Organocatalytic diastereo- and atroposelective construction of N-N axially chiral pyrroles and indoles.

The construction of N-N axially chiral motifs is an important research topic, owing to their wide occurrence in natural products, pharmaceuticals and chiral ligands. One efficient method is the atroposelective dihydropyrimidin-4-one formation. We present herein a direct catalytic synthesis of N-N atropisomers with simultaneous creation of contiguous axial and central chirality by oxidative NHC (N-heterocyclic carbenes) catalyzed (3 + 3) cycloaddition. Using our method, we are able to synthesize structurally diverse N-N axially chiral pyrroles and indoles with vicinal central chirality or bearing a 2,3-dihydropyrimidin-4-one moiety in moderate to good yields and excellent enantioselectivities. Further synthetic transformations of the obtained axially chiral pyrroles and indoles derivative products are demonstrated. The reaction mechanism and the origin of enantioselectivity are understood through DFT calculations.

Kinetic Resolution of Acyclic Tertiary Propargylic Alcohols by NHC-Catalyzed Enantioselective Acylation.

We report herein an efficient NHC-catalyzed kinetic resolution of acyclic tertiary propargylic alcohols that provides them in high to excellent enantioselectivity. This is the first example of kinetic resolution realized by enantioselective acylation. The recovered enantioenriched alcohols can be facilely converted into other valuable compounds such as densely functionalized tertiary alcohols and carbmates in high yields and excellent stereopurity. Density functional theory calculations were performed to determine the reaction mechanism and to understand the origin of enantiodiscrimination.

Enhancing silicon-nitride formation through ammonolysis of silanes with pseudo-halide substituents.

Considering the challenges in reactivity, potential contamination, and substrate selectivity, the ammonolysis of traditional halosilanes in silicon nitride (SiN) thin film processing motivates the exploration of alternative precursors. In this pioneering study, we employed density functional theory calculations at the M06-2X/6-311++G(3df,2p) level to comprehensively screen potential pseudo-halide substituents on silane compounds as substitutes for conventional halosilanes. Initially, we investigated the ammonolysis mechanism of halosilanes, exploring factors influencing activation barriers, with the aid of frontier molecular orbital and charge density analyses. Subsequently, a systematic screening of silane substituents from group 14 to group 16 was conducted to identify pseudo-halides with low reaction barriers. Additionally, we examined the inductive effects on pseudohalide substituents. Using cluster models to represent the silicon surface validates the realistic prediction of ammonolysis barriers with a simplified model. Our findings indicate that pseudo-halide substituents from group 16, particularly those with electron-withdrawing groups, present as practical alternatives to traditional halosilanes in SiN thin film processing, including applications such as low-temperature atomic layer deposition (ALD) techniques.

Highly Selective On-Surface Ring-Opening of Aromatic Azulene Moiety.

Controllable ring-opening of polycyclic aromatic hydrocarbons plays a crucial role in various chemical and biological processes. However, breaking down aromatic covalent C-C bonds is exceptionally challenging due to their high stability and strong aromaticity. This study presents a seminal report on the precise and highly selective on-surface ring-opening of the seven-membered ring within the aromatic azulene moieties under mild conditions. The chemical structures of the resulting products were identified using bond-resolved scanning probe microscopy. Furthermore, through density functional theory calculations, we uncovered the mechanism behind the ring-opening process and elucidated its chemical driving force. The key to achieving this ring-opening process lies in manipulating the local aromaticity of the aromatic azulene moiety through strain-induced internal ring rearrangement and cyclodehydrogenation. By precisely controlling these factors, we successfully triggered the desired ring-opening reaction. Our findings not only provide valuable insights into the ring-opening process of polycyclic aromatic hydrocarbons but also open up new possibilities for the manipulation and reconstruction of these important chemical structures.

Dispersion-Corrected DFT-D4 Study of the Adsorption of Halobenzenes and 1,3,5-Trihalobenzenes on the Cu(111) Surface─Effect of Sigma Hole Properties.

Halogen bonds, characterized by directionality, tunability, hydrophobicity, and variable sizes, are ideal noncovalent interactions to design and control the formation of self-assembled nanostructures. The specific self-assembly cases formed by the halogen-bonding interaction have been well studied by scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. However, there is a lack of systematic theoretical adsorption studies on halogenated molecules. In this work, the adsorption of halobenzenes and 1,3,5-trihalobenzenes on the Cu(111) surface was examined by dispersion-corrected DFT methods. The adsorption geometries, noncovalent molecule-surface interactions, electronic densities, and electrostatic potential maps were examined for their most stable adsorption sites using the DFT-D4 method. Our calculations revealed that the iodo compounds favor a different adsorption geometry from aryl chlorides and bromides. Down the halogen group (Cl to I), the adsorption energy increases and the distance between the halogen atom and Cu surface decreases, which indicates stronger molecule-surface interactions. This is supported by the changes in the density of states upon adsorption. Noncovalent interaction analysis was also employed to further understand the nature and relative strength of the molecule-surface interactions. Electrostatic potential maps revealed that the positive character of the halogen sigma hole becomes stronger upon adsorption. Thus, surface adsorption of the halogenated molecule will enhance the formation of intermolecular halogen bonds. The present theoretical findings are expected to contribute toward a more comprehensive understanding of halogen bonding on the Cu(111) surface.

A Computational Study on the Reaction Mechanism of Stereocontrolled Synthesis of ß-Lactam within [2]Rotaxane.

The macrocycle effect of [2]rotaxane on the highly trans-stereoselective cyclization reaction of N-benzylfumaramide was extensively investigated by various computational methods, including DFT and high-level DLPNO-CCSD(T) methods. Our computational results suggest that the most favorable mechanism of the CsOH-promoted cyclization of the fumaramide into trans-ß-lactam within [2]rotaxane initiates with deprotonation of a N-benzyl group of the interlocked fumaramide substrate by CsOH, followed by the trans-selective C-C bond formation and protonation by one amide functional group of the macrocycle. Our distortion/interaction analysis further shows that the uncommon trans-stereoselective cyclization forming ß-lactam within the rotaxane may be attributed to a higher distortion energy (mainly from the distortion of the twisted cis-fumaramide conformation enforced by the rotaxane). Our systematic study should give deeper mechanistic insight into the reaction mechanism influenced by a supramolecular host.

Targeting Pathogenic Formate-Dependent Bacteria with a Bioinspired Metallo-Nitroreductase Complex.

Nitroreductases (NTRs) constitute an important class of oxidoreductase enzymes that have evolved to metabolize nitro-containing compounds. Their unique characteristics have spurred an array of potential uses in medicinal chemistry, chemical biology, and bioengineering toward harnessing nitro caging groups and constructing NTR variants for niche applications. Inspired by how they carry out enzymatic reduction via a cascade of hydride transfer reactions, we sought to develop a synthetic small-molecule NTR system based on transfer hydrogenation mediated by transition metal complexes harnessing native cofactors. We report the first water-stable Ru-arene complex capable of selectively and fully reducing nitroaromatics into anilines in a biocompatible buffered aqueous environment using formate as the hydride source. We further demonstrated its application to activate nitro-caged sulfanilamide prodrug in formate-abundant bacteria, specifically pathogenic methicillin-resistant Staphylococcus aureus. This proof of concept paves the way for a new targeted antibacterial chemotherapeutic approach leveraging on redox-active metal complexes for prodrug activation via bioinspired nitroreduction.

Hybrid Electrolyte Design for High-Performance Zinc-Sulfur Battery.

Rechargeable aqueous Zn/S batteries exhibit high capacity and energy density. However, the long-term battery performance is bottlenecked by the sulfur side reactions and serious Zn anode dendritic growth in the aqueous electrolyte medium. This work addresses the problem of sulfur side reactions and zinc dendrite growth simultaneously by developing a unique hybrid aqueous electrolyte using ethylene glycol as a co-solvent. The designed hybrid electrolyte enables the fabricated Zn/S battery to deliver an unprecedented capacity of 1435 mAh g-1 and an excellent energy density of 730 Wh kg-1 at 0.1 Ag-1 . In addition, the battery exhibits capacity retention of 70% after 250 cycles even at 3 Ag-1 . Moreover, the cathode charge-discharge mechanism studies demonstrate a multi-step conversion reaction. During discharge, the elemental sulfur is sequentially reduced by Zn to S2- ( S 8 → S x 2 - → S 2 2 - + S 2 - ) ${{\rm{S}}_8}{\bm{ \to }}{\rm{S}}_{\rm{x}}^{2{\bm{ - }}}{\bm{ \to }}{\rm{S}}_2^{2{\bm{ - }}}{\bm{ + }}{{\rm{S}}^{2{\bm{ - }}}})$ , forming ZnS. On charging, the ZnS and short-chain polysulfides will oxidize back to elemental sulfur. This electrolyte design strategy and unique multi-step electrochemistry of the Zn/S system provide a new pathway in tackling both key issues of Zn dendritic growth and sulfur side reactions, and also in designing better Zn/S batteries in the future.

In Silico Screening of Multi-Domain Targeted Inhibitors for PTK6: A Strategy Integrating Drug Repurposing and Consensus Docking.

Protein tyrosine kinase 6 (PTK6), also known as breast tumor kinase (BRK), serves as a non-receptor intracellular tyrosine kinase within the Src kinases family. Structurally resembling other Src kinases, PTK6 possesses an Src homology 3 (SH3) domain, an Src homology 2 (SH2) domain, and a tyrosine kinase domain (SH1). While considerable efforts have been dedicated to designing PTK6 inhibitors targeting the SH1 domain, which is responsible for kinase activity in various pathways, it has been observed that solely inhibiting the SH1 domain does not effectively suppress PTK6 activity. Subsequent investigations have revealed the involvement of SH2 and SH3 domains in intramolecular and substrate binding interactions, which are crucial for PTK6 function. Consequently, the identification of PTK6 inhibitors targeting not only the SH1 domain but also the SH2 and SH3 domains becomes imperative. Through an in silico structural-based virtual screening approach, incorporating drug repurposing and a consensus docking approach, we have successfully identified four potential ligands capable of concurrently inhibiting the tyrosine kinase domain and SH2/SH3 domains of PT6K simultaneously. This finding suggests potential pathways for therapeutic interventions in PTK6 inhibition.

Functionalization of Alpha-Lactalbumin by Zinc Ions.

Alpha-lactalbumin (α-LA) and binding of zinc cations to protein were studied. Molecular characteristics of protein was determined by MALDI-TOF/MS and electrophoresis SDS-PAGE, and also, for complexes, it was determined by spectroscopic techniques (ATR-FT-IR and Raman) and microscopic techniques (SEM along with an EDX detector and also TEM). The pH dependence of zeta potential of α-LA was determined in saline solution. The zinc binding to the protein mechanism was investigated; zinc binding to protein kinetics, the molecular modeling by the DFT method, and electron microscopy (SEM and TEM) for microstructure observation were performed. The experiments performed indicate a quick binding process (equilibrium takes place after 2 min of incubation) which occurs onto the surface of α-LA. Zinc cations change the conformation of the protein and create spherical particles from the morphological point of view. DFT studies indicate the participation of acidic functional groups of the protein (aspartic acid and glutamic acid residues), and these have a decisive influence on the interaction with zinc cations. Application studies of general toxicity and cytotoxicity and bioavailability were conducted.

Study on silver ions binding to ß-lactoglobulin.

The drug-resistant pathogen phenomenon, resulting in infections and deaths that are increasingly difficult to treat, requires research into searching new potential antimicrobial agents. The presented study is focused on the investigation of impact of silver ions (Ag+ ions) to ß-lactoglobulin (ßLG) structure and mechanism formation of silver-ß-lactoglobulin nanocomposites, that could find potential applications in medicine. To determine the physicochemical characteristics of silver ion binding, kinetics and isothermal models were used. The presence of functional groups involved in the binding process was investigated by spectroscopic methods (FTIR-ATR, Raman spectroscopy). The binding ability and nanocomplexes formation was determined by instrumental analyses (SEM, TEM, EDX). Based on the obtained results, the binding of Ag+ ions to ßLG were heterogeneous in nature consisting of three main steps: rapid sorption of Ag+ ions on the ßLG surface, intramolecular diffusion of Ag+ ions, and chemical equilibrium. Microscopic studies showed a change in the surface morphology of ßLG and the appearance of silver nanoparticles. Spectroscopic studies indicated that acidic (Glu-, Asp-) and Lys, Tyr, Met amino groups play a key role in the formation of the AgßLG nanocomplex. Finally, molecular dynamics (MD) and density functional theory (DFT) calculated studies as a comparative and complementary method have proven contribution of respective amino acids in the binding process.

Three-Dimensional Quantitative Structure and Activity Relationship of Flavones on Their Hypochlorite Scavenging Capacity.

Flavonoids, a class of polyphenolic substances widely present in the plant realm, are considered as ideal hypochlorite scavengers. However, to our knowledge, little study has focused on the structure-activity relationship between flavonoids and hypochlorite scavenging capacity. Herein, we report for the first time the three-dimensional quantitative structure and activity relationship (3D-QSAR) combined with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Four models derived from CoMFA and CoMSIA with different combinations of descriptors were built and compared; the CoMFA model, which included both steric and electrostatic fields, showed great potential (R2 = 0.989; Q2 = 0.818) in predictive quality according to both internal and external validation criteria. Additionally, the average local ionization energy (ALIE), electrostatic potential (ESP), and orbital weighted dual descriptor (OWDD) were determined to identify the key structural moiety for scavenging capacity of flavonoids against hypochlorite. The computational results indicated that hypochlorous acid (HClO) serves as an electrophile undergoing electrophilic addition to the C6 carbon, which has the highest negative charge density, which are influenced by the functional groups on the flavones. The DFT calculated mechanism revealed the catalytic role of water of mono- and di-chlorination reactions, characterized by low activation barriers, and the involvement of neutral, instead of high-energy carbocation, intermediates.

Polymerization-like mechanism for fixation of CO2 with epoxides by multifunctional organocatalysts.

The commonly accepted mechanism of CO2 fixation of epoxides to cyclic carbonates catalyzed by multifunctional non-halide organocatalysts is challenged by our computational DFT-D3 study, which revealed a new polymerization-like mechanism comprising alternate epoxide and CO2 activation steps and a nested CO2 activation pathway. We investigated a recently reported CO2 coupling with epoxide reaction catalyzed by a bis-phenolic multifunctional catalyst. The predicted cis/trans product ratio is in excellent agreement with experimental results. The general applicability of the new mechanism is supported by another diamine-diacid catalyzed CO2 fixation reaction.

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations.

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand-protein complexes may shed light on rational design of potent ligands in the future.

Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization.

Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.

Tailoring long-range superlattice chirality in molecular self-assemblies via weak fluorine-mediated interactions.

Controllable fabrication of enantiospecific molecular superlattices is a matter of imminent scientific and technological interest. Herein, we demonstrate that long-range superlattice chirality in molecular self-assemblies can be tailored by tuning the interplay of weak intermolecular non-covalent interactions between hexaphenylbenzene-based enantiomers. By means of high-resolution scanning tunneling microscopy measurements, we demonstrate that the functionalization of a hexaphenylbenzene-based molecule with fluorine (F) atoms leads to the formation of molecular self-assemblies with distinct long-range chiral recognition patterns. We employed density functional theory calculations to quantify F-mediated lone pair F⋯π, C-H⋯F, and F⋯F interactions attributed to the distinct enantiospecific molecular self-organizations. Our findings underpin a viable route to fabricate long-range chiral recognition patterns in supramolecular assemblies by engineering the weak non-covalent intermolecular interactions.

In silico characterization and prediction of thiourea-like neutral bidentate halogen bond catalysts.

Preorganization is a common strategy to align halogen bond (XB) donors to form two or more halogen bonds simultaneously. Previous approaches have utilized various non-covalent interactions such as steric interactions, ππ stacking, and hydrogen bond interactions. However, some of the introduced aligning interactions may compete with halogen bond interactions if the donors are employed in catalysis. To achieve thiourea-like properties, we have designed in silico several neutral bidentate halogen bond donors in whose structures the donor moieties are connected via covalent bonds. Compared to previous XB catalyst designs, the new design does not involve other potentially competitive non-covalent interactions such as hydrogen bonds. One of the designed XB donors can deliver strong halogen bonds, with a O-I distance as short as 2.64 Å. Density functional theory (DFT) calculations predicted that our designed catalysts may catalyze important organic reactions on their own, particularly for those reactions that involve (developing) soft anions such as thiolates.

The study of the molecular mechanism of Lactobacillus paracasei clumping via divalent metal ions by electrophoretic separation.

In this work, the molecular mechanism of Lactobacillus paracasei bio-colloid clumping under divalent metal ions treatment such as zinc, copper and magnesium at constant concentrations was studied. The work involved experimental (electrophoretic - capillary electrophoresis in pseudo-isotachophoresis mode, spectroscopic and spectrometric - FT-IR and MALDI-TOF-MS, microscopic - fluorescent microscopy, and flow cytometry) and theoretical (DFT calculations of model complex systems) characterization. Electrophoretic results have pointed out the formation of aggregates under the Zn2+ and Cu2+ modification, whereas the use of the Mg2+ allowed focusing the zone of L. paracasei biocolloid. According to the FT-IR analysis, the major functional groups involved in the aggregation are deprotonated carboxyl and amide groups derived from the bacterial surface structure. Nature of the divalent metal ions was shown to be one of the key factors influencing the bacterial aggregation process. Proteomic analysis showed that surface modification had a considerable impact on bacteria molecular profiles and protein expression, mainly linked to the activation of carbohydrate and nucleotides metabolism as well with the transcription regulation and membrane transport. Density-functional theory (DFT) calculations of modeled Cu2+, Mg2+ and Zn2+ coordination complexes support the interaction between the divalent metal ions and bacterial proteins. Consequently, the possible mechanism of the aggregation phenomenon was proposed. Therefore, this comprehensive study could be further applied in evaluation of biocolloid aggregation under different types of metal ions.

Asymmetric Nucleophilic Allylation of α-Chloro Glycinate via Squaramide Anion-Abstraction Catalysis: SN1 or SN2 Mechanism, or Both?

The nucleophilic substitution mechanism of enantioselective allylation of α-chloro glycinate catalyzed by squaramide organocatalysts was studied using density functional theory. Based on a comprehensive study of SN1 and SN2 pathways of a catalyst-free reaction, we found that the catalytic reaction slightly favors the SN1 mechanism, instead of the previously proposed SN2 mechanism. Further investigation of different leaving groups and nucleophiles revealed that this is not limited to the present reaction, and the SN1 mechanism might have been generally overlooked. For the squaramide-catalyzed reactions, the SN1 mechanism was predicted to be preferred. However, the rate-determining step of the SN1 pathway has changed from the chloride-leaving step to the C-C bond-formation step. Therefore, a first-order dependence on both substrates was predicted, in agreement with the observed second-order kinetics. Intriguingly, the lowest-energy enantioselective transition states (TSs) originate from different pathways; R-inducing TS corresponds to the SN1 pathway, while S-inducing TS corresponds to SN2. The calculated enantiomeric excesses of two squaramide catalysts agree well with the experimental values. Given the ubiquity of nucleophilic substitution reactions in chemistry and biology, we believe that our finding will inspire more studies that will lead to an improved mechanistic understanding of important chemical reactions, and it may even lead to better catalysts.

Anion Texturing Towards Dendrite-Free Zn Anode for Aqueous Rechargeable Batteries.

The reversibility of metal anode is a fundamental challenge to the lifetime of rechargeable batteries. Though being widely employed in aqueous energy storage systems, metallic zinc suffers from dendrite formation that severely hinders its applications. Here we report texturing Zn as an effective way to address the issue of zinc dendrite. An in-plane oriented Zn texture with preferentially exposed (002) basal plane is demonstrated via a sulfonate anion-induced electrodeposition, noting no solid report on (002) textured Zn till now. Anion-induced reconstruction of zinc coordination is revealed to be responsible for the texture formation. Benchmarking against its (101) textured-counterpart by the conventional sulphate-based electrolyte, the Zn (002) texture enables highly reversible stripping/plating at a high current density of 10 mA cm-2 , showing its dendrite-free characteristics. The Zn (002) texture-based aqueous zinc battery exhibits excellent cycling stability. The developed anion texturing approach provides a pathway towards exploring zinc chemistry and prospering aqueous rechargeable batteries.