Hybrid Cyclopeptide-Based Chemical Models for Allosteric Disulfide and Amyloid Self-Assembly

We present here a series of isomeric disulfide-based hybrid cyclic peptides with different ring sizes. The water soluble pseudopeptidic macrocycles display a high intrinsic tendency to self-assemble. Microscopic investigations revealed amyloid like fibrillar morphology with autofluorescence. X-ray crystal structure of 23-membered macrocycle showed the presence of intramolecular hydrogen bonding and a unique S···O interaction. We delineate that the macrocyclic framework is an ideal platform to generate various classes of disulfide conformations. X-ray structure of the macrocycle further revealed the presence of an allosteric disulfide bond with -LHHook geometry.

Intramolecular Hydrogen Bond Modulated the Formation of Exciplex for Highly Efficient Organic Light-Emitting Diodes

Although exciplexes with thermally activated delayed fluorescence (TADF) properties have been applied in high-efficiency organic electroluminescent devices, the development of exciplexes has been hindered due to the limited material systems and unclear formation mechanisms. Inspired by the unusual exciplex emission discovered in the pyridine solution of 2,12-di-tert-butyl-5,9-dithia-13b-boranaphtho[3,2,1-de]anthracene (TSBA) in this work, the formation mechanism of exciplexes based on two groups of pyridine-based derivative isomeric acceptors 26DCzPPy, 35DCzPPy and B2PyPB, B3PyPB and B4PyPB was explored accordingly. The difference in the position of the substituted pyridine in the isomeric acceptors can effectively regulate the formation of intramolecular N···H hydrogen bonds, which further affects their interaction with the electron-donating unit in TSBA through a conformational locking effect-induced topological rigidification of the molecule, ultimately determining the formation of the exciplex. Based on this mechanism, 35DCzPPy, B3PyPB and B4PyPB acceptors, combined with the TSBA donor, display TADF exciplex emission as expected. Among these, 35DCzPPy:TSBA shows the excellent TADF property with a high photoluminescent quantum yield reaching 78%, and the corresponding device achieves a high external quantum efficiency of 18.72% along with a small efficiency roll-off. An in-depth investigation into the influence mechanisms of intramolecular interactions on exciplex construction in this work will provide crucial theoretical guidance and design strategies for developing novel, highly efficient exciplex materials.

Redox-Responsive Side Chain Structural Changes in a Seven-Membered Cyclic α,α-Disubstituted α-Amino Acid with a Disulfide Bond Enable Reversible Conformational Changes in Peptides

We report the development of a redox-responsive system that induces reversible conformational changes in peptides through the design of a seven-membered cyclic α,α-disubstituted α-amino acid with a disulfide bond, 5-amino-1,2-dithiepane-5-carboxylic acid (Dtp). Upon reduction, the disulfide bond in Dtp was cleaved to form thiols, converting Dtp into (2-mercaptoethyl)homocysteine (Mhc), and this process was reversed by oxidation. Dtp-containing peptides predominantly adopted 310-helical conformation in solution, whereas Mhc-containing peptides exhibited a mixture of helical and other conformations. This redox-responsive mechanism allows for precise control over peptide secondary structures, making it a promising approach for designing functional helical peptides capable of acting molecular switches in response to intracellular reductive environments.

Exploring the influence of (n - 1)d subvalence correlation and of spin-orbit coupling on chalcogen bonding

This article presents a comprehensive computational investigation into chalcogen bonding interactions, focusing specifically on elucidating the role of subvalence (n - 1)d and (n - 1)sp correlation. The incorporation of inner-shell (n - 1)d correlation leads to a decrease in interaction energies for chalcogen-bonded systems (at least those studied herein), contradicting the observations regarding halogen bonding documented by Kesharwani et al. in J. Phys. Chem. A, 2018, 122 (8), 2184-2197. The significance of (n - 1)sp subvalence correlation appears to be lower by an order of magnitude. Notably, among the various components of interaction energies computed at the PNO-LCCSD(T) or DF-CCSD levels, we identify the PNO-LMP2 or DF-MP2 component of the (n - 1)d correlation as predominant. Furthermore, we delve into the impact of second-order spin-orbit coupling (SOC2) on these interactions. The SOC2 effects appear to be less significant than the (n - 1)d correlation; however, they remain non-trivial, particularly for Te complexes. For the Se complexes, SOC2 is much less important. Generally, SOC2 stabilizes monomers more than dimers, resulting in reduced binding of the latter. Notably, at equilibrium and stretched geometries, SOC2 and (n - 1)d destabilize the complex; however, at compressed geometries, they exhibit opposing effects, with (n - 1)d becoming stabilizing.

Self-contacting Cys, Ser, and Thr residues in high-resolution protein crystal structures: Tertiary constraints or hydrogen bonds?

Functional groups in the side-chains of at least 10 amino acids are mainly involved in tertiary interactions. However, structural and functional significance of intra-residue interactions has not been fully recognized. In this study, we have analyzed ~5800 non-redundant high-resolution protein structures and identified 1166 self-contacts between the side-chain S-H/O-H and backbone C=O groups in Cys, Ser, and Thr residues that satisfied the geometric criteria to form hydrogen bonds. Quantum chemical calculations using model compounds were used to evaluate single point energy for 45 representative examples from different allowed regions of Ramachandran map. Relative energy profiles obtained by varying the side-chain dihedral angle χ1 revealed that the energy difference between the crystal structure and the minimum energy conformations is between 0 and 3 kcal/mol. Natural bond orbital analysis (NBO) of self-contacting Cys residues revealed no charge transfer between Cys side-chain S-H and the backbone C=O groups. However, side-chain hydroxyl and the backbone C=O groups of 90%-95% of all self-contacting Ser and Thr residues are involved in charge transfer and the second order perturbation energy of majority of them is above 1 kcal/mol. Interaction energies calculated for model compounds along with NBO and NCIPLOT analyses demonstrate that the self-contacts observed in Ser and Thr residues can be described as hydrogen bonds. These interactions may provide stability to the loop/coil conformations. Self-contacting Cys residues are buried and the self-contacts appear to be mostly due to tertiary constraints. Dispersion between the self-contacting groups is one way to explain the close approach in Cys residues. Mutation studies will further validate and reveal the structural and functional significance of these self-contacting residues.

Mixed H2S and H2O Clusters─New Insights into Dispersion-Dominated Hydrogen Bonding

Here, we report the results of an IR spectroscopy study on heteroclusters of H2S and H2O and several of their isotopomers using mass-selective IR spectroscopy in superfluid helium nanodroplets in the range of 2560-2800 cm-1. Based on DFT calculations on the B3LYP-D3/6-311++G(d,p) level of theory, we were able to assign the experimentally observed O-D stretching bands to heterodimer and heterotrimer clusters. Since no bands of the S-H-bound conformer HSH···OH2 could be observed, we were able to determine the O-H-bound conformer HOH···SH2 to be the global minimum structure. A trapping of the local minima in helium nanodroplets was not observed. This is in line with the weaker hydrogen bond expected for H2S complexes. In these clusters, the interaction energy is expected to be more dominated by dispersion and less dictated by highly directional electrostatic forces.

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.

Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I

Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.

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.

Probing the Directionality of S···O/N Chalcogen Bond and Its Interplay with Weak C-H···O/N/S Hydrogen Bond Using Molecular Electrostatic Potential

The directionality of the chalcogen bond (Ch-bond) formed by S and its interplay with other weak interactions have important chemical and biological implications. Here, dimers made of CH₃-S-X and O/N containing nucleophiles are studied and found to be stabilized by coexisting S···O/N and C-H···O/N interactions. Based on experimentally accessible electron density and molecular electrostatic potentials (MESPs), we showed that reciprocity between S···O/N and C-H···O/N interactions in the stability of cumulative molecular interaction (ΔE) was dependent on the strength of the σ-hole on S (V_s,max). Direct correlation between ΔE of dimers with V_s,max of S supports the electrostatic nature of the Ch-bond. Such interplay of the Ch-bond is necessary for its directionality in complex nucleophiles (carbonyl groups) with multiple electron-rich centers, which is explained using MESP. A correlation between the MESP minima in the π-region and the strength of the S-π interaction explains the directional selectivity of the Ch-bond.

Various Sorts of Chalcogen Bonds Formed by an Aromatic System

The chalcogen Y atom in the aromatic ring of thiophene and its derivatives YC₄H₄ (Y = S, Se, Te) can engage in a number of different interactions with another such unit within the homodimer. Quantum calculations show that the two rings can be oriented perpendicular to one another in a T-shaped dimer in which the Y atom accepts electron density from the π-system of the other unit in a Y···π chalcogen bond (ChB). This geometry best takes advantage of attractions between the electrostatic potentials surrounding the two monomers. There are two other geometries in which the two Y atoms engage in a ChB with one another. However, instead of a simple interaction between a σ-hole on one Y and the lone pair of its neighbor, the interaction is better described as a pair of symmetrically equivalent Y···Y interactions, in which charge is transferred in both directions simultaneously, thereby effectively doubling the strength of the bond. These geometries differ from what might be expected based simply on the juxtaposition of the electrostatic potentials of the two monomers.

Principles Guiding the Square Bonding Motif Containing a Pair of Chalcogen Bonds between Chalcogenadiazoles

The bonding motif adopted by a dimer of chalcogenadiazole molecules is characterized by a pair of equivalent Ch···N chalcogen bonds. Quantum calculations show that the interaction energy is substantial, varying between 4 kcal/mol for Ch = S and 17 kcal/mol for Te. The interaction is cooperative in that the total bond strength is greater than either chalcogen bond individually. Neither the addition of a phenyl ring nor the addition of a pair of cyano substituents to the diazole ring has much influence on this binding. Removal of one N from the diazole weakens the binding, and addition of two nitrogens has little effect. The largest perturbation arises with three N atoms in each ring, for which the binding energy increases by some 25%. The ring size plays a minor role in most cases, although a near doubling of bond strength occurs if there are two N atoms present on a four-membered ring.

An isotropic three-dimensional organic semiconductor 2-(thiopyran-4-ylidene)-1,3-benzodithiole (TP-BT): asymmetric molecular design to suppress access resistance

We report the synthesis of P-BT and TP-BT and their OTFT properties based on electronic dimensionality and access resistance (Racc). TP-BT can suppress Racc due to its 3D electronic structure.

Synthesis and absolute structure of (R)-2-(benzyl-selan-yl)-1-phenyl-ethanaminium hydrogen sulfate monohydrate: crystal structure and Hirshfeld surface analyses

A hydrogen sulfate salt, C15H18NSe+·HSO4 -·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 -), of a chiral selenated amine (R)-2-(benzyl-selan-yl)-1-phenyl-ethan-amine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT-IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitro-gen atom is chiral and in the R configuration, and, the -C-C- bond of the -CH2-CH- fragment has a staggered conformation. In the crystal structure, two HSO4 - anions and two water mol-ecules form an R 4 4(12) tetra-meric type of assembly comprised of alternating HSO4 - anions and water mol-ecules via discrete D(2) O-H⋯O hydrogen bonds. This tetra-meric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are inter-connected via discrete D(2) N-H⋯O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 - anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C-H⋯π inter-actions between adjacent cations running as chains down the [010] axis. Secondary Se⋯O [3.1474 (4) Å] inter-actions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent mol-ecule, was carried out to confirm the presence of various inter-actions in the crystal structure.

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.

CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions?

We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

Design, synthesis, and photophysics of bi- and tricyclic fused pyrazolines

A three series of bi-cyclic and tri-cyclic functionalised pyrazoline fluorophores with high quantum yields and positive solvato(fluoro)chromism were designed and synthesised by improved method.

Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects

In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6^γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6^γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6^γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type C[double bond, length as m-dash]O⋯H(N)⋯SR₂, while the trimer adopts two C5-C6^γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.

What is the preferred geometry of sulfur–disulfide interactions?

Combined crystallographic and quantum chemical studies showed that in most cases, in crystal structures, interactions between sulphur atoms and disulphide bonds are bifurcated.

Secondary Forces in Protein Folding

A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.

Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone

Oxidation and protonation/deprotonation strongly impact intermolecular noncovalent interactions. For example, S-aromatic interactions are stabilized up to three-fold in the gas phase on oxidation of the sulfur ligand or protonation/deprotonation of the aromatic. To probe if such stabilizing effects are additive and to model interactions of oxidized methionine (MetOn) with protonated histidine and deprotonated tyrosine residues in proteins, we examined Me2SOn (n = 1, 2) binding to imidazolium, phenolate and their 4-methylated forms. Ab initio MP2(full)/6-311++G(d,p) gas-phase calculations reveal that the Me2SOn-imidazolium complexes adopt edge-on geometry with σ-type (N/C-HarO) H-bonding and interaction energies of -17.2 to -31.1 kcal mol-1. The less stable (-13.8 to -21.0 kcal mol-1) Me2SOn-phenolates possess en-face geometry stabilized by π-type (C-Hπar) H-bonding. Comparing these energies with those reported for the Me2S-neutral aromatics affirms the additive effects of ligand protonation/deprotonation and oxidation on gas-phase stability. However, this is not the case in water although the aqueous complexes retain their preferred gas-phase σ- and π-type H-bonded structures. Binding free energies (kcal mol-1) calculated from molecular dynamics simulations in bulk water (preceded by CHARMM36 force field calibration where necessary) reveal that Me2SO-imidazolium (-4.4) is more stable than Me2SO-phenolate (-2.4) but Me2SO2-imidazolium (-0.6) is less stable than Me2SO2-phenolate (-3.8). Vertical ionization potentials (IPV) calculated for the gas-phase complexes indicate that the Me2SOn-phenolates, but not the Me2SOn-imidazoles, are oxidizable under biological conditions. Charge transfer from the phenolate increases its IPV by ∼20%, decreasing its susceptibility to oxidation. Overall, this work provides fundamental data to predict the behaviour of protein-based MetOn-aromatic-ion interactions.

Nature of the E⋯E′ interactions (E, E′ = O, S, Se, and Te) at naphthalene 1,8-positions with fine details of the structures: experimental and theoretical investigations

The nature of E⋯E′ in 1-RE–8-R′E′C₁₀H₆ (E/E′ = O, S, Se and Te) is clarified with the QTAIM approach and NBO analysis, after structural determinations.

Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H₂S, MeSH) and Met (Me₂S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-H_ar···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-H_ar···S or S-H···O_ar/N_ar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.

From Noncovalent Chalcogen-Chalcogen Interactions to Supramolecular Aggregates: Experiments and Calculations

This review considers noncovalent bonds between divalent chalcogen centers. In the first part we present X-ray data taken from the solid state structures of dimethyl- and diphenyl-dichalcogenides as well as oligoalkynes kept by alkyl-sulfur, -selenium, and -tellurium groups. Furthermore, we analyzed the solid state structures of medium sized (12-24 ring size) selenium coronands and medium to large rings with alkyne and alkene units between two chalcogen centers. The crystal structures of the cyclic structures revealed columnar stacks with close contacts between neighboring rings via noncovalent interactions between the chalcogen centers. To get larger space within the cavities, rings with diyne units between the chalcogen centers were used. These molecules showed channel-like structures in the solid state. The flexibility of the rings permits inclusion of guest molecules such as five-membered heterocycles and aromatic six-membered rings. In the second part we discuss the results of quantum chemical calculations. To treat properly the noncovalent bonding between chalcogens, we use diffuse augmented split valence basis sets in combination with electron correlation methods. Our model substances were 16 dimers consisting of two Me-X-Me (X = O, S, Se, Te) pairs and dimers of Me-X-Me/Me-X-CN (X = O, S, Se, Te) pairs. The calculations show the anticipated increase of the interaction energy from (Me-O-Me)₂ (-2.15 kcal/mol) to (Me-O-Me/Me-Te-CN) (-6.59 kcal/mol). An analysis by the NBO method reveals that in the case of the chalcogen centers O and S the hydrogen bridges between the molecules dominate. However, in the case of Se and Te the major bonding between the pairs originates from dispersion forces between the chalcogen centers. It varies between -1.7 and -4.0 kcal/mol.

Predicting structural and energetic changes in Met–aromatic motifs on methionine oxidation to the sulfoxide and sulfone

Methionine oxidation increases its affinity for aromatics in the gas phase but lowers it for most complexes in water.

The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy

A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone pair orbital into a π* orbital. New polymeric materials based on chalcogen bonds should take advantage of the extra stabilization granted by multiple chalcogen bonds, as is shown for 1,2,5-telluradiazole dimers.

Hydrogen bonding liquid crystalline benzoic acids with alkylthio groups: phase transition behavior and insights into the cybotactic nematic phase

A novel class of hydrogen bonding liquid crystalline benzoic acids with alkylthio groups was established and their phase transition behavior was investigated in detail.

S···O and S···N Sulfur Bonding Interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function

Sulfur bonding interactions between organosulfur compounds and proteins were examined using crystal structures deposited to-date in the PDB. The data was analyzed as a function of sulfur-σ-hole-bonding (i.e., sulfur bonds) to main chain Lewis bases, viz. oxygen and nitrogen atoms of the backbone amide linkages. The analyses also included an examination of sulfur bonding to side chain Lewis bases (O, N, and S) and to the "non-classical" Lewis bases present in electron-rich aromatic amino acids as-well-as to donor-acceptor bond angle distributions. The interactions analyzed included those restricted to the sum of van der Waals radii of the respective atoms or to a distance of 4 Å. The surveyed data revealed that sulfur bonding tendencies (C-S-C bond angles) were impacted not only by steric effects but perhaps also by enthalpic features present in both the donor and acceptor participants. This knowledge is not only of fundamental interest but is also important in terms of materials and drug-design involving moieties incorporating the sulfur atom. Additionally, a new empirical scoring function was developed to address the anisotropy of sulfur in protein-ligand interactions. This newly developed scoring function is incorporated into AutoDock Vina molecular docking program and is valuable for modeling and drug design.

A crucial role of Cys218 in configuring an unprecedented auto-inhibition form of MAP2K7

Mitogen-activated protein kinase kinase 7 (MAP2K7) is an indispensable kinase of the c-Jun N-terminal kinase signal cascade and is rigorously regulated via phosphorylation. To investigate the regulatory mechanism of the inactive non-phosphorylated state of MAP2K7, the crystal structures of the wild-type and C218S mutant were solved. The wild-type apo-structure revealed an unprecedented auto-inhibition form that occluded the ATP site. This closed form was configured by the n-σ* interaction of Cys218, a non-conserved residue among the MAP2K family kinases, with Gly145 in the glycine-rich loop. The interaction was unaltered in the presence of an ATP analog, whereas the C218S mutation precluded the closed configuration. These structural insights are potentially valuable for drug discovery of highly selective MAP2K7 inhibitors.

Structures of potent anticancer compounds bound to tubulin

Small molecules that bind to tubulin exert powerful effects on cell division and apoptosis (programmed cell death). Cell-based high-throughput screening combined with chemo/bioinformatic and biochemical analyses recently revealed a novel compound MI-181 as a potent mitotic inhibitor with heightened activity towards melanomas. MI-181 causes tubulin depolymerization, activates the spindle assembly checkpoint arresting cells in mitosis, and induces apoptotic cell death. C2 is an unrelated compound previously shown to have lethal effects on microtubules in tumorigenic cell lines. We report 2.60 Å and 3.75 Å resolution structures of MI-181 and C2, respectively, bound to a ternary complex of αβ-tubulin, the tubulin-binding protein stathmin, and tubulin tyrosine ligase. In the first of these structures, our crystallographic results reveal a unique binding mode for MI-181 extending unusually deep into the well-studied colchicine-binding site on β-tubulin. In the second structure the C2 compound occupies the colchicine-binding site on β-tubulin with two chemical moieties recapitulating contacts made by colchicine, in combination with another system of atomic contacts. These insights reveal the source of the observed effects of MI-181 and C2 on microtubules, mitosis, and cultured cancer cell lines. The structural details of the interaction between tubulin and the described compounds may guide the development of improved derivative compounds as therapeutic candidates or molecular probes to study cancer cell division.

Charge-displacement analysis as a tool to study chalcogen bonded adducts and predict their association constants in solution

The secondary interaction between an atom of tellurium and different Lewis bases has been studied by charge displacement analysis, providing a detailed description of the interaction and a computational insight into experimental data.

Assembly of thioether-containing rod-like liquid crystalline materials assisted by hydrogen-bonding terminal carboxyl groups

A hydrogen-bonding-tolane-based liquid crystalline material with an alkylsulfanyl group was synthesized, which exhibited a long-range correlated mesophase compared with analogs with alkyl and alkoxy groups.

Optimization of pyrrolamide topoisomerase II inhibitors toward identification of an antibacterial clinical candidate (AZD5099)

AZD5099 (compound 63) is an antibacterial agent that entered phase 1 clinical trials targeting infections caused by Gram-positive and fastidious Gram-negative bacteria. It was derived from previously reported pyrrolamide antibacterials and a fragment-based approach targeting the ATP binding site of bacterial type II topoisomerases. The program described herein varied a 3-piperidine substituent and incorporated 4-thiazole substituents that form a seven-membered ring intramolecular hydrogen bond with a 5-position carboxylic acid. Improved antibacterial activity and lower in vivo clearances were achieved. The lower clearances were attributed, in part, to reduced recognition by the multidrug resistant transporter Mrp2. Compound 63 showed notable efficacy in a mouse neutropenic Staphylococcus aureus infection model. Resistance frequency versus the drug was low, and reports of clinical resistance due to alteration of the target are few. Hence, 63 could offer a novel treatment for serious issues of resistance to currently used antibacterials.

Discovery and development of hepatitis C virus NS5A replication complex inhibitors

Lead inhibitors that target the function of the hepatitis C virus (HCV) nonstructural 5A (NS5A) protein have been identified by phenotypic screening campaigns using HCV subgenomic replicons. The demonstration of antiviral activity in HCV-infected subjects by the HCV NS5A replication complex inhibitor (RCI) daclatasvir (1) spawned considerable interest in this mechanistic approach. In this Perspective, we summarize the medicinal chemistry studies that led to the discovery of 1 and other chemotypes for which resistance maps to the NS5A protein and provide synopses of the profiles of many of the compounds currently in clinical trials. We also summarize what is currently known about the NS5A protein and the studies using NS5A RCIs and labeled analogues that are helping to illuminate aspects of both protein function and inhibitor interaction. We conclude with a synopsis of the results of notable clinical trials with HCV NS5A RCIs.

Conformational analysis of some N,N-diethyl-2-[(4'-substituted) phenylthio] acetamides

The conformational analysis of some N,N-diethyl-2[(4'-substituted)phenylthio]acetamides bearing the substituents OMe 1, Me 2, H 3, Cl 4, Br 5 and NO26, was performed by νCO IR analysis, along with B3LYP/6-311++G(d,p) and Polarisable Continuum Model (PCM) calculations, as well as NBO analysis for 1, 3, and 6 and X-ray diffraction for 4. The results of the calculations indicated the existence of two stable conformation pairs, i.e. gauche (anti; syn) (most stable) and cis (anti; syn) in the gas phase. The gauche conformers were less polar with respect to the cis ones for 1 and 3, but more polar for 6. The most intense IR carbonyl doublet component observed at the lower frequency can be ascribed to the gauche conformers g(anti; syn) for 3-6 in n-C6H14, which is in agreement with the gauche and cis relative stabilities and frequencies resulting from the PCM calculations. Similarly, the single IR band for 1 and 2 in n-hexane may be attributed to the gauche conformers. The PCM calculations compared well with the IR data for the compounds in solution, showing that there is a progressive increase of the cis/gauche population ratio as the solvent polarity increases. The NBO analysis indicated that the gauche(anti; syn) conformation in the gas phase was stabilized by the relevant LPS4→πC2O1(∗),πC2O1→σC3S4(∗),σC3S4→πC2O1(∗),πC2O1(∗)→σC3S4(∗), and LPO1→σ(∗)C11H28 orbital interactions, which were absent in the cis(anti; syn) conformer. On the contrary, the cis conformer for derivatives 1, 3, and 6 were stabilized by the σC3-S4(∗)→σ(∗)C2N5 orbital interaction (through bond coupling), along with the additional LPO1→σ(∗)S4C10 interaction for 6. Moreover, the electrostatic repulsion between the C(δ+)S(δ-) and C(δ+)O(δ-) dipoles (Repulsive Field Effect) contributed to both the larger destabilization and increase of the νCO frequency of the cis conformer with respect to the gauche conformer. X-ray single crystal analysis indicates that compound 4 assumes the c2(anti) conformation in the solid state, which is the conformation obtained by compound 6 in the gas phase. To obtain the largest energy gain, the molecules were arranged in the crystal in a six-molecules synthon mediated by CH⋯O and Cl⋯Cl interactions, where the chlorine atoms were related by a crystallographic inversion center.