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Crystals, Volume 9, Issue 5 (May 2019)

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Open AccessReview
Reading and Misreading 8-oxoguanine, a Paradigmatic Ambiguous Nucleobase
Crystals 2019, 9(5), 269; https://doi.org/10.3390/cryst9050269 (registering DOI)
Received: 26 April 2019 / Revised: 17 May 2019 / Accepted: 19 May 2019 / Published: 23 May 2019
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Abstract
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG [...] Read more.
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases. Full article
(This article belongs to the Special Issue Noncanonical Nucleobases)
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Open AccessArticle
Effect of Sectional Polymerization Process on Tunable Twist Structure Liquid Crystal Filters
Crystals 2019, 9(5), 268; https://doi.org/10.3390/cryst9050268 (registering DOI)
Received: 26 March 2019 / Revised: 25 April 2019 / Accepted: 20 May 2019 / Published: 23 May 2019
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Abstract
The effect of sectional polymerization process on tunable filters with cholesteric liquid crystal (CLC) and blue phase liquid crystal (BPLC) is demonstrated. The bandwidths of the polymer-stabilized cholesteric liquid crystal (PSCLC) and polymer-stabilized blue phase liquid crystal (PSBPLC) filters can be broadened by [...] Read more.
The effect of sectional polymerization process on tunable filters with cholesteric liquid crystal (CLC) and blue phase liquid crystal (BPLC) is demonstrated. The bandwidths of the polymer-stabilized cholesteric liquid crystal (PSCLC) and polymer-stabilized blue phase liquid crystal (PSBPLC) filters can be broadened by the holding treatment without distortion. The reflection bandwidth of the CLC filter can be broadened from 120 nm to 220 nm, and that of the BPLC filter can be broadened from 45 nm to 140 nm. Meanwhile, the intensity of reflection can be retained very well. The central wavelength of polymer-stabilized CLC filter can be thermally tuned from 1614 nm to 1460 nm with a stable wide bandwidth. The tunable C-band CLC filter and BPLC filter show great potential application in multi- and hyper-spectral systems and wide-band color filters. Full article
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Open AccessEditorial
Compounds with Polar Metallic Bonding
Crystals 2019, 9(5), 267; https://doi.org/10.3390/cryst9050267
Received: 14 May 2019 / Revised: 16 May 2019 / Accepted: 16 May 2019 / Published: 22 May 2019
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Abstract
Recently, I witnessed a discussion amongst solid state chemists whether the term polar intermetallic
bonding was necessary or dispensable, whether a conceptual discernation of this special class of
intermetallic compounds was indicated or spurious[...] Full article
(This article belongs to the Special Issue Compounds with Polar Metallic Bonding)
Open AccessArticle
Transformation of the Topological Phase and the Edge Modes of Double-Bilayer Bismuthene with Inter-Bilayer Spacing
Crystals 2019, 9(5), 266; https://doi.org/10.3390/cryst9050266
Received: 4 April 2019 / Revised: 18 May 2019 / Accepted: 20 May 2019 / Published: 22 May 2019
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Abstract
The transformations of the topological phase and the edge modes of a double-bilayer bismuthene were investigated with first-principles calculations and Green’s function as the inter-bilayer spacing increased from 0 Å to 10 Å. At a critical spacing of 2 Å, a topological phase [...] Read more.
The transformations of the topological phase and the edge modes of a double-bilayer bismuthene were investigated with first-principles calculations and Green’s function as the inter-bilayer spacing increased from 0 Å to 10 Å. At a critical spacing of 2 Å, a topological phase transition from a topological insulator to a band insulator resulting from a band inversion between the highest valence band and the second lowest conduction band, was observed, and this was understood based on the particular orbital characters of the band inversion involved states. The edge modes of double-bilayer bismuthene survived the phase transition. When d was 2 Å < d < 4 Å, the interaction between the edge modes of two separated bismuthene bilayers induced an anti-crossing gap and resulted in a trivial band connection. At and beyond 4 Å, the two bilayers behavior decoupled entirely. The results demonstrate the transformability of the topological phase and the edge modes with the inter-bilayer spacing in double-bilayer bismuthene, which may be useful for spintronic applications. Full article
(This article belongs to the Special Issue Recent Advances in Novel Topological Materials)
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Open AccessArticle
Ordering of Rods near Surfaces: Concentration Effects
Crystals 2019, 9(5), 265; https://doi.org/10.3390/cryst9050265
Received: 24 February 2019 / Revised: 6 May 2019 / Accepted: 16 May 2019 / Published: 21 May 2019
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Abstract
We study the orientation of rods in the neighborhood of a surface. A semi-infinite region in two different situations is considered: (i) the rods are located close to a flat wall and (ii) the rods occupy the space that surrounds a sphere. In [...] Read more.
We study the orientation of rods in the neighborhood of a surface. A semi-infinite region in two different situations is considered: (i) the rods are located close to a flat wall and (ii) the rods occupy the space that surrounds a sphere. In a recent paper we investigated a similar problem: the interior of a sphere, with a fixed concentration of rods. Here, we allow for varying concentration, the rods are driven from a reservoir to the neighborhood of the surface by means of a tunable chemical potential. In the planar case, the particle dimensions are irrelevant. In the curved case, we consider cylinders with dimensions comparable to the radius of curvature of the sphere; as they come close to the surface, they have to accommodate to fill the available space, leading to a rich orientational profile. These systems are studied by a mapping onto a three-state Potts model with annealed disorder on a semi-infinite lattice; two order parameters describe the system: the occupancy and the orientation. The Hamiltonian is solved using a mean-field approach producing recurrence relations that are iterated numerically and we obtain various interesting results: the system undergoes a first order transition just as in the bulk case; the profiles do not have a smooth decay but may present a step and we search for the factors that determine their shape. The prediction of such steps may be relevant in the field of self-assembly of colloids and nanotechnology. Full article
(This article belongs to the Special Issue New Trends in Lyotropic Liquid Crystals)
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Open AccessArticle
Semiperiodic Ultra-Broadband Double-Grating to Improve c-Si Thin-Film Solar Cell’s Optical Absorption, through Numerical Structural Optimization
Crystals 2019, 9(5), 264; https://doi.org/10.3390/cryst9050264
Received: 30 April 2019 / Revised: 15 May 2019 / Accepted: 17 May 2019 / Published: 21 May 2019
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Abstract
Plasmonic gratings provide effective photon management techniques in thin-film solar cells, capable of extending the optical thickness of the solar cell’s active layer. However, the ultra-broadband nature of such application makes an optimal design of the grating structure quite challenging, since a fully [...] Read more.
Plasmonic gratings provide effective photon management techniques in thin-film solar cells, capable of extending the optical thickness of the solar cell’s active layer. However, the ultra-broadband nature of such application makes an optimal design of the grating structure quite challenging, since a fully periodic grating operates only in specific spectral ranges. To achieve a more broadband design, semiperiodicity is introduced, which, due to having controllable disorder, is an apt solution in broadband optical applications. In this work, semiperiodic double gratings as a broadband photon management technique are introduced in order to improve the optical absorption of c-Si thin-film solar cells, and optimized through numerical structural optimization. Physical parameters of both front and back gratings are determined taking the spectrally integrated optical absorption as the figure of merit and subsequently a semiperiodic double grating is established through adding defects to the fully periodic structure. It is shown that such semiperiodic structure is capable of enhancing the spectrally integrated optical absorption 88.6 % compared to a reference structure without gratings. Full article
(This article belongs to the Special Issue Advances in Thin Film Solar Cells)
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Open AccessReview
Magnetron Sputtering for ZnO:Ga Scintillation Film Production and Its Application Research Status in Nuclear Detection
Crystals 2019, 9(5), 263; https://doi.org/10.3390/cryst9050263
Received: 24 April 2019 / Revised: 13 May 2019 / Accepted: 15 May 2019 / Published: 20 May 2019
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Abstract
As a wide band-gap and direct transition semiconductor material, ZnO has good scintillation performance and strong radiation resistance, but it also has a serious self-absorption phenomenon that affects its light output. After being doped with Ga, it can be used for the scintillator [...] Read more.
As a wide band-gap and direct transition semiconductor material, ZnO has good scintillation performance and strong radiation resistance, but it also has a serious self-absorption phenomenon that affects its light output. After being doped with Ga, it can be used for the scintillator of ultra-fast scintillating detectors to detect X-ray, gamma, neutron, and charged particles with extremely fast response and high light output. Firstly, the basic properties, defects, and scintillation mechanism of ZnO crystals are introduced. Thereafter, magnetron sputtering, one of the most attractive production methods for producing ZnO:Ga film, is introduced including the principle of magnetron sputtering and its technical parameters’ influence on the performance of ZnO:Ga. Finally, ZnO:Ga film’s application research status is presented as a scintillation material in the field of radiation detection, and it is concluded that some problems need to be urgently solved for its wider application. Full article
(This article belongs to the Special Issue Crystals, Films and Nanocomposite Scintillators)
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Open AccessReview
Peculiarities in the Director Reorientation and the NMR Spectra Evolution in a Nematic Liquid Crystals under the Effect of Crossed Electric and Magnetic Fields
Crystals 2019, 9(5), 262; https://doi.org/10.3390/cryst9050262
Received: 6 May 2019 / Revised: 14 May 2019 / Accepted: 15 May 2019 / Published: 20 May 2019
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Abstract
The illustrative description of the field-induced peculiarities of the director reorientation in the microsized nematic volumes under the effect of crossed magnetic B and electric E fields have been proposed. The most interesting feature of such configuration is that the nematic phase becomes [...] Read more.
The illustrative description of the field-induced peculiarities of the director reorientation in the microsized nematic volumes under the effect of crossed magnetic B and electric E fields have been proposed. The most interesting feature of such configuration is that the nematic phase becomes unstable after applying the strong E . The theoretical analysis of the reorientational dynamics of the director field provides an evidence for the appearance of the spatially periodic patterns in response to applied large E directed at an angle α to B . The feature of this approach is that the periodic distortions arise spontaneously from a homogeneously aligned nematic sample that ultimately induces a faster response than in the uniform mode. The nonuniform rotational modes involve additional internal elastic distortions of the conservative nematic system and, as a result, these deformations decrease of the viscous contribution U vis to the total energy U of the nematic phase. In turn, that decreasing of U vis leads to decrease of the effective rotational viscosity coefficient γ eff ( α ) . That is, a lower value of γ eff ( α ) , which is less than one in the bulk nematic phase, gives the less relaxation time τ on ( α ) γ eff ( α ) , when α is bigger than the threshold value α th . The results obtained by Deuterium NMR spectroscopy confirm theoretically obtained dependencies of τ on ( α ) on α . Full article
(This article belongs to the Special Issue Nuclear Magnetic Resonance of Liquid Crystals)
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Open AccessArticle
A Magnetic-Dependent Vibration Energy Harvester Based on the Tunable Point Defect in 2D Magneto-Elastic Phononic Crystals
Crystals 2019, 9(5), 261; https://doi.org/10.3390/cryst9050261
Received: 22 April 2019 / Revised: 10 May 2019 / Accepted: 16 May 2019 / Published: 19 May 2019
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Abstract
In this work, an innovative vibration energy harvester is designed by using the point defect effect of two-dimensional (2D) magneto-elastic phononic crystals (PCs) and the piezoelectric effect of piezoelectric material. A point defect is formed by removing the central Tenfenol-D rod to confine [...] Read more.
In this work, an innovative vibration energy harvester is designed by using the point defect effect of two-dimensional (2D) magneto-elastic phononic crystals (PCs) and the piezoelectric effect of piezoelectric material. A point defect is formed by removing the central Tenfenol-D rod to confine and enhance vibration energy into a spot, after which the vibration energy is electromechanically converted into electrical energy by attaching a piezoelectric patch into the area of the point defect. Numerical analysis of the point defect can be carried out by the finite element method in combination with the supercell technique. A 3D Zheng-Liu (Z-L) model which accurately describes the magneto-mechanical coupling constitutive behavior of magnetostrictive material is adopted to obtain variable band structures by applied magnetic field and pre-stress along the z direction. The piezoelectric material is utilized to predict the output voltage and power based on the capacity to convert vibration energy into electrical energy. For the proposed tunable vibration energy harvesting system, numerical results illuminate that band gaps (BGs) and defect bands of the in-plane mixed wave modes (XY modes) can be adjusted to a great extent by applied magnetic field and pre-stress, and thus a much larger range of vibration frequency and more broad-distributed energy can be obtained. The defect bands in the anti-plane wave mode (Z mode), however, have a slight change with applied magnetic field, which leads to a certain frequency range of energy harvesting. These results can provide guidance for the intelligent control of vibration insulation and the active design of continuous power supply for low power devices in engineering. Full article
(This article belongs to the Special Issue Sonic and Photonic Crystals)
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Open AccessArticle
Theoretical Model and Experimental Investigations on Solution-Mediated Polymorphic Transformation of Theophylline: From Polymorph I to Polymorph II
Crystals 2019, 9(5), 260; https://doi.org/10.3390/cryst9050260
Received: 8 May 2019 / Accepted: 17 May 2019 / Published: 19 May 2019
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Abstract
In this work, theophylline was selected as the model compound to study and simulate the solution-mediated polymorphic transformation. The polymorph I and polymorph II of theophylline were prepared and fully characterized. Raman and UV spectra methods were carried out to observe the phase [...] Read more.
In this work, theophylline was selected as the model compound to study and simulate the solution-mediated polymorphic transformation. The polymorph I and polymorph II of theophylline were prepared and fully characterized. Raman and UV spectra methods were carried out to observe the phase transformation of theophylline from polymorph I to polymorph II at different temperatures. The theoretical models, including dissolution model, nucleation model, and growth model, were established to describe and simulate the transformation processes. By combination of experiments and simulations, the controlling steps of the transformation processes were discussed. The effects of temperature and/or solvent on the transformation processes were evaluated. This work can shed light on the polymorphic transformation processes. Full article
(This article belongs to the Special Issue Anti-Solvent Crystallization)
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Open AccessArticle
Bacterial Effect on the Crystallization of Mineral Phases in a Solution Simulating Human Urine
Crystals 2019, 9(5), 259; https://doi.org/10.3390/cryst9050259
Received: 24 April 2019 / Revised: 11 May 2019 / Accepted: 16 May 2019 / Published: 18 May 2019
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Abstract
The effect of bacteria that present in the human urine (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus) was studied under the conditions of biomimetic synthesis. It was shown that the addition of bacteria significantly affects both the phase composition [...] Read more.
The effect of bacteria that present in the human urine (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus) was studied under the conditions of biomimetic synthesis. It was shown that the addition of bacteria significantly affects both the phase composition of the synthesized material and the position of crystallization boundaries of the resulting phosphate phases, which can shift toward more acidic (struvite, apatite) or toward more alkaline (brushite) conditions. Under conditions of oxalate mineralization, bacteria accelerate the nucleation of calcium oxalates by almost two times and also increase the amount of oxalate precipitates along with phosphates and stabilize the calcium oxalate dihydrate (weddellite). The multidirectional changes in the pH values of the solutions, which are the result of the interaction of all system components and the crystallization process, were analyzed. The obtained results are the scientific basis for understanding the mechanisms of bacterial involvement in stone formation within the human body and the creation of biotechnological methods that inhibit this process. Full article
(This article belongs to the Special Issue Mineralogical Crystallography)
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Open AccessCommunication
Morphologically Controlled Synthesis of Cs2SnCl6 Perovskite Crystals and Their Photoluminescence Activity
Crystals 2019, 9(5), 258; https://doi.org/10.3390/cryst9050258
Received: 17 April 2019 / Revised: 14 May 2019 / Accepted: 16 May 2019 / Published: 18 May 2019
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Abstract
The Cs2SnX6 perovskites have attracted much attention due to excellent optoelectronic properties and high stability. In the present work, we have focused on the morphology control and photoluminescence characteristics of the Cs2SnCl6 perovskite crystals. The synthesis process [...] Read more.
The Cs2SnX6 perovskites have attracted much attention due to excellent optoelectronic properties and high stability. In the present work, we have focused on the morphology control and photoluminescence characteristics of the Cs2SnCl6 perovskite crystals. The synthesis process of the Cs2SnCl6 crystals includes two stages composed of the formation of initial crystals and the growth of Cs2SnCl6; the later originated from the oxidization of CsSnCl3. This process has been confirmed by Scanning electron microscope (SEM) and X-rays diffraction (XRD). By controlling the concentration of the initial reactants and hydrochloric acid in the solution to change the supersaturation of the solution, different crystal morphologies, such as truncated octahedron, octahedron, hexapod, quasi-sphere, have been obtained. In relatively a low supersaturation solution, the amount of growth units dominates the crystal growth process to obtain the hexapod and self-assembly crystals. In contrast, in relatively high supersaturation solution, nucleation predominates to yield small size truncated octahedrons and near-spherical Cs2SnCl6 crystals. The synthesized Cs2SnCl6 crystals have shown a wide emission band peaking at 450 nm with full width at half maximum (FWHM) 63 nm due to the defects introduced by Sn2+. The photoluminescence intensities of crystals synthesized at various conditions exhibited considerable difference, which was about 60 times between the highest and the lowest. Full article
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Open AccessReview
Historical Perspective on Diffraction Line-Profile Analyses for Crystals Containing Defect Clusters
Crystals 2019, 9(5), 257; https://doi.org/10.3390/cryst9050257
Received: 6 April 2019 / Revised: 29 April 2019 / Accepted: 30 April 2019 / Published: 17 May 2019
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Abstract
Deviations of crystal diffraction line profiles from those predicted by the dynamical theory of diffraction for perfect crystals provide a window into the microscopic distributions of defects within non-perfect crystals. This overview provides a perspective on key theoretical, computational, and experimental developments associated [...] Read more.
Deviations of crystal diffraction line profiles from those predicted by the dynamical theory of diffraction for perfect crystals provide a window into the microscopic distributions of defects within non-perfect crystals. This overview provides a perspective on key theoretical, computational, and experimental developments associated with the analysis of diffraction line profiles for crystals containing statistical distributions of point defect clusters, e.g., dislocation loops, precipitates, and stacking fault tetrahedra. Pivotal theoretical developments beginning in the 1940s are recalled and discussed in terms of their impact on the direction of theoretical and experimental investigations of lattice defects in the 1960s, the 1970s, and beyond, as both experimental and computational capabilities advanced. The evolution of experimental measurements and analysis techniques, as stimulated by theoretical and computational progress in understanding the distortion fields surrounding defect clusters, is discussed. In particular, consideration is given to determining dislocation loop densities and separate size distributions for vacancy and interstitial type loops, and to the internal strain and size distributions for coherent precipitates. Full article
(This article belongs to the Special Issue X-ray and neutron Line Profile Analysis of Microstructures)
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Open AccessArticle
Crystal Structure Optimization and Gibbs Free Energy Comparison of Five Sulfathiazole Polymorphs by the Embedded Fragment QM Method at the DFT Level
Crystals 2019, 9(5), 256; https://doi.org/10.3390/cryst9050256
Received: 27 April 2019 / Revised: 9 May 2019 / Accepted: 13 May 2019 / Published: 17 May 2019
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Abstract
Molecular crystal plays an important role in many fields of science and technology, but it often crystallizes in different polymorphs with different physical properties. To guide the experimental synthesis of candidate materials, the atomic-scale model is frequently used to predict the most stable [...] Read more.
Molecular crystal plays an important role in many fields of science and technology, but it often crystallizes in different polymorphs with different physical properties. To guide the experimental synthesis of candidate materials, the atomic-scale model is frequently used to predict the most stable polymorph and its structural properties. Here, we show how an ab initio method can be used to achieve a rapid and accurate prediction of sulfathiazole crystal polymorphs (an antibiotic drug), based on the Gibbs free energy calculation and Raman spectra analysis. At the atmospheric pressure and the temperature of 300 K, we demonstrate that form III (FIII) is the most stable structure of sulfathiazole. The agreement between the predicted and experimental crystal structures corresponds to the order of stability for five sulfathiazole polymorphs as FI < FV < FIV < FII < FIII, which is achieved by employing the density functional theory (DFT) calculations. Full article
(This article belongs to the Special Issue Polymorphism in Crystals)
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Open AccessArticle
The Fabrication of Calcium Alginate Beads as a Green Sorbent for Selective Recovery of Cu(Ⅱ) from Metal Mixtures
Crystals 2019, 9(5), 255; https://doi.org/10.3390/cryst9050255
Received: 3 April 2019 / Revised: 13 May 2019 / Accepted: 13 May 2019 / Published: 17 May 2019
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Abstract
Calcium alginate (CA) beads as a green sorbent were easily fabricated in this study using sodium alginate crosslinking with CaCl2, and the crosslinking pathway was the exchange between the sodium ion of α-L-guluronic acid and Ca(II). The experimental study was conducted [...] Read more.
Calcium alginate (CA) beads as a green sorbent were easily fabricated in this study using sodium alginate crosslinking with CaCl2, and the crosslinking pathway was the exchange between the sodium ion of α-L-guluronic acid and Ca(II). The experimental study was conducted on Cu(II), Cd(II), Ni(II) and Zn(II) as the model heavy metals and the concentration was determined by inductively coupled plasma optical emission spectrometry (ICP-OES). The characterization and sorption behavior of the CA beads were analyzed in detail via using scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The adsorption experiments demonstrated that the CA beads exhibited a high removal efficiency for the selective adsorption of Cu(II) from the tetra metallic mixture solution and an excellent adsorption capacity of the heavy metals separately. According to the isotherm studies, the maximum uptake of Cu(II) could reach 107.53 mg/g, which was significantly higher than the other three heavy metal ions in the tetra metallic mixture solution. Additionally, after five cycles of adsorption and desorption, the uptake rate of Cu(II) on CA beads was maintained at 92%. According to the properties mentioned above, this material was assumed to be applied to reduce heavy metal pollution or recover valuable metals from waste water. Full article
(This article belongs to the Special Issue Layered Double Hydroxides)
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Open AccessArticle
Atomistic Modeling of Various Doped Mg2NiH4 as Conversion Electrode Materials for Lithium Storage
Crystals 2019, 9(5), 254; https://doi.org/10.3390/cryst9050254
Received: 16 April 2019 / Revised: 4 May 2019 / Accepted: 15 May 2019 / Published: 17 May 2019
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Abstract
In this work, we have compared the potential applications of nine different elements doped Mg2NiH4 as conversion-type electrode materials in Li-ion batteries by means of state-of-the-art Density functional theory calculations. The electrochemical properties, such as specific capacity, volume change and [...] Read more.
In this work, we have compared the potential applications of nine different elements doped Mg2NiH4 as conversion-type electrode materials in Li-ion batteries by means of state-of-the-art Density functional theory calculations. The electrochemical properties, such as specific capacity, volume change and average voltage, as well as the atomic and electronic structures of different doped systems have been investigated. The Na doping can improve the electrochemical capacity of the pristine material. Si and Ti doping can reduce the band gap and benefit the electronic conductivity of electrode materials. All of the nine doping elements can help to reduce the average voltage of negative electrodes and lead to reasonable volume changes. According to the computational screening, the Na, Si and Ti doping elements are thought to be promising to enhance the comprehensive properties of pure material. This theoretical study is proposed to encourage and expedite the development of metal-hydrides based lithium-storage materials. Full article
(This article belongs to the Special Issue Ab Initio Study of the Energy Storage Crystalline Materials)
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Open AccessArticle
Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes
Crystals 2019, 9(5), 253; https://doi.org/10.3390/cryst9050253
Received: 22 March 2019 / Revised: 14 May 2019 / Accepted: 15 May 2019 / Published: 17 May 2019
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Abstract
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have [...] Read more.
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have been used here as material capable of supporting protein crystallization and hosting grown crystals. We found that IL-HCMs affect the selection mechanism of glucose isomerase (GI) polymorphs and make GI crystals grow completely immersed into the hydrogel layer. X-ray diffraction studies show that IL ions do not bind to the protein, likely because IL molecules are constrained in the polymeric framework. Our GI crystal structures have been compared with many existing GI crystal structures using multivariate analysis tools, allowing a comprehensive overview of factors determining structural similarities, i.e., temperature variations and external stresses exerted during or after crystal growth, such as dehydration or presence of hydrogel of a different nature. GI crystals grown on IL-HCM fit perfectly in this framework, showing typical features induced by external forces. Overall, protein crystallization by IL-HCMs show potential for biotechnological applications, as it could constitute a natural means for containing crystallized enzymes in working conditions. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Open AccessArticle
The Effect of Internal Free Surfaces on Void Swelling of Irradiated Pure Iron Containing Subsurface Trenches
Crystals 2019, 9(5), 252; https://doi.org/10.3390/cryst9050252
Received: 8 April 2019 / Revised: 5 May 2019 / Accepted: 11 May 2019 / Published: 15 May 2019
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Abstract
We studied the effects of internal free surfaces on the evolution of ion-induced void swelling in pure iron. The study was initially driven by the motivation to introduce a planar free-surface defect sink at depths that would remove the injected interstitial effect from [...] Read more.
We studied the effects of internal free surfaces on the evolution of ion-induced void swelling in pure iron. The study was initially driven by the motivation to introduce a planar free-surface defect sink at depths that would remove the injected interstitial effect from ion irradiation, possibly enhancing swelling. Using the focused ion beam technique, deep trenches were created on a cross section of pure iron at various depths, so as to create bridges of thickness ranging from 0.88 μm to 1.70 μm. Samples were then irradiated with 3.5 MeV Fe2+ ions at 475 °C to a fluence corresponding to a peak displacement per atom dose of 150 dpa. The projected range of 3.5 MeV Fe2+ ions is about 1.2 μm so the chosen bridge thicknesses involved fractions of the ion range, thicknesses comparable to the mean ion range (peak of injected interstitial distribution), and thicknesses beyond the full range. It was found that introduction of such surfaces did not enhance swelling but actually decreased it, primarily because there were now two denuded zones with a combined stronger influence than that of the injected interstitial. The study suggests that such strong surface effects must be considered for ion irradiation studies of thin films or bridge-like structures. Full article
(This article belongs to the Special Issue Nanostructured Ferritic Alloys)
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Open AccessArticle
Magnetic Properties of Quasi-One-Dimensional Crystals Formed by Graphene Nanoclusters and Embedded Atoms of the Transition Metals
Crystals 2019, 9(5), 251; https://doi.org/10.3390/cryst9050251
Received: 31 March 2019 / Revised: 1 May 2019 / Accepted: 8 May 2019 / Published: 15 May 2019
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Abstract
Using the density-matrix renormalization group method and quantum Monte Carlo simulation, we studied numerically the energy spectrum and thermodynamics of the quantum Heisenberg spin model for narrow graphene nanoribbons and their derivatives with periodically embedded heteroatoms. For several nanoribbon structures we found macroscopic [...] Read more.
Using the density-matrix renormalization group method and quantum Monte Carlo simulation, we studied numerically the energy spectrum and thermodynamics of the quantum Heisenberg spin model for narrow graphene nanoribbons and their derivatives with periodically embedded heteroatoms. For several nanoribbon structures we found macroscopic ground state spin, gapless lowest excitation spectra and intermediate magnetization plateaus at low temperatures. We also studied the lowest energy states of frustrated systems formed by triangular graphitic clusters connected by bridged ions of transition metals. On the base of many-body perturbation theory and the exact diagonalization method, we showed the possibility of spin switching for this model due to the change the corresponding coupling parameters. Full article
(This article belongs to the Special Issue Quantum and Molecular Mechanic Analysis of Crystalline Materials)
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Open AccessArticle
Quasi-Liquid Layer on Ice and Its Effect on the Confined Freezing of Porous Materials
Crystals 2019, 9(5), 250; https://doi.org/10.3390/cryst9050250
Received: 31 March 2019 / Revised: 2 May 2019 / Accepted: 6 May 2019 / Published: 14 May 2019
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Abstract
Freezing of the water confined in thin pores can be destructive to the porous frame, but the effect of the quasi-liquid layer (QLL) between the confined ice and the pore walls remains still far from being fully understood. In the present study, the [...] Read more.
Freezing of the water confined in thin pores can be destructive to the porous frame, but the effect of the quasi-liquid layer (QLL) between the confined ice and the pore walls remains still far from being fully understood. In the present study, the physical origins of the intermediate phase of QLL were discussed by thermodynamic analyses. Different interactions on QLL bring different models to estimate its thickness, which generally decays with temperature decreasing. Four representative models of QLL thickness were selected to unveil its effect on the growing rates and extents of ice in a concrete. The engineering consequences of the confined freezing were then discussed in the aspects of effective pore pressures built from the confined ice growth and deformations framed by a poro-elastic model. Overall, thickening QLL depresses ice growing rates and contents and, consequentially, decreases pore pressures and material deformations during freezing. The QLL corrections also narrow the gaps between the predicted and measured freezing deformations. The findings of this study contribute to profound understandings of confined freezing that may bridge over physical principles and engineering observations. Full article
(This article belongs to the Special Issue Ice Crystals)
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Open AccessArticle
Nematic and Cholesteric Liquid Crystal Structures in Cells with Tangential-Conical Boundary Conditions
Crystals 2019, 9(5), 249; https://doi.org/10.3390/cryst9050249
Received: 27 March 2019 / Revised: 7 May 2019 / Accepted: 9 May 2019 / Published: 14 May 2019
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Abstract
Orientational structures formed in nematic and cholesteric layers with tangential-conical boundary conditions have been investigated. LC cells with one substrate specifying the conical surface anchoring and another substrate specifying the tangential one have been considered. The director configurations and topological defects have been [...] Read more.
Orientational structures formed in nematic and cholesteric layers with tangential-conical boundary conditions have been investigated. LC cells with one substrate specifying the conical surface anchoring and another substrate specifying the tangential one have been considered. The director configurations and topological defects have been identified analyzing the texture patterns obtained by polarizing microscope in comparison with the structures and optical textures calculated by free energy minimization procedure of director field and finite-difference time-domain method, respectively. The domains, periodic structures and two-dimensional defects proper to the LC cells with tangential-conical anchoring have been studied depending on the layer thickness and cholesteric pitch. Full article
(This article belongs to the Special Issue Advances in Cholesteric Liquid Crystals)
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Open AccessArticle
Negative Thermal Expansivity of Ice: Comparison of the Monatomic mW Model with the All-Atom TIP4P/2005 Water Model
Crystals 2019, 9(5), 248; https://doi.org/10.3390/cryst9050248
Received: 28 March 2019 / Revised: 10 May 2019 / Accepted: 12 May 2019 / Published: 14 May 2019
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Abstract
We calculate the thermal expansivity of ice I for the monatomic mW model using the quasi-harmonic approximation. It is found that the original mW model is unable to reproduce the negative thermal expansivity experimentally observed at low temperatures. A simple prescription is proposed [...] Read more.
We calculate the thermal expansivity of ice I for the monatomic mW model using the quasi-harmonic approximation. It is found that the original mW model is unable to reproduce the negative thermal expansivity experimentally observed at low temperatures. A simple prescription is proposed to recover the negative thermal expansion by re-adjusting the so-called tetrahedrality parameter, λ. We investigate the relation between the λ value and the Grüneisen parameter to explain the origin of negative thermal expansion in the mW model and compare it with an all-atom water model that allows the examination of the effect of the rotational motions on the volume of ice. Full article
(This article belongs to the Special Issue Ice Crystals)
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Open AccessArticle
Insight into the Optoelectronic and Thermoelectric Properties of Mn Doped ZnTe from First Principles Calculation
Crystals 2019, 9(5), 247; https://doi.org/10.3390/cryst9050247
Received: 2 April 2019 / Revised: 23 April 2019 / Accepted: 7 May 2019 / Published: 13 May 2019
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Abstract
Using DFT band structure simulations together with semi-classical Boltzmann transport kinetics equations, we have explored the optoelectronic and transport features of MnxZn1−xTe (x = 8% and 16%) crystals. Optimization of the doping and related technological processes it is extremely [...] Read more.
Using DFT band structure simulations together with semi-classical Boltzmann transport kinetics equations, we have explored the optoelectronic and transport features of MnxZn1−xTe (x = 8% and 16%) crystals. Optimization of the doping and related technological processes it is extremely important for optimization of the technological parameters. The Generalized Gradient Approximation is applied to compute the corresponding band structure parameters. We have applied the Generalized Gradient Approximation Plus U (GGA+U). We have demonstrated that MnxZn1−xTe (x = 8% and 16%) is a direct type band semiconductor with principal energy gap values equal to 2.20 and 2.0 eV for x = 8% and 16%, respectively. The energy gap demonstrates significant decrease with increasing Mn content. Additionally, the origin of the corresponding bands is explored from the electronic density of states. The optical dispersion functions are calculated from the spectra of dielectric function. The theoretical simulations performed unambiguously showed that the titled materials are simultaneously promising optoelectronic and thermoelectric devices. The theoretical simulations performed showed ways for amendment of their transport properties by replacement of particular ions. Full article
(This article belongs to the Special Issue First-Principles Prediction of Structures and Properties in Crystals)
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Open AccessArticle
Structural Chemistry of Akdalaite, Al10O14(OH)2, the Isostructural Aluminum Analogue of Ferrihydrite
Crystals 2019, 9(5), 246; https://doi.org/10.3390/cryst9050246
Received: 21 April 2019 / Revised: 7 May 2019 / Accepted: 9 May 2019 / Published: 12 May 2019
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Abstract
As part of an effort to characterize clusters and intermediate phases likely to be encountered along solution reaction pathways that produce iron and aluminum oxide-hydroxides from Fe and Al precursors, the complete structure of Al10O14(OH)2 (akdalaite) was determined [...] Read more.
As part of an effort to characterize clusters and intermediate phases likely to be encountered along solution reaction pathways that produce iron and aluminum oxide-hydroxides from Fe and Al precursors, the complete structure of Al10O14(OH)2 (akdalaite) was determined from a combination of single-crystal X-ray diffraction (SC-XRD) data collected at 100 K to define the Al and O positions, and solid-state nuclear magnetic resonance (NMR) and neutron powder diffraction (NPD) data collected at room temperature (~300 K) to precisely determine the nature of hydrogen in the structure. Two different synthesis routes produced different crystal morphologies. Using an aluminum oxyhydroxide floc made from mixing AlCl3 and 0.48 M NaOH, the product had uniform needle morphology, while using nanocrystalline boehmite (Vista Chemical Company Catapal D alumina) as the starting material produced hexagonal plates. Akdalaite crystallizes in the space group P63mc with lattice parameters of a = 5.6244(3) Å and c = 8.8417(3) Å (SC-XRD) and a = 5.57610(2) Å and c = 8.77247(6) Å (NPD). The crystal structure features Al13O40 Keggin clusters. The structural chemistry of akdalaite is nonideal but broadly conforms to that of ferrihydrite, the nanomineral with which it is isostructural. Full article
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Open AccessArticle
Czochralski Growth, Magnetic Properties and Faraday Characteristics of CeAlO3 Crystals
Crystals 2019, 9(5), 245; https://doi.org/10.3390/cryst9050245
Received: 3 April 2019 / Revised: 2 May 2019 / Accepted: 8 May 2019 / Published: 11 May 2019
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Abstract
CeAlO3 crystals were grown in different growth atmospheres by the Czochralski method. The lattice parameters and space group of CeAlO3 crystal were determined by Rietveld structure refinement of X-ray diffraction (XRD) data. The influence of Ce4+ ions in the crystal [...] Read more.
CeAlO3 crystals were grown in different growth atmospheres by the Czochralski method. The lattice parameters and space group of CeAlO3 crystal were determined by Rietveld structure refinement of X-ray diffraction (XRD) data. The influence of Ce4+ ions in the crystal on the transmittance and crystal color was confirmed by XPS analysis. Magnetization curve at room temperature and temperature dependencies of the magnetic susceptibility in two different directions were measured, indicating that CeAlO3 crystal has remarkable magnetic anisotropy and there is an abnormal magnetic behavior in the vertical <001> direction in the temperature range of 50–150 K. Faraday characteristics of CeAlO3 crystal were investigated at room temperature. Verdet constants of CeAlO3 at 532, 635 and 1064 nm are about 2.1 times as large as those of CeF3. The reason of large Verdet constants was analyzed based on the Van Vleck–Hebb theory and the magnetic circular dichroism (MCD) spectrum. Full article
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Open AccessArticle
Extending the pool of compatible peptide hydrogels for protein crystallization
Crystals 2019, 9(5), 244; https://doi.org/10.3390/cryst9050244
Received: 5 April 2019 / Revised: 3 May 2019 / Accepted: 7 May 2019 / Published: 10 May 2019
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Abstract
Short-peptide supramolecular (SPS) hydrogels are a class of materials that have been found to be useful for (bio)technological applications thanks to their biocompatible nature. Among the advantages reported for these peptides, their economic affordability and easy functionalization or modulation have turned them into [...] Read more.
Short-peptide supramolecular (SPS) hydrogels are a class of materials that have been found to be useful for (bio)technological applications thanks to their biocompatible nature. Among the advantages reported for these peptides, their economic affordability and easy functionalization or modulation have turned them into excellent candidates for the development of functional biomaterials. We have recently demonstrated that SPS hydrogels can be used to produce high-quality protein crystals, improve their properties, or incorporate relevant materials within the crystals. In this work, we prove that hydrogels based on methionine and tyrosine are also good candidates for growing high-quality crystals of the three model proteins: lysozyme, glucose isomerase, and thaumatin. Full article
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Open AccessArticle
Van der Waals Density Functional Theory vdW-DFq for Semihard Materials
Crystals 2019, 9(5), 243; https://doi.org/10.3390/cryst9050243
Received: 9 April 2019 / Revised: 1 May 2019 / Accepted: 2 May 2019 / Published: 8 May 2019
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Abstract
There are a large number of materials with mild stiffness, which are not as soft as tissues and not as strong as metals. These semihard materials include energetic materials, molecular crystals, layered materials, and van der Waals crystals. The integrity and mechanical stability [...] Read more.
There are a large number of materials with mild stiffness, which are not as soft as tissues and not as strong as metals. These semihard materials include energetic materials, molecular crystals, layered materials, and van der Waals crystals. The integrity and mechanical stability are mainly determined by the interactions between instantaneously induced dipoles, the so called London dispersion force or van der Waals force. It is challenging to accurately model the structural and mechanical properties of these semihard materials in the frame of density functional theory where the non-local correlation functionals are not well known. Here, we propose a van der Waals density functional named vdW-DFq to accurately model the density and geometry of semihard materials. Using β -cyclotetramethylene tetranitramine as a prototype, we adjust the enhancement factor of the exchange energy functional with generalized gradient approximations. We find this method to be simple and robust over a wide tuning range when calibrating the functional on-demand with experimental data. With a calibrated value q = 1.05 , the proposed vdW-DFq method shows good performance in predicting the geometries of 11 common energetic material molecular crystals and three typical layered van der Waals crystals. This success could be attributed to the similar electronic charge density gradients, suggesting a wide use in modeling semihard materials. This method could be useful in developing non-empirical density functional theories for semihard and soft materials. Full article
(This article belongs to the Special Issue First-Principles Prediction of Structures and Properties in Crystals)
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Open AccessArticle
Molecular Structures Polymorphism the Role of F…F Interactions in Crystal Packing of Fluorinated Tosylates
Crystals 2019, 9(5), 242; https://doi.org/10.3390/cryst9050242
Received: 19 April 2019 / Revised: 4 May 2019 / Accepted: 5 May 2019 / Published: 7 May 2019
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Abstract
The peculiarities of interatomic interactions formed by fluorine atoms were studied in four tosylate derivatives p-CH3C6H4OSO2CH2CF2CF3 and p-CH3C6H4OSO2CH2(CF2) [...] Read more.
The peculiarities of interatomic interactions formed by fluorine atoms were studied in four tosylate derivatives p-CH3C6H4OSO2CH2CF2CF3 and p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5, 7) using X-ray diffraction and quantum chemical calculations. Compounds p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) were crystallized in several polymorph modifications. Analysis of intermolecular bonding was carried out using QTAIM approach and energy partitioning. All compounds are characterized by crystal packing of similar type and the contribution of intermolecular interactions formed by fluorine atoms to lattice energy is raised along with the increase of their amount. The energy of intra- and intermolecular F…F interactions is varied in range 0.5–13.0 kJ/mol. Total contribution of F…F interactions to lattice energy does not exceed 40%. Crystal structures of studied compounds are stabilized mainly by C-H…O and C-H…F weak hydrogen bonds. The analysis of intermolecular interactions and lattice energies in polymorphs of p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) has shown that most stabilized are characterized by the least contribution of F…F interactions. Full article
(This article belongs to the Special Issue Chemical Bonding in Crystals and Their Properties)
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Open AccessArticle
Dielectric Relaxor and Conductivity Mechanism in Fe-Substituted PMN-32PT Ferroelectric Crystal
Crystals 2019, 9(5), 241; https://doi.org/10.3390/cryst9050241
Received: 15 March 2019 / Revised: 3 May 2019 / Accepted: 4 May 2019 / Published: 7 May 2019
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Abstract
Fe-substituted PMN-32PT relaxor ferroelectric crystals were grown by a high-temperature flux method. The effects of charged defects on the dielectric relaxor and conductivity mechanism were discussed in detail. The Fe-substituted PMN-32PT crystal showed a high coercive field (Ec = 765 V/mm), [...] Read more.
Fe-substituted PMN-32PT relaxor ferroelectric crystals were grown by a high-temperature flux method. The effects of charged defects on the dielectric relaxor and conductivity mechanism were discussed in detail. The Fe-substituted PMN-32PT crystal showed a high coercive field (Ec = 765 V/mm), due to domain wall-pinning, induced by charged defect dipoles. Three dielectric anomaly peaks were observed, and the two dielectric relaxation peaks at low temperature were associated with the diffusion phase transition, while the high temperature one resulted from the short-range hopping of oxygen vacancies. At temperature T ≤ 150 °C, the dominating conduction carriers were electrons coming from the first ionization of oxygen vacancies. For the temperature range from 200 to 500 °C, the conductivity was composed of the bulk and interface between sample and electrode, and the oxygen vacancies were suggested to be the conduction mechanism. Above 550 °C, the trapped electrons from the Ti3+ center were excited and played a major role in electrical conduction. Our results are helpful for better understanding the relationship between dielectric relaxation and the conduction mechanism. Full article
(This article belongs to the Special Issue Synthesis and Characterization of Ferroelectrics)
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Open AccessArticle
Nanoscale Mechanical and Mechanically-Induced Electrical Properties of Silicon Nanowires
Crystals 2019, 9(5), 240; https://doi.org/10.3390/cryst9050240
Received: 21 March 2019 / Revised: 29 April 2019 / Accepted: 6 May 2019 / Published: 7 May 2019
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Abstract
Molecular dynamics (MD) simulation was employed to examine the deformation and phase transformation of mono-crystalline Si nanowire (SiNW) subjected to tensile stress. The techniques of coordination number (CN) and centro-symmetry parameter (CSP) were used to monitor and elucidate the detailed mechanisms of the [...] Read more.
Molecular dynamics (MD) simulation was employed to examine the deformation and phase transformation of mono-crystalline Si nanowire (SiNW) subjected to tensile stress. The techniques of coordination number (CN) and centro-symmetry parameter (CSP) were used to monitor and elucidate the detailed mechanisms of the phase transformation throughout the loading process in which the evolution of structural phase change and the dislocation pattern were identified. Therefore, the relationship between phase transformation and dislocation pattern was established and illustrated. In addition, the electrical resistance and conductivity of SiNW were evaluated by using the concept of virtual electric source during loading and unloading similar to in situ electrical measurements. The effects of temperature on phase transformation of mono-crystalline SiNWs for three different crystallographically oriented surfaces were investigated and discussed. Simulation results show that, with the increase of applied stress, the dislocations are initiated first and then the phase transformation such that the total energy of the system tends to approach a minimum level. Moreover, the electrical resistance of (001)- rather than (011)- and (111)-oriented SiNWs was changed before failure. As the stress level of the (001) SiNW reaches 24 GPa, a significant amount of metallic Si-II and amorphous phases is produced from the semiconducting Si-I phase and leads to a pronounced decrease of electrical resistance. It was also found that as the temperature of the system is higher than 500 K, the electrical resistance of (001) SiNW is significantly reduced through the process of axial elongation. Full article
(This article belongs to the Special Issue Elasticity and Micro- and Macro- Plasticity of Crystals)
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