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Crystals, Volume 9, Issue 10 (October 2019)

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Open AccessArticle
Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)
Crystals 2019, 9(10), 533; https://doi.org/10.3390/cryst9100533 (registering DOI) - 16 Oct 2019
Abstract
A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the [...] Read more.
A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the hybrid input–output (HIO) algorithm. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Open AccessArticle
Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation
Crystals 2019, 9(10), 532; https://doi.org/10.3390/cryst9100532 (registering DOI) - 16 Oct 2019
Abstract
The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed [...] Read more.
The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking. Full article
(This article belongs to the Special Issue Nucleic Acid Crystallography)
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Open AccessArticle
LED as Transmitter and Receiver of Light: A Simple Tool to Demonstration Photoelectric Effect
Crystals 2019, 9(10), 531; https://doi.org/10.3390/cryst9100531 - 15 Oct 2019
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Abstract
The experimental observations of the photoelectric effect show the properties of quantum mechanics of the electromagnetic field. For this reason, this important effect is commonly used as an introductory topic for the study of quantum physics. The “classical” demonstration of the photoelectric effect [...] Read more.
The experimental observations of the photoelectric effect show the properties of quantum mechanics of the electromagnetic field. For this reason, this important effect is commonly used as an introductory topic for the study of quantum physics. The “classical” demonstration of the photoelectric effect is very incisive; unfortunately, the experimental apparatus is not cheap and easy to realize. The typical use of LEDs is as light emitters, but they can be used even as photosensors and, in this case, they are sensitive to wavelengths equal to or shorter than the predominant wavelength it emits. Furthermore, a LED used as detector is sensitive to wavelengths equal to or shorter than the predominant wavelength it emits. This ability of LEDs offers the possibility of developing a simple tool able to demonstrate the photoelectric effect. This paper describes the realization of an economic, simple, easy and safe system to use for the experimental demonstration of the photoelectric effect, based on the LED to LED structure. The paper has educational purposes, oriented towards laboratory teaching activities. Full article
(This article belongs to the Special Issue Recent Advances in Light-Emitting Diodes (LEDs))
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Open AccessArticle
Size and Shape Evolution of GaAsSb-Capped InAs/GaAs Quantum Dots: Dependence on the Sb Content
Crystals 2019, 9(10), 530; https://doi.org/10.3390/cryst9100530 - 15 Oct 2019
Viewed by 117
Abstract
Capping InAs/GaAs quantum dots (QDs) with a thin GaAsSb layer alters the QDs structural properties, leading to considerable changes in their optical properties. The increase of the Sb content induces a redshift of the emission energies, indicating a change in the buried QDs [...] Read more.
Capping InAs/GaAs quantum dots (QDs) with a thin GaAsSb layer alters the QDs structural properties, leading to considerable changes in their optical properties. The increase of the Sb content induces a redshift of the emission energies, indicating a change in the buried QDs shape and size. The presence of well-defined ground- and excited-state emission bands in all the photoluminescence spectra allow an accurate estimation of the buried QDs size and shape by numerical evaluation and tuning of the theoretical emission energies. For an Sb content below 14%, the QDs are found to have a type I band alignment with a truncated height pyramidal form. However, for higher Sb content (22%), the QDs are present in a full pyramidal shape. The observed behavior is interpreted in terms of increasing prevention of InAs QDs decomposition with increasing the Sb content in the cap layer. Full article
(This article belongs to the Special Issue Nanowires and Quantum Dots for IoT Applications)
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Open AccessArticle
Trinodal Self-Penetrating Nets from Reactions of 1,4-Bis(alkoxy)-2,5-bis(3,2’:6’,3’’-terpyridin-4’-yl)benzene Ligands with Cobalt(II) Thiocyanate
Crystals 2019, 9(10), 529; https://doi.org/10.3390/cryst9100529 - 15 Oct 2019
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Abstract
The tetratopic ligands 1,4-bis(2-ethylbutoxy)-2,5-bis(3,2’:6’,3’’-terpyridin-4’-yl)benzene (1) and 1,4-bis(3-methylbutoxy)-2,5-bis(3,2’:6’,3’’-terpyridin-4’-yl)benzene (2) have been prepared and characterized by 1H and 13C{1H} NMR, IR, and absorption spectroscopies and mass spectrometry. Reactions of 1 and 2 with cobalt(II) thiocyanate under conditions [...] Read more.
The tetratopic ligands 1,4-bis(2-ethylbutoxy)-2,5-bis(3,2’:6’,3’’-terpyridin-4’-yl)benzene (1) and 1,4-bis(3-methylbutoxy)-2,5-bis(3,2’:6’,3’’-terpyridin-4’-yl)benzene (2) have been prepared and characterized by 1H and 13C{1H} NMR, IR, and absorption spectroscopies and mass spectrometry. Reactions of 1 and 2 with cobalt(II) thiocyanate under conditions of crystal growth at room temperature result in the formation of [{Co(1)(NCS)2}·MeOH·3CHCl3]n and [{Co(2)(NCS)2}·0.8MeOH·1.8CHCl3]n. Single-crystal X-ray diffraction reveals that each crystal lattice consists of a trinodal self-penetrating (62.84)(64.82)(65.8)2 net. The nodes are defined by two independent cobalt centres and the centroids of two crystallographically independent ligands which are topologically equivalent. Full article
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Open AccessArticle
Effect of Pressure Treatment on the Specific Surface Area in Kaolin Group Minerals
Crystals 2019, 9(10), 528; https://doi.org/10.3390/cryst9100528 - 14 Oct 2019
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Abstract
Pressure can tailor the properties of a material by changing its atomistic arrangements and/or crystal morphology. We have investigated the changes in the adsorption properties of kaolin group minerals as a function of pressure treatment in the gigapascal range. External pressures have been [...] Read more.
Pressure can tailor the properties of a material by changing its atomistic arrangements and/or crystal morphology. We have investigated the changes in the adsorption properties of kaolin group minerals as a function of pressure treatment in the gigapascal range. External pressures have been applied using a large volume press (LVP) to kaolinite (Al2Si2O5(OH)4) and halloysite (H4Al2O9Si2·2H2O), which represent natural 2D layered and 1D nanowire structures, respectively. Powdered samples have been compressed up to 3 GPa in 1 GPa steps at room temperature and recovered by up to ca. 0.35 g from each pressure step. Brunauer–Emmett–Teller (BET) measurements were conducted using N2 gas to measure the specific surface area, pore size distribution, and pore volume of the pressure-treated samples. As the treatment pressure increased, kaolinite showed an increase in the adsorption behavior from nonpores to mesopores, whereas halloysite responded in an opposite manner to show a decrease in its adsorption capability. We discuss the contrasting effects of pressure-treatment on the two morphologically distinct kaolin group minerals based on field-emission scanning electron microscope (FE-SEM) images measured on each recovered material. We observed that the layers in kaolinite separate into smaller units upon increasing pressure treatment, whereas the tubes in halloysite become flattened, which led to the contrasting changes in surface area. Further study is in progress to compare this effect to when water is used as the pressure-transmitting medium. Full article
(This article belongs to the Special Issue High Pressure Synthesis in Crystalline Materials)
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Open AccessArticle
New Tetragonal ReGa5(M) (M = Sn, Pb, Bi) Single Crystals Grown from Delicate Electrons Changing
Crystals 2019, 9(10), 527; https://doi.org/10.3390/cryst9100527 - 14 Oct 2019
Viewed by 114
Abstract
Single crystals of the new Ga-rich phases ReGa~5(Sn), ReGa~5(Pb) and ReGa~5(Bi) were successfully obtained from the flux method. The new tetragonal phases crystallize in the space group P4/mnc (No. 128) with vertex-sharing capped Re2@Ga14 [...] Read more.
Single crystals of the new Ga-rich phases ReGa~5(Sn), ReGa~5(Pb) and ReGa~5(Bi) were successfully obtained from the flux method. The new tetragonal phases crystallize in the space group P4/mnc (No. 128) with vertex-sharing capped Re2@Ga14 oblong chains. Vacancies were discovered on the Ga4 and Ga5 sites, which can be understood as the direct inclusion of elemental Sn, Pb and Bi into the structure. Heat capacity measurements were performed on all three compounds resulting in a small anomaly which resembles the superconductivity transition temperature from the impurity ReGa5 phase. The three compounds were not superconducting above 1.85 K. Subsequently, electronic structure calculations revealed a high density of states around the Fermi level, as well as non-bonding interactions that likely indicate the stability of these new phases. Full article
(This article belongs to the Special Issue High Pressure Synthesis in Crystalline Materials)
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Open AccessArticle
Structure of Cubic Al73.8Pd13.6Fe12.6 Phase with High Al Content
Crystals 2019, 9(10), 526; https://doi.org/10.3390/cryst9100526 - 13 Oct 2019
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Abstract
A cubic ternary phase Al73.8Pd13.6Fe12.6 (designated C′ phase), with very high Al content (Al/TM = 2.82, TM denotes transition metal) was prepared by spark plasma sintering (SPS). Its crystal structure was determined by combing single-crystal X-ray diffraction (SXRD) [...] Read more.
A cubic ternary phase Al73.8Pd13.6Fe12.6 (designated C′ phase), with very high Al content (Al/TM = 2.82, TM denotes transition metal) was prepared by spark plasma sintering (SPS). Its crystal structure was determined by combing single-crystal X-ray diffraction (SXRD) and scanning electron microscope (SEM) equipped with energy dispersive X-ray spectroscopy (EDS) measurements. The crystal structure of the new phase can be described with a small unit cell (a = 7.6403(2) Å; space group Pm3, No. 200) as that of Al2.63Rh (a = 7.6692(1) Å; space group P23, No. 195) while different from those of the reported Al39Pd21Fe2 (a = 15.515(1) Å; space group Fm3, No. 202) and Al69Pd17Fe14 (a = 15.3982(2) Å; space group Im3, No. 204) compounds, which both adopt a double length unit cell in the Al–Pd–Fe system. The mechanism of distributing more Al atoms in the new phase was compared with that of the Al2.63Rh phase by analyzing their site symmetry and the corresponding site of occupancies (SOF). Furthermore, relations of the C′ phase to the reported Al69Pd17Fe14 (designated C1 phase) and Al39Pd21Fe2 (designated C2 phase) phases were investigated by analyzing their building units with the “nanocluster” method in the ToposPro package. Full article
Open AccessArticle
Revisit the Role of Steps/Disconnections on Misfit Cancellation at Semi-Coherent Interface—Bridging the O-Line Model and the Topological Model
Crystals 2019, 9(10), 525; https://doi.org/10.3390/cryst9100525 - 13 Oct 2019
Viewed by 200
Abstract
It has been a long-standing topic how the lattice misfit is cancelled at a semi-coherent interphase boundary consisting of terraces and steps. Apart from a set of misfit dislocations separating the coherent patches, the role of steps (which is frequently called ‘disconnections’) on [...] Read more.
It has been a long-standing topic how the lattice misfit is cancelled at a semi-coherent interphase boundary consisting of terraces and steps. Apart from a set of misfit dislocations separating the coherent patches, the role of steps (which is frequently called ‘disconnections’) on misfit cancellation remains ambiguous because these steps do not destroy the continuity of lattice planes across the interface. This paper aims to clarify such ambiguity through identification of a set of secondary dislocations through a rigorous constrained coincidence site lattice (CCSL)/constrained displacive shift complete lattice (CDSCL) analysis. A semi-coherent interface between body-centred cubic (BCC) Cr-rich precipitate and face-centred cubic (FCC) Cu-rich matrix that holds a near N-W orientation relationship (OR) is used as an example to demonstrate the procedure to determine the secondary dislocations that are coincident with steps along the interface. The current approach does not only redefine the disconnections in the topological model, but also extends the description of interface structure from the O-line model. As a result, the ‘discrepancy’ between these two popular crystallographic models can be completely eliminated when the interface is required to contain a pair of parallel close-packed directions. Full article
(This article belongs to the Special Issue Crystallography of Structural Phase Transformations)
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Open AccessArticle
Design of an LED Spot Light System with a Projection Distance of 10 km
Crystals 2019, 9(10), 524; https://doi.org/10.3390/cryst9100524 - 13 Oct 2019
Viewed by 234
Abstract
We designed a spot light system with an illumination range of 10 km. In the designed system, an appropriate white light-emitting diode (LED) was selected according to the exitance and injection power required. Subsequently, through a first-order optical design, the geometry of the [...] Read more.
We designed a spot light system with an illumination range of 10 km. In the designed system, an appropriate white light-emitting diode (LED) was selected according to the exitance and injection power required. Subsequently, through a first-order optical design, the geometry of the lens and reflector was determined using geometrical calculation. Because the central illuminance of the projection spot of the reflector was 2.5 times that of the cover lens, we first considered the fabrication error of the reflector. According to the adjustment of the optimized distance between the white LED and reflector, we modified the design of the cover lens to fit the new location of the white LED. An LED spot light module containing 16 spot light units was used. The module’s power injection was only 68.2 W. Because of the excellent performance of the designed system in terms of the divergence angle of the projection beam and maximum luminous intensity, which were 1.6° and 2,840,000 cd, respectively, the projection distance of the LED spot light module was 3.37 Km, according to the ANSI regulation. Finally, a spot light system with nine modules and capable of achieving a projection distance of 10 km was successfully fabricated. Full article
(This article belongs to the Special Issue Advanced LED Solid-state Lighting Optics)
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Open AccessEditorial
Liquid Crystal Optical Devices
Crystals 2019, 9(10), 523; https://doi.org/10.3390/cryst9100523 - 12 Oct 2019
Viewed by 139
Abstract
It has been approximately 125 years since the Austrian scientist Friedrich Reinitzer in 1888 observed the curious behavior of the double melting points of cholesterol benzoate, a discovery that today is widely recognized as liquid crystal science [...] Full article
(This article belongs to the Special Issue Liquid Crystal Optical Device)
Open AccessArticle
Anion Influence on the Packing of 1,3-Bis(4-Ethynyl-3-Iodopyridinium)-Benzene Halogen Bond Receptors
Crystals 2019, 9(10), 522; https://doi.org/10.3390/cryst9100522 - 11 Oct 2019
Viewed by 149
Abstract
Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focused on the receptor conformation, anion [...] Read more.
Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focused on the receptor conformation, anion shape, solvation, and long range packing of these systems. Coupled with our previously reported structures, we concluded that anions can be classified as building units within this family of halogen bonding receptors. Two kinds of antiparallel dimers were observed for these dicationic receptors. An off-centered species was most frequent, present among geometrically diverse anions and assorted receptor conformations. In contrast, the centered antiparallel dimers were observed with receptors adopting a bidentate conformation in the solid-state. While anions support the solid-state formation of dimers, the molecular geometry and characteristics (planarity, rigidity, and directionality) of arylethynyl systems increase the likelihood of dimer formation by limiting efficient packing arrangements. The significantly larger cation may have considerable influence on the solid-state packing, as similar cationic arylethynyl systems also display these dimers. Full article
(This article belongs to the Special Issue Halogen-Bonded Cocrystals)
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Open AccessArticle
A New High-Pressure Phase Transition in Natural Gedrite
Crystals 2019, 9(10), 521; https://doi.org/10.3390/cryst9100521 - 11 Oct 2019
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Abstract
High-pressure diamond-anvil cell synchrotron X-ray diffraction experiments were conducted on single-crystal samples of natural orthoamphibole; gedrite; with composition; (K0.002Na0.394)(Mg2)(Mg1.637Fe2.245Mn0.004Ca0.022Cr0.003Na0.037Al1.052)(Si6.517Al1.483)O [...] Read more.
High-pressure diamond-anvil cell synchrotron X-ray diffraction experiments were conducted on single-crystal samples of natural orthoamphibole; gedrite; with composition; (K0.002Na0.394)(Mg2)(Mg1.637Fe2.245Mn0.004Ca0.022Cr0.003Na0.037Al1.052)(Si6.517Al1.483)O22(OH)2. The samples were compressed at 298 K up to a maximum pressure of 27(1) GPa. In this pressure regime, we observed a displacive phase transition between 15.1(7) and 21(1) GPa from the orthorhombic Pnma phase to a new structure with space group P21/m; which is different from the familiar P21/m structure of cummingtonite and retains the (+, +, −, −) I-beam stacking sequence of the orthorhombic structure. The unit cell parameters for the new phase at 21(1) GPa are a = 17.514(3), b = 17.077(1), c = 4.9907(2) Å and β = 92.882(6)°. The high-pressure P21/m phase is the first amphibole structure to show the existence of four crystallographically distinct silicate double chains. The orthorhombic to monoclinic phase transition is characterized by an increase in the degree of kinking of the double silicate chains and is analogous to displacive phase changes recently reported in orthopyroxenes, highlighting the parallel structural relations and phase transformation behavior of orthorhombic single- and double-chain silicates. Full article
(This article belongs to the Special Issue High Pressure Synthesis in Crystalline Materials)
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Open AccessArticle
Co-Crystal with Unusual High Z′ and Z′′ Values Derived from Hexamethylenetetramine and 4-fluorophenol (1/1)
Crystals 2019, 9(10), 520; https://doi.org/10.3390/cryst9100520 - 10 Oct 2019
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Abstract
The title co-crystal, 1,3,5,7-tetraazatricyclo[3.3.1.13,7]decane (HMTA, 1)–4-fluorophenol (4-FP) (1/1), C6H12N4·C6H5FO, shows an unusual asymmetric unit that comprises eight independent molecules (Z′′ = 8), four for each component, with four formula units per [...] Read more.
The title co-crystal, 1,3,5,7-tetraazatricyclo[3.3.1.13,7]decane (HMTA, 1)–4-fluorophenol (4-FP) (1/1), C6H12N4·C6H5FO, shows an unusual asymmetric unit that comprises eight independent molecules (Z′′ = 8), four for each component, with four formula units per asymmetric unit (Z′ = 4). In the molecular packing, each HMTA molecule bridges one 4-FP molecule via an O−H···N hydrogen bond to form a two-molecule aggregate. Differences can be observed between the bond lengths and angles of the independent HMTA and 4-FP molecules and those of the molecules in the aggregate. The C−N bonds exhibit different bond lengths in the tetrahedral cage-like structure of the HMTA molecules, but the largest differences between the molecular aggregates are in the bond lengths in the 4-fluorophenol ring. In the crystal, the HMTA and 4-FP molecules form two hydrogen-bonded (O−H···N, C−H···F and C−H···O) dimers of HMTA and 4-FP molecules, A···D and B···C inversion dimers, which generate enlarged R88(34) ring motifs in both supramolecular structures. In both structures, the crystal packing also features additional C−H···F and C−H···O interactions. The A···D and B···C dimers are linked by additional C−H···F and C−H···O hydrogen bonds, forming columns along the a and b axes, respectively. The importance of the C−H···F interaction to the structure and crystal packing has been demonstrated. Full article
(This article belongs to the Section Crystal Engineering)
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Open AccessArticle
Twisted Graphene Bilayers and Quasicrystals: A Cut and Projection Approach
Crystals 2019, 9(10), 519; https://doi.org/10.3390/cryst9100519 - 10 Oct 2019
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Abstract
In this work, a modified version of the cut and projection approach is proposed to describe the structure of graphene bilayers with twist angles. With this method, the rotation between two graphene layers is viewed as a rotation of the projection space and [...] Read more.
In this work, a modified version of the cut and projection approach is proposed to describe the structure of graphene bilayers with twist angles. With this method, the rotation between two graphene layers is viewed as a rotation of the projection space and the resulting projected structure is interpreted as the set of points of best fit between the two rotated structures. Additionally, focus is given to the pertinence of the many algebraic and geometric tools used in grain boundaries and in quasicrystals to graphene bilayer system (or any other bilayer system, for that matter) case. Full article
(This article belongs to the collection Structure and Properties of Quasicrystals)
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Open AccessArticle
Dissimilar Infrared Brazing of CoCrFe(Mn)Ni Equiatomic High Entropy Alloys and 316 Stainless Steel
Crystals 2019, 9(10), 518; https://doi.org/10.3390/cryst9100518 - 09 Oct 2019
Viewed by 178
Abstract
Dissimilar infrared brazing of CoCrFeMnNi/CoCrFeNi equiatomic high entropy alloys and 316 stainless steel using MBF601 and BNi-2 foils was evaluated. The wetting angles of the two fillers at 50 °C above their liquidus temperatures on the three substrates were below 40 degrees. The [...] Read more.
Dissimilar infrared brazing of CoCrFeMnNi/CoCrFeNi equiatomic high entropy alloys and 316 stainless steel using MBF601 and BNi-2 foils was evaluated. The wetting angles of the two fillers at 50 °C above their liquidus temperatures on the three substrates were below 40 degrees. The CoCrFeMnNi/316 SS joint had the highest shear strength of 361 MPa with BNi-2 filler brazing at 1020 °C for 180 s, and fractured at the CrB compound in the joint. The CoCrFeMnNi/MBF601/316 SS joint contained a CoCrFeMnNi-based matrix, phosphides and B-containing compounds. The CoCrFeNi/316 SS joint had the highest shear strength of 374 MPa when brazed with BNi-2 filler at 1020 °C for 600 s, and fractured at the CrB in the joint. The CoCrFeNi/MBF601/316 SS joint consisted of a (Fe,Ni)-rich matrix, phosphides and B/Cr/Fe/P compounds, and the highest shear strength of 324 MPa was achieved when it was brazed at 1080 °C for 600 s. Full article
(This article belongs to the Special Issue Mechanical and Microstructural Characterization of Metals and Alloys)
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Open AccessArticle
The Behavior of NH3+ Torsional Vibration in Amino Acids: A Raman Spectroscopic Study
Crystals 2019, 9(10), 517; https://doi.org/10.3390/cryst9100517 - 09 Oct 2019
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Abstract
In this work we present the continuation of studies carried out on the changes of geometric parameters of the hydrogen bonds in amino acid crystals subjected to temperature or pressure variations. Changes in geometric parameters of the hydrogen bonds are correlated with the [...] Read more.
In this work we present the continuation of studies carried out on the changes of geometric parameters of the hydrogen bonds in amino acid crystals subjected to temperature or pressure variations. Changes in geometric parameters of the hydrogen bonds are correlated with the temperature behavior of the Raman wavenumber of NH3+ torsional band. Now four monocrystals, L-valine, L-isoleucine, taurine, and L-arginine hydrochloride monohydrate, are studied. Temperature evolution of the Raman wavenumber of NH3+ torsional band, with positive slope (dν/dT = 0.023 cm−1/K) of L-isoleucine, can be related to the stability of the crystal structure and the hydrogen bonds strengths on heating due to different temperature lattice parameters variation. Full article
(This article belongs to the Special Issue Raman Spectroscopy of Crystals)
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Open AccessArticle
Numerical Investigation of Thermal Buoyancy, the Electromagnetic Force and Forced Convection in Conventional RF Systems for 4-Inch Sic by TSSG
Crystals 2019, 9(10), 516; https://doi.org/10.3390/cryst9100516 - 08 Oct 2019
Viewed by 151
Abstract
In this paper, we study thermal buoyancy, the electromagnetic force and forced convection in a conventional radio frequency (RF) furnace for growing large-sized (4-inch) silicon carbide ingots using the top-seeded solution method. The thermal buoyancy and electromagnetic force are analyzed qualitatively and quantitatively [...] Read more.
In this paper, we study thermal buoyancy, the electromagnetic force and forced convection in a conventional radio frequency (RF) furnace for growing large-sized (4-inch) silicon carbide ingots using the top-seeded solution method. The thermal buoyancy and electromagnetic force are analyzed qualitatively and quantitatively under real working conditions, and a method to increase the growth stability of large-sized (4-inch) SiC is proposed through the study of forced convection. Full article
(This article belongs to the Section Crystalline Materials)
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Open AccessArticle
Miniaturized Metalens Based Optical Tweezers on Liquid Crystal Droplets for Lab-on-a-Chip Optical Motors
Crystals 2019, 9(10), 515; https://doi.org/10.3390/cryst9100515 - 07 Oct 2019
Viewed by 232
Abstract
Surfaces covered with layers of ultrathin nanoantenna structures—so called metasurfaces have recently been proven capable of completely controlling phase of light. Metalenses have emerged from the advance in the development of metasurfaces providing a new basis for recasting traditional lenses into thin, planar [...] Read more.
Surfaces covered with layers of ultrathin nanoantenna structures—so called metasurfaces have recently been proven capable of completely controlling phase of light. Metalenses have emerged from the advance in the development of metasurfaces providing a new basis for recasting traditional lenses into thin, planar optical components capable of focusing light. The lens made of arrays of plasmonic gold nanorods were fabricated on a glass substrate by using electron beam lithography. A 1064 nm laser was used to create a high intensity circularly polarized light focal spot through metalens of focal length 800 µm, N.A. = 0.6 fabricated based on Pancharatnam-Berry phase principle. We demonstrated that optical rotation of birefringent nematic liquid crystal droplets trapped in the laser beam was possible through this metalens. The rotation of birefringent droplets convinced that the optical trap possesses strong enough angular momentum of light from radiation of each nanostructure acting like a local half waveplate and introducing an orientation-dependent phase to light. Here, we show the success in creating a miniaturized and robust metalens based optical tweezers system capable of rotating liquid crystals droplets to imitate an optical motor for future lab-on-a-chip applications. Full article
(This article belongs to the Special Issue Localized Optical Modes in Liquid Crystals)
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Open AccessArticle
Synthesis of MgFe Layered Double Hydroxide from Iron-Containing Acidic Residual Solution and Its Adsorption Performance
Crystals 2019, 9(10), 514; https://doi.org/10.3390/cryst9100514 - 03 Oct 2019
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Abstract
The paper presents a new method of layered double hydroxide (LDH) synthesis starting from secondary sources, namely acidic residual solutions. The iron content of the acidic solution resulting from the pickling step of the hot-dip galvanizing process make it suitable to be used [...] Read more.
The paper presents a new method of layered double hydroxide (LDH) synthesis starting from secondary sources, namely acidic residual solutions. The iron content of the acidic solution resulting from the pickling step of the hot-dip galvanizing process make it suitable to be used as an iron precursor in LDH synthesis. Here, Mg4Fe–LDH synthesized through the newly proposed method presented structural and morphological characteristics similar to the properties of layered double hydroxides synthesized from analytical-grade reagents. Moreover, the as-synthesized LDH and its calcined product presented efficient adsorption properties in the removal process of Mo(VI) from aqueous solutions. The adsorption studies are discussed from the equilibrium, kinetic, and thermodynamic points of view. The proposed novel technologies present both economic and environmental protection benefits. Full article
(This article belongs to the Special Issue Layered Double Hydroxides)
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Open AccessArticle
Characterization of Coals and Coal Ashes with High Si Content Using Combined Second-Derivative Infrared Spectroscopy and Raman Spectroscopy
Crystals 2019, 9(10), 513; https://doi.org/10.3390/cryst9100513 - 02 Oct 2019
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Abstract
The organic and mineral components in two coals and resulting high-temperature ashes with high silicon content were characterized by second-derivative infrared spectroscopy, Raman spectroscopy, and X-ray diffraction (XRD). The infrared spectra of raw coals show weak organic functional groups bands but strong kaolinite [...] Read more.
The organic and mineral components in two coals and resulting high-temperature ashes with high silicon content were characterized by second-derivative infrared spectroscopy, Raman spectroscopy, and X-ray diffraction (XRD). The infrared spectra of raw coals show weak organic functional groups bands but strong kaolinite bands because of the relatively high silicates content. In contrast, the Raman spectra of raw coals show strong disordered carbon bands but no mineral bands since Raman spectroscopy is highly sensitive to carbonaceous phases. The overlapping bands of mineral components (e.g., calcite, feldspar, and muscovite) were successfully resolved by the method of second-derivative infrared spectroscopy. The results of infrared spectra indicate the presence of metakaolinite in coal ashes, suggesting the thermal transformation of kaolinite during ashing. Intense quartz bands were shown in both infrared and Raman spectra of coal ashes. In addition, Raman spectra of coal ashes show a very strong characteristic band of anatase (149 cm–1), although the titanium oxides content is very low. Combined use of second-derivative infrared spectroscopy and Raman spectroscopy provides valuable insight into the analyses of mineralogical composition. The XRD results generally agree with those of FTIR and Raman spectroscopic analyses. Full article
(This article belongs to the Special Issue Raman Spectroscopy of Crystals)
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Open AccessArticle
Structure, Optical, and Thermal Properties of 9, 10-Diphenylanthracene Crystals
Crystals 2019, 9(10), 512; https://doi.org/10.3390/cryst9100512 - 01 Oct 2019
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Abstract
9,10-diphenylanthracene (DPA) single crystal is a promising scintillator material for fast-neutron detection. Two centimetre-sized polymorph crystals of DPA were grown by melting and solution methods (DPA-Melt and DPA-Solution, respectively), and characterised by single-crystal X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectroscopy, fluorescence spectroscopy, UV-Vis [...] Read more.
9,10-diphenylanthracene (DPA) single crystal is a promising scintillator material for fast-neutron detection. Two centimetre-sized polymorph crystals of DPA were grown by melting and solution methods (DPA-Melt and DPA-Solution, respectively), and characterised by single-crystal X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectroscopy, fluorescence spectroscopy, UV-Vis absorbance spectroscopy, and thermogravimetric/differential scanning calorimetry. The DPA-Melt crystal possessed a P21/n structure, with excitation bands at approximately 331, 348, 367, and 387 nm, and the strongest emission wavelength at approximately 454 nm. On the other hand, the DPA-Solution crystal possessed a C2/c structure, with excitation bands at approximately 335, 353, 372, and 396 nm, and the strongest emission wavelength at approximately 468 nm. The two kinds of DPA crystals have the same molecular formula but different crystal structures, crystal lattice constants, and cell parameters. The theoretical density of the DPA-Solution crystal was 1.239 g/cm3, while that of the DPA-Melt crystal was 1.211 g/cm3. The two types of crystals exhibited the same melting point, but the thermal stability of the DPA-Solution crystal is better than that of the DPA-Melt crystal. Full article
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Open AccessArticle
Synthesis of Manganese Mononitride with Tetragonal Structure under Pressure
Crystals 2019, 9(10), 511; https://doi.org/10.3390/cryst9100511 - 30 Sep 2019
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Abstract
The exploration of the vast phase space of transition metal nitrides is critical for discovering novel materials and potential technological applications. Manganese mononitride with a tetragonal structure (space group I4/mmm) was synthesized in a laser-heating diamond anvil cell, which could [...] Read more.
The exploration of the vast phase space of transition metal nitrides is critical for discovering novel materials and potential technological applications. Manganese mononitride with a tetragonal structure (space group I4/mmm) was synthesized in a laser-heating diamond anvil cell, which could be quenched to ambient pressure. The bulk modulus of 173 GPa was measured using in situ high-pressure diffraction, and the axial compressibility shows that, under pressure, the a direction is much more compressible than the c direction in tetragonal MnN. DFT results with correction of the on-site repulsion (GGA + U) confirm that tetragonal MnN is energetically stable and antiferromagnetic. This study highlights the need to include on-site repulsion to understand 3d metal nitrides. Full article
(This article belongs to the Special Issue High Pressure Synthesis in Crystalline Materials)
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Open AccessArticle
Band Topology of Bismuth Quantum Films
Crystals 2019, 9(10), 510; https://doi.org/10.3390/cryst9100510 - 30 Sep 2019
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Abstract
Bismuth has been the key element in the discovery and development of topological insulator materials. Previous theoretical studies indicated that Bi is topologically trivial and it can transform into the topological phase by alloying with Sb. However, recent high-resolution angle-resolved photoemission spectroscopy (ARPES) [...] Read more.
Bismuth has been the key element in the discovery and development of topological insulator materials. Previous theoretical studies indicated that Bi is topologically trivial and it can transform into the topological phase by alloying with Sb. However, recent high-resolution angle-resolved photoemission spectroscopy (ARPES) measurements strongly suggested a topological band structure in pure Bi, conflicting with the theoretical results. To address this issue, we studied the band structure of Bi and Sb films by ARPES and first-principles calculations. The quantum confinement effectively enlarges the energy gap in the band structure of Bi films and enables a direct visualization of the Z 2 topological invariant of Bi. We find that Bi quantum films in topologically trivial and nontrivial phases respond differently to surface perturbations. This way, we establish experimental criteria for detecting the band topology of Bi by spectroscopic methods. Full article
(This article belongs to the Special Issue Recent Advances in Novel Topological Materials)
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Open AccessArticle
Investigating Differences and Similarities between Betaxolol Polymorphs
Crystals 2019, 9(10), 509; https://doi.org/10.3390/cryst9100509 - 29 Sep 2019
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Abstract
Betaxolol belongs to the class of β1-adrenergic blocking agent. Several polymorphs of racemic betaxolol have been reported in the literature, but only one of them (BE_I) had the crystal structure determined from single-crystal X-ray diffraction. Here, we present a new crystalline [...] Read more.
Betaxolol belongs to the class of β1-adrenergic blocking agent. Several polymorphs of racemic betaxolol have been reported in the literature, but only one of them (BE_I) had the crystal structure determined from single-crystal X-ray diffraction. Here, we present a new crystalline phase of betaxolol (BE_IV). Its solid-state structure has been obtained from single-crystal X-ray diffraction data. The molecular and crystal arrangements of betaxolol in BE_IV have been further investigated by molecular modelling, by Cambridge Structural Database (CSD) surveys and by Hirshfeld surface analysis. A comparison with the solid-state structure of BE_I have been carried out. In the two polymorphs the 2-hydroxy-3-(isopropylamino)-propoxy chain, which is common to other β-blocker drugs, adopts a different conformation. In addition, the rotational isomer found in BE_IV is different with respect to the four already observed in the solid-state structure of analogous compounds. In both the polymorphs, the most significant interaction is due to the H-bonds involving the OH group as donor and the NH as acceptor, while the interaction where OH works as acceptor (NH acts as donor) is definitely less important. The resulting H-bond patterns are however different: Alternate R2,2(10) a > a (OH donors) and R2,2(10) b > b (OH acceptors) in BE_I vs. alternate R4,4 (8) a > b > a > b (OH donors) and R2,2 (10) b > b (OH acceptor) in BE_IV. Full article
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Open AccessArticle
2D Monte Carlo Simulation of Patchy Particles Association and Protein Crystal Polymorph Selection
Crystals 2019, 9(10), 508; https://doi.org/10.3390/cryst9100508 - 28 Sep 2019
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Abstract
Typically, protein crystals inherit the polymorphic form selected by nuclei arising in the solution. However, a transition of a polymorphic form may also occur at a later crystal growth stage. Unfortunately, due to the molecular-scale processes involved, the earliest stages of protein crystal [...] Read more.
Typically, protein crystals inherit the polymorphic form selected by nuclei arising in the solution. However, a transition of a polymorphic form may also occur at a later crystal growth stage. Unfortunately, due to the molecular-scale processes involved, the earliest stages of protein crystal nucleation and polymorph selection remain poorly understood. This paper attempts to elucidate the polymorph selection and crystal growth process in proteins (and colloidal crystals) using 2D Monte Carlo simulations and a computational model with short-range attraction for ‘protein-like’ patchy particles (PPs) of a specific patch geometry, bond width and strength. A relatively narrow temperature range is established whereby parts of the PPs monomers arrange initially in a rapidly growing unstable rhombohedral lattice (Rh). Stable trimers form simultaneously from the monomers remaining in the solution and monomers released from the Rh lattice. These trimers serve as building blocks of a more stable Kagome trihexagonal lattice (TriHex), which appears after a prolonged simulation time. The step-by-step scenario of this polymorphic transition and the specific role of PPs’ geometric and interaction anisotropies are discussed in detail. Full article
(This article belongs to the Special Issue Polymorphism in Crystals)
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The Predictive Power of Different Projector-Augmented Wave Potentials for Nuclear Quadrupole Resonance
Crystals 2019, 9(10), 507; https://doi.org/10.3390/cryst9100507 - 28 Sep 2019
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Abstract
The projector-augmented wave (PAW) method is used to calculate electric field gradients (EFG) for various PAW potentials. A variety of crystals containing reactive nonmetal, simple metal, and transition elements, are evaluated in order to determine the predictive ability of the PAW method for [...] Read more.
The projector-augmented wave (PAW) method is used to calculate electric field gradients (EFG) for various PAW potentials. A variety of crystals containing reactive nonmetal, simple metal, and transition elements, are evaluated in order to determine the predictive ability of the PAW method for the determination of nuclear quadrupole resonance frequencies in previously unstudied materials and their polymorphs. All results were compared to experimental results and, where possible, to previous density functional theory (DFT) calculations. The EFG at the 14N site of NaNO2 is calculated by DFT for the first time. The reactive nonmetal elements were not very sensitive to the variation in PAW potentials, and calculations were quite close to experimental values. For the other elements, the various PAW potentials led to a clear spread in EFG values, with no one universal potential emerging. Within the spread, there was agreement with other ab initio models. Full article
(This article belongs to the Special Issue NQR of Polymorphic Crystals)
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Open AccessArticle
Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides
Crystals 2019, 9(10), 506; https://doi.org/10.3390/cryst9100506 - 28 Sep 2019
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Abstract
The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed [...] Read more.
The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating. Full article
(This article belongs to the Special Issue Chemical Bonding in Crystals and Their Properties)
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Open AccessReview
ZnO as a Functional Material, a Review
Crystals 2019, 9(10), 505; https://doi.org/10.3390/cryst9100505 - 28 Sep 2019
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Abstract
Zinc oxide (ZnO) is a fascinating wide band gap semiconductor material with many properties that make it widely studied in the material science, physics, chemistry, biochemistry, and solid-state electronics communities. Its transparency, possibility of bandgap engineering, the possibility to dope it into high [...] Read more.
Zinc oxide (ZnO) is a fascinating wide band gap semiconductor material with many properties that make it widely studied in the material science, physics, chemistry, biochemistry, and solid-state electronics communities. Its transparency, possibility of bandgap engineering, the possibility to dope it into high electron concentrations, or with many transition or rare earth metals, as well as the many structures it can form, all explain the intensive interest and broad applications. This review aims to showcase ZnO as a very versatile material lending itself both to bottom-up and top-down fabrication, with a focus on the many devices it enables, based on epitaxial structures, thin films, thick films, and nanostructures, but also with a significant number of unresolved issues, such as the challenge of efficient p-type doping. The aim of this article is to provide a wide-ranging cross-section of the current state of ZnO structures and technologies, with the main development directions underlined, serving as an introduction, a reference, and an inspiration for future research. Full article
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Open AccessArticle
Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1
Crystals 2019, 9(10), 504; https://doi.org/10.3390/cryst9100504 - 27 Sep 2019
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Abstract
Soluble fumarate reductase is essential for survival under anaerobic conditions. This enzyme can maintain the redox balance in the cell by catalyzing the reduction of fumarate to succinate. Although the overall reaction mechanism of soluble fumarate reductase in yeast, Osm1, has been proposed [...] Read more.
Soluble fumarate reductase is essential for survival under anaerobic conditions. This enzyme can maintain the redox balance in the cell by catalyzing the reduction of fumarate to succinate. Although the overall reaction mechanism of soluble fumarate reductase in yeast, Osm1, has been proposed by a previous structural study, the details of the underlying mechanism are not completely elucidated. The present study provides the structural information regarding the active site mutant form of Osm1 (R326A), thus, revealing that R326A mutation does not affect the substrate binding. Structural alterations of the residues surrounding the active site, and the missing 2nd flavin adenine dinucleotide (FAD) in the previously defined 2nd FAD binding site, were observed as characteristic features of the Osm1 R326A crystal structure. Based on these findings, we provided a clue that can explain the loss of activity of Osm1 R326A. Full article
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
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