⁻ (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO−LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A⁻ to D₂Ch.     

Observations on the Crystal Structures of Electron Donor-Acceptor Complexes

The theoretical interpretation of electron donor-acceptor complex formation in terms of charge transfer interactions has stimulated many structure determinations for these complexes. These fall into three classes, depending on the type of orbitals involved in charge transfer. In σ-σ complexes, intermolecular bonds become shorter and intramolecular bonds become longer as charge transfer increases. Relative orientations correspond to overlap of donor and acceptor molecules in directions of “preferred polarizability”. Intermolecular bond lengths in σ-π complexes show similar trends, and the axial orientation in the benzene-halogen complexes is probably the result of the best compromise between orbital overlap and energy factors. π-π Complexes contain stacks of alternate plane-to-plane donor and acceptor molecules, arranged in three characteristic ways. There is little correlation between interplanar spacing in these stacks and charge transfer properties. The relative orientations of donor and acceptor molecules within the stacks are determined by a combination of charge transfer interactions (maximized when aromatic rings of donor and acceptor molecules are displaced by half a ring diameter) and dipole-induced dipole interactions (maximized, for example, when a polar bond of one molecule overlaps a polarizable region of another). Crystal packing requirements and dispersion forces modify these effects, and no satisfactory theoretical treatment of this complex combination of interactions is yet available.     

A new noncovalent force: comparison of P···N interaction with hydrogen and halogen bonds

When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(?) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(?) orbital that is closest to the P. In contrast to halogen bonds, there is no requirement of a σ-hole of positive electrostatic potential on the P atom, nor is it necessary for the two interacting atoms to be of differing potential. In fact, the two atoms can be identical, as the global minimum of the PH(3) homodimer has the same structure, characterized by a P···P attraction. Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction.     

Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments

Molecules of the type XYT = Ch (T = C, Si, Ge; Ch = S, Se; X,Y = H, CH₃, Cl, Br, I) contain a σ-hole along the T = Ch bond extension. This hole can engage with the N lone pair of NCH and NCCH₃ so as to form a chalcogen bond. In the case of T = C, these bonds are rather weak, less than 3 kcal/mol, and are slightly weakened in acetone or water. They owe their stability to attractive electrostatic energy, supplemented by dispersion, and a much smaller polarization term. Immersion in solvent reverses the electrostatic interaction to repulsive, while amplifying the polarization energy. The σ-holes are smaller for T = Si and Ge, even negative in many cases. These Lewis acids can nonetheless engage in a weak chalcogen bond. This bond owes its stability to dispersion in the gas phase, but it is polarization that dominates in solution.