The dielectric response of phenothiazine-based glass-formers with different molecular complexity

AbstractWe examined a series of structurally related glass-forming liquids in which a phenothiazine-based tricyclic core (PTZ) was modified by attaching n-alkyl chains of different lengths (n = 4, 8, 10). We systematically disentangled the impact of chemical structure modification on the intermolecular organization and molecular dynamics probed by broadband dielectric spectroscopy (BDS). X-ray diffraction (XRD) patterns evidenced that all PTZ-derivatives are not ‘ordinary’ liquids and form nanoscale clusters. The chain length has a decisive impact on properties, exerting a plasticizing effect on the dynamics. Its elongation decreases glass transition temperature with slight impact on fragility. The increase in the medium-range order was manifested as a broadening of the dielectric loss peak reflected in the lower value of stretching parameter βKWW. A disagreement with the behavior observed for non-associating liquids was found as a deviation from the anti-correlation between the value of βKWW and the relaxation strength of the α-process. Besides, to explain the broadening of loss peak in PTZ with the longest (decyl) chain a slow Debye process was postulated. In contrast, the sample with the shortest alkyl chain and a less complex structure with predominant supramolecular assembly through π–π stacking exhibits no clear Debye-mode fingerprints. The possible reasons are also discussed.

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XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798316002837 ◽

2016 ◽

Vol 72 (4) ◽

pp. 586-598 ◽

Cited By ~ 11

Author(s):

Oleg Borbulevych ◽

Roger I. Martin ◽

Ian J. Tickle ◽

Lance M. Westerhoff

Keyword(s):

Quantum Mechanics ◽

Drug Discovery ◽

Neutron Diffraction ◽

Diffraction Data ◽

Complex Structure ◽

Urate Oxidase ◽

X Ray Diffraction ◽

Protonation State ◽

X Ray ◽

The Impact

Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, calledXModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that usingXModeScoreit is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case,XModeScoreapplied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinementversusconventional refinement onXModeScoreis also discussed.

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Bond length (Ti–O) dependence of nano ATO3-based (A = Pb, Ba, Sr) perovskite structures: Optical investigation in IR range

Modern Physics Letters B ◽

10.1142/s0217984917503560 ◽

2018 ◽

Vol 32 (01) ◽

pp. 1750356

Author(s):

Mahdi Ghasemifard ◽

Misagh Ghamari ◽

Cengiz Okay

Keyword(s):

Bond Length ◽

Complex Refractive Index ◽

Average Crystallite Size ◽

Optical Investigation ◽

X Ray Diffraction ◽

Xrd Pattern ◽

Polyhedral Particles ◽

Auto Combustion ◽

Xrd Patterns ◽

The Impact

In the current study, ABO3 (A = Pb, Ba, Sr and B = Ti) perovskite structures are produced by the auto-combustion route by using citric acid (CA) and nitric acid (NA) as fuel and oxidizer. The X-ray diffraction (XRD) patterns confirmed the perovskite nanostructure with cubic, tetragonal, and rhombohedral for SrTiO3, PbTiO3, and BaTiO3, respectively. Using Scherrer’s equation and XRD pattern, the average crystallite size of the samples were acquired. The effect of Ti–O bond length on the structure of the samples was evaluated. The type of structures obtained depends on Ti–O bond length which is in turn influenced by A[Formula: see text] substitutions. Microstructural studies of nanostructures calcined at 850[Formula: see text]C confirmed the formation of polyhedral particles with a narrow size distribution. The values of optical band gaps were measured and the impact of A[Formula: see text] was discussed. The optical properties such as the complex refractive index and dielectric function were calculated by IR spectroscopy and Kramers–Kronig (K–K) relations. Lead, as the element with the highest density as compared to other elements, changes the optical constants, remarkably due to altering titanium and oxygen distance in TO6 groups.

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Composition Dependence of Phase Separation and Crystallization in Deeply Undercooled Zr-(Ti-)Cu-Ni-Al Alloys

MRS Proceedings ◽

10.1557/proc-644-l5.6 ◽

2000 ◽

Vol 644 ◽

Author(s):

Andreas A. Kündig ◽

Jörg F. Löffler ◽

William L. Johnson

Keyword(s):

Glass Transition ◽

Transition Temperature ◽

Glass Transition Temperature ◽

Scale Up ◽

X Ray Diffraction ◽

Scanning Calorimetry ◽

Glass Forming ◽

The Difference ◽

Xrd Patterns ◽

Thermal Stability Of

AbstractDifferent bulk glass forming alloys in the neighborhood of Zr52.5Cu17.9Ni14.6Al10Ti5 (Vit105) have been investigated by differential scanning calorimetry (DSC), x-ray diffraction (XRD) and small-angle neutron scattering (SANS). Along the Ti/Al line in composition space, Zr52.5Cu17.9Ni14.6Al10−xTi5+x with – ≤ x ≤ +2.5, the glass transition temperature, Tg, and the undercooled liquid regime (the difference between the first crystallization temperature and the glass transition temperature) continually decrease with increasing x. SANS measurements of annealed alloys show interference maxima, giving evidence for decomposition on the nanometer scale, up to a critical temperature Tc. In contrast to Tg, Tc increases with x and thus intercepts with Tg in the range –2.5 ≤ x ≤ –1.25, depending on the time scale of the experiment. At this composi- tion, significant changes in DSC traces and XRD patterns are observed. Additional isothermal DSC experiments show that the onset times for crystallization are significantly different for temperatures below and above Tc. We conclude that Tc, respectively the relation between Tc and Tg, determines the crystallization behavior and the thermal stability of these bulk metallic glasses.

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The 3-Dimensional Molecular Structure of the Actin Filament Revisited

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100119223 ◽

1985 ◽

Vol 43 ◽

pp. 480-481

Author(s):

U. Aebi ◽

R. Millonig ◽

H. Salvo

Keyword(s):

Actin Filament ◽

Supramolecular Assembly ◽

Specimen Preparation ◽

X Ray Diffraction ◽

Single Filament ◽

X Ray ◽

3 Dimensional ◽

Filament Diameter ◽

Preparation Conditions ◽

Apparent Diameter

To date, most 3-D reconstructions of undecorated actin filaments have been obtained from actin filament paracrystal data (for refs, see 1,2). However, due to the fact that (a) the paracrystals may be several filament layers thick, and (b) adjacent filaments may sustantially interdigitate, these reconstructions may be subject to significant artifacts. None of these reconstructions has permitted unambiguous tracing or orientation of the actin subunits within the filament. Furthermore, measured values for the maximal filament diameter both determined by EM and by X-ray diffraction analysis, vary between 6 and 10 nm. Obviously, the apparent diameter of the actin filament revealed in the EM will critically depend on specimen preparation, since it is a rather flexible supramolecular assembly which can easily be bent or distorted. To resolve some of these ambiguities, we have explored specimen preparation conditions which may preserve single filaments sufficiently straight and helically ordered to be suitable for single filament 3-D reconstructions, possibly revealing molecular detail.

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Structural and Magnetic Hysteresis Properties of Co-Zr Substituted Hexagonal Barium Ferrites

JOURNAL OF ADVANCES IN PHYSICS ◽

10.24297/jap.v7i1.1739 ◽

2015 ◽

Vol 7 (1) ◽

pp. 1346-1351

Author(s):

Ch.Gopal Reddy ◽

Ch. Venkateshwarlu ◽

P. Vijaya Bhasker Reddy

Keyword(s):

Magnetic Properties ◽

Single Phase ◽

Magnetic Hysteresis ◽

Grain Morphology ◽

Hexagonal Structure ◽

Ion Composition ◽

X Ray Diffraction ◽

Ceramic Method ◽

Barium Ferrites ◽

Xrd Patterns

Co-Zr substituted M-type hexagonal barium ferrites, with chemical formula BaCoxZrxFe12-2xO19 (where x = 0.0, 0.2, 0.4, 0.6, 0.8 and 1.0), have been synthesized by double sintering ceramic method. The crystallographic properties, grain morphology and magnetic properties of these ferrites have been investigated by X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Vibrating Sample Magnetometer (VSM). The XRD patterns confirm the single phase with hexagonal structure of prepared ferrites. The magnetic properties have been investigated as a function of Co and Zr ion composition at an applied field in the range of 20 KOe. These studies indicate that the saturation magnetization (Ms) in the samples increases initially up to the Co-Zr composition of x=0.6 and decreases thereafter. On the other hand, the coercivity (Hc) and Remanent magnetization (Mr) are found to decrease continuously with increasing Co-Zr content. This property is most useful in permanent magnetic recording. The observed results are explained on the basis of site occupation of Co and Zr ions in the samples.

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The impact of point defects in n-type GaN layers on thermal decomposition of InGaN/GaN QWs

Scientific Reports ◽

10.1038/s41598-021-81017-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mikolaj Grabowski ◽

Ewa Grzanka ◽

Szymon Grzanka ◽

Artur Lachowski ◽

Julita Smalc-Koziorowska ◽

...

Keyword(s):

Quantum Wells ◽

High Temperatures ◽

Point Defects ◽

X Ray Diffraction ◽

Helium Ions ◽

X Ray ◽

Sapphire Substrates ◽

Transmission Electron ◽

The Impact ◽

Ingan Quantum Wells

AbstractThe aim of this paper is to give an experimental evidence that point defects (most probably gallium vacancies) induce decomposition of InGaN quantum wells (QWs) at high temperatures. In the experiment performed, we implanted GaN:Si/sapphire substrates with helium ions in order to introduce a high density of point defects. Then, we grew InGaN QWs on such substrates at temperature of 730 °C, what caused elimination of most (but not all) of the implantation-induced point defects expanding the crystal lattice. The InGaN QWs were almost identical to those grown on unimplanted GaN substrates. In the next step of the experiment, we annealed samples grown on unimplanted and implanted GaN at temperatures of 900 °C, 920 °C and 940 °C for half an hour. The samples were examined using Photoluminescence, X-ray Diffraction and Transmission Electron Microscopy. We found out that the decomposition of InGaN QWs started at lower temperatures for the samples grown on the implanted GaN substrates what provides a strong experimental support that point defects play important role in InGaN decomposition at high temperatures.

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Deep Neural Network and Polynomial Chaos Expansion-Based Surrogate Models for Sensitivity and Uncertainty Propagation: An Application to a Rockfill Dam

Water ◽

10.3390/w13131830 ◽

2021 ◽

Vol 13 (13) ◽

pp. 1830

Author(s):

Gullnaz Shahzadi ◽

Azzeddine Soulaïmani

Keyword(s):

Polynomial Chaos ◽

Complex Structure ◽

Uncertainty Propagation ◽

Surrogate Models ◽

Polynomial Chaos Expansion ◽

Soil Parameters ◽

Chaos Expansion ◽

Rockfill Dam ◽

Parametric Studies ◽

The Impact

Computational modeling plays a significant role in the design of rockfill dams. Various constitutive soil parameters are used to design such models, which often involve high uncertainties due to the complex structure of rockfill dams comprising various zones of different soil parameters. This study performs an uncertainty analysis and a global sensitivity analysis to assess the effect of constitutive soil parameters on the behavior of a rockfill dam. A Finite Element code (Plaxis) is utilized for the structure analysis. A database of the computed displacements at inclinometers installed in the dam is generated and compared to in situ measurements. Surrogate models are significant tools for approximating the relationship between input soil parameters and displacements and thereby reducing the computational costs of parametric studies. Polynomial chaos expansion and deep neural networks are used to build surrogate models to compute the Sobol indices required to identify the impact of soil parameters on dam behavior.

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Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01819-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Olga V. Bondareva ◽

Nadezhda A. Potapova ◽

Kirill A. Konovalov ◽

Tatyana V. Petrova ◽

Natalia I. Abramson

Keyword(s):

Amino Acid ◽

Oxidative Phosphorylation ◽

Adaptive Evolution ◽

Complex Structure ◽

Subterranean Rodents ◽

Amino Acid Sequence Variation ◽

Tertiary Protein Structure ◽

Metabolic Performance ◽

The Impact ◽

Subterranean Species

Abstract Background Mitochondrial genes encode proteins involved in oxidative phosphorylation. Variations in lifestyle and ecological niche can be directly reflected in metabolic performance. Subterranean rodents represent a good model for testing hypotheses on adaptive evolution driven by important ecological shifts. Voles and lemmings of the subfamily Arvicolinae (Rodentia: Cricetidae) provide a good example for studies of adaptive radiation. This is the youngest group within the order Rodentia showing the fastest rates of diversification, including the transition to the subterranean lifestyle in several phylogenetically independent lineages. Results We evaluated the signatures of selection in the mitochondrial cytochrome b (cytB) gene in 62 Arvicolinae species characterized by either subterranean or surface-dwelling lifestyle by assessing amino acid sequence variation, exploring the functional consequences of the observed variation in the tertiary protein structure, and estimating selection pressure. Our analysis revealed that: (1) three of the convergent amino acid substitutions were found among phylogenetically distant subterranean species and (2) these substitutions may have an influence on the protein complex structure, (3) cytB showed an increased ω and evidence of relaxed selection in subterranean lineages, relative to non-subterranean, and (4) eight protein domains possess increased nonsynonymous substitutions ratio in subterranean species. Conclusions Our study provides insights into the adaptive evolution of the cytochrome b gene in the Arvicolinae subfamily and its potential implications in the molecular mechanism of adaptation. We present a framework for future characterizations of the impact of specific mutations on the function, physiology, and interactions of the mtDNA-encoded proteins involved in oxidative phosphorylation.

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A Study of the Effects of Rain, Snow and Hail on the Atmospheric Electric Field near Ground

Atmosphere ◽

10.3390/atmos12080996 ◽

2021 ◽

Vol 12 (8) ◽

pp. 996

Author(s):

Athanasios Karagioras ◽

Konstantinos Kourtidis

Keyword(s):

Frequency Distribution ◽

Complex Structure ◽

Potential Gradient ◽

Weather Conditions ◽

The Other ◽

Fair Weather ◽

Northern Greece ◽

Rain Events ◽

The Impact ◽

Bounce Back

The purpose of the present study is to investigate the impact of rain, snow and hail on potential gradient (PG), as observed in a period of ten years in Xanthi, northern Greece. An anticorrelation between PG and rainfall was observed for rain events that lasted several hours. When the precipitation rate was up to 2 mm/h, the decrease in PG was between 200 and 1300 V/m, in most cases being around 500 V/m. An event with rainfall rates up to 11 mm/h produced the largest drop in PG, of 2 kV/m. Shortly after rain, PG appeared to bounce back to somewhat higher values than the ones of fair-weather conditions. A decrease in mean hourly PG was observed, which was around 2–4 kV/m during the hail events which occurred concurrently with rain and from 0 to 3.5 kV/m for hail events with no rain. In the case of no drop, no concurrent drop in temperature was observed, while, for the other cases, it appeared that, for each degree drop in temperature, the drop in hourly mean PG was 1000 V/m; hence, we assume that the intensity of the hail event regulates the drop in PG. The frequency distribution of 1-minute PG exhibits a complex structure during hail events and extend from −18 to 11 kV/m, with most of the values in the negative range. During snow events, 1-minute PG exhibited rapid fluctuations between high positive and high negative values, its frequency distribution extending from −10 to 18 kV/m, with peaks at −10 and 3 kV/m.

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Glass-Forming Ability and Corrosion Resistance of Al88Y8−xFe4+x (x = 0, 1, 2 at.%) Alloys

Materials ◽

10.3390/ma14071581 ◽

2021 ◽

Vol 14 (7) ◽

pp. 1581

Author(s):

Rafał Babilas ◽

Monika Spilka ◽

Katarzyna Młynarek ◽

Wojciech Łoński ◽

Dariusz Łukowiec ◽

...

Keyword(s):

Corrosion Resistance ◽

Analytical Techniques ◽

Corrosion Current ◽

Glass Forming Ability ◽

Electrochemical Tests ◽

Glass Forming ◽

Transmission Electron ◽

Composition And Structure ◽

Amorphous Structures ◽

The Impact

The effect of iron and yttrium additions on glass forming ability and corrosion resistance of Al88Y8-xFe4+x (x = 0, 1, 2 at.%) alloys in the form of ingots and melt-spun ribbons was investigated. The crystalline multiphase structure of ingots and amorphous-crystalline structure of ribbons were examined by a number of analytical techniques including X-ray diffraction, Mössbauer spectroscopy, and transmission electron microscopy. It was confirmed that the higher Fe additions contributed to formation of amorphous structures. The impact of chemical composition and structure of alloys on their corrosion resistance was characterized by electrochemical tests in 3.5% NaCl solution at 25 °C. The identification of the mechanism of chemical reactions taking place during polarization test along with the morphology and internal structure of the surface oxide films generated was performed. It was revealed that the best corrosion resistance was achieved for the Al88Y7Fe5 alloy in the form of ribbon, which exhibited the lowest corrosion current density (jcorr = 0.09 μA/cm2) and the highest polarization resistance (Rp = 96.7 kΩ∙cm2).

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