Dynamics of Linkers in Metal-Organic Framework Glasses.

Metal-organic framework (MOF) glasses have emerged as a new class of organic-inorganic hybrid glass materials. Considerable efforts have been devoted to unraveling the macroscopic dynamics of MOF glasses by studying their rheological behavior; however, their microscopic dynamics remain unclear. In this work, we studied the effect of vitrification on linker dynamics in ZIF-62 by solid-state 2H nuclear magnetic resonance (NMR) spectroscopy. 2H NMR relaxation analysis provided a detailed picture of the mobility of the ZIF-62 linkers, including local restricted librations and a large-amplitude twist; these details were verified by molecular dynamics. A comparison of ZIF-62 crystals and glasses revealed that vitrification does not drastically affect the fast individual flipping motions with large-amplitude twists, whereas it facilitates slow cooperative large-amplitude twist motions with a decrease in the activation barrier. These observations support the findings of previous studies, indicating that glassy ZIF-62 retains permanent porosity and that short-range disorder exists in the alignment of ligands because of distortion of the coordination angle.

Understanding Alkene Interaction with Metal-Modified Zeolites: Thermodynamics and Mechanism of Bonding in the π-Complex.

Zeolites modified with metal cations are perspective catalysts for converting light alkenes to valuable chemicals. A crucial step of the transformation is an alkene interaction with zeolite to afford π-complex with metal cations. The mechanism of alkene bonding with cations is still unclear. To address this problem, propene adsorption on H+ (BroÌ·nsted acid site), Na+, Ca2+, Zn2+, Co2+, Cu2+, Cu+, and Ag+ cationic sites in ZSM-5 zeolite has been studied by quantum chemical calculations in terms of adsorption enthalpy, νC═C frequency, and natural bond orbital (NBO) analysis together with natural energy decomposition analysis (NEDA). It is revealed that the conventional concept of σ- and π-bonding is only partially applicable to alkene interaction with metal cations in zeolites. The orbital interaction between an alkene molecule and a metal site is more complex. Several different bonding mechanisms have been identified depending on the nature and electron configuration of the metal cation. This finding explains the complex correlations observed for propene π-complex stability and νC═C frequency shift or charge transfer from the alkene molecule. The results provide the basis for further understanding the interactions between alkenes and inorganic solid BroÌ·nsted and Lewis acids.

Tuning the Mechanism of H/D Exchange for Isobutane on H-BEA by Loading Zn Species in Zeolite.

Kinetics of H/D hydrogen exchange between deuterated isobutane-d10 and Brønsted acid sites (BAS) of three zeolite samples (H-BEA, ZnO/H-BEA, Zn2+ /H-BEA) were monitored with 1 H MAS NMR in situ at 343-468 K. The regioselective H/D exchange in the methyl groups detected on H-BEA can be rationalized in terms of the mechanism of indirect exchange, which involves protonation of the intermediate olefin and further hydride abstraction from the other alkane molecule by the formed carbenium ion. Loading of Zn species in the zeolite results in a decrease of the rate and an increase of the activation energy of the exchange. The loaded Zn species provide the tuning effect on the reaction occurrence, changing the mechanism from the indirect one to the mechanism of the direct exchange.

Mobility and separation of linear and branched C5 alkanes in UiO-66 (Zr) probed by 2H NMR and MD simulations.

The UiO-66 (Zr) metal-organic framework (MOF) is of notable interest due to its facile synthesis, robustness under a wide range of chemical and physical conditions and its capability to separate industrially relevant hydrocarbons mixtures. However, the knowledge of the molecular mechanisms behind these process remains limited. Here, we present a combined experimental (2H NMR) and computational study of the molecular mobility, transport and adsorption of C5 alkanes isomers in a dehydroxylated UiO-66 (Zr) MOF. We show that the tetrahedral cages of the MOF are the preferred adsorption location for both n-pentane and isopentane. In a binary mixture of the isomers, isopentane interacts more strongly with the material leading it to occupy more of the tetrahedral cages than n-pentane, resulting in an isopentane/n-pentane adsorption selectivity of αads = 2 (at 373 K). At the same time, the microscopic diffusivity for n-pentane, Dn (En = 18 kJ mol-1), is significantly lower than for isopentane, Diso (Eiso = 28 kJ mol-1), which results in a high separation selectivity for a n-pentane/isopentane mixture of α ≈ 13 (at 300 K). This shows that the UiO-66 MOF is indeed a promising active material for use in light hydrocarbon separation processes.

Quantitative 67Zn, 27Al and 1H MAS NMR spectroscopy for the characterization of Zn species in ZSM-5 catalysts.

67Zn MAS NMR spectroscopy was used to characterize the state of Zn in Zn-modified zeolites ZSM-5. Two 67Zn enriched zeolite samples were prepared: by solid-state exchange with metal 67Zn (Zn2+/ZSM-5 sample) and by ion exchange with zinc formate solution (ZnO/H-ZSM-5 sample), both containing ca. 3.8 wt% Zn. The elemental analysis, TEM, and quantitative BAS and aluminum analyses with 1H and 27Al MAS NMR have shown that Zn2+/ZSM-5 contains zinc in the form of Zn2+ cations, while both ZnO species and Zn2+ cations are present in ZnO/H-ZSM-5 besides BAS. 67Zn MAS NMR has detected the signal of Zn in a tetrahedral environment from ZnO species for both the activated and hydrated ZnO/H-ZSM-5 zeolite. The signal of Zn in an octahedral environment was detected for the hydrated Zn2+/ZSM-5 and ZnO/H-ZSM-5 zeolites. This signal may belong to zinc cation [HOZn]+ or Zn(OH)2 species surrounded by water molecules. Quantitative 67Zn MAS NMR analysis has shown that only 27 and 38% of zinc loaded in the zeolite is visible for the activated and hydrated ZnO/H-ZSM-5 zeolite, and 24% of Zn is visible for the hydrated Zn2+/ZSM-5. Zinc in the form of ZnO species is entirely visible in both the activated and hydrated ZnO/H-ZSM-5 zeolite, while Zn2+ cations are not detected at all for the activated sample and only 29% of Zn2+ cations is visible for the hydrated zeolite. Detection of only a part of Zn2+ cations in the form of [HOZn]+ or Zn(OH)2 species in octahedral environment presumes only partial hydrolysis of the bond of Zn2+ cation with framework oxygen and further solvation of the Zn species formed at hydrolysis by the adsorbed water.

Comparison of the Patency and Regenerative Potential of Biodegradable Vascular Prostheses of Different Polymer Compositions in an Ovine Model.

The lack of suitable autologous grafts and the impossibility of using synthetic prostheses for small artery reconstruction make it necessary to develop alternative efficient vascular grafts. In this study, we fabricated an electrospun biodegradable poly(ε-caprolactone) (PCL) prosthesis and poly(3-hydroxybutyrate-co-3-hydroxyvalerate)/poly(ε-caprolactone) (PHBV/PCL) prosthesis loaded with iloprost (a prostacyclin analog) as an antithrombotic drug and cationic amphiphile with antibacterial activity. The prostheses were characterized in terms of their drug release, mechanical properties, and hemocompatibility. We then compared the long-term patency and remodeling features of PCL and PHBV/PCL prostheses in a sheep carotid artery interposition model. The research findings verified that the drug coating of both types of prostheses improved their hemocompatibility and tensile strength. The 6-month primary patency of the PCL/Ilo/A prostheses was 50%, while all PHBV/PCL/Ilo/A implants were occluded at the same time point. The PCL/Ilo/A prostheses were completely endothelialized, in contrast to the PHBV/PCL/Ilo/A conduits, which had no endothelial cells on the inner layer. The polymeric material of both prostheses degraded and was replaced with neotissue containing smooth-muscle cells; macrophages; proteins of the extracellular matrix such as type I, III, and IV collagens; and vasa vasorum. Thus, the biodegradable PCL/Ilo/A prostheses demonstrate better regenerative potential than PHBV/PCL-based implants and are more suitable for clinical use.

High-Temperature Quantum Tunneling and Hydrogen Bonding Rearrangements Characterize the Solid-Solid Phase Transitions in a Phosphonium-Based Protic Ionic Liquid.

We report the complex phase behavior of the glass forming protic ionic liquid (PIL) d3-octylphosphonium bis(trifluoromethylsulfonyl)imide [C8 H17 PD3 ][NTf2 ] by means of solid-state NMR spectroscopy. Combined line shape and spin relaxation studies of the deuterons in the PD3 group of the octylphosphonium cation allow to map and correlate the phase behavior for a broad temperature range from 71 K to 343 K. In the solid PIL at 71 K, we observed a static state, characterized by the first deuteron quadrupole coupling constant reported for PD3 deuterons. A transition enthalpy of about 12 kJ mol-1 from the static to the mobile state with increasing temperature suggests the breaking of a weak, charge-enhanced hydrogen bond between cation and anion. The highly mobile phase above 100 K exhibits an almost disappearing activation barrier, strongly indicating quantum tunneling. Thus, we provide first evidence of tunneling driven mobility of the hydrogen bonded P-D moieties in the glassy state of PILs, already at surprisingly high temperatures up to 200 K. Above 250 K, the mobile phase turns from anisotropic to isotropic motion, and indicates strong internal rotation of the PD3 group. The analyzed line shapes and spin relaxation times allow us to link the structural and dynamical behavior at molecular level with the phase behavior beyond the DSC traces.

The Influence of Deuterium Isotope Effects on Structural Rearrangements, Ensemble Equilibria, and Hydrogen Bonding in Protic Ionic Liquids.

We report strong isotope effects for the protic ionic liquid triethylammonium methanesulfonate [TEA][OMs] by means of deuterium solid-state NMR spectroscopy covering broad temperature ranges from 65 K to 313 K. Both isotopically labelled PILs differ in non-deuterated and fully deuterated ethyl groups of the triethyl ammonium cations. The N-D bond of both cations is used as sensitive probe for hydrogen bonding and structural ordering. The 2 H NMR line shape analysis provides the deuteron quadrupole coupling constants and the characteristics of a broad heterogeneous phase with simultaneously present static and mobile states indicating plastic crystal behavior. The temperatures where both states are equally populated differ by about 80 K for the two PILs, showing that deuteration of the ethyl groups in the trialkylammonium cations tremendously shifts the equilibrium towards the static state. In addition, it leads to a significant less cooperative transition, associated with a significantly reduced standard molar transition entropy.

Isobutane Transformation to Aromatics on Zn-Modified Zeolites: Intermediates and the Effect of Zn2+ and ZnO Species on the Reaction Occurrence Revealed by 13 C MAS NMR.

To clarify the effects of different Zn species, zeolite topology and acidity (quantity of Brønsted acid sites, BAS) on alkane aromatization, isobutane transformation on Zn2+ /H-ZSM-5, Zn2+ /H-BEA, and ZnO/H-BEA zeolites has been monitored with 13 C MAS NMR. The alkane transformation has been established to occur by aromatization and hydrogenolysis pathways. Zn2+ species is more efficient for the aromatization reaction because aromatic products are formed at lower temperatures on Zn2+ /H-BEA and Zn2+ /H-ZSM-5 than on ZnO/H-BEA. The larger quantity of BAS in ZnO/H-BEA seems to provide a higher degree of the hydrogenolysis pathway on this catalyst. The mechanism of the alkane aromatization is similar for the zeolites of different topology and containing different Zn species, with the main reaction steps being the following: (i) isobutane dehydrogenation to isobutene via isobutylzinc; (ii) isobutene stabilization as a π-complex on Zn sites; (iii) isobutene oligomerization via the alkene insertion into Zn-C bond of methyl-σ-allylzinc formed from the π-complex; (iv) oligomer dehydrogenation with intermediate formation of polyene carbanionic structures; (v) aromatics formation via further polyene dehydrogenation, protonation, cyclization, deprotonation steps with BAS involvement.

The DFT Approach to predict 13C NMR chemical shifts of hydrocarbon species adsorbed on Zn-modified zeolites.

13C MAS NMR spectroscopy is a powerful technique to study the mechanisms of hydrocarbon transformations on heterogeneous catalysts. It can reliably identify the surface intermediates and the adsorbed products based on the analysis of their 13C chemical shifts, δ(13C). However, the unambiguous assignment of the detected signals is always a challenge due to the uncertainty of the nature of the surface intermediates formed and the mechanism of adsorbed species interaction with active sites. The way to solve this problem is the application of DFT calculations to predict chemical shifts for the expected intermediate hydrocarbon species. Herein, the methodology for δ(13C) chemical shift calculations for adsorbed species has been proposed. It includes: (i) zeolite framework optimization with periodic DFT (pPBE); (ii) medium-sized cluster geometry optimization with hybrid GGA (PBE0), and (iii) σ(13C) values calculation followed by δ(13C) estimation using the linear regression method. It is inferred that the TPSS/cc-pVTZ method provides the best computational cost/accuracy ratio for the set of adsorbed hydrocarbon species that was previously detected experimentally on the surface of Zn-containing zeolites. The drawbacks of the computation method have also been revealed and discussed.

Structure, hydrogen bond dynamics and phase transition in a model ionic liquid electrolyte.

We show that solid-state NMR spectroscopy is a suitable method for characterizing the structure, hydrogen bond dynamics and phase transition behavior in protic ionic liquids (PILs). Deuteron line shape and spin relaxation time analysis provide a description of the structural and dynamical heterogeneity in the solid state of the model PIL triethyl ammonium bis(trifluoromethanesulfonyl)amide [TEA][NTf2]. Therein, we observed two deuteron quadrupole coupling constant for the ND bond of the TEA cation, indicating differently strong hydrogen bonds to the nitrogen and oxygen atoms of the NTf2 anion, as we could confirm by DFT calculations. The transition processes in the dynamically heterogeneous phase are characterized by two standard molar enthalpies and thus different stages of melting. We provide geometry, rates and energetics of the cation in the solid and liquid states of the PIL. Comparison with PILs having stronger interacting anions shows higher enthalpy change between the solid and liquid states, lower activation barriers of tumbling motion and higher amplitude of librational motion for the TEA cation in the presence of the weakly interacting anion NTf2. We provide reasonable relations between microscopic and macroscopic properties, as is relevant for any kind of application.

Property-activity relations of multifunctional reactive ensembles in cation-exchanged zeolites: a case study of methane activation on Zn2+-modified zeolite BEA.

The reactivity theories and characterization studies for metal-containing zeolites are often focused on probing the metal sites. We present a detailed computational study of the reactivity of Zn-modified BEA zeolite towards C-H bond activation of the methane molecule as a model system that highlights the importance of representing the active site as the whole reactive ensemble integrating the extra-framework ZnEF2+ cations, framework oxygens (OF2-), and the confined space of the zeolite pores. We demonstrate that for our model system the relationship between the Lewis acidity, defined by the probe molecule adsorption energy, and the activation energy for methane C-H bond cleavage performs with a determination coefficient R2 = 0.55. This suggests that the acid properties of the localized extra-framework cations can be used only for a rough assessment of the reactivity of the cations in the metal-containing zeolites. In turn, studying the relationship between the activation energy and pyrrole adsorption energy revealed a correlation, with R2 = 0.80. This observation was accounted for by the similarity between the local geometries of the pyrrole adsorption complexes and the transition states for methane C-H bond cleavage. The inclusion of a simple descriptor for zeolite local confinement allows transferability of the obtained property-activity relations to other zeolite topologies. Our results demonstrate that the representation of the metal cationic species as a synergistically cooperating active site ensembles allows reliable detection of the relationship between the acid properties and reactivity of the metal cation in zeolite materials.

Butane isomers mobility and framework dynamics in UiO-66 (Zr) MOF: Impact of the hydroxyl groups in zirconia cluster.

UiO-66 (Zr) is a metal-organic framework (MOF) known for its thermal and chemical stability and wide range of adsorption-based applications. This MOF exhibits high separation selectivity for butane isomers. It has been earlier inferred that the separation performance of the material depends on the hydroxylation state of the zirconia cluster. In this contribution, we apply 2H solid-state NMR to characterize the dynamics of both the MOF organic framework itself and butane isomers in hydroxylated and dehydroxylated forms of UiO-66. It is established that the rate of π-flipping and the amplitude of the phenylene ring plane librations in the framework are higher for the dehydroxylated form. Self-diffusion coefficients of butane isomers have been estimated for both forms of UiO-66. The diffusivity is higher for n-butane in the dehydroxylated form, whereas the diffusion of isobutane is not affected by the presence of OH groups in the zirconia cluster of the MOF. Higher diffusivity of n-butane in dehydroxylated form is accounted for by the larger effective diameter of the window between the adjacent cages in this form, which arises from faster rotation and larger amplitude of framework linker libration. This rationalizes the higher efficiency of the dehydroxylated form of UiO-66(Zr) material for butane isomers separation.

Application of different approaches to generate virtual patient populations for the quantitative systems pharmacology model of erythropoiesis.

In a standard situation, a quantitative systems pharmacology model describes a "reference patient," and the model parameters are fixed values allowing only the mean values to be described. However, the results of clinical trials include a description of variability in patients' responses to a drug, which is typically expressed in terms of conventional statistical parameters, such as standard deviations (SDs) from mean values. Therefore, in this study, we propose and compare four different approaches: (1) Monte Carlo Markov Chain (MCMC); (2) model fitting to Monte Carlo sample; (3) population of clones; (4) stochastically bounded selection to generate virtual patient populations based on experimentally measured mean data and SDs. We applied these approaches to generate virtual patient populations in the QSP model of erythropoiesis. According to the results of our research, stochastically bounded selection showed slightly better results than the other three methods as it allowed the description of any number of patients from clinical trials and could be applied in the case of complex models with a large number of variable parameters.

Tear Proteome Revealed Association of S100A Family Proteins and Mesothelin with Thrombosis in Elderly Patients with Retinal Vein Occlusion.

Tear samples collected from patients with central retinal vein occlusion (CRVO; n = 28) and healthy volunteers (n = 29) were analyzed using a proteomic label-free absolute quantitative approach. A large proportion (458 proteins with a frequency > 0.6) of tear proteomes was found to be shared between the study groups. Comparative proteomic analysis revealed 29 proteins (p < 0.05) significantly differed between CRVO patients and the control group. Among them, S100A6 (log (2) FC = 1.11, p < 0.001), S100A8 (log (2) FC = 2.45, p < 0.001), S100A9 (log2 (FC) = 2.08, p < 0.001), and mesothelin ((log2 (FC) = 0.82, p < 0.001) were the most abundantly represented upregulated proteins, and ß2-microglobulin was the most downregulated protein (log2 (FC) = −2.13, p < 0.001). The selected up- and downregulated proteins were gathered to customize a map of CRVO-related critical protein interactions with quantitative properties. The customized map (FDR < 0.01) revealed inflammation, impairment of retinal hemostasis, and immune response as the main set of processes associated with CRVO ischemic condition. The semantic analysis displayed the prevalence of core biological processes covering dysregulation of mitochondrial organization and utilization of improperly or topologically incorrect folded proteins as a consequence of oxidative stress, and escalating of the ischemic condition caused by the local retinal hemostasis dysregulation. The most significantly different proteins (S100A6, S100A8, S100A9, MSLN, and ß2-microglobulin) were applied for the ROC analysis, and their AUC varied from 0.772 to 0.952, suggesting probable association with the CRVO.

In Silico Study of the Interactions of Anle138b Isomer, an Inhibitor of Amyloid Aggregation, with Partner Proteins.

Herein, we aimed to highlight current "gaps" in the understanding of the potential interactions between the Anle138b isomer ligand, a promising agent for clinical research, and the intrinsically disordered alpha-synuclein protein. The presence of extensive unstructured areas in alpha-synuclein determines its existence in the cell of partner proteins, including the cyclophilin A chaperone, which prevents the aggregation of alpha-synuclein molecules that are destructive to cell life. Using flexible and cascaded molecular docking techniques, we aimed to expand our understanding of the molecular architecture of the protein complex between alpha-synuclein, cyclophilin A and the Anle138b isomer ligand. We demonstrated the possibility of intricate complex formation under cellular conditions and revealed that the main interactions that stabilize the complex are hydrophobic and involve hydrogen.

3ß-Corner Stability by Comparative Molecular Dynamics Simulations.

This study explored the mechanisms by which the stability of super-secondary structures of the 3ß-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3ß-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3ß-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3ß-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or "ready-made" building block in protein folding. The 3ß-corner can also be considered as an independent object for study in field of structural biology.

Atomic Simulation of the Binding of JAK1 and JAK2 with the Selective Inhibitor Ruxolitinib.

Rheumatoid arthritis belongs to the group of chronic systemic autoimmune diseases characterized by the development of destructive synovitis and extra-articular manifestations. Cytokines regulate a wide range of inflammatory processes involved in the pathogenesis of rheumatoid arthritis and contribute to the induction of autoimmunity and chronic inflammation. Janus-associated kinase (JAK) and signal transducer and activator of transcription (STAT) proteins mediate cell signaling from cytokine receptors, and are involved in the pathogenesis of autoimmune and inflammatory diseases. Targeted small-molecule drugs that inhibit the functional activity of JAK proteins are used in clinical practice for the treatment of rheumatoid arthritis. In our study, we modeled the interactions of the small-molecule drug ruxolitinib with JAK1 and JAK2 isoforms and determined the binding selectivity using molecular docking. Molecular modeling data show that ruxolitinib selectively binds the JAK1 and JAK2 isoforms with a binding affinity of -8.3 and -8.0 kcal/mol, respectively. The stabilization of ligands in the cavity of kinases occurs primarily through hydrophobic interactions. The amino acid residues of the protein globules of kinases that are responsible for the correct positioning of the drug ruxolitinib and its retention have been determined.

The Role of Bile Acids in the Human Body and in the Development of Diseases.

Bile acids are specific and quantitatively important organic components of bile, which are synthesized by hepatocytes from cholesterol and are involved in the osmotic process that ensures the outflow of bile. Bile acids include many varieties of amphipathic acid steroids. These are molecules that play a major role in the digestion of fats and the intestinal absorption of hydrophobic compounds and are also involved in the regulation of many functions of the liver, cholangiocytes, and extrahepatic tissues, acting essentially as hormones. The biological effects are realized through variable membrane or nuclear receptors. Hepatic synthesis, intestinal modifications, intestinal peristalsis and permeability, and receptor activity can affect the quantitative and qualitative bile acids composition significantly leading to extrahepatic pathologies. The complexity of bile acids receptors and the effects of cross-activations makes interpretation of the results of the studies rather difficult. In spite, this is a very perspective direction for pharmacology.

A Recent Ten-Year Perspective: Bile Acid Metabolism and Signaling.

Bile acids are important physiological agents required for the absorption, distribution, metabolism, and excretion of nutrients. In addition, bile acids act as sensors of intestinal contents, which are determined by the change in the spectrum of bile acids during microbial transformation, as well as by gradual intestinal absorption. Entering the liver through the portal vein, bile acids regulate the activity of nuclear receptors, modify metabolic processes and the rate of formation of new bile acids from cholesterol, and also, in all likelihood, can significantly affect the detoxification of xenobiotics. Bile acids not absorbed by the liver can interact with a variety of cellular recipes in extrahepatic tissues. This provides review information on the synthesis of bile acids in various parts of the digestive tract, its regulation, and the physiological role of bile acids. Moreover, the present study describes the involvement of bile acids in micelle formation, the mechanism of intestinal absorption, and the influence of the intestinal microbiota on this process.