Production of Alkyl Aryl Sulfides from Aromatic Disulfides and Alkyl Carboxylates via a Disilathiane–Disulfide Interchange Reaction

The results of this study show that disilathiane is an effective mediator in the synthesis of alkyl aryl sulfides with disulfides and alkyl carboxylates. Mechanistic studies suggest that disilathiane promotes cleavage of the sulfur–sulfur bond of disulfides to generate thiosilane as a key intermediate. Diselenides were also applicable to this transformation to produce the corresponding selenides.     

Conformational polymorphs of 3‐cyclopropyl‐5‐(3‐methyl‐[1,2,4]triazolo[4,3‐a]pyridin‐7‐yl)‐1,2,4‐oxadiazole

The dipharmacophore compound 3‐cyclopropyl‐5‐(3‐methyl‐[1,2,4]triazolo[4,3‐a]pyridin‐7‐yl)‐1,2,4‐oxadiazole, C₁₂H₁₁N₅O, was studied on the assumption of its potential biological activity. Two polymorphic forms differ in both their molecular and crystal structures. The monoclinic polymorphic form was crystallized from more volatile solvents and contains a conformer with a higher relative energy. The basic molecule forms an abundance of interactions with relatively close energies. The orthorhombic polymorph was crystallized very slowly from isoamyl alcohol and contains a conformer with a much lower energy. The basic molecule forms two strong interactions and a large number of weak interactions. Stacking interactions of the `head‐to‐head' type in the monoclinic structure and of the `head‐to‐tail' type in the orthorhombic structure proved to be the strongest and form stacked columns in the two polymorphs. The main structural motif of the monoclinic structure is a double column where two stacked columns interact through weak C—H…N hydrogen bonds and dispersive interactions. In the orthorhombic structure, a single stacked column is the main structural motif. Periodic calculations confirmed that the orthorhombic structure obtained by slow evaporation has a lower lattice energy (0.97 kcal mol^?1) compared to the monoclinic structure.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

Elucidating the Binding Mode between Heparin and Inflammatory Cytokines by Molecular Modeling

Heparan sulfate (HS) interacts with a broad spectrum of inflammatory cytokines, thereby modulating their biological activities. It is believed that there is a structural-functional correlation between each protein and sugar sequences in the HS polysaccharides, however, the information in this regard is limited. In this study, we compared the binding of four inflammatory cytokines (CCL8, IL-1beta, IL-2 and IL-6) to immobilized heparin by an SPR analysis. To define the molecular base of the binding, we used a heparin pentasaccharide as representative structure to dock into the 3D-molecular structure of the cytokines. The results show a discrepancy in K_D values obtained by SPR analysis and theoretical calculation, pointing to the importance to apply more than one method when describing affinity between proteins and HS. By cluster analysis of the complex formed between the pentasaccharide and cytokines, we have identified several groups in heparin forming strong hydrogen bonds with all four cytokines, which is a significant finding. This molecular and conformational information should be valuable for rational design of HS/heparin-mimetics to interfere cytokine-HS interactions.     

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.     

Probing the Interactions of Porphyrins with Macromolecules Using NMR Spectroscopy Techniques

Porphyrinic compounds are widespread in nature and play key roles in biological processes such as oxygen transport in blood, enzymatic redox reactions or photosynthesis. In addition, both naturally derived as well as synthetic porphyrinic compounds are extensively explored for biomedical and technical applications such as photodynamic therapy (PDT) or photovoltaic systems, respectively. Their unique electronic structures and photophysical properties make this class of compounds so interesting for the multiple functions encountered. It is therefore not surprising that optical methods are typically the prevalent analytical tool applied in characterization and processes involving porphyrinic compounds. However, a wealth of complementary information can be obtained from NMR spectroscopic techniques. Based on the advantage of providing structural and dynamic information with atomic resolution simultaneously, NMR spectroscopy is a powerful method for studying molecular interactions between porphyrinic compounds and macromolecules. Such interactions are of special interest in medical applications of porphyrinic photosensitizers that are mostly combined with macromolecular carrier systems. The macromolecular surrounding typically stabilizes the encapsulated drug and may also modify its physical properties. Moreover, the interaction with macromolecular physiological components needs to be explored to understand and control mechanisms of action and therapeutic efficacy. This review focuses on such non-covalent interactions of porphyrinic drugs with synthetic polymers as well as with biomolecules such as phospholipids or proteins. A brief introduction into various NMR spectroscopic techniques is given including chemical shift perturbation methods, NOE enhancement spectroscopy, relaxation time measurements and diffusion-ordered spectroscopy. How these NMR tools are used to address porphyrin–macromolecule interactions with respect to their function in biomedical applications is the central point of the current review.     

Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol—A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling

The CB₁ cannabinoid receptor (CB₁R) contains one of the longest N termini among class A G protein-coupled receptors. Mutagenesis studies suggest that the allosteric binding site of cannabidiol (CBD) involves residues from the N terminal domain. In order to study the allosteric binding of CBD to CB₁R we modeled the whole N-terminus of this receptor using the replica exchange molecular dynamics with solute tempering (REST2) approach. Then, the obtained structures of CB₁R with the N terminus were used for ligand docking. A natural cannabinoid receptor agonist, Δ⁹-THC, was docked to the orthosteric site and a negative allosteric modulator, CBD, to the allosteric site positioned between extracellular ends of helices TM1 and TM2. The molecular dynamics simulations were then performed for CB₁R with ligands: (i) CBD together with THC, and (ii) THC-only. Analyses of the differences in the residue-residue interaction patterns between those two cases allowed us to elucidate the allosteric network responsible for the modulation of the CB₁R by CBD. In addition, we identified the changes in the orthosteric binding mode of Δ⁹-THC, as well as the changes in its binding energy, caused by the CBD allosteric binding. We have also found that the presence of a complete N-terminal domain is essential for a stable binding of CBD in the allosteric site of CB₁R as well as for the allosteric-orthosteric coupling mechanism.     

Spatiotemporal organization of coacervate microdroplets

Liquid–liquid phase separation (LLPS) has emerged as a new paradigm in the fields of soft matter, colloid chemistry, prebiotic chemistry, and cell biology. As phase separation is a dynamic assembly process, how to spatiotemporally regulate the assembly and disassembly of these micrometre-sized droplets, which are referred as biomolecular condensates in biology is essential for their diverse applications in various disciplines. Herein, we discuss recent advances in the spatiotemporal control of phase separation using different physical tools and external environmental stimuli in bulk solutions and living cells. Specifically, the exploration of phase transition in a compartmentalized protocellular system, which can bridge the gap between synthetic and intracellular LLPS systems, is summarized, and the challenges and future research directions are discussed.     

Theoretical investigation of nonlinear optical behavior for rod and T-Shaped phenothiazine based D-π-A organic compounds and their derivatives

The exploration of novel materials with excellent nonlinear optical (NLO) features is an area of frontline investigation for scientific community from technological point of view. This study reports the novel phenothiazine-based rod-shaped and T-shaped NLO molecules which are quantum chemically designed from synthesized compounds: rod-shaped (CFA and CBA) and T-shaped (CTA, CCA and CPA). Structural tailoring was performed on D-π-π-A centered CPA chromophore and the effect of various π-spacers, as well as solvents on NLO response properties is investigated. Density functional theory (DFT) along with time dependent DFT (TDDFT) calculations have been executed at B3LYP/6-311G(d,p) functional to examine entire analysis. Results showed a smaller energy gap in structurally modified compounds as compared to reference CPA. Global reactivity parameters analysis revealed smaller hardness and larger softness values in T-shaped compounds. UV–Vis analysis of investigated molecules displayed a red shift in absorption maximum value as compared to CPA. Natural bond orbital (NBO) and frontier molecular orbital (FMO) analysis revealed the stability and intra-molecular electron transferring (ICT) process in investigated molecules. ICT showed the effective charge shift from donor to acceptor via π-spacers. Overall, promising NLO response exists in gas phase and different solvents (acetonitrile, ethyl alcohol and water). Interestingly, proposed molecule CPP presented a maximum value of linear polarizability < α > as 1518.23 a.u and first hyperpolarizability (β_tot) as 755322.39 a.u in acetonitrile solvent. In short, entitled chromophores exhibited excellent NLO properties due to their lower charge transport resistance. This NLO study may open a new topic for researchers to discover novel NLO for hi-tech submissions of modern era.     

Changes in the physical properties of low bandgap polymer after interaction with ionic liquids

Over the past few years, polymers shown comprehensive utilization in optical devices, solar cells, sensors, and other such devices. However, the efficiency of these devices remains a problem. We have synthesized new thiophene based, lowband gap polymer, poly(2-heptadecyl-4-vinylthieno[3,4-d] [1,3] selenazole) (PHVTS) and investigated the interactions between the PHVTS and ionic liquids (ILs), in this study. We have used imidazolium- and ammonium-family ILs, and studied the interactions using various spectroscopic techniques such UV–visible, FTIR, and confocal Raman spectroscopies. Additionally, we studied surface morphology of the polymer-IL film. Spectroscopic studies show that both families of ILs can interact with the newly synthesized polymer poly(2-heptadecyl-4-vinylthieno[3,4-d] [1,3] selenazole). However, the imidazolium-family Ionic Liquid-polymer (IL-polymer) mixture films show higher conductivities than ammonium-family IL–polymer mixture films.