Introducing Cationic Selenium-Containing Triazapentadiene Ligand Framework: Synthesis, Coordination Chemistry, and Antifungal Activity

Positively charged ligands are scarce. Here, we report the synthesis of unprecedented cationic selenium-containing triazapentadiene ligand framework. The reaction between 2-pyridylselenyl reagents and NaN(CN)2 in a 2:1 ratio produces the sodium complexes featuring the cationic selenium-containing triazapentadiene (SeTAP) ligand. The sodium-to-metal transmetalation allows facile preparation of SeTAP metal complexes, as exemplified by the reactions with CuCl2, AgNO3, NaAuCl4, and FeCl3. Density functional theory calculations have been used to analyze and characterize the chalcogen bonding interactions observed in the solid state for these compounds. Moreover, antifungal properties of the SeTAP ligand and its metal complexes were screened for in vitro activity against several phytopathogenic fungi. Phoma eupyrena exhibited prominent sensitivity against the action of most of the tested compounds.

Chalcogen bonding interaction between ebselen and nitrite promote N-nitrosation of amines

Ebselen (EbSe), a therapeutically significant molecule, is shown to exhibit chalcogen bonding interaction with nitrite anion (ONO-). This report suggests that the σ-holes of EbSe are powerful for offering weak but influential interactions towards biologically relevant ONO-, thereby assisting oxidative transformations like N-nitrosation of aromatic amines.

Fingerprints of Chalcogen Bonding Revealed Through 77Se-NMR

77Se-NMR is used to characterise several chalcogen bonded complexes of derivatives of the organoselenium drug ebselen, exploring a range of electron demand. NMR titration experiments support the intuitive understanding that chalcogen bond donors bearing more electron withdrawing substituents give rise stronger chalcogen bonds. The chemical shift of the selenium nucleus is also shown to move upfield as it participates in a chalcogen bond. Solid-state NMR is used to explore chalcogen bonding in co-crystals. Due to the lack of molecular reorientation on the NMR timescale in the solid state, the shape of the chemical shift tensor can be determined using this technique. A range of co-crystals are shown to have extremely large chemical shift anisotropy, which suggests a strongly anisotropic electron density distribution around the selenium atom. A single crystal NMR experiment was conducted using one of the co-crystals, affording the absolute orientation of the chemical shift tensor within the crystal. This showed that the selenium nucleus is strongly shielded in the direction of the chalcogen bond (due to the approach of the lone pair of the Lewis base), and strongly deshielded in the perpendicular direction. The orientation of the deshielded axis is consistent with the presence of a second σ-hole which is not participating in a chalcogen bond, showing the profound effect of electron density anisotropy on the chemical shift.

Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank

The presence of chalcogen bonds in native proteins was investigated on a non-redundant and high-resolution (≤ 1 Angstrom) set of protein crystal structures deposited in the Protein Data Bank. It was observed that about one half of the sulfur atoms of methionines and disulfide bridges from chalcogen bonds with nucleophiles (oxygen and sulfur atoms, and aromatic rings). This suggests that chalcogen bonds are a non-bonding interaction important for protein stability. Quite numerous chalcogen bonds involve water molecules. Interestingly, in the case of disulfide bridges, chalcogen bonds have a marked tendency to occur along the S-S bond extension rather than along the C-S bond extension. Additionally, it has been observed that closer residues have a higher probability of being connected by a chalcogen bonds, while the secondary structure of the two residues connected by a chalcogen bond do not correlate with its formation.Communicated by Ramaswamy H. Sarma.

Interplay between hydrogen and chalcogen bonds in cysteine

Protein structures are stabilized by several types of chemical interactions between amino acids, which can compete with each other. This is the case of chalcogen and hydrogen bonds formed by the thiol group of cysteine, which can form three hydrogen bonds with one hydrogen acceptor and two hydrogen donors and a chalcogen bond with a nucleophile along the extension of the CS bond. A survey of the Protein Data Bank shows that hydrogen bonds are about 40-50 more common than chalcogen bonds, suggesting that they are stronger and, consequently, prevail, though not always. It is also observed that frequently a thiol group that forms a chalcogen bond is also involved, as a hydrogen donor, in a hydrogen bond.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

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.

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.

Ebselen and Analogues: Pharmacological Properties and Synthetic Strategies for Their Preparation

Ebselen is the leader of selenorganic compounds, and starting from its identification as mimetic of the key antioxidant enzyme glutathione peroxidase, several papers have appeared in literature claiming its biological activities. It was the subject of several clinical trials and it is currently in clinical evaluation for the treatment of COVID-19 patients. Given our interest in the synthesis and pharmacological evaluation of selenorganic derivatives with this review, we aimed to collect all the papers focused on the biological evaluation of ebselen and its close analogues, covering the timeline between 2016 and most of 2021. Our analysis evidences that, even if it lacks specificity when tested in vitro, being able to bind to every reactive cysteine, it proved to be always well tolerated in vivo, exerting no sign of toxicity whatever the administered doses. Besides, looking at the literature, we realized that no review article dealing with the synthetic approaches for the construction of the benzo[d][1,2]-selenazol-3(2H)-one scaffold is available; thus, a section of the present review article is completely devoted to this specific topic.

Anion⋅⋅⋅Anion Coinage Bonds: The Case of Tetrachloridoaurate

Interactions in crystalline tetrachloridoaurates of acetylcholine and dimethylpropiothetine are characterized by Au⋅⋅⋅Cl and Au⋅⋅⋅O short contacts. The former interactions assemble the AuCl4 - units into supramolecular anionic polymers, while the latter interactions append the acetylcholine and propiothetine units to the polymer. The distorted octahedral geometry of the bonding pattern around the gold center is rationalized on the basis of the anisotropic distribution of the electron density, which enables gold to behave as an electrophile (π-hole coinage-bond donor). Computational studies prove that gold atoms in negatively charged species can function as acceptors of electron density. The attractive nature of the Au⋅⋅⋅Cl/O interactions described here complement the known aurophilic bonds involved in gold-centered interactions.

Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.