Argentophilic Interactions, Flexibility, and Dynamics of Pyrrole Cages Encapsulating Silver(I) Clusters.

Recently, pyrrole cages have been synthesized that encapsulate ion pairs and silver(I) clusters to form intricate supramolecular capsules. We report here a computational analysis of these structures using density functional theory combined with a semiempirical tight-binding approach. We find that for neutral pyrrole cages, the Gibbs free energies of formation provide reliable predictions for the ratio of bound ions. For charged pyrrole cages, we find strong argentophilic interactions between Ag ions on the basis of the calculated bond indices and molecular orbitals. For the cage with the Ag4 cluster, we find two minimum-geometry conformations that differ by only 6.5 kcal/mol, with an energy barrier <1 kcal/mol, suggesting a very flexible structure as indicated by molecular dynamics. The predicted energies of formation of [Agn⊂1]n-3+ (n = 1-5) cryptands provide low energy barriers of formation of 5-20 kcal/mol for all cases, which is consistent with the experimental data. Furthermore, we also examined the structural variability of mixed-valence silver clusters to test whether additional geometrical conformations inside the organic cage are thermodynamically accessible. In this context, we show that the time-dependent density functional theory UV-vis spectra may potentially serve as a diagnostic probe to characterize mixed-valence and geometrical configurations of silver clusters encapsulated into cryptands.

The Conjugates of Indolo[2,3-b]quinoline as Anti-Pancreatic Cancer Agents: Design, Synthesis, Molecular Docking and Biological Evaluations.

New amide conjugates of hydroxycinnamic acids (HCAs) and the known antineoplastic 5,11-dimethyl-5H-indolo[2,3-b]quinoline (DiMIQ), an analog of the natural alkaloid neocryptolepine, were synthesized and tested in vitro for anticancer activity. The compound 9-[((2-hydroxy)cinnamoyl)amino]-5,11-dimethyl-5H-indolo[2,3-b]quinoline (2), which contains the ortho-coumaric acid fragment, demonstrated dose-dependent effectiveness against both normal BxPC-3 and metastatic AsPC-1 pancreatic cancer cells. The IC50 values for AsPC-1 and BxPC-3 were 336.5 nM and 347.5 nM, respectively, with a selectivity index of approximately 5 for both pancreatic cancer cells compared to normal dermal fibroblasts. Conjugate 2 did not exhibit any hemolytic activity against human erythrocytes at the tested concentration. Computational studies were performed to predict the pharmacokinetic profile and potential mechanism of action of the synthesized conjugates. These studies focused on the ADME properties of the conjugates and their interactions with DNA, as well as DNA-topoisomerase alpha and beta complexes. All of the conjugates studied showed approximately one order of magnitude stronger binding to DNA compared to the reference DiMIQ, and approximately two orders of magnitude stronger binding to the topoisomerase II-DNA complex compared to DiMIQ. Conjugate 2 was predicted to have the strongest binding to the enzyme-DNA complex, with a Ki value of 2.8 nM.

Iminopyrrole-Based Self-Assembly: A Route to Intrinsically Flexible Molecular Links and Knots.

The use of 2,5-diformylpyrrole in self-assembly reactions with diamines and Zn(II)/Cd(II) salts allowed the preparation of [2]catenane, trefoil knot, and Borromean rings. The intrinsically dynamic nature of the diiminopyrrole motif rendered all of the formed assemblies intramolecularly flexible. The presence of diiminopyrrole revealed new coordination motifs and influenced the host-guest chemistry of the systems, as illustrated by hexafluorophosphate encapsulation by Borromean rings.

Inhibition of the Decomposition Pathways of Ruthenium Olefin Metathesis Catalysts: Development of Highly Efficient Catalysts for Ethenolysis.

Ruthenium-based Hoveyda-type olefin metathesis catalysts bearing novel rigid spirocyclic alkyl amino carbenes (CAACs) have been developed. They are characterized by exceptional stability toward decomposition through ß-elimination and bimolecular pathways, thus enabling unprecedented efficiency in the cross-metathesis of seed oil-derived fatty acid esters with ethylene (ethenolysis). Catalyst loading as low as 100 ppb was applied to the ethenolysis of the model substrate methyl oleate, leading to a remarkable turnover number (TON) of 2.6 million, significantly higher than previously reported (TON 340 000 at 1 ppm and 744 000 at 0.5 ppm catalyst loading). Ethenolysis of methyl esters derived from high oleic sunflower oil and rapeseed oil, readily available on an industrial scale, inexpensive, and renewable feedstocks, was for the first time effectively carried out with 0.5 ppm catalyst loading with TON as high as 964 000.

Iminoboranes With Parent B=NH Entity: Imino Group Metathesis, Nucleophilic Reactivity and N-N Coupling.

While R2 C=N-R double bonds in organic imines are well established, the related iminoboranes R-B=N-R are either prone to oligomerization or can only be stabilized at sufficient steric congestion. In particular, the examples of unsubstituted parent B=N-H entity are rare. We demonstrate that the amino imidazoline-2-imine ligand system (HAmIm) not only gives rise to the isolation of a parent (AmIm)B=N-H iminoborane, but also to species of type (AmIm)B=N-SiMe3 with concomitant stabilization by lithium bromide. The double bond character in these systems is unambiguously corroborated by DFT calculations. The steric accessibility of the (AmIm)B=NH unit allows facile reactivity including metathesis reactions with C=O and C=S bonds, nucleophilic addition toward organic and organometallic carbonyl compounds, but also oxidative N-N coupling within a dimeric unit. Thus, the chemical behavior of the (AmIm)B=N-H and (AmIm)B=N-SiMe3 is distinctly different from that of organic imines.

An Anthracene-Thiolate-Ligated Ruthenium Complex: Computational Insights into Z-Stereoselective Cross Metathesis.

Stereoselective control of the cross metathesis of olefins is a crucial aspect of synthetic procedures. In this study, we utilized density functional theory methods to calculate thermodynamic and kinetic descriptors to explore the stereoselectivity of cross metathesis between allylbenzene and 2-butene-1,4-diyl diacetate. A ruthenium-based complex, characterized primarily by an anthracene-9-thiolate ligand, was designed in silico to completely restrict the E conformation of olefins through a bottom-bound mechanism. Our investigation of the kinetics of all feasible propagation routes demonstrated that Z-stereoisomers of metathesis products can be synthesized with an energy cost of only 13 kcal/mol. As a result, we encourage further research into the synthetic strategies outlined in this work.

New Piperazine Derivatives of 6-Acetyl-7-hydroxy-4-methylcoumarin as 5-HT1A Receptor Agents.

A series of 15 new derivatives of 6-acetyl-7-hydroxy-4-methylcoumarin containing a piperazine group were designed with the help of computational methods and were synthesized to study their affinity for the serotonin 5-HT1A and 5-HT2A receptors. Among them, 6-acetyl-7-{4-[4-(3-bromophenyl)piperazin-1-yl]butoxy}-4-methylchromen-2-one (4) and 6-acetyl-7-{4-[4-(2-chlorophenyl)piperazin-1-yl]butoxy}-4-methylchromen-2-one (7) exhibited excellent activity for 5-HT1A receptors with Ki values 0.78 (0.4-1.4) nM and 0.57 (0.2-1.3) nM, respectively, comparable to the Ki values of 8-OH-DPAT (0.25 (0.097-0.66) nM). The equilibrium dissociation constant values of the tested compounds showed differential intrinsic activities of the agonist and antagonist modes.

Synthesis, Biological Activity, ADME and Molecular Docking Studies of Novel Ursolic Acid Derivatives as Potent Anticancer Agents.

A series of new ursolic acid (UA) derivatives substituted with various amino acids (AAs) or dipeptides (DP) at the C-3 position of the steroid skeleton was designed and synthesized. The compounds were obtained by the esterification of UA with the corresponding AAs. The cytotoxic activity of the synthesized conjugates was determined using the hormone-dependent breast cancer cell line MCF-7 and the triple-negative breast cancer cell line MDA. Three derivatives (l-seryloxy-, l-prolyloxy- and l-alanyl-l-isoleucyloxy-) showed micromolar IC50 values and reduced the concentrations of matrix metalloproteinases 2 and 9. Further studies revealed that for two compounds (l-seryloxy- and l-alanyl-l-isoleucyloxy-), a possible mechanism of their antiproliferative action is the activation of caspase-7 and the proapoptotic Bax protein in the apoptotic pathway. The third compound (l-prolyloxy- derivative) showed a different mechanism of action as it induced autophagy as measured by an increase in the concentrations of three autophagy markers: LC3A, LC3B, and beclin-1. This derivative also showed statistically significant inhibition of the proinflammatory cytokines TNF-α and IL-6. Finally, for all synthesized compounds, we computationally predicted their ADME properties as well as performed molecular docking to the estrogen receptor to assess their potential for further development as anticancer agents.

New, Low-Molecular Weight Chemical Compounds Inhibiting Biological Activity of Interleukin 15.

Chronic overproduction of IL-15 contributes to the pathogenesis of numerous inflammatory and autoimmune disorders. Experimental methods used to reduce the cytokine activity show promise as potential therapeutic approaches to modify IL-15 signaling and alleviate the development and progression of IL-15-related diseases. We previously demonstrated that an efficient reduction of IL-15 activity can be obtained by selective blocking of the specific, high affinity subunit alpha of the IL-15 receptor (IL-15Rα) with small-molecule inhibitors. In this study, we determined the structure-activity relationship of currently known IL-15Rα inhibitors in order to define the critical structural features required for their activity. To validate our predictions, we designed, analyzed in silico, and assessed in vitro function of 16 new potential IL-15Rα inhibitors. All newly synthesized molecules were benzoic acid derivatives with favorable ADME properties and they efficiently reduced IL-15 dependent peripheral blood mononuclear cells (PBMCs) proliferation, as well as TNF-α and IL-17 secretion. The rational design of IL-15 inhibitors may propel the identification of potential lead molecules for the development of safe and effective therapeutic agents.

Structural and Electronic Properties of Boranes Containing Boron-Chalcogen Multiple Bonds and Stabilized by Amido Imidazoline-2-imine Ligands.

The stabilization of elusive monomeric species containing multiple boron-chalcogen bonds has motivated the investigation of sophisticated ligand systems in the past few years. Recently, a series of neutral, Lewis acid-free chalcogenboranes were prepared by incorporation of an amido imidazoline-2-imine as the supporting ligand (Frank et al., Angew. Chem. Int. Ed. 2021, 60, 4633), resulting in well-defined molecular entities with pronounced multiple bond character, B=X (X=O, S, Se, Te). In view of the potential use of N-heterocyclic boranes (NHB=X) as ligands in catalysis and fine chemistry, we evaluated in this work the bonding properties of the new B=X compounds based on a π-backdonation model. The electronic properties of systems in question were modulated via systematic modifications of the NHB ring with respect to ligand variation, saturation, size, and heteroatom substitutions. Investigations into the B=X bond length and order, calculated by means of density functional theory methods, reveal enhanced B=X bonding properties for NHB rings with high electron delocalization in the NHB ring and bearing electron-withdrawing substituents; a fact that was also confirmed by computational assessment of electron interactions of the B=X species with a dicarbonyl manganese complex. We expect that the analysis will contribute to the rational optimization of existing ligands as well as the development of new moieties, which would further allow for exploration of new boron chemistry.

Reactions of a Four-Membered Borete with Carbon, Silicon, and Gallium Donor Ligands: Fused and Spiro-Type Boracycles.

Donor-acceptor cyclopropanes or cyclobutanes are dipolar reagents, which are widely used in the synthesis of complex organic (hetero)cycles in ring expansion reactions. Applying this concept to boron containing heterocycles, the four-membered borete cyclo-iPr2 N-BC10 H6 reacted with the carbon donor ligands 2,6-xylylisonitrile and the carbene IMes :C(NMesCH)2 with ring expansion and ring fusion, respectively. In particular, the tetracyclic structure formed with IMes displays zwitterionic character and absorption in the visible region. In contrast to the carbene IMes, the heavier carbenoids :Si(NDippCH)2 and :Ga(AmIm) with a two-coordinate donor atom afford spiro-type bicyclic compounds, which display four-coordinate geometry at silicon or gallium. (TD-)DFT calculations provide deeper insight into the mechanism of formation and the absorption properties of these new compounds.

Electrophilicity of Hoveyda-Grubbs Olefin Metathesis Catalysts as the Driving Force that Controls Initiation Rates.

The dissociative mechanism of initiation for a series of Hoveyda-Grubbs type metathesis catalysts modified at the para and meta positions in the isopropoxybenzylidene ligand is investigated by means of DFT calculations. The electron donating/withdrawing capacity of the ligand was screened through the incorporation of various substituents such as halogens, nitro, alkoxides, ketones, esters, amines, and amides. Variations in structural parameters, energy barriers for the Ru-O bond dissociation, and Ru-O bond strength were examined as a function of the Hammett constant. It was found that electronic properties of the catalysts such as chemical potential, hardness, and electrophilicity correlate linearly with the dissociative energy barriers. These findings enable a systematic rationalization and prediction of rate of precatalyst initiation through the calculation of only the HOMO-LUMO gap of catalysts, as the faster the initiation, the more electrophilic the catalyst.

Olefin Metathesis Catalyzed by a Hoveyda-Grubbs-like Complex Chelated to Bis(2-mercaptoimidazolyl) Methane: A Predictive DFT Study.

Although highly selective complexes for the cross-metathesis of olefins, particularly oriented toward the productive metathesis of Z-olefins, have been reported in recent years, there is a constant need to design and prepare new and improved catalysts for this challenging reaction. In this work, guided by density functional theory (DFT) calculations, the performance of a Ru-based catalyst chelated to a sulfurated pincer in the olefin metathesis was computationally assessed. The catalyst was designed based on the Hoveyda-Grubbs catalyst (SIMes)Cl2Ru(═CH-o-OiPrC6H4) through the substitution of chlorides with the chelator bis(2-mercaptoimidazolyl)methane. The obtained thermodynamic and kinetic data of the initiation phase through side- and bottom-bound mechanisms suggest that this system is a versatile catalyst for olefin metathesis, as DFT predicts the highest energy barrier of the catalytic cycle of ca. 20 kcal/mol, which is comparable to those corresponding to the Hoveyda-Grubbs-type catalysts. Moreover, in terms of the stereoselectivity evaluated through the propagation phase in the metathesis of propene-propene to 2-butene, our study reveals that the Z isomer can be formed under a kinetic control. We believe that this is an interesting outcome in the context of future exploration of Ru-based catalysts with sulfurated chelates in the search for high stereoselectivity in selected reactions.

Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and cellular receptors ACE2 and CD147, and a reference anti-RBD antibody (IgG2B) based on a functionalised boron-doped diamond (BDD) electrode. The DEIS was supported by a multivariate data analysis of a SARS-CoV-2 Spike RBD assay and cross-correlated with the atomic-level information revealed by molecular dynamics simulations. This approach allowed us to study and detect subtle changes in the electrical properties responsible for the susceptibility of cellular receptors to SARS-CoV-2, revealing their interactions. Changes in electrical homogeneity in the function of the RBD concentration led to the conclusion that the ACE2 receptor delivers the most homogeneous surface, delivered by the high electrostatic potential of the relevant docking regions. For higher RBD concentrations, the differences in electrical homogeneity between electrodes with different receptors vanish. Collectively, this study reveals interdependent virus entry pathways involving separately ACE2, CD147, and spike protein, as assessed using a biosensing platform for the rapid screening of cellular interactions (i.e. testing various mutations of SARS-CoV-2 or screening of therapeutic drugs).

The Interplay of Conjugation and Metal Coordination in Tuning the Electron Transfer Abilities of NTA-Graphene Based Interfaces.

An artificial leaf is a concept that not only replicates the processes taking place during natural photosynthesis but also provides a source of clean, renewable energy. One important part of such a device are molecules that stabilize the connection between the bioactive side and the electrode, as well as tune the electron transfer between them. In particular, nitrilotriacetic acid (NTA) derivatives used to form a self-assembly monolayer chemisorbed on a graphene monolayer can be seen as a prototypical interface that can be tuned to optimize the electron transfer. In the following work, interfaces with modifications of the metal nature, backbone saturation, and surface coverage density are presented by means of theoretical calculations. Effects of the type of the metal and the surface coverage density on the electronic properties are found to be key to tuning the electron transfer, while only a minor influence of backbone saturation is present. For all of the studied interfaces, the charge transfer flow goes from graphene to the SAM. We suggest that, in light of the strength of electron transfer, Co2+ should be considered as the preferred metal center for efficient charge transfer.

Reductive Al-B σ-Bond Formation in Alumaboranes: Facile Scission of Polar Multiple Bonds.

We present facile access to an alumaborane species with electron precise Al-B σ-bond. The reductive rearrangement of 1-(AlI2 ), 8-(BMes2 ) naphthalene (Mes=2,4,6-Me3 C6 H2 ) affords the alumaborane species cyclo-(1,8-C10 H6 )-[1-Al(Mes)(OEt2 )-8-B(Mes)] with a covalent Al-B σ-bond. The Al-B σ-bond performs the reductive scission of multiple bonds: S=C(NiPrCMe)2 affords the naphthalene bridged motif B-S-Al(NHC), NHC=N-heterocyclic carbene, while O=CPh2 is deoxygenated to afford an B-O-Al bridged species with incorporation of the remaining ≡CPh2 fragment into the naphthalene scaffold. The reaction with isonitrile Xyl-N≡C (Xyl=2,6-Me2 C6 H4 ) proceeds via a proposed (amino boryl) carbene species; which adds a second equivalent of isonitrile to ultimately form the Al-N-B bridged species cyclo-(1,8-C10 H6 )-[1-Al(Mes)-N(Xyl)-8-B{C(Mes)=C-N-Xyl}] with complete scission of the C≡N triple bond. The latter reaction is supported with isolated intermediates and by DFT calculations.

Ruthenium Olefin Metathesis Catalysts Bearing a Macrocyclic N-Heterocyclic Carbene Ligand: Improved Stability and Activity.

Formation of sterically hindered C-C double bonds via catalytic olefin metathesis is considered a very challenging task for Ru catalysts. This limitation led to the development of specialised catalysts bearing sterically reduced N-heterocyclic carbene (NHC) ligands that are very active in such transformations, yet significantly less stable as compared to general purpose catalysts. To decrease the small-size NHC catalysts susceptibility to decomposition, a new NHC ligand was designed, in which two sterically reduced aryl arms were tied together by a C-8 alkyl chain. The installation of this macrocyclic ligand on the ruthenium centre led to the formation of an olefin metathesis catalyst (trans-Ru6). Interestingly, this complex undergoes transformation into an isomer bearing two Cl ligands in the cis-arrangement (cis-Ru6). These two isomeric complexes exhibit similarly high thermodynamic stability, yet different application profiles in catalysis.

Superseding ß-Diketiminato Ligands: An Amido Imidazoline-2-Imine Ligand Stabilizes the Exhaustive Series of B=X Boranes (X=O, S, Se, Te).

Boron reluctantly forms B=X (X=O, S, Se, Te) moieties, which has stimulated the quest for such species in the past few years. Based on the N,N'-chelating ß-diketiminato ligand (HNacNac), a new amido imidazoline-2-imine ligand system (HAmIm) is presented, giving rise to the isolation of an exhaustive series of Lewis acid free, monomeric chalcogen B=X boranes with documented π-bond character between boron and the chalcogen. The chalcogenoboranes are isoelectronic and isolobal to the respective ketones. The chemical behavior of the oxoborane (B=O) strongly resembles the classical carbonyl reactivity in C=O bonds. The improved stability provided by HAmIm arises from the formation of more-stable five-membered boron chelates versus the six-membered NacNac analogues and from the imidazoline-2-imine moiety providing enhanced σ- and π-donation. The HAmIm ligand class may supersede the widely employed NacNac system in certain applications.

Impact of the olefin structure on the catalytic cycle and decomposition rates of Hoveyda-Grubbs metathesis catalysts.

A relatively fast degradation of ruthenium catalysts in the presence of selected olefins, and ethylene in particular, is one of the bottlenecks in their use in metathesis reactions. Here we explore the structure-activity relationships between the rate of degradation of Hoveyda-Grubbs catalysts and the structure of olefins by means of DFT calculations. We show that (Z)-1,2-dichloroethene can't form stable complexes with a 14-electron active complex due to a strong inductive electron withdrawal effect. Hoveyda-Grubbs catalysts can be, however, used to convert (Z)-1,2-dichloroethene to (E)-1,2-dichloroethene due to differences in crucial barriers in the catalytic cycle for E/Z isomers. Hoveyda-Grubbs catalysts in the presence of both isomers of 1,2-dimethoxyethene and 1,2-dichloroethene are predicted to be very stable in the unproductive metathesis, while for monosubstituted olefins the methoxyethene presence gives relatively low barriers for crucial degradation transition states and can readily undergo decomposition.

Rate-Limiting Steps in the Intramolecular C-H Activation of Ruthenium N-Heterocyclic Carbene Complexes.

Ruthenium (II) complexes with N-heterocyclic carbenes (NHC) are commonly used as efficient catalysts in hydrogenation of olefins with simultaneous intramolecular C-H activation. Using the DFT approach, we have investigated the entire hydrogenation reaction pathway for four new potential catalysts and ethylene, a model substrate. Our calculations imply that the dissociation of phosphine is the rate-limiting step of hydrogenation, contrary to recent computational results. We also found that catalysts bearing NHCs with aliphatic and aromatic side groups are energetically favorable over other aliphatic cyclohexyl-substituted NHC. To examine how electronic properties of various catalysts influence the energetic barrier in the crucial steps of the reaction, we applied the Noncovalent Interaction analysis, which allowed us to reveal crucial interactions which stabilize/destabilize important intermediates and transition states in the hydrogenation reaction.