Ligand Structure Research Articles

A comprehensive study on the steric impact of phosphine ligands on propene hydroformylation

This research examines the steric impact of ligand structure on Rhodium-catalyzed hydroformylation, specifically, the significant impact of substituent positioning of monodentate phosphine ligands on the catalytic activity in propene hydroformylation. Focusing on methyl-substituted triphenylphosphine ligands, it explores how the placement of methyl groups influences the selection between mono- and bis-ligated coordination modes and, consequently, the selectivity towards linear versus branched aldehydes. Findings highlight that substituents' proximity to the ligand's phosphorus atom alters the dominant reaction step, depending on the coordination mode favored by the ligand's structural configuration. Substituents positioned further from the phosphorus atom tend to favor a bis-ligated coordination mode, wherein olefin insertion predominantly influences the aldehyde product profile. Conversely, closer substituents lead to a preference for a mono-ligated mode, shifting the decisive step from olefin insertion to other reactions, changing selectivity and catalytic activity. The result refined understanding facilitates catalyst optimization through targeted modifications of ligand structures, advancing the more effective design of hydroformylation catalysis.

Triazole-based Mn(II), Fe(II), Ni(II), Cu(II) and Zn(II) complexes as potential anticancer agents – Physicochemical properties, in silico predictions and in vitro activity

A series of solid-state coordination compounds of Mn(II), Fe(II), Ni(II), Cu(II) and Zn(II) with 5-((1-methyl-pyrrol-2-yl)methyl)-4-(2-chlorophenyl)-1,2,4-triazoline-3-thione as a ligand were synthesized and studied in terms of their chemical composition (elemental analysis, ICP), spectroscopic properties (FTIR) and magnetic measurements. Single crystal X-ray diffraction analysis (SC-XRD), HRMS and NMR studies were carried out to confirm the structure of the organic ligand. Its biological potential was evaluated in silico, using molecular docking studies and ADME analysis. The anticancer activity of all five metal complexes and the organic ligand were tested in vitro against A549 and HT-29 cancer cells. We found that the metal complexes in general exhibited better anticancer activity in comparison with the free ligand, with the Cu(II) complex exhibiting the highest activity against both tested cell lines.

Congestion of steric and electronic factors in α-diimine nickel precatalysts for high-temperature ethylene polymerization in accessing direct PE elastomer

In α-diimine-nickel catalysts mediated ethylene polymerization, the synergistic impact of steric and electronic factors plays an instrumental role in fine-tuning catalytic activity, polymer molecular weights, microstructure, as well as mechanical and elastic properties. In this study, a new series of nonsymmetrical bis(arylimino)-acenaphthene-nickel complexes was prepared and investigated for ethylene polymerization. These complexes feature both bulky N-2,6-dibenzhydryl-3,4,5-fluorophenyl imine and smaller N-2,6-di(R)-4-(R1)phenyl imine units [Ni2Me (R, = Me, R1 = H), Ni2Et (R, = Et, R1 = H) and Ni2iPr (R, = iPr, R1 = H), Ni3Me (R, R1 = Me), Ni2Et,Me (R, = Et, R1 = Me)]. The incorporation of both steric congestion and strong electronic withdrawal groups into the catalyst structure resulted in significantly improved catalytic performance: high thermal stability and exceptional activity were observed at both ambient temperature (21.24 × 106 at 30 °C) and industrially relevant temperatures (1.65 × 106 at 100 °C). Polymer molecular weights and branching degree were tunable by adjusting the ligand structure and reaction conditions. This correlation extended to mechanical and elastic properties, demonstrating high tensile strength at low temperatures and good elastic recovery at high reaction temperatures, consistent with typical polyolefin elastomers.

Investigation of Enantioselectivity Using TADDOL Derivatives as Chiral Ligands in Asymmetric Cyanation Reactions.

This study investigates the enantioselectivity challenges of asymmetric cyanation reactions using TADDOL derivatives as chiral ligands, specifically focusing on the cyanosilylation of aldehydes and the cyanation of imines. Despite extensive optimization efforts, the highest achieved ee was only modest, peaking at 71% for the cyanosilylation reaction, while the cyanation of imines consistently resulted in racemic mixtures. Our comprehensive analysis, supported by experimental data and computational modeling, reveals significant barriers to enhancing the enantioselectivity. The results highlight a complex interplay between ligand structure and reaction conditions, demonstrating that even promising ligands such as TADDOL derivatives face substantial challenges in these reaction types. This study underscores the importance of understanding the mechanistic details through computational insights to guide future improvements in asymmetric catalysis.

Structure–performance relationship of Au nanoclusters in electrocatalysis: Metal core and ligand structure

AbstractRemarkable progress has characterized the field of electrocatalysis in recent decades, driven in part by an enhanced comprehension of catalyst structures and mechanisms at the nanoscale. Atomically precise metal nanoclusters, serving as exemplary models, significantly expand the range of accessible structures through diverse cores and ligands, creating an exceptional platform for the investigation of catalytic reactions. Notably, ligand‐protected Au nanoclusters (NCs) with precisely defined core numbers offer a distinct advantage in elucidating the correlation between their specific structures and the reaction mechanisms in electrocatalysis. The strategic modulation of the fine microstructures of Au NCs presents crucial opportunities for tailoring their electrocatalytic performance across various reactions. This review delves into the profound structural effects of Au NC cores and ligands in electrocatalysis, elucidating their underlying mechanisms. A detailed exploration of the fundamentals of Au NCs, considering core and ligand structures, follows. Subsequently, the interaction between the core and ligand structures of Au NCs and their impact on electrocatalytic performance in diverse reactions are examined. Concluding the discourse, challenges and personal prospects are presented to guide the rational design of efficient electrocatalysts and advance electrocatalytic reactions.

The Structural Basis of the Activity Cliff in Modafinil-Based Dopamine Transporter Inhibitors.

Modafinil analogs with either a sulfoxide or sulfide moiety have improved binding affinities at the human dopamine transporter (hDAT) compared to modafinil, with lead sulfoxide-substituted analogs showing characteristics of atypical inhibition (e.g., JJC8-091). Interestingly, the only distinction between sulfoxide and sulfide substitution is the presence of one additional oxygen atom. To elucidate why such a subtle difference in ligand structure can result in different typical or atypical profiles, we investigated two pairs of analogs. Our quantum mechanical calculations revealed a more negatively charged distribution of the electrostatic potential surface of the sulfoxide substitution. Using molecular dynamics simulations, we demonstrated that sulfoxide-substituted modafinil analogs have a propensity to attract more water into the binding pocket. They also exhibited a tendency to dissociate from Asp79 and form a new interaction with Asp421, consequently promoting an inward-facing conformation of hDAT. In contrast, sulfide-substituted analogs did not display these effects. These findings elucidate the structural basis of the activity cliff observed with modafinil analogs and also enhance our understanding of the functionally relevant conformational spectrum of hDAT.

Catalysis-mediated dynamic ligand presentation regulates mechanosensing–metabolism coupling of stem cells

The dynamic presentation of ligands on biomaterial surfaces can greatly affect cellular behaviors. However, there have been no prior studies that utilize catalysis-mediated dynamic bonds for dynamic ligand presentation and explore its impact on cellular events. In this work we employ aniline as a catalyst to enhance the dynamics of the hydrazone bond in the tether structure of ligands attached to biomaterial substrate to study the impact of such controlled dynamic ligand presentation on the mechanosensing–metabolism coupling of adherent stem cells. Gold nanoparticles, decorated with polyethylene glycol (PEG)-hydrazide, are linked to benzaldehyde-modified glass substrates through hydrazone bonds. The catalytic aniline, combined with the cell adhesive arginyl-glycyl-aspartic acid (RGD) peptide, is conjugated on the nanoparticle surface to facilitate the disassociation and reassociation of hydrazone bonds in the RGD tether structure. This catalysis-mediated dynamic presentation of RGD effectively regulates the Ras-related C3 botulinum toxin substrate 1 (Rac1)-dependent mechanosensing and stimulates the actin cytoskeleton rearrangement in stem cells. The enhanced release of a glycolytic enzyme (Aldolase A) due to the cytoskeleton rearrangement leads to increased glycolysis, adenosine triphosphate (ATP) generation, oxidative phosphorylation, thereby contributing to the osteogenic differentiation of human mesenchymal stem cells (hMSCs). These findings highlight the importance of chemically manipulating the dynamic ligand presentation in regulating mechanosensing–metabolism coupling and the differentiation of stem cells.

Therapeutic Use of G4-Ligands in Cancer: State-of-the-Art and Future Perspectives.

G-quadruplexes (G4s) are guanine-rich non-canonical secondary structures of nucleic acids that were identified in vitro almost half a century ago. Starting from the early 1980s, these structures were also observed in eukaryotic cells, first at the telomeric level and later in regulatory regions of cancer-related genes, in regulatory RNAs and within specific cell compartments such as lysosomes, mitochondria, and ribosomes. Because of the involvement of these structures in a large number of biological processes and in the pathogenesis of several diseases, including cancer, the interest in G4 targeting has exponentially increased in the last few years, and a great number of novel G4 ligands have been developed. Notably, G4 ligands represent a large family of heterogeneous molecules that can exert their functions by recognizing, binding, and stabilizing G4 structures in multiple ways. Regarding anti-cancer activity, the efficacy of G4 ligands was originally attributed to the capability of these molecules to inhibit the activity of telomerase, an enzyme that elongates telomeres and promotes endless replication in cancer cells. Thereafter, novel mechanisms through which G4 ligands exert their antitumoral activities have been defined, including the induction of DNA damage, control of gene expression, and regulation of metabolic pathways, among others. Here, we provided a perspective on the structure and function of G4 ligands with particular emphasis on their potential role as antitumoral agents. In particular, we critically examined the problems associated with the clinical translation of these molecules, trying to highlight the main aspects that should be taken into account during the phases of drug design and development. Indeed, taking advantage of the successes and failures, and the more recent technological progresses in the field, it would be possible to hypothesize the development of these molecules in the future that would represent a valid option for those cancers still missing effective therapies.

Impact of POM's coordination mode and Mo-hybrid constituents on the binding, stability, and catalytic properties of hybrid (pre)catalysts.

The assembly of MoVIO2 2+ and methoxy-substituted salicylaldehyde nicotinoyl hydrazone ligands afforded two classes of hybrid polyoxometalates (POMs). In the Class I architectures, [MoO2(HL1-3)(D)]2[Mo6O19]·xCH3COCH3 (D = CH3COCH3 or H2O, x = 0 or 2, and L1-3 = ligands bearing the OMe group at position 3, 4 and 5, respectively), the main driving force for self-assembly is the electrostatic interaction between the components. Class II architectures are composed of a POM anion covalently linked to two Mo-complex units through the terminal Ot or bridging μ2-OPOM oxygen atoms, as found in Lindqvist-based hybrids [{MoO2(HL1-3)}2Mo6O19]·xCH3CN (x = 0 or 2) and the asymmetrical β-octamolybdate-based hybrid [{Mo2O4(HL2)(H2L)}{MoO2(HL2)}2Mo8O26]·CH3CN·H2O. Quantum chemical calculations were applied to evaluate the impact of the POM hybrid constituents on the hybrid-type stability, showing that it strongly depends on the ligand substituent position and ancillary ligand nature. Hybrids were tested as catalysts for cyclooctene epoxidation using tert-butyl hydroperoxide (TBHP in water or decane) and with or without the addition of acetonitrile (CH3CN) as an organic solvent. The catalytic results provided by the use of TBHP in decane are the best ones and classify all the prepared catalysts as very active, with the conversion of cyclooctene >90%, and high selectivity towards epoxide, >80%. We also examined the influence of the ligand structure, POM's hybrid type, and coordination mode on the Mo-hybrid activity and selectivity.

Covalent and Visible‐Light Photoswitchable Derivatives of the Potent Synthetic Opioid Isotonitazene and Other Nitazenes

AbstractIsotonitazene belongs to a potent class of μ‐opioid receptor (μOR) ligands, known as nitazenes. The lack of knowledge surrounding this agonist and others in its class has sparked thorough re‐investigations. To aid in these investigations, the purportedly covalent yet underexplored nitazene BIT was biochemically re‐evaluated in this work, along with a newly synthesized analogue, Iso‐BIT. Moreover, in the pursuit of understanding the mechanism, function and interactions of the μOR, this study involved developing photoswitchable nitazene derivatives as potential probe molecules. Converting known ligands into azo‐containing photoswitchable derivatives offers the opportunity to modulate ligand structure with light, allowing for photocontrol of compound activity. While photocontrol of μOR activity could not be entirely achieved, photophysical evaluation of these 2‐benzimidazole azo‐arenes revealed a novel photoswitch scaffold that responds to visible light. Furthermore, azo‐containing 2 e and 3 e emerged as promising nitazene derivatives that were able to form an exceptionally high fraction of covalent‐ligand receptor complexes with wild‐type μOR at physiological pH.

Discovery of novel CDK9 inhibitor with tridentate ligand: Design, synthesis and biological evaluation

Cyclin-dependent kinase 9 (CDK9) plays a role in transcriptional regulation, which had become an attractive target for discovery of antitumor agent. In this work, beyond traditional CDK9 inhibitor with bidentate ligands in ATP binding domain, a series of novel CDK9 inhibitor with tridentate ligand were designed and synthesized. Surprisingly, this unique tridentate ligand structure endows better CDK9 inhibition selectivity compared to other CDK subtypes, and the lead candidate compound Z4-7a showed effective proliferation inhibition in HCT116 cells with acceptable pharmacokinetic properties. Research on the mechanism indicated that Z4-7a could induce apoptosis in the HCT116 cell line by inhibiting phosphorylation of RNA polymerase II at Ser2, which resulted in the inhibition of apoptosis-related genes and proteins expression. In brief, introduction of tridentate ligand might work as a promising strategy for the development of novel selective CDK9 inhibitor.

Fragment-Based Discovery of Novel MUS81 Inhibitors.

MUS81 is a structure-selective endonuclease that cleaves various branched DNA structures arising from natural physiological processes such as homologous recombination and mitosis. Due to this, MUS81 is able to relieve replication stress, and its function has been reported to be critical to the survival of many cancers, particularly those with dysfunctional DNA-repair machinery. There is therefore interest in MUS81 as a cancer drug target, yet there are currently few small molecule inhibitors of this enzyme reported, and no liganded crystal structures are available to guide hit optimization. Here we report the fragment-based discovery of novel small molecule MUS81 inhibitors with sub-μM biochemical activity. These inhibitors were used to develop a novel crystal system, providing the first structural insight into the inhibition of MUS81 with small molecules.

Si Single-Atom Sites Anchored Carbon Anode Achieving the Zero-Strain Feature and Superior Li+ Storage Performance.

Overcoming the significant volume strain in silicon-based anodes has been the focus of research for decades. The strain/stress in silicon-based anodes is inversely proportional to their size. In this study, we design atomic Si sites to achieve the ultimate size effect, which indeed exhibits a zero-strain feature. Compared with conventional silicon-based anodes with alloying addition reactions, the lithium-ion storage mechanism of atomic Si sites is solid-solution reactions, which brings about the zero-strain feature. Additionally, the ligand structure of atomic Si sites remains constant during cycling. This zero-strain feature results in excellent cycling stability. Furthermore, the exposed atomic Si sites enhance the electrochemical reaction kinetics, leading to outstanding rate performance. Moreover, the anode inherits the advantages of silicon-based anodes, including a low working voltage (~0.21 V) and high specific capacity (~2300 mAh g-1 or ~1203 mAh cm-3). This work establishes a novel pathway for designing low/zero-strain anodes.

Understanding the Role of Ligand Structure on Extraction of Neptunium by N-Pivot Tripodal Diglycolamides in an Ionic Liquid

ABSTRACT The extraction of Np4+ was studied by a series of N-pivot tripodal diglycolamides, with varying substituents (alkyl groups with varying branching and chain length) and varying spacer length, dissolved in an ionic liquid, i.e. [C4mim][Tf2N]. Out of a series of four ligands, L I (propylene spacer) and L II (ethylene spacer) differ only in the spacer length connecting the three diglycolamide units with the tripodal N platform. While L II – L IV have the same spacer length (ethylene spacer), but L II has a hydrogen atom, L III has methyl group, and L IV has isopropyl group as a substituent at the amidic N atom close to the central N atom. A reversal extraction mechanism of Np4+ was observed when the spacer chain length reduced from a propylene group in L I to an ethylene group in L II – L IV . While a cation-exchange mechanism was observed in case of L I , a solvation extraction mechanism was seen for the other three ligands with the extracted species being Np(NO3)2(L)2+ for L I , and [Np(NO3)4·L] for L II – L IV . The extraction efficiencies of Np4+ with L II – L IV were significantly affected by the nature of the alkyl substituents and follow the order: L II > L III > L IV . This trend in the extraction pattern affirms that the alkyl substitution at the amidic N atom creates steric strain in the ligand while complexing with the metal ion.

Synthesis, characterization and analytical study of new azo ligand driven from benzocaine and its metal complexes

The synthesis and spectrum of of a new azo ligand derived from acetylacetone and benzocaine (Ethyl p-aminobenzoate)). Spectral investigations such as 1H NMR,FT.IR, 13C-NMR and Mass spectra were performed to investigate the azo dye ligand's structure. Several physiochemical approaches, FT-IR, electronic spectra, molar conductivity, atom absorption, and magnetic susceptibility were used to identify new complexes with CO(II), and Zn(II) ions Complexes that are all 1:2 [M:L] were formed using the procedures described, and an tetrahedral geometry with sp3 hybridization. At several pH ranges (2–12), the electronic spectra of these azo dyes have been examined in terms of their acid–base properties, which included determining their isosbestic points and protonation and ionization constants. In the other study, azodye were used as an inductor for acid-base titration.

Exploring the binding properties of DNA/BSA and cytotoxicity studies with new terpyridine-ester-based metal complexes (M = Fe(III), Ni(II), Cu(II) and Ru(III)) – A comparative analysis

Many terpyridines and their metal complexes are known to exhibit remarkable potential for the interaction of biological targets. Notably, a subtle change in the structure of the ligand can influence these interactions significantly. In this regard, it would be very interesting to assess the binding affinity of functionalized molecules with DNA/BSA. In this work, a novel ester-based terpyridine (L) and the corresponding four metal complexes with Ni(II) (MC1), Cu(II) (MC2), Fe(III) (MC3) and Ru(III) (MC4) were prepared and structurally characterized using various spectroscopic and analytical techniques including the validation of molecular structures of ligand (L) and Ni(II)-Tpy complex (MC1). The EPR data demonstrate that MC1 is diamagnetic and other complexes (MC2-MC4) exhibit paramagnetic behavior. Additionally, the structures of ligands and metal complexes were determined using DFT studies and the same were utilized for the docking studies. Interestingly, MC3 and MC4 exhibit a predominant lowest binding energy of −9.62 Kcal/mol (with DNA) and −10.05 Kcal/mol (with BSA) respectively. The binding affinity of the ligand and its complexes with protein and DNA was evaluated by spectroscopic techniques. Notably, the cytotoxicity studies of L and MC1-MC4 were performed against the MCF-7 (human breast cancer) cell lines. The complex MC4 displayed great activity with an IC50 of 3.5 ± 1.75 μM among all synthesized compounds and comparable with cisplatin.

Highly biased agonism for GPCR ligands via nanobody tethering

Ligand-induced activation of G protein-coupled receptors (GPCRs) can initiate signaling through multiple distinct pathways with differing biological and physiological outcomes. There is intense interest in understanding how variation in GPCR ligand structure can be used to promote pathway selective signaling (“biased agonism”) with the goal of promoting desirable responses and avoiding deleterious side effects. Here we present an approach in which a conventional peptide ligand for the type 1 parathyroid hormone receptor (PTHR1) is converted from an agonist which induces signaling through all relevant pathways to a compound that is highly selective for a single pathway. This is achieved not through variation in the core structure of the agonist, but rather by linking it to a nanobody tethering agent that binds with high affinity to a separate site on the receptor not involved in signal transduction. The resulting conjugate represents the most biased agonist of PTHR1 reported to date. This approach holds promise for facile generation of pathway selective ligands for other GPCRs.

Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.

Histones are keys to many epigenetic events and their complexes have therapeutic and diagnostic importance. The determination of the structures of histone complexes is fundamental in the design of new drugs. Computational molecular docking is widely used for the prediction of target-ligand complexes. Large, linear peptides like the tail regions of histones are challenging ligands for docking due to their large conformational flexibility, extensive hydration, and weak interactions with the shallow binding pockets of their reader proteins. Thus, fast docking methods often fail to produce complex structures of such peptide ligands at a level appropriate for drug design. To address this challenge, and improve the structural quality of the docked complexes, post-docking refinement has been applied using various molecular dynamics (MD) approaches. However, a final consensus has not been reached on the desired MD refinement protocol. In this present study, MD refinement strategies were systematically explored on a set of problematic complexes of histone peptide ligands with relatively large errors in their docked geometries. Six protocols were compared that differ in their MD simulation parameters. In all cases, pre-MD hydration of the complex interface regions was applied to avoid the unwanted presence of empty cavities. The best-performing protocol achieved a median of 32% improvement over the docked structures in terms of the change in root mean squared deviations from the experimental references. The influence of structural factors and explicit hydration on the performance of post-docking MD refinements are also discussed to help with their implementation in future methods and applications.

Understanding Flexdispersion: Structure-Function Relationship Studies of Organic Amphiphilic Ligands.

Since inorganic nanoparticles have unique properties that differ from those of bulk materials, their material applications have attracted attention in various fields. In order to utilize inorganic nanoparticles for functional materials, they must be dispersed without agglomeration. Therefore, the surfaces of inorganic nanoparticles are typically modified with organic ligands to improve their dispersibility. Nevertheless, the relationship between the tail group structure in organic ligands and the dispersibility of inorganic nanoparticles in organic solvents remains poorly understood. We previously developed amphiphilic ligands that consist of ethylene glycol chains and alkyl chains to disperse inorganic nanoparticles in a variety of organic solvents. However, the structural requirements for amphiphilic ligands to "flexibly" disperse nanoparticles in less polar to polar solvents are still unclear. Here, we designed and synthesized several phosphonic acid ligands for structure-function relationship studies of flexdispersion. Dynamic light scattering analysis and visible light transmittance measurements revealed that the ratio of alkyl/ethylene glycol chains in organic ligands alone does not determine the dispersibility of the nanoparticles in organic solvents, but the arrangement of the individual chains also has an effect. From a practical application standpoint, it is preferable to design ligands with ethylene glycol chains on the outside relative to the particle surface.

Novel Drug Repurposing Strategy as an Alternative Therapeutic Concept for Scrub Typhus Using Computational Studies

Scrub typhus is one of the most underdiagnosed and unreported febrile illnesses caused by an obligate intracellular bacterium named Orientia tsutsugamushi and the antibiotics were the commonly prescribed drugs to treat the condition. Due to the widespread development of antimicrobial resistance to the standard drugs, the new therapeutic approach is warranted. The drug repurposing approach plays a novel concept in identifying alternative therapies to fight against pathogens. To investigate the anti-scrub typhus activity of nine newly FDA-approved antibiotics from 2018-2019 against Orientia tsutsugamushi deubiquitylase (OtDUB) compared with standard drugs. The structure of ligands was retrieved from the PubChem database and the crystal structure of target OtDUB (PDB ID: 6UPU) with a resolution of 2.2 Ao was retrieved from the Protein data bank. Molecular docking studies were performed using PyRx version 0.8 and the amino acid interactions were visualized using BIOVIA Discovery studio and the pharmacokinetic properties of the drugs were analysed by SWISS ADME software. The binding affinity of the drugs to deubiquitylase and amino acids was determined using the In silico approach, the drug Omadacycline shows superior activity when compared with other drugs. Based on our preliminary in-silico docking studies, we conclude that Omadacycline may be repurposed for the treatment of scrub typhus as it shows a higher binding affinity of -8.6 kcal/mol when compared to the standard drugs. For the further advancement of the study, in vitro and in vivo studies should be performed.