Substrate Orientation Research Articles

Ferromagnetism and two magnetic phases in rutile (TiO<sub>2</sub>) implanted with cobalt ions: effect of substrate temperature and orientation

Room-temperature ferromagnetism and two magnetic phases: cobalt metal nanoparticles and a solid solution of divalent cobalt ions have been observed in single-crystal rutile (TiO2) implanted with cobalt ions to high dose level. Here we present the results of our structural and magnetic studies showing an influence both the temperature and the orientation of TiO2 substrate during a cobalt ion implantation, as well the effect of post-implantation thermal annealing (in air or in vacuum) on ferromagnetism value and magnetic phase composition of Co-implanted rutile.

Ferromagnetism and Two Magnetic Phases in Rutile (TiO2) Implanted with Cobalt Ions: Effects of Substrate Temperature and Orientation

Ferromagnetism and Two Magnetic Phases in Rutile (TiO2) Implanted with Cobalt Ions: Effects of Substrate Temperature and Orientation

The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn2+ for substrate orientation and activation

Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate (D2HG) dehydrogenase (PaD2HGDH) oxidizes D2HG to 2-ketoglutarate during the vital l-serine biosynthesis and is a potential therapeutic target against P.aeruginosa. PaD2HGDH, which oxidizes d-malate as an alternative substrate, has been demonstrated to be a metallo flavoprotein that requires Zn2+ for activity. However, the role of Zn2+ in the enzyme has not been elucidated, making it difficult to rationalize why nature employs both a redox center and a metal ion for catalysis in PaD2HGDH and other metallo flavoenzymes. In this study, recombinant His-tagged PaD2HGDH was purified to high levels in the presence of Zn2+ or Co2+ to investigate the metal's role in catalysis. We found that the flavin reduction step was reversible and partially rate limiting for the enzyme's turnover at pH 7.4 with either D2HG or d-malate with similar rate constants for both substrates, irrespective of whether Zn2+ or Co2+ was bound to the enzyme. The steady-state pL profiles of the kcat and kcat/Km values with d-malate demonstrate that Zn2+ mediates the activation of water coordinated to the metal. Our data are consistent with a dual role for the metal, which orients the hydroxy acid substrate in the enzyme's active site and rapidly deprotonates the substrate to yield an alkoxide species for hydride transfer to the flavin. Thus, we propose a catalytic mechanism for PaD2HGDH oxidation that establishes Zn2+ as a cofactor required for substrate orientation and activation during enzymatic turnover.

Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1?

Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.

Analysis of mixed optical transitions in dilute magnetic AlAs/GaAs/GaMnAs quantum wells grown on high substrate index by molecular beam epitaxy

In this study, we report the influence of high-index substrate orientation on the optical properties of dilute Mn containing a single quantum well (QW) structure grown by molecular beam epitaxy (MBE). The electronic band structure of the samples is calculated with finite element methods (FEM). Photomodulated reflectance (PR) spectroscopy is employed to determine the optical transition energies at room temperature. PR experimental results are analyzed with the Third Derivative Functional Form (TDFF) signal function. TDFF fitting shows that the optical transition starts below the fundamental GaAs bandgap energy for the samples grown on (311) B and (411) B-oriented substrates. Comparing TDFF fitting and calculated optical transition energies with FEM show that the optical transition occurs in type-I and type-II as direct and indirect transitions, respectively. Type-I and -II optical transitions are addressed concerning the electronic band structure of the sample grown on oriented substrates.

The effect of temperature on the contact angle of a water drop on graphene and graphene synthesized on copper

The influence of temperature on the graphene wettability in the range from 2 °C to 97 °C was investigated. The experimental and theoretical studies have shown that the water temperature, the roughness of the wall and the crystal orientation of the copper substrate significantly affect the wettability of graphene, as well as the structuring of water molecules and hydrogen bonds in the vicinity of the graphene surface. The lowest contact angle is obtained on graphene coating on copper with orientation (111). The lowest wettability of graphene corresponds to a copper substrate with orientation (110). Temperature noticeably distorts the structuring of water molecules near the graphene layer. Defects on the surface of the substrate in the form of a “spike” lead to the formation of graphene wrinkles, which result in local exfoliation of copper and graphene and in a change in the wettability of the graphene layer.

Comparative investigation of ligand binding of heme-containing dioxygenases by computer modeling.

Heme-containing enzymes are typically used as catalysts of oxidation-reduction reactions. These enzymes range from monooxygenases and dioxygenases to peroxidases and catalases to oxidases and dehydrogenases. Mechanistic aspects of these enzymes, including heme chemistry, have been extensively studied. Cyclooxygenase (COX), a heme-containing dioxygenase, has a cyclooxygenase activity and an associated peroxidase activity. COX shows similarity in the organization of the peroxidase active site to the other peroxidases. Cyclooxygenase active site, to which arachidonic acid binds, is on the proximal side of the heme and is the main target of explosive research interest, which results in great success. In plants, pathogen-inducible oxygenase (PIOX), another heme-containing enzyme, generates a potent lipid mediator by oxygenating 14-20 fatty acid substrates. COX and PIOX exhibit catalytic and structural similarities. The ligand-protein interactions of COX and PIOX have been characterized by crystallographic and mutagenic studies. Interestingly, the orientation of the fatty acid substrate inside the PIOX active site is different from the case of COX because of the α-dioxygenation of a cognate substrate by PIOX. This paper analyzes the characteristics of the substrate binding of mammalian and plant heme-containing dioxygenases using computer-aided modeling.

Experimental investigation of the loading speed effects on the performances of ultrasonically welded PA66/glass fabric composites

These past decades, the ability of thermoplastic composites to be welded has been of great interest, with numerous studies investigating the process and mechanical strength of joints for quasi-static loadings. The present study aims to determine the loading speed influence on the behaviour of these structures, as crashworthiness is of tremendous interest in the transport industry for safety issues. The polyamide-based composite used in this work is sensitive to strain rate, which may influence the interface and the entire structure's behaviour. Tensile tests were performed on single lap joint specimens for loading speeds from 1.2 mm min−1 to 7 m s−1, considering several substrate orientations. Loading speed influences the lap shear strength for the different configurations: increasing loading speed induces a performance enhancement of 11.2%–22.9%. This phenomenon is caused by the matrix strain rate sensitivity, which stiffens and strengthens the substrate shear behaviour and the welded joint behaviour. Finally, the fractography analysis confirms that fracture mechanisms observed are similar for each loading speed tested with primarily fibre/matrix debonding. Therefore, improvement in the welded structures' performance is due to the mechanical performance of its constituents and their influence on the interfacial strength.

Strain effects on the optoelectronic performance of ultra-wide band gap polycrystalline β-Ga2O3 thin film grown on differently-oriented Silicon substrates for solar blind photodetector

β-Ga2O3 based photodetectors are being intensively researched as possible substitutes to conventional Silicon deep-UV PDs. However, high cost of single-crystalline Ga2O3 poses hindrance towards commercialization by semiconductor industry still monopolized by Si. An easier integration with existing technology can be achieved by growing Ga2O3 thin films on Si directly, but growth of lattice mismatched substrates is often tricky and complicated with various parameters such as interfacial energies, surface energies, etc. playing important roles. Thus, it becomes imperative to investigate the role of each of these on film growth and devices thereof. Herein, polycrystalline β-Ga2O3 thin films are grown on different orientations of Si namely (100), (110) and (111), offering varied surface energies for film growth even under identical conditions. Best growth is observed on Si (111) substrate, deduced by largest crystallite size and lowest strain using Williamson-Hall method. This leads to devices of Ga2O3 on Si (111) having improved performance compared to other orientations. To validate effect of strain on device performance, a well-known method of reducing strain further – introduction of seed layer – is utilized, leading to further enhancement. This implies that PD performance is highly dependent on orientation of substrate used as the strain induced ultimately affects film growth.

Self-Assembly of Nanocrystalline Structures from Freestanding Oxide Membranes.

The exploration of crystalline nanostructures enhances the understanding of quantum phenomena occurring in spatially confined quantum matter and may lead to functional materials with unforeseen applications. A novel route to fabricating nanocrystalline oxide structures of exceptional quality is presented. This is achieved by utilizing a self-assembly process of ultrathin membranes composed of the desired oxide. The thermally induced self-assembly of nanocrystalline structures is driven by dewetting the oxide membranes once they are lifted off and transferred onto sapphire surfaces. In three successive steps, the process provides nanovoids, nanowires, and nanocrystals. Regardless of substrate orientation, the nanostructures are highly anisotropic in shape due to material retraction favoring low-index crystalline lattice directions of the membranes. The orientation of the nanostructures is provided precisely by the crystal lattice of the transferred membrane. The microstructure of the nanocrystals exhibits exceptional quality, characterized by a pristine crystal structure and uniform stoichiometry, both maintained all the way down to the well-developed crystalline facets. The demonstrated self-assembly process holds the potential to improve the understanding of surface diffusion phenomena at the interface of materials, which is important for advancing epitaxial growth technology and paves the way to fabricating crystalline nanostructures by the transfer and self-assembly of membranes.

Improving the catalytic ability of a peptide-based artificial glycosidase through a tyrosine strategy.

Recently, peptide-based artificial enzymes have attracted growing interest due to the similar composition of peptide assemblies to natural enzymes. However, low catalytic activity and stability are still the main challenges for these enzyme-like catalysts. In this study, a tyrosine strategy was developed to construct a peptide-based artificial glycosidase through engaging the Tyr residue into the peptide sequence. We found that the appropriate substitution of Tyr produced an enhanced catalytic ability, because the proximal Tyr residue around catalytic sites acts as a nucleophile, playing an important role in the substrate orientation and proton transfer. Moreover, inspired by the biological function of dityrosine bonds in structural proteins, a photo-crosslinking reaction between the phenolic side chains of Tyr was also employed to form intermolecular covalent bonds in peptide assemblies, which further improved the activity and stability of the artificial glycosidase. This work provides a simple avenue for the designing and construction of efficient glycosidase-like catalysts based on a peptide-based material platform.

Enzymatic synthesis, characterization and molecular docking of a new functionalized polyphenol: Resveratrol-3,4′-⍺-diglucoside

Transglucosylation of resveratrol by the Q345F variant of sucrose phosphorylase from Bifidobacterium adolescentis (BaSP) was extensively studied during the last decade. Indeed, Q345F is able to catalyze the synthesis of resveratrol-3-O-⍺-D-glucoside (RES-3) with yield up to 97% using a cost-effective glucosyl donor, sucrose (Kraus et al., Chemical Communications, 53(90), 12182–12184 (2017)). Despite the fact that two further products were detectable in low amounts after glucoside synthesis, they were never identified. Here, we isolated and fully characterized one of those two minor products: resveratrol-3,4′-O-⍺-D-diglucoside (RES-3,4′). This original compound had never been described before. Using bioinformatics models, we successfully explained the formation of this diglucosylated product. Indeed, with RES-3 as acceptor substrate, Q345F is able to transfer a glucosyl moiety in position 4′-OH, what had been reported as impossible in the literature. The low yield observed is due to the steric hindrance into the catalytic site between RES-3 and residues Tyr132 and Tyr344. Nevertheless, the substrate orientation in the active site is favored by stabilizing interactions. Ring A of RES-3 bearing the diol moiety is stabilized by hydrogen bonds with residues Asp50, Arg135, Asn347 and Arg399. Hydroxyl group OH-4′ shares hydrogen bonds with the catalytic residues Asp192 and Glu232. Multiple hydrophobic contacts complete the stabilization of the substrate to favor the glucosylation at position 4′. Understanding of the mechanisms allowing the glucosylation at position 4′ of resveratrol will help the development of enzymatic tools to target and control the enzymatic synthesis of original ⍺-glucosylated polyphenols with high added value and better biodisponibility.

Изучение кинетики сближения ступеней поверхности Si(100)

In this work, the convergence kinetics investigations of the SA and SB steps on Si(100) substrates with inclination 0.5o and 0.1o were carried out. Analysis of the time dependence of reflection high-energy electron diffraction (RHEED) intensity was used to establish the growth kinetics character on vicinal Si(100) surfaces. It is shown that, in a Si flow at the growth rate of 0.37 ML/s, the step convergence velocity has a decreasing exponential dependence with the temperature increase. It is determined that the single-domain surface formation velocity increases with an increase in the terrace width on the surface, which may be due to the partial participation of growth due to the formation of two-dimensional islands. Above a temperature of 650°C, the dominant growth mode is due to the step movement and the single-domain surface formation velocity decreases with an increase in the terrace width. Thus, the single-layer step convergence is determined by both the MBE growth conditions and the Si(100) substrate orientation. The convergence of SA and SB steps of the Si(100) surface is explained by the slowdown of the step SA motion, which is associated with complex permeability mechanisms and a kink formation of steps. It is assumed that the reason for the slowdown of the step convergence with increasing temperature is an increase in the kink density at the SA step, which reduces the step SA permeability coefficient.

Study of Si(100) surface step convergence kinetics

In this work, the convergence kinetics investigations of the SA- and SB-steps on Si(100) substrates with inclination 0.5o and 0.1o were carried out. Analysis of the time dependence of reflection high-energy electron diffraction (RHEED) intensity was used to establish the growth kinetics character on vicinal Si(100) surfaces. It is shown that, in a Si flow at the growth rate of 0.37 ML/s, the step convergence velocity has a decreasing exponential dependence with the temperature increase. It is determined that the single-domain surface formation velocity increases with an increase in the terrace width on the surface, which may be due to the partial participation of growth due to the formation of two-dimensional islands. Above a temperature of 650oC, the dominant growth mode is due to the step movement and the single-domain surface formation velocity decreases with an increase in the terrace width. Thus, the single-layer step convergence is determined by both the MBE growth conditions and the Si(100) substrate orientation. The convergence of SA- and SB-steps of the Si(100) surface is explained by the slowdown of the step SA-motion, which is associated with complex permeability mechanisms and a kink formation of steps. It is assumed that the reason for the slowdown of the step convergence with increasing temperature is an increase in the kink density at the SA-step, which reduces the step SA-permeability coefficient. Keywords:: Molecular-beam epitaxy, reflection high-energy electron diffraction, surface, terraces, steps, kinks.

Влияние механической деформации на магнитные свойства и магнитокалорический эффект в пленках Gd

In W/Gd/W/MgO heterostructures, the dependence of mechanical stresses in the Gd film on the crystallographic orientation of the MgO substrate was revealed. Variations in the interplanar spacings in MgO in different orientations create tensile elastic stresses up to 0.22 GPa in the Gd film, which are transferred through the damping layer W. It is found that these stresses affect the isothermal magnetization curves, the corresponding change in the magnetic part of the entropy at the Curie point Tc = 293 K, and the relative cooling capacity (RCP). This allows us to consider mechanical stresses as a factor in controlling the magnetocaloric cycle, which increases the efficiency of the refrigeration machine, when mechanical loading is synchronized with the heating-cooling cycles of the ferromagnet.

Influence of mechanical deformation on magnetic properties and magnetocaloric effect in Gd films

In W/Gd/W/MgO heterostructures, the dependence of mechanical stresses in the Gd film on the crystallographic orientation of the MgO substrate was revealed. Variations in the interplanar spacings in MgO in different orientations create tensile elastic stresses up to 0.22 GPa in the Gd film, which are transferred through the damping layer W. It is found that these stresses affect the isothermal magnetization curves, the corresponding change in the magnetic part of the entropy at the Curie point T_c=293 K, and the relative cooling capacity (RCP). This allows us to consider mechanical stresses as a factor in controlling the magnetocaloric cycle, which increases the efficiency of the refrigeration machine, when mechanical loading is synchronized with the heating-cooling cycles of the ferromagnet. Keywords: magnetocaloric effect, entropy, microdeformations, microstresses.

Structure of the green heme isolated from allylbenzene-modified chloroperoxidase: A novel heme architecture implicating the mechanisms of CPO inactivation and epoxidation

The chemical identification of the modified heme (the green heme) during chloroperoxidase catalyzed epoxidation of allylbenzene remains unestablished due to its high instability within the protein matrix, the absence of paramagnetically shifted signals, and the difficulty in obtaining crystals of the modified enzyme. We have established the unambiguous structure of the modified prosthetic heme group, which was extracted from the protein matrix using 2D NMR spectroscopy and LC-MS spectrometry. The modified heme was isolated as a µ-oxo dimer that can be quantitatively converted to the corresponding monomer. The depolymerized green heme displayed characteristic NMR signatures of iron porphyrin complexes, but no Nuclear Overhauser Effect was observable to assist in signal assignment. An alternative strategy was applied by removing the iron center of the green heme, resulting in a stable demetallated green porphyrin species. Complete assignment of all the NMR resonances in the demetallated green heme allowed us to establish the molecular architecture of the modified species as a novel N-alkylated heme. Decisive space correlations between the propyl protons of allylbenzene and the γ meso proton coupled with clear dipolar connectivities between the propyl-2H of the substrate and the β proton in the side chain of the propionic acid at carbon-6 of the porphyrin ring, clearly indicate that allylbenzene was covalently attached to the nitrogen atom of the pyrrole ring III of the prosthetic heme. In this study, the mechanism of green CPO formation and its relation to CPO catalyzed chiral transformations are also discussed. It is concluded that the double-phenyl clamp formed by two phenylalanine residues at the distal heme pocket plays a critical role in fine-tuning substrate orientation that determines the outcome of CPO catalyzed epoxidation of substituted styrenes.

Growth and characterization of the β-Ga2O3 (011) plane without line-shaped defects

The β-Ga2O3 (011) plane could be a potential substrate orientation for power devices because it avoids a kind of dislocation which leads to leakage current and breakdown of power devices as the dislocations propagate parallel to the (011) plane.

Defect structure of α-Ga-=SUB=-2-=/SUB=-O-=SUB=-3-=/SUB=- film grown on a m-face sapphire substrate, according to transmission electron microscopy investigation

The results of a study by transmission electron microscopy of the structural state of α-Ga2O3 film with a thickness of about 1 micron, grown on the prismatic m-face sapphire by the method of chloride vapor phase epitaxy, are presented. The influence of the substrate orientation on the formation of the dislocation structure is discussed. Threading dislocations, including those with the Burgers vector 1/3< 1120 >, and dislocation half-loops are revealed. The inclined propagation of dislocations and the formation of dislocation half-loops result in the reduction of the threading dislocation density near the surface.. Keywords: dislocations, gallium oxide, TEM.

Дефектная структура пленки α-Ga-=SUB=-2-=/SUB=-O-=SUB=-3-=/SUB=-, выращенной на m-грани подложки сапфира, по данным просвечивающей электронной микроскопии

The results of a study by transmission electron microscopy of the structural state of α-Ga2O3 film with a thickness of about 1 micron, grown on the prismatic m-face sapphire by the method of chloride vapor phase epitaxy, are presented. The influence of the substrate orientation on the formation of the dislocation structure is discussed. Threading dislocations, including those with the Burgers vector 1/3<11-20> , and dislocation half-loops are revealed. The inclined propagation of dislocations and the formation of dislocation half-loops result in the reduction of the threading dislocation density near the surface.