Substrate Orientation Research Articles

Engineering of carbonyl reductase for asymmetric reduction of difficult-to-reduce ketone tetrahydrofuran-3-one

Tetrahydrofuran-3-one (3TF) was regarded as a difficult-to-reduce ketone for carbonyl reductases due to its high stereosymmetry, result of which, the biosynthesis of chiral 3-hydroxytetrahydrofuran (3HTF), a key precursor of pharmaceuticals for treatment of HIV or diabetes, has been limited. Present study mined a robust carbonyl reductase CmCR from Candida metapsilosis with high activity towards 3TF using isopropanol as co-substrate (500 mM, 22 g/L/h space-time yield, 67% ee). Based on the orientation of substrate's etheryl oxygen in the substrate binding pocket, CmCR was rationally designed and two mutants MuR and MuS were screened out to completely reduce 3TF into (R)-HTF and (S)-HTF respectively with the highest 3TF loading and productivity (200 mM, 4.4 g/L/h space-time yield, 99% ee for MuR while 500 mM, 11 g/L/h space-time yield, 99% ee for MuS). The structural mechanism for the enhanced stereoselectivity was revealed that the mutagenesis changed the electrostatic potential surrounding the substrate entrance and promoted 3TF to approach, bind and form prereaction state with MuR or MuS in one certain direction, by which 3TF was converted into 3HTF with excellent optical purity. The success in this study provides a viable approach for rational design of carbonyl reductases with high enantioselectivity towards target substrates of high symmetry.

Computationally guided epitaxial synthesis of (Sr/Ba)MnO[formula omitted] films on (Sr/Ba)TiO[formula omitted] substrates

Density functional theory (DFT) was used in the computation of thermodynamic terms relevant to the competition between epitaxial polytypes during nucleation of (Sr/Ba)MnO3 on (100), (110), and (111) cubic (Sr/Ba)TiO3 substrates. Values for volumetric formation energies, volumetric strain energies, and area-specific interface energies were computed for different polytypes (3C, 4H, and 2H) and were incorporated in a standard (capillarity) model for epitaxial nucleation. Experimental orientation relationships (ORs) for SrMnO3 were used in the construction of strained and interface cells for (Sr/Ba)MnO3. For 3C polytypes, the OR is simply cube-on-cube, or (111)[11̄0]3C,film||(111)[11̄0]3C,sub, and is isostructural with cubic (Sr/Ba)TiO3. For 4H/2H polytypes, the orientation relationship is (001)[100]4H/2H,film||(111)[11̄0]3C,sub, which can only be modeled with a coherent interface on the (111) substrate. Results indicate that 3C SrMnO3 has increased energies (becomes less stable) on moving from SrTiO3 substrate orientations (100) to (110) to (111), consistent with experimental observations. For BaMnO3, similar trends are predicted, although no experimental data is available for comparison. We use the DFT results to discuss the different thermodynamic contributions to polytype stability, and assess the feasibility of stabilizing a 3C BaMnO3 film on (Sr/Ba)TiO3 substrates.

Investigation of interdiffusion in thin films of ZnO/ZnCdO grown by molecular beam epitaxy

Rutherford backscattering spectrometry (RBS) was used to determine the composition, uniformity, impurity, and elemental depth profiles of Zn, Cd, and O in ZnCdO/ZnO thin film deposited on differently oriented Al2O3 substrates using molecular beam epitaxy technique. For the films deposited under the same condition, it was observed that the variation of Zn/Cd/O ratios is dependent on substrate orientation and highly depends on the growth parameters. The composition and thickness variation, in relationship with two different substrates orientations, were explored with RBS, scanning electron microscopy, and photoluminescence measurements. It was found that ZnCdO films deposited on r- oriented ZnO buffers exhibit much less surface roughness and intermixing after the rapid thermal processing annealing is less extensive.

Dimensionality Engineering of Single-Atom Nanozyme for Efficient Peroxidase-Mimicking.

In nature, enzymatic reactions occur in well-functioning catalytic pockets, where substrates bind and react by properly arranging the catalytic sites and amino acids in a three-dimensional (3D) space. Single-atom nanozymes (SAzymes) are a new type of nanozymes with active sites similar to those of natural metalloenzymes. However, the catalytic centers in current SAzymes are two-dimensional (2D) architectures and the lack of collaborative substrate-binding features limits their catalytic activity. Herein, we report a dimensionality engineering strategy to convert conventional 2D Fe-N-4 centers into 3D structures by integrating oxidized sulfur functionalities onto the carbon plane. Our results suggest that oxidized sulfur functionalities could serve as binding sites for assisting substrate orientation and facilitating the desorption of H2O, resulting in an outstanding specific activity of up to 119.77 U mg-1, which is 6.8 times higher than that of conventional FeN4C SAzymes. This study paves the way for the rational design of highly active single-atom nanozymes.

Effect of silicon surface orientation on the Au droplet motion

The Monte Carlo simulation results of the gold droplet motion along the silicon surface during the gold deposition are presented in this paper. The droplet behavior on silicon substrates with (111), (011) and (311) orientations at temperatures above the eutectic temperature of the Au-Si system was considered. The reason for the droplet movement is the substrate dissolution by the liquid droplet in an attempt to maintain the equilibrium Au-Si melt concentration. It was demonstrated that the gold droplet movement in 〈110〉 directions is determined by the etch pit asymmetry under the droplet, which depends on the substrate orientation. On the Si(111) surface the etch pit shape is symmetric. In this case, the droplet moves only along the vicinal surface, where the vicinal steps provide the lateral droplet-crystal interface asymmetry. The average droplet velocity on the vicinal Si(111) surface increases with an increase in the misorientation angle. On Si(011) and Si(311) surfaces the lateral droplet-crystal interface is asymmetric. A lower droplet velocity on the Si(311) surface, compared to the Si(011) surface, is due to a different etch pit shape under the droplet for these surface orientations.

Effect of substrate and growth method on vanadium dioxide thin films by RF magnetron sputtering: Vanadium metal oxidation vs reactive sputtering

Vanadium dioxide (VO2) undergoes a metal–insulator phase transition at ∼70 °C and has attracted substantial interest for potential applications in electronics, including those in neuromorphic computing. The vanadium–oxygen system has a rather complicated phase diagram, and controlling the stoichiometry and the phase of thin films of vanadium oxides is a well-known challenge. We explore the novel combination of two methods of VO2 thin film deposition using off-axis RF magnetron sputtering on (100)- and (111)-oriented yttria-stabilized zirconia (YSZ) substrates: reactive sputtering of vanadium in an oxygen environment and sputtering of vanadium metal followed by oxidation to VO2. Interestingly, the reactive sputtering process on both substrate orientations yields the metastable semiconducting VO2 (B) phase, which is structurally stabilized by the YSZ surface. The metal sputtering and oxidation process on YSZ produces mainly the equilibrium monoclinic (or M1) phase of VO2 that exhibits a metal–insulator transition. Using this method, we obtained thin films of (010)-textured polycrystalline VO2 (M1) that show a metal–insulator transition with an on/off ratio larger than 1000.

Spatiotemporal walking gait kinematics of semi-arboreal red pandas (Ailurus fulgens).

Semi-arboreal mammals must routinely cope with the differing biomechanical challenges of terrestrial versus arboreal locomotion; however, it is not clear to what extent semi-arboreal mammals adjust footfall patterns when moving on different substrates. We opportunistically filmed quadrupedal locomotion (n = 132 walking strides) of semi-arboreal red pandas (Ailurus fulgens; n = 3) housed at Cleveland Metroparks Zoo and examined the effects of substrate type on spatiotemporal gait kinematic variables using linear mixed models. We further investigated the effects of substrate diameter and orientation on arboreal gait kinematics. Red pandas exclusively used lateral sequence (LS) gaits and most frequently utilized LS lateral couplet gaits across terrestrial and arboreal substrates. Red pandas moved significantly slower (p < 0.001), and controlling for speed, had significantly greater relative stride length (p < 0.001), mean stride duration (p = 0.002), mean duty factor (p < 0.001), and mean number of supporting limbs (p < 0.001) during arboreal locomotion. Arboreal strides on inclined substrates were characterized by significantly faster relative speeds and increased limb phase values compared with those horizontal and declined substrates. These kinematics adjustments help to reduce substrate oscillations thereby promoting stability on potentially precarious arboreal substrates. Red panda limb phase values are similar to those of (primarily terrestrial) Carnivora examined to date. Despite the similarity in footfall patterns during arboreal and terrestrial locomotion, flexibility in other kinematic variables is important for semi-arboreal red pandas that must navigate disparate biomechanical challenges inherent to arboreal versus terrestrial locomotion.

Crystal orientation dependent spin pumping in a Bi0.1Y2.9Fe5O12/Pt interface

Ferromagnetic resonance (FMR) based spin pumping is a versatile tool to quantify the spin-mixing conductance and spin-to-charge conversion (S2CC) efficiency of ferromagnet–normal metal (FM/NM) heterostructures. The spin-mixing conductance at the FM–NM interface can also be tuned by the crystal orientation symmetry of epitaxial FM. In this work, we study the S2CC in epitaxial bismuth-substituted yttrium iron garnet (Bi0.1Y2.9Fe5O12) thin-film Bi–YIG (100 nm) interfaced with heavy metal platinum (Pt, 8 nm) deposited by pulsed laser deposition on different crystal orientations of Gd3Ga5O12 substrates, i.e. [100] and [111]. The crystal structure and surface roughness characterized by x-ray diffraction and atomic force microscopy measurements establish epitaxial Bi–YIG [100] and Bi–YIG [111] orientations, and atomically flat surfaces, respectively. The S2CC quantification was realized using two complementary techniques, namely (i) FMR-based spin pumping and the inverse spin Hall effect (ISHE) at GHz frequencies and (ii) temperature-dependent spin Seebeck measurements. The FMR-ISHE results demonstrate that the [111]-oriented Bi–YIG/Pt sample shows significantly higher values of spin mixing conductance ((2.31 ± 0.23) × 1018 m−2) and spin Hall angle (0.01 ± 0.001) as compared to the [100]-oriented Bi–YIG/Pt. Longitudinal spin Seebeck measurements reveal that the [111]-oriented sample has a higher spin Seebeck coefficient (106.40 ± 10 nV mm−1 K−1). The anisotropic nature of the spin-mixing conductance and spin Seebeck coefficient in the [111] and [100] orientations are discussed using the magnetic environment elongation along the surface normal or parallel to the growth direction. Our results aid in understanding the role of crystal orientation symmetry in S2CC-based spintronics devices.

Formation of hexagonal phase 9R-Si in SiO2/Si system upon Kr+ ion implantation

Hexagonal silicon polytypes are attracting significant attention from the scientific community due to their potential applications in next-generation electronics and photonics. However, obtaining stable heterostructures based on both cubic and hexagonal polytypes is a complicated task. In the present work, the possibility of formation of hexagonal silicon of the 9R-Si phase using the traditional method of microelectronics, i.e. ion implantation, is shown. Implantation of Kr+ ions was carried out through a SiO2 layer, the thickness of which was approximately twice the projected range of Kr+ followed by high temperature annealing. High resolution transmission electron microscopy reveals that a thin amorphous layer forms in a Si substrate at the interface with the SiO2 film under implantation, upon recrystallization of which the formation of the 9R-Si polytype occurs during annealing. It is assumed that mechanical stresses are created during implantation through the oxide layer, that contributes to hexagonalization during high-temperature annealing. The dependence of the efficiency of hexagonalization on the substrate orientation is established. In addition to the formation of the 9R-Si phase, at the implantation and annealing parameters used, light-emitting defects are formed in silicon, the photoluminescence of which at a wavelength of ∼1240 nm is observed up to a temperature of ∼120 K. The obtained results can stimulate and expand the range of applications of ion-irradiated silicon in micro-, nano-, and optoelectronics

A polyamine acetyltransferase regulates the motility and biofilm formation of Acinetobacter baumannii

Acinetobacter baumannii is a nosocomial pathogen highly resistant to environmental changes and antimicrobial treatments. Regulation of cellular motility and biofilm formation is important for its virulence, although it is poorly described at the molecular level. It has been previously reported that Acinetobacter genus specifically produces a small positively charged metabolite, polyamine 1,3-diaminopropane, that has been associated with cell motility and virulence. Here we show that A. baumannii encodes novel acetyltransferase, Dpa, that acetylates 1,3-diaminopropane, directly affecting the bacterium motility. Expression of dpa increases in bacteria that form pellicle and adhere to eukaryotic cells as compared to planktonic bacterial cells, suggesting that cell motility is linked to the pool of non-modified 1,3-diaminopropane. Indeed, deletion of dpa hinders biofilm formation and increases twitching motion confirming the impact of balancing the levels of 1,3-diaminopropane on cell motility. The crystal structure of Dpa reveals topological and functional differences from other bacterial polyamine acetyltransferases, adopting a β-swapped quaternary arrangement similar to that of eukaryotic polyamine acetyltransferases with a central size exclusion channel that sieves through the cellular polyamine pool. The structure of catalytically impaired DpaY128F in complex with the reaction product shows that binding and orientation of the polyamine substrates are conserved between different polyamine-acetyltransferases.

N2O grown high Al composition nitrogen doped β-(AlGa)2O3/β-Ga2O3 using MOCVD

We report on the MOCVD growth of smooth (010) (AlxGa1–x)2O3 and (100) (AlyGa1–y)2O3 epitaxial films on β-Ga2O3 substrates with (010) and (100) orientations, respectively, using N2O for oxidation. High resolution x-ray diffraction was used to evaluate the phase purity and strain characteristics of the (AlGa)2O3 layers and estimate the Al composition. The incorporation efficiency of Al into the (AlGa)2O3 films depends on process conditions, including chamber pressure, growth temperature, and gas phase Al concentration. Layers grown at lower reactor pressure and substrate temperature and higher gas phase Al concentration showed higher Al incorporation. Pure beta phase (AlGa)2O3 films with a record high Al composition of x = 30% for a film grown on a (010) β-Ga2O3 substrate and with an Al composition of up to y = 45% on the (100) β-Ga2O3 substrate was realized by introducing ∼18% Al mole fraction into the reactor. N2O grown β-(AlGa)2O3/β-Ga2O3 superlattice structures with an Al composition of 5% were also demonstrated on both substrate orientations. When higher gas phase Al concentration is introduced into the reactor, pure γ-phase (AlxGa1–x)2O3 is grown on (010) β-Ga2O3 substrates. In contrast, on the (100) β-Ga2O3 substrate, the (AlyGa1–y)2O3 layers are β-phase, but with two separate Al compositions owing to the local Al segregation. The nitrogen doping of (010) β-(AlxGa1–x)2O3 with [N] ranging 6 × 1017–2 × 1019 cm−3 was achieved using N2O. Higher Al composition and lower substrate temperature lead to higher N incorporation. The results show that using N2O as an oxygen source can lead to the growth of high Al content β-(AlGa)2O3, which paves the way for the realization of efficient power devices, such as modulation-doped field effect transistors.

Magnetron sputtering of the high entropy alloy CoCrFeMnNi on 316L: Influence of substrate grain orientations

This study explores the influence of a 316 L stainless steel substrate on growth of CoCrFeMnNi coatings deposited using magnetron sputtering at different substrate bias. The study was carried out on a polycrystalline 316 L substrate where the growth behavior of the coating could be investigated on grains with different orientations. By combining electron backscatter diffraction (EBSD) before and after deposition and characterization of the same area, it was possible to determine growth behavior and surface morphologies on individual substrate grains. No strong influence of the substrate was observed at a floating bias. At a bias of -100 V, however, the coating was strongly influenced by the orientation of the individual substrate grains. Epitaxial growth with a smooth coating grain surface was observed on the <102>-oriented grains while a more columnar growth was observed on <111>-oriented substrate grains. Furthermore, a small difference in growth rate was observed on different substrate orientations. The growth behavior could be related to differences in energy transfer from incoming ions and diffusion rates during growth on different orientations.

Substrate orientation effect in covalent organic frameworks/2D materials heterostructure by high-resolution atomic force microscopy

Substrate orientation effect in covalent organic frameworks/2D materials heterostructure by high-resolution atomic force microscopy

Ohmic contact structures on β-Ga2O3 with n+ β-Ga2O3 pulsed laser deposition layers

Thin (40–150 nm), highly doped n+ (1019–1020 cm−3) Ga2O3 layers deposited using pulsed laser deposition (PLD) were incorporated into Ti/Au ohmic contacts on (001) and (010) β-Ga2O3 substrates with carrier concentrations between 2.5 and 5.1 × 1018 cm−3. Specific contact resistivity values were calculated for contact structures both without and with a PLD layer having different thicknesses up to 150 nm. With the exception of a 40 nm PLD layer on the (001) substrate, the specific contact resistivity values decreased with increasing PLD layer thickness: up to 8× on (001) Ga2O3 and up to 16× on (010) Ga2O3 compared with samples without a PLD layer. The lowest average specific contact resistivities were achieved with 150 nm PLD layers: 3.48 × 10−5 Ω cm2 on (001) Ga2O3 and 4.79 × 10−5 Ω cm2 on (010) Ga2O3. Cross-sectional transmission electron microscopy images revealed differences in the microstructure and morphology of the PLD layers on the different substrate orientations. This study describes a low-temperature process that could be used to reduce the contact resistance in Ga2O3 devices.

13C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N-Linked Glycosylated Lipoxygenase.

Lipoxygenase (LOX) enzymes produce important cell-signaling mediators, yet attempts to capture and characterize LOX-substrate complexes by X-ray co-crystallography are commonly unsuccessful, requiring development of alternative structural methods. We previously reported the structure of the complex of soybean lipoxygenase, SLO, with substrate linoleic acid (LA), as visualized through the integration of 13C/1H electron nuclear double resonance (ENDOR) spectroscopy and molecular dynamics (MD) computations. However, this required substitution of the catalytic mononuclear, nonheme iron by the structurally faithful, yet inactive Mn2+ ion as a spin probe. Unlike canonical Fe-LOXs from plants and animals, LOXs from pathogenic fungi contain active mononuclear Mn2+ metallocenters. Here, we report the ground-state active-site structure of the native, fully glycosylated fungal LOX from rice blast pathogen Magnaporthe oryzae, MoLOX complexed with LA, as obtained through the 13C/1H ENDOR-guided MD approach. The catalytically important distance between the hydrogen donor, carbon-11 (C11), and the acceptor, Mn-bound oxygen, (donor-acceptor distance, DAD) for the MoLOX-LA complex derived in this fashion is 3.4 ± 0.1 Å. The difference of the MoLOX-LA DAD from that of the SLO-LA complex, 3.1 ± 0.1 Å, is functionally important, although is only 0.3 Å, despite the MoLOX complex having a Mn-C11 distance of 5.4 Å and a "carboxylate-out" substrate-binding orientation, whereas the SLO complex has a 4.9 Å Mn-C11 distance and a "carboxylate-in" substrate orientation. The results provide structural insights into reactivity differences across the LOX family, give a foundation for guiding development of MoLOX inhibitors, and highlight the robustness of the ENDOR-guided MD approach to describe LOX-substrate structures.

Understanding substrate-driven growth mechanism of copper silicide nanoforms and their applications

The growth mechanism of various nanoforms of copper/copper silicide on Si substrates with different orientations is reported here. The triangular, square and rectangular copper/copper silicide nanostructures are deposited on silicon substrates with (111), (100) and (110) orientations respectively, by thermal evaporation of metallic copper at different substrate temperatures. Investigations confirm that the nanostructures consist of a pure copper layer on top of a copper silicide layer. The morphology and growth behaviour studies confirmed for the first time that the formation of well-defined structures and shapes are governed by the Si substrate orientation and the surface reconstruction of the Si planes. The copper silicide nanostructures are used in field emission applications and also serve as a template for the growth of carbon nano-fibre.

Interface structure between Nb thin film and MgO(112) substrate: A first-principles prediction

The crystal orientation of ceramic substrates is an important factor affecting the interface structure of metal/ceramic composite materials. However, there is little information about the interface composed of metal films and ceramic substrates with a high-index plane. In this work, we predicted the interface structure between a Nb film and a MgO(112) substrate by calculating the interface separation works of different interface models by using the first-principles calculation method. The results showed that the preferred growth direction is Nb [120], and that the value of the interface separation work is 0.35 eV/Å2. The lattice mismatch between the film and substrate is less than 3%, implying that a coherent interface type is highly realizable in Nb/MgO(112). Furthermore, we analyzed the interface structures of Nb/MgO(100), Nb/MgO(110), Nb/MgO(111), and Nb/MgO(112) and found that the unique atomic configuration of the MgO substrate is the main factor determining the preferred interface structure of Nb/MgO.

A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments

Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdusluminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P.luminescens. Activity assays invitro and deletion experiments invivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found invitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.

Fatigue properties of resistance spot‐welded maraging steel produced by selective laser melting

AbstractThis research study investigates the fatigue properties of resistance spot welds (RSWs) made from selective laser‐melted (SLMed) maraging steel (MS1) and compares them with dual‐phase (DP) steel RSWs. The findings reveal that MS1 spot welds exhibit superior fatigue properties compared with DP steel RSWs, regardless of the printing orientation of the MS1 substrate. Furthermore, fatigue fracture occurs at the MS1 substrate, with a transition of fracture location observed from MS1 to itself and MS1‐to‐DP600 dissimilar welds. The results of structural stress analysis indicate that the weld nugget diameter is not the only factor affecting the fatigue life. The study also highlights the importance of considering materials inhomogeneity and fracture modes in fatigue life assessment. Based on the findings, the study recommends the development of a new fatigue life prediction curve for spot welds of additive manufacturing (AM) materials. Such a curve would be beneficial in promoting the further application of AM technology for functional parts of design verification vehicles (DCV) and production cars. Overall, the research contributes to the understanding of the fatigue properties of RSWs made from SLMed MS1 and DP steel, which has implications for the design and manufacturing of parts in the automotive industry.

New approaches to study of mismatched interfaces structure on low-index surfaces by molecular dynamics simulation

We used molecular dynamics simulations to study the structure of mismatched Al/Ni and Ag/Cu interfaces, considering low-index surfaces of the substrate. Embedded Atom Potentials are being employed to mimic atomic interactions between the different elements. The effect of the substrate orientation on the adlayer structure is investigated. The results showed that, on the (111) substrate, the adlayer presents a coincidence site lattice characterized by a rotation (labeled α) with respect to the substrate. This coincidence site lattice may contain dislocations and twin boundary that can be produced by the occurrence of a twin spirals (with opposite directions). To accommodate the adlayer deposition on the substrate, a slight shuffling of some atoms occurs in the substrate and leads to a rectangular structures producing a dislocation. Furthermore, on the (001) substrate, the accommodation of the triangular structure on the square lattice (substrate) is produced by a shift of some atomic rows producing a dislocation. But, the agglomeration of several square structures of 2d shape gives rise to a polycrystal delimited by a disclination forming grain boundaries and vacancies. However, the inward adsorption on the (110) substrate restricts the space of extension of adsorbed atoms, producing linear cracks. The relaxation of atoms adsorbed on these cracks change the linear shape of vacancies towards a staircase structure.