Chalcogen Bonds Research Articles

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective.

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Fluorogenic In Situ Thioacetalization: Expanding the Chemical Space of Fluorescent Probes, Including Unorthodox, Bifurcated, and Mechanosensitive Chalcogen Bonds.

Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ. Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds.

Influence of Internal Noncovalent Bonds on Rotational Dynamics.

While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.

Synthesis, computational and experimental pharmacological studies for (thio)ether-triazine 5-HT6R ligands with noticeable action on AChE/BChE and chalcogen-dependent intrinsic activity in search for new class of drugs against Alzheimer's disease

Alzheimer's disease is becoming a growing problem increasing at a tremendous rate. Serotonin 5-HT6 receptors appear to be a particularly attractive target from a therapeutic perspective, due to their involvement not only in cognitive processes, but also in depression and psychosis. In this work, we present the synthesis and broad biological characterization of a new series of 18 compounds with a unique 1,3,5-triazine backbone, as potent 5-HT6 receptor ligands. The main aim of this research is to compare the biological activity of the newly synthesized sulfur derivatives with their oxygen analogues and their N-demethylated O- and S-metabolites obtained for the first time. Most of the new triazines displayed high affinity (Ki < 200 nM) and selectivity towards 5-HT6R, with respect to 5-HT2AR, 5-HT7R, and D2R, in the radioligand binding assays. For selected, active compounds crystallographic studies, functional bioassays, and ADME-Tox profile in vitro were performed. The exciting novelty is that the sulfur derivatives exhibit an agonistic mode of action contrary to all other compounds obtained to date in this chemical class herein and previously reported. Advanced computational studies indicated that this intriguing functional shift might be caused by presence of chalcogen bonds formed only by the sulfur atom. In addition, the N-demethylated derivatives have emerged highly potent antioxidants and, moreover, show a significant improvement in metabolic stability compared to the parent structures. The cholinesterase study present micromolar inhibitory AChE and BChE activity for both 5-HT6 agonist 19 and potent antagonist 5. Finally, the behavioral experiments of compound 19 demonstrated its antidepressant-like properties and slight ability to improve cognitive deficits, without inducing memory impairments by itself. Described pharmacological properties of both compounds (5 and 19) allow to give a design clue for the development of multitarget compounds with 5-HT6 (both agonist and antagonist)/AChE and/or BChE mechanism in the group of 1,3,5-triazine derivatives.

Competition between Binding to Various Sites of Substituted Imidazoliums.

The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery.

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Automated identification of chalcogen bonds in AlphaFold protein structure database files: is it possible?

Protein structure prediction and structural biology have entered a new era with an artificial intelligence-based approach encoded in the AlphaFold2 and the analogous RoseTTAfold methods. More than 200 million structures have been predicted by AlphaFold2 from their primary sequences and the models as well as the approach itself have naturally been examined from different points of view by experimentalists and bioinformaticians. Here, we assessed the degree to which these computational models can provide information on subtle structural details with potential implications for diverse applications in protein engineering and chemical biology and focused the attention on chalcogen bonds formed by disulphide bridges. We found that only 43% of the chalcogen bonds observed in the experimental structures are present in the computational models, suggesting that the accuracy of the computational models is, in the majority of the cases, insufficient to allow the detection of chalcogen bonds, according to the usual stereochemical criteria. High-resolution experimentally derived structures are therefore still necessary when the structure must be investigated in depth based on fine structural aspects.

Cocrystal of 4-Nitrophenol and 2,1,3-Benzoselenadizole

The 1:1 cocrystal of 4-nitrophenol (NP) and 2,1,3-benzoselenadiazole (BSA) was successfully synthesized. The X-ray single-crystal diffraction analysis revealed that the structure contained a [Se–N]2 cyclic supramolecular synthon. The synthons were connected into a one-dimensional ribbon by O–H···N hydrogen bonds and N–Se···O chalcogen bonds. Furthermore, adjacent ribbons were stabilized by the π···π stacking interactions between two 2,1,3-benzoselenadiazole molecules, leading to the formation of a two-dimensional network.

Transmembrane anion transport mediated by sigma-hole interactions

Supramolecular transmembrane anion transporters are promising therapeutics for channelopathies and typically operate via hydrogen bonding. Sigma-hole interactions including halogen bonding (XB), chalcogen bonding (ChB), and pnictogen bonding (PnB) have emerged as promising alternatives in both transport activity and selectivity. This forum highlights recent advances and identifies anion transport properties unique to sigma-hole interactions.

Comparison of the Ability of N-Bases to Engage in Noncovalent Bonds.

The lone pair of the N atom is a common electron donor in noncovalent bonds. Quantum calculations examine how various aspects of the base on which the N is located affect the strength and other properties of complexes formed with Lewis acids FH, FBr, F2 Se, and F3 As that respectively encompass hydrogen, halogen, chalcogen, and pnicogen bonds. In most cases the halogen bond is the strongest, followed in order by chalcogen, hydrogen, and pnicogen. The noncovalent bond strength increases in the sp<sp2 <sp3 order of hybridization of N. Replacement of H substituents on the base by a methyl group or substituting N by C atom to which the base N is attached, strengthens the bond. The strongest bonds occur for trimethylamine and the weakest for N2 .

The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function.

Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.

Matrix isolation infrared study of complexes between and : Evidence of formation of hydrogen bond and chalcogen bond

Among the non-covalent interactions, the most well studied is the hydrogen bonding interaction. A new type of non-covalent interaction is the chalcogen bonding interaction. In the present work 1:1 complex of [▪] has been characterised using matrix isolation infrared spectroscopy and electronic structure calculations. Two minima have been obtained on the dimer potential energy surface at the MP2 level of calculations with 6-311++G(d,p) and 6-311++G(3df,2pd) basis sets. One of the minima is stabilised by ▪ hydrogen bond and the other minima is stabilised by ▪ chalcogen bond along with secondary ▪ hydrogen bond. Vibrational spectra in the ▪ stretching, ▪ stretching, and ▪ bending modes have been monitored to understand the complex formation. The formation of the hydrogen- and chalcogen-bonded complex in ▪ and ▪ matrices are confirmed by comparison of the experimental and simulated vibrational frequencies. Stabilisation energy, energy decomposition analysis, natural bond orbital analysis, and atoms in molecules analysis provide insight into the nature of the interactions. This work presents the first experimental report where both the hydrogen- and chalcogen-bonded complexes are formed simultaneously. This work also provides the first impression of the ▪ hydrogen bonding and ▪ chalcogen bonding interaction between ▪ and ▪.

Molecular Switching through Chalcogen-Bond-Induced Isomerization of Binuclear (Diaminocarbene)PdII Complexes

Binuclear diaminocarbene complexes, which form as a regioisomer mixture in the reaction between isocyanide–palladium(II) complex cis-[PdCl2(CNXyl)2] and 1,3-thiazol-2-amine, are able to exchange an anionic chloride ligand with other halides, such as Br or I. This process also affords binuclear complexes as mixtures of kinetically and thermodynamically controlled regioisomers. In CDCl3 solutions, we observed interconversion of kinetically and thermodynamically controlled regioisomers. The results of the DFT calculations revealed that in CHCl3 solution, each pair of the isomers exhibited two different types of chalcogen bonding such as S···X or S···N; the presence of CBs for two complexes in the solid state was also proven through X-ray crystallographic study. Based on the combined experimental and theoretical data, it could be concluded that thermodynamic favorability for the formation of thermodynamically controlled regioisomers increases in the Cl &lt; Br ≈ I row and correlate well with the energy difference between S···N and S···X (X = Cl, Br, I) chalcogen bonds in kinetically and thermodynamically controlled products. This means that it is possible to change the structure of metallocycles in binuclear diaminocarbene complexes by simply replacing one halide ligand with another.

Chalcogen-Bond-Induced Double Helix Based on Self-Assembly of a Small Planar Building Block.

As a rule, helical structures at the molecular level are formed by non-planar units. This makes the design of helices, starting from planar building blocks via self-assembly, even more fascinating. Until now, however, this has only been achieved in rare cases, where hydrogen and halogen bonds were involved. Here, we show that the carbonyl-tellurium interaction motif is suitable to assemble even small planar units into helical structures in solid phase. We found two different types of helices: both single and double helices, depending on the substitution pattern. In the double helix, the strands are connected by additional Te⋅⋅⋅Te chalcogen bonds. In the case of the single helix, a spontaneous enantiomeric resolution occurs in the crystal. This underlines the potential of the carbonyl-tellurium chalcogen bond to generate complex three-dimensional patterns.

Interaction Modes between SF4 and Ketones; Study of Intermediates in Deoxofluorination Reactions.

Interactions between ketones and SF4 are studied for the simplest ketone, acetone, and the bulky polycyclic 2-adamantanone. Acetone forms the 1:2 adduct SF4·[O=C(CH-3)2]2, as well as the dimeric 1:1 adducts [SF4·O=C(CH-3)2]2 as identified by low-temperature Raman spectroscopy and, for the latter, X-ray crystallography. In both adducts, SF4 acts as a double chalcogen-bond donor to two keto groups. In contrast 2-adamantanone does not form an isolable solid adduct with SF4; in the presence of HF, however, it forms SF4·O=C10H14O·HF, which comprises chains with weak S---O and S---FH chalcogen bonds in the crystal structure. Sulfur tetrafluoride in this compound is readily lost at -85 °C, leading to the isolation of C10H14O·HF at low temperature. Density functional theory (DFT) calculations aid in vibrational assignments and serve to describe the interactions of the keto group with SF4 and HF, as well as interactions between SF4 with HF. It is found that separate and combined CO---HF and CO---SF4 chalcogen bonds do not polarize the C=O group to any significant degree.

Chalcogen-Peierls Transition: Single-Crystal-to-Single-Crystal Transition from a Two-Dimensional to a One-Dimensional Network of Chalcogen Bonds at Low Temperature

Abstract Due to inherent structural instability, low-dimensional materials often undergo the Peierls transition upon cooling, which is suppressed by an increase in dimensionality of their solid-state electronic structures using secondary bonding interactions such as chalcogen bonds (ChB). We revealed here that ChB themselves have an inherent structural instability when a chalcogen atom participates in simultaneous formation of two ChB, demonstrating for the first time a Peierls-like transition (chalcogen-Peierls transition) of ChB-based organic solids upon cooling. Thus, a lattice dimerization occurs at 220–230 K that changes the two-dimensional ChB network into an accumulated one-dimensional ribbon network in the tetracyanoquinodimethane fused with two [1,2,5]thiadiazoles (1). Negative cooperativity of two ChB formation is weakened on the Se atom due to greater polarizability. Thus, the selenadiazole analogues (2 and 3) undergo a similar chalcogen-Peierls transition at lower temperatures, such as at 160–170 K and at 110–120 K, respectively, depending on the number of Se atom incorporated (one or two, respectively).

Crystal Engineering, Electron Conduction, Molecular Recognition and Reactivity by Chalcogen Bonds in Tetracyanoquinodimethanes Fused with [1,2,5]Chalcogenadiazoles

AbstractStudies on a series of tetracyanoquinodimethanes (TCNQs) fused with [1,2,5]chalcogenadiazole rings reveals that chalcogen bonds (ChBs), through E•••N≡C (E = S or Se) contacts, are a decisive factor in determining their crystal structures, with the formation of one- or two-dimensional networks in a lateral direction. For anion-radical salts generated by one-electron reduction, electron conduction occurs in the direction of the network due to intermolecular electronic interactions involving ChBs. Based on the reliable synthon E•••N≡C for crystal engineering, molecular recognition occurs so that solid-state molecular complexes are selectively formed with certain donors, such as xylenes, among their isomers by charge-transfer-type clathrate formation. The inclusion cavity of the clathrate might provide a reaction environment for photoinduced electron transfer in the solid state. The accommodation of multiple conformers of overcrowded ethylene exhibiting thermo/mechanochromism is another example of a novel function that can be realized by ChBs through E•••N≡C contacts. Therefore, these chalcogenadiazolo-TCNQs endowed with the ability to form ChBs are promising materials for the development of novel solid-state functions.1 Introduction2 Bis[1,2,5]thiadiazolo-TCNQ (BTDA)2.1 Chalcogen Bonds in Crystal Structures of BTDA and its Se Analogues2.2 Electronic Effects of Chalcogen Bonds in Organic Conductors Consisting of BTDA2.3 Molecular Recognition by Chalcogen Bonds in Molecular Complexes of BTDA2.4 Single-Crystalline-State Photoreactions of Molecular Complexes of BTDA2.5 Overcrowded Ethylene Composed of a BTDA Substructure3 TCNQ Analogues Fused with a [1,2,5]Chalcogenadiazole3.1 Crystal Structures of Chalcogenadiazolo-TCNQs3.2 Crystal Structures of Chalcogenadiazolo-TCNNQs: An E•••N≡C Chalcogen Bond versus a Weak C–H•••N≡C Hydrogen Bond3.3 Molecular Recognition by Chalcogen Bonds in TCNNQ Derivatives4 Outlook

Halogen bonds, chalcogen bonds, pnictogen bonds, tetrel bonds and other σ-hole interactions: a snapshot of current progress.

We report here on the status of research on halogen bonds and other σ-hole interactions involving p-block elements in Lewis acidic roles, such as chalcogen bonds, pnictogen bonds and tetrel bonds. A brief overview of the available literature in this area is provided via a survey of the many review articles that address this field. Our focus has been to collect together most review articles published since 2013 to provide an easy entry into the extensive literature in this area. A snapshot of current research in the area is provided by an introduction to the virtual special issue compiled in this journal, comprising 11 articles and entitled `Halogen, chalcogen, pnictogen and tetrel bonds: structural chemistry and beyond.'

A highly effective halide anion sponge containing tellurium σ-hole

Chalcogen bonding has attracted lots of attention recently due to possessing good tunability and significant directionality. A novel and highly effective anion sponge ligand (L) capable of capturing halide anions was designed using chalcogen bond. Quantum chemistry calculations show the sponge can bind the halide anions by one or two chalcogen bonds through several binding modes. The binding free energies range from −40.0 to −77.0 kcal mol−1 in gas phase, from −11.0 to −35.0 kcal mol−1 in aqueous solution, with a common trend of F->Cl-> Br->I-. L shows extremely high selectivity for F- with respect to other halide anions. Electronic structure analyses further reveal the chalcogen bonding between halide anions and Te σ-hole may be regarded as an ionic bond.

Chalcogen Bonds, Halogen Bonds and Halogen···Halogen Contacts in Di- and Tri-iododiorganyltellurium(IV) Derivatives

In this manuscript, we have examined the CSD (Cambridge Structural Database) to investigate the relative ability of Te and I (in practice, the heaviest chalcogen and halogen atoms) in di- and tri-iododiorganyltellurium(IV) derivatives to establish σ-hole interactions. The geometry around the Te(IV) in this type of compound is trigonal bipyramidal where the stereoactive lone pair at Te(IV) occupies one of the equatorial positions. In the solid state, Te(IV) tends to form pseudo-octahedral coordination by establishing strong noncovalent interactions opposite to the two covalent bonds of the equatorial plane. Such contacts can also be classified as chalcogen bonds following the recommendation of the International Union of Pure and Applied Chemistry (IUPAC). Such contacts have been analyzed energetically in this work using density functional theory (DFT) calculations, rationalized using molecular electrostatic potential (MEP) surface analysis and characterized using a combination of the quantum theory of atoms in molecules (QTAIM) and noncovalent interaction plot (NCIplot) computational tools. Finally, the observation of halogen bonds and type I halogen···halogen contacts is also emphasized and compared to the chalcogen bonds. Energy decomposition analysis has also been performed to compare the physical nature of chalcogen, halogen and type I interactions.