Structural Lability Research Articles

The Influence of Sulfur Doping on Composition and Stability of Cathode Material-Electrolyte Interface Basing on Lithium-Manganese Spinel Studies

The solid-electrolyte interface (SEI) in lithium-ion batteries systems has crucial influence on the cell performance and its lifetime. The composition and properties of passivation layer which is formed at this interface depend on many factors like electrode material and electrolyte composition, the morphology of the electrode, potential range in which electrode is working or current densities. Therefore, appropriate selection of all of those parameters is essential to ensure the optimal properties of final battery. Lithium-manganese spinel LiMn2O4 (LMO) is relatively well known and successfully used cathode material in some commercial application (18% of whole cathode materials market according to Avicenne ENERGY reports from 2013). Despite the fact that LMO is used to power electric tools, medical devices or powertrains, its applicability is greatly limited due to the LMO’s poor capacity retention. This restricted cyclability is related to material’s structural lability and its limited stability versus organic solvents used in electrolytes for Li-ion batteries. LMO at room temperatures can undergo reversible phase transition from cubic (Fd-3m) to orthorhombic (Fddd) structure [1]. This transition which is related to the Jahn-Teller distortion of high-spin Mn3+ ions causes irreversible loss of capacity during subsequent charging/discharging cycles [1-6]. Stabilization of LMO is possible by distorting long-range order of crystalline structure. This can be achieved by partial substitution in cationic or anionic sublattice. Substitution of manganese ions with other transition metals (Co and Ni are most often used) leads to good stabilization but in the same time have negative impact on material cost. Izoelectronic partial substitution of oxygen atoms in spinel structure with sulfur seems to be better approach because it not only inhibit undesirable phase transition, which improves columbic efficiency of electrochemical reaction and cycle life of battery, but also significantly increase the capacity of the material [7]. Moreover, electrochemical impedance spectroscopy studies of the sulfur doped LMO (LiMn2O4-ySy) indicate that the surface of such modified material is more stable than pristine LMO. The goal of this studies is to analyze the influence of sulfur presence in the cathode material’s structure on the composition and stability of solid-electrolyte interface in working Li-ion battery cell. The stability and lifetime of working spinel electrode is strongly dependent on the properties of the material’s passivation layer. The composition of this interface and its stability in the electrolyte in the potential range of 3-4.5 V at different current densities were analyzed during electrochemical reaction for pristine LMO and sulfur doped samples. ACKNOWLEDGMENT This work is supported by National Centre for Research and Development, Poland under research grant No. LIDER/463/L-6/14/NCBR/2015. REFERENCES G. Li, Y. Iijima, Y. Kudo, H. Azuma Solid State Ionics, 146 (2002) 55-63G. Pistoia, A. Antonini, R. Rosati, D. Zane Electrochimica Acta, 41 (1996) 2683-2689G.G. Amatucci, C.N. Schmutz, A. Blyr, C. Sigala, A.S. Gozdz, D. Larcher, J.M. Tarascon Journal Power Sources, 69 (1997) 11-25A. Yamada, M. Tanaka, K. Tanaka, K. Sekai Journal Power Sources, 81-82 (1999) 73-78E. Iwata, K. Takahashi, K. Maeda, T. Mouri Journal Power Sources, 81-82 (1999) 430-433L. Yang, M. Takahashi, B. Wang Electrochimica Acta, 51 (2006) 3228-3234M. Molenda, M. Bakierska, D. Majda, M. Świętosławski, R. Dziembaj Solid State Ionics, 272 (2015) 127–132

Hybrid Nanogels Based on Chitosan Hydrochloride-Ascorbate Derived by Sol-Gel Biomimetic Synthesis

Nanostructured hydrogels obtained by the in situ sol-gel technology represent innovative systems for theranostic applications. Controlled self-assembly of charged macromolecular chains to form a polymer network due to specific non-covalent interactions is one of the methods to produce ionic biopolymer-based nanoscale gels. However, the structural lability and kinetic instability of such systems are significant disadvantages. In this study, we propose a preparation process of hybrid nanogels based on chitosan hydrochloride-ascorbate by biomimetic sol-gel synthesis at 20 and 80 °С using an organic-inorganic precursor. With the influence of the concentrations of the precursor, the binary chitosan salt, and a low-molecular-weight accelerator, the temperature of the sol-gel synthesis on the gelation time of our multicomponent chitosan-containing systems was evaluated. An increased concentration of the polymer salt, the introduction of an accelerator, and an increased temperature are shown to accelerate the gelation process. The refractive index (nD25) and pH of the silicon-chitosan-containing hydrogels were measured. A solid phase in these hydrogels was isolated by cold extraction combined with cryotreatment. Scanning electron microscopy shows that the solid phase of the hybrid nanogels is a matrix of agglomerated particles whose sizes increase with the chitosan concentration in the system.

Stable J-aggregation enabled dual photoacoustic and fluorescence nanoparticles for intraoperative cancer imaging.

J-aggregates display nanoscale optical properties which enable their use in fluorescence and photoacoustic imaging applications. However, control over their optical properties in an in vivo setting is hampered by the conformational lability of the J-aggregate structure in complex biological environments. J-aggregating nanoparticles (JNP) formed by self-assembly of bacteriopheophorbide-lipid (Bchl-lipid) in lipid nanovesicles represents a novel strategy to stabilize J-aggregates for in vivo bioimaging applications. We find that 15 mol% Bchl-lipid embedded within a saturated phospholipid bilayer vesicle was optimal in terms of maximizing Bchl-lipid dye loading, while maintaining a spherical nanoparticle morphology and retaining spectral properties characteristic of J-aggregates. The addition of cholesterol maintains the stability of the J-aggregate absorption band for up to 6 hours in the presence of 90% FBS. In a proof-of-concept experiment, we successfully applied JNPs as a fluorescence contrast agent for real-time intraoperative detection of metastatic lymph nodes in a rabbit head-and-neck cancer model. Lymph node metastasis delineation was further verified by visualizing the JNP within the excised lymph node using photoacoustic imaging. Using JNPs, we demonstrate the possibility of using J-aggregates as fluorescence and photoacoustic contrast agents and may potentially spur the development of other nanomaterials that can stably induce J-aggregation for in vivo cancer bioimaging applications.

Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding.

The energy required for mechanical inhibition of target proteases is stored in the native structure of inhibitory serpins and accessed by serpin structural remodeling. The overall serpin fold is ellipsoidal with one long and two short axes. Most of the structural remodeling required for function occurs along the long axis, while expansion of the short axes is associated with misfolded, inactive forms. This suggests that ellipticity, as typified by the long axis, may be important for both function and folding. Placement of donor and acceptor fluorophores approximately along the long axis or one of the short axes allows single-pair Förster resonance energy transfer (spFRET) to report on both unfolding transitions and the time-averaged shape of different conformations. Equilibrium unfolding and refolding studies of the well-characterized inhibitory serpin α1-antitrypsin reveal that the long axis collapses in the folding intermediates while the monitored short axis expands. These energetically distinct intermediates are thus more spherical than the native state. Our spFRET studies agree with other equilibrium unfolding studies that found that the region around one of the β strands, s5A, which helps define the long axis and must move for functionally required loop insertion, unfolds at low denaturant concentrations. This supports a connection between functionally important structural lability and unfolding in the inhibitory serpins.

Molecular Motions in Functional Self-Assembled Nanostructures

The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted.

Indirect Evidences of Conformational Regulation in Protein Reactions: How Much Can Be Learnt?

Almost all reactions of proteins manifest deviations from the simple behaviour prescribed by standard (bio)chemical kinetics. This is caused by the extraordinary structural lability of protein macromolecules which is often not less important for the reaction efficiency than the properties of the active center. Unveiling the mechanisms of structural regulation encounters serious difficulties because of their hidden character, as either modern experiments or computational methods still fall short of monitoring simultaneously the reaction events and concomitant conformational changes, so that one has to decipher the reaction kinetics only. Nevertheless, it is possible to come to reliable conclusions on the mode of operation of proteins and the character of their structural relaxation with the help of a convenient and computationally accessible approach expounded in the present paper.

Template synthesis and structures of bis-ferrocenylboronate macrobicyclic iron(ii) tris-dioximates

A series of ferrocenylboron-capped tris-dioximate iron(ii) clathrochelates was synthesized by the template condensation of three molecules of dimethylglyoxime (H2Dm), cyclohexanedione 1,2-dioxime (H2Nx), or cyclooctanedione 1,2-dioxime (H2Ox) and two molecules of ferrocenylboronic acid (FcB(OH)2) on the Fe2+ ion matrix. The yields of the clathrochelate derivatives of alicyclic dioximes were substantially higher than that of their acyclic analog, because the molecules of alicyclic H2Nx and H2Ox α-dioximes have the s-cis-configuration suitable for complex formation, whereas the H2Dm molecules in solution have the s-trans-configuration. The synthesized compounds were characterized using elemental analysis, IR and UV-Vis spectroscopies, MALDI-TOF mass spectrometry, 1H and 13C{1H} NMR and 57Fe Mossbauer spectroscopies, and X-ray diffraction analysis. The crystal of FeDm3(BFc)2·CHCl3 contains two types of crystallographically nonequivalent clathrochelate molecules. The intermolecular contacts C-H⋯Cp formed by the ferrocenyl fragments and cyclooctane carbocycles and the interactions Cp-H⋯O were observed in the crystal of FeOx3(BFc)2. The structural lability of the cyclooctane substituents allows the FeOx3(BFc)2 molecules to arrange by the “bump-into-hollow” mode because of attractive H⋯H interactions between the ribbed substituents of the neighboring molecules. The geometry of the ferrocenylborate iron(ii) clathrochelates is intermediate between a trigonal prism and a trigonal antiprism.

General Access to theVincaandTacamanAlkaloids Using a Rh(II)-Catalyzed Cyclization/Cycloaddition Cascade

The total synthesis of several members of the vinca and tacaman classes of indole alkaloids has been accomplished. The central step in the synthesis consists of an intramolecular [3+2]-cycloaddition reaction of an alpha-diazo indoloamide which delivers the pentacyclic skeleton of the natural product in excellent yield. The acid lability of the oxabicyclic structure was exploited to establish the trans-D/E ring fusion of (+/-)-3H-epivincamine (3). Finally, a base induced keto-amide ring contraction was utilized to generate the E-ring of the natural product. A variation of the cascade sequence of reactions used to synthesize (+/-)-3H-epivincamine was also employed for the synthesis of the tacaman alkaloids (+/-)-tacamonine and (+/-)-apotacamine.

Structural Lability in Stem–Loop 1 Drives a 5′ UTR–3′ UTR Interaction in Coronavirus Replication

The leader RNA of the 5′ untranslated region (UTR) of coronaviral genomes contains two stem–loop structures denoted SL1 and SL2. Herein, we show that SL1 is functionally and structurally bipartite. While the upper region of SL1 is required to be paired, we observe strong genetic selection against viruses that contain a deletion of A35, an extrahelical nucleotide that destabilizes SL1, in favor of genomes that contain a diverse panel of destabilizing second-site mutations, due to introduction of a noncanonical base pair near A35. Viruses containing destabilizing SL1-ΔA35 mutations also contain one of two specific mutations in the 3′ UTR. Thermal denaturation and imino proton solvent exchange experiments reveal that the lower half of SL1 is unstable and that second-site SL1-ΔA35 substitutions are characterized by one or more features of the wild-type SL1. We propose a “dynamic SL1” model, in which the base of SL1 has an optimized lability required to mediate a physical interaction between the 5′ UTR and the 3′ UTR that stimulates subgenomic RNA synthesis. Although not conserved at the nucleotide sequence level, these general structural characteristics of SL1 appear to be conserved in other coronaviral genomes.

Optimized Sample Preparation for MALDI Mass Spectrometry Analysis of Protected Synthetic Peptides

The recent development and commercialization of Fuzeon (enfuvirtide) demonstrated that a convergent strategy comprised of both solid- and solution-phase synthetic methodologies presents a viable route for peptide manufacturing on a multi-ton scale. In this strategy, the target sequence is prepared by stepwise solid-phase synthesis of protected peptide fragments, which are then coupled together in the solution-phase to give the full-length sequence. These synthetic methodologies pose a unique challenge for mass spectrometry (MS), as protected peptide intermediates are often marked by poor solubility, structural lability, and low ionization potential. Matrix-assisted laser desorption/ionization (MALDI) MS is uniquely suited to such analytes; however, generalized protocols for MALDI analysis of protected peptides have yet to be demonstrated. Herein, we report an operationally simple sample preparation method for MALDI analysis of protected peptides, which greatly facilitates the collection and interpretation of MS data. In this method, the difficulty in MS analysis of protected peptides has been greatly diminished by use of dithranol as a matrix and CsCl as an additive, giving rise to intentionally-formed Cs(+) adducts. With greatly reduced fragmentation, better crystalline morphology, and easier data interpretation, we anticipate that these findings will find utility in peptide process development and manufacturing settings for reaction monitoring, troubleshooting, and quality control.

Structural changes in the erythrocyte membrane of the trout Salmo irideus at seasonal acclimatization

Differences of thermostability were studied in red blood cells of the trout Salmo irideus differing in sex and age, as well as structural-dynamic characteristics of erythrocyte membrane proteins at seasonal acclimatization in the interval of reservoir water temperature of 0–19°C. An increase of resistance of erythrocytes to temperature lysis with elevation of the environmental temperature was revealed to be accompanied by a rise of the proteins segmental mobility and a decrease of intermolecular interactions in spectrin-actin cytoskeleton from the data of the ESR spin labeling method. Regulation of erythrocyte stability during acclimation was concluded to occur both changes of the fatty acids chain package at the variations of lipid composition and by changes of the cytoskeleton structural lability. Thereby this provides an increase of the bilayer firmness, on the one hand, while, on the other hand, a rise of elasticity and expansibility of the membrane on the whole, which increases resistance of cells to colloidal-osmotic hemolysis. Changes of concentration of oxygen dissolved in water, which are caused by temperature fluctuations, do not deem to be of crucial importance for structural stability of erythrocytes, as it can be compensated by another mechanism, specifically by changes of affinity of hemoglobin to oxygen.

Embryological evidence for developmental lability during early angiosperm evolution

Recent advances in angiosperm phylogeny reconstruction, palaeobotany and comparative organismic biology have provided the impetus for a major re-evaluation of the earliest phases of the diversification of flowering plants. We now know that within the first fifteen million years of angiosperm history, three major lineages of flowering plants-monocotyledons, eumagnoliids and eudicotyledons-were established, and that within this window of time, tremendous variation in vegetative and floral characteristics evolved. Here I report on a novel type of embryo sac (angiosperm female gametophyte or haploid egg-producing structure) in Amborella trichopoda, the sole member of the most ancient extant angiosperm lineage. This is the first new pattern of embryo sac structure to be discovered among angiosperms in well over half a century. This discovery also supports the emerging view that the earliest phases of angiosperm evolution were characterized by an extensive degree of developmental experimentation and structural lability, and may provide evidence of a critical link to the gymnospermous ancestors of flowering plants.

Intermolecular Transfer of Copper Ions from the CopC Protein of Pseudomonas syringae. Crystal Structures of Fully Loaded CuICuII Forms

CopC is a small soluble protein expressed in the periplasm of Pseudomonas syringae pathovar tomato as part of its copper resistance response (cop operon). Equilibrium competition reactions confirmed two separated binding sites with high affinities for Cu(I) (10(-7) > or = K(D) > or = 10(-13) M) and Cu(II) (K(D) = 10(-13(1)) M), respectively. While Cu(I)-CopC was converted cleanly by O2 to Cu(II)-CopC, the fully loaded form Cu(I)Cu(II)-CopC was stable in air. Variant forms H1F and H91F exhibited a lower affinity for Cu(II) than does the wild-type protein while variant E27G exhibited a higher affinity. Cation exchange chromatography detected each of the four different types of intermolecular copper transfer reactions possible between wild type and variant forms: Cu(I) site to Cu(II) site; Cu(II) site to Cu(I) site; Cu(I) site to Cu(I) site; Cu(II) site to Cu(II) site. The availability of an unoccupied site of higher affinity induced intermolecular transfer of either Cu(I) or Cu(II) in the presence of O2 while buffering concentrations of cupric ion at sub-picomolar levels. Crystal structures of two crystal forms of wild-type Cu(I)Cu(II)-CopC and of the apo-H91F variant demonstrate that the core structures of the molecules in the three crystal forms are conserved. However, the conformations of the amino terminus (a Cu(II) ligand) and the two copper-binding loops (at each end of the molecule) differ significantly, providing the structural lability needed to allow transfer of copper between partners, with or without change of oxidation state. CopC has the potential to interact directly with each of the four cop proteins coexpressed to the periplasm.

Lipid-destabilising properties of a peptide with structural plasticity

The Chameleon peptide (Cham) is a peptide designed from two regions of the GB1 protein, one folded as an α-helix and the other as a β structure. Depending on the environment, the Cham peptide adopts an α or a β conformation when inserted in different locations of GB1. This environment dependence is also observed for tilted peptides. These short protein fragments, able to destabilise organised system, are mainly folded in β structure in water and in α helix in a hydrophobic environment, like the lipid bilayer. In this paper, we tested whether the Cham peptide can be qualified as a tilted peptide. For this, we have compared the properties of Cham peptide (hydrophobicity, destabilising properties, conformation) to those of tilted peptides. The results suggest that Cham is a tilted peptide. Our study, together the presence of tilted fragments in transconformational proteins, suggests a relationship between tilted peptides and structural lability.

Rapid Monitoring of the Nature and Interconversion of Supported Catalyst Phases and of Their Influence upon Performance: CO Oxidation to CO2 by γ‐Al2O3 Supported Rh Catalysts

Spatially and temporally resolved energy-dispersive EXAFS (EDE) has been utilised in situ to study supported Rh nanoparticles during CO oxidation by O2 under plug-flow conditions. Three distinct phases of Rh supported upon Al2O3 were identified by using EDE at the Rh K-edge during CO oxidation. Their presence and interconversion are related to the efficiency of the catalysts in oxidising CO to CO2. A metallic phase is only found at higher temperatures (>450 K) and CO fractions (CO/O2 > 1); an oxidic phase resembling Rh2O3 dominates the active catalyst under oxygen-rich conditions. Below about 573 K, and in CO-rich environments, high proportions of isolated Rh(I)(CO)2 species are found to co-exist with metallic Rh nanoparticles. Alongside these discrete situations a large proportion of the active phase space comprises small Rh cores surrounded by layers of active oxide. Confinement of Rh to nanoscale domains induces structural lability that influences catalytic behaviour. For CO oxidation over Rh/Al2O3 there are two redox phase equilibria alongside the chemistry of CO and O adsorbed upon extended Rh surfaces.

XAFS study of TiO2/SiO2 system prepared by sol–gel from inorganic precursors

Abstract The samples of 5%TiO 2 /SiO 2 prepared by sol–gel method from inorganic precursors calcinated at the various temperatures were studied by XAFS spectroscopy at Siberian Synchrotron Radiation Center. It was established that structural lability of this system and the change of symmetry of the oxygen coordination around the Ti(+4) ions depends on the calcination temperature. It seems that the mechanism of dissolution of the Ti(4+) ions in SiO 2 depends on the calcination temperature and consists in the formation of Wadsley defects following the incorporation of SiO 2 in TiO 2 particles.

Purification and stability of glutaryl-7-ACA acylase from Pseudomonas sp.

The enzyme glutaryl-7-ACA acylase from Pseudomonas sp. NCIMB 40474, produced by a recombinant Escherichia coli host, was purified to homogeneity. The enzyme is a tetramer composed of two couples of asymmetric dimers, each of them constituted of two subunits of mol wt 18 and 52 kDa, respectively. It was found that glutaric acid, one of the products of the substrate hydrolysis, is an effective acylase inhibitor. Between pH 6.0 and pH 10.0, the enzymatic activity is almost constant, but below pH 6.0 it progressively declines. The acylase activity decreased sharply as a function of guanidine HCl concentration. The loss is significant even at concentrations of denaturant lower than those causing unfolding, as suggested by UV spectroscopy and fluorescence emission studies. In these conditions (low denaturant concentration and low pH) the inactivation of the enzyme is caused by the tetramer dissociation into dimers. The lability of the quaternary structure of the enzyme is a key feature that must be taken into account for the improvement of the catalyst stability.

Thermophysical properties of cytidine and deoxycytidine mono- and hemiphosphates

The calorimetric (DSC) and derivative thermogravimetric (DTG) measurements for crystalline mono- and hemiphosphates of cytidine and deoxycytidine have been performed. The results for four examined salts confirm the influence of presence (or absence) of 2'OH group in ribose ring on stability (or lability) of the crystal structure of examined salts.

Synthese, Struktur und Reaktivität eines Stanna(II)‐nickela(II)‐cyclobuten‐Komplexes

Synthesis, Structure, and Reactivity of a Stanna(II)‐nickela(III)‐cyclobutene KomplexesThe (ethyne)nickel(0) complex (iPr2PC2H4PiPr2)Ni(C2H2) (1) reacts with the stannene Sn[CH(SiMe3)2]2 below −30°C to yield the stanna(II)‐nickela(II)‐cyclobutene complex (iPr2PC2H4PiPr2)YYNiCH=YYCHSn[CH(SiMe3)2]2 (2; 83%) as the kinetically controlled product; 2 has been characterized by IR and NMR spectroscopy and an X‐ray crystal‐structure determination. The latter shows the central four‐membered ring to be planar with a long Ni—Sn bond [2.626(1) Å]. According to the temperature‐dependent NMR spectra, 2 dissociates reversibly in solution to the starting components. The synthesis reaction thus represents an equilibrium as long as the temperature is below 20°C. These observations indicate that the structural lability of the stanna(II)‐nickela(II)‐cyclobutene moiety is associated with the weakness of the Ni—Sn bond. The bonding situation in 2 is best described as an “inner complex” in which a stannyl anion is coordinated to a nickel(II) cation. An ethereal solution of 2 undergoes an oxidative addition of one ethyne C—H bond to the stannene at 20°C to give the Ni(0)/Sn(IV) complex iPr2PC2H4PiPr2)Ni({η2‐HC≡CSn(H)[CH(SiMe3)2]2} (3) as the thermodynamically controlled product. Reaction of 3 with CO liberates the new alkyne ligand.

Breakage of the human Y-chromosome short arm between two blocks of tandemly repeated DNA sequences

Y-chromosomal rearrangements, a common cause of sex reversal in man, frequently occur between two blocks of repeated DNA. Both blocks are composed of 20-kb tandemly repeated Y-chromosome-specific DNA sequences. They are located in the proximal portion of the Y short arm on a NotI restriction fragment of approximately 5.3 Mb and on an MluI fragment of approximately 5.5 Mb. Chromosome breaks positioned between the two blocks were detected in two of three 46,XY females with deletions of Yp and in five of six 46,XX males positive for the repeat sequences. The rearranged NotI fragments in the 46,XX males were 4.4 Mb and the MluI fragments were 2.0 Mb in length. This indicates that breaks occur within a small region of Yp defined by the two blocks of specific repeated DNA sequences. The region between the two blocks thus appears to be a focus of structural lability in the human Y chromosome.