Step Rearrangement Research Articles

Structural Analysis of Neutral Nitrogen Compounds Refractory to the Hydrodenitrogenation Process of Heavy Oil Fractions by High-Resolution Tandem Mass Spectrometry and Ion Mobility–Mass Spectrometry

This study aims to identify and characterize compounds refractory to hydrodenitrogenation (HDN). The efficiency of a vacuum hydrocracking unit in removing nitrogen-containing compounds to produce a low-nitrogen-content effluent is examined. Molecular, structural, and compositional knowledge is a requisite for the optimization development of the hydrotreatment step processing unit because changes in the chemical composition of petroleum have a direct impact on physical properties and, thus, overall vacuum gas oil (VGO) upgrading processes. Two samples, a VGO and a effluent obtained after the HDN process containing 10 wppm of N, were analyzed by negative-mode electrospray ionization ultra-high-resolution tandem mass spectrometry (ESI–FT-ICR) and ion mobility spectrometry–mass spectrometry (IMS–MS). FT-ICR mass spectrometry provides ultrahigh mass resolving power to separate and characterize compounds in the highly complex petroleum samples. The fragments generated by MS/MS of selected N₁ refractory compounds were used for structural elucidation. Species with a double bond equivalent of 10 and 13, which proved to be highly refractory, were analyzed in more detail. On the other hand, the TWIMS–TOF MS measurements enabled the entire ion mobility analysis of refractory species to hydrotreatment processes. The MS/MS spectra revealed a specific pattern allowing for the identification of the molecular nucleus. Furthermore, it allowed for the understanding of the fragmentation pathways: loss of alkyl chains in the first step and opening and rearrangement of the nuclei after that. Ion mobility separation, in combination with MS/MS, allowed for the identification of the different conformations and the revealment of the typical fragments of these molecular nuclei. In particular, the ion mobility peak width indicates isomeric diversity and collision cross section (CCS) determination and provides structural information. The IMS analysis of the identified refractory precursor shows the evolution of its compounds at different processing stages and indicates that some families and structural conformations of N₁ species are more resistant to hydrotreatment. Isomers presenting low CCS values in negative mode are more resistant to HDN processes. The combination of TWIMS–TOF MS and ultra-high-resolution mass spectrometry opens exciting and promising prospects for structural determination of complex mixtures, in particular, problematic compounds in petroleum refining processes.

PH conditioning is a crucial step in primary recovery - A case study for a recombinant Fab from E. coli

Primary recovery of recombinant proteins from E. coli often describes a major challenge in downstream processing. After product release, the target protein usually accounts for only a small amount of total protein and has to be separated from a complex mixture of host cell proteins (HCPs) and non-proteinogenic impurities, such as DNA and lipids. Non-optimized procedures as well as unfavorable conditions at the extraction step and conditioning cause significant product loss already prior capture. In this study, we investigated pH conditioning during primary recovery for a subsequent cation exchange chromatography (CEX)-based capture of a recombinant Fab produced in E. coli. We showed that pH ≤ 5.0, which is necessary for CEX, led to high product loss due to protein precipitation during cell disruption and pH conditioning. Thus, we developed a procedure that resulted in a 25% increased Fab recovery prior capture based on simple re-arrangement of process steps and the use of a low-cost stabilizing agent. Summarizing, we show the huge potential for simple and cheap improvement of overall downstream process recovery by optimization of pH conditioning during primary product recovery.

A Heuristic Approach to Overcome Architectural Barriers Using a Robotic Wheelchair.

The Mobility Enhancement roBotic (MEBot) wheelchair was developed to improve the safety and accessibility of wheelchair users when facing architectural barriers. MEBot uses pneumatic actuators attached to its frame and six wheels to provide curb ascending/descending for heights up to 20.3 cm. To improve MEBot's application, this study used a heuristic approach with power wheelchair users to evaluate and improve the MEBot application at different curb heights. Wheelchair users were trained on MEBot's features to operate its curb ascending/descending application. Three trials were carried out with wheelchair users ascending and descending three curbs of different height. Quantitative variables were analyzed to improve the sequential steps to ascend/descend curbs. Additionally, the application's effectiveness and efficiency were measured by the number of completed tasks, change in seat angle, and task completion time. Results showed that participants completed each trial and applied alternative strategies to traverse different curb heights. Furthermore, results suggested the combination and/or re-arrangement of steps to reduce task completion time. MEBot demonstrated its effectiveness to ascend/descend different curb heights with a heterogeneous participant sample. Future work will incorporate participant's most efficient strategies to improve the ascending/ascending process and the efficiency of the MEBot application.

Перераспределение атомных ступеней на поверхности кремния (001) при сублимации в условиях нагрева постоянным электрическим током

Перераспределение атомных ступеней на поверхности кремния (001) при сублимации в условиях нагрева постоянным электрическим током

Effects of Ga-induced reconstructed surfaces and atomic steps on the morphology of GaSb islands on Si(1 0 0)

The effects of the Ga-induced reconstructed surface and atomic step type on the shape and morphology of GaSb islands on a Si(100) surface were studied using ultrahigh-vacuum scanning tunneling microscopy and atomic force microscopy. Though both anisotropic elongated islands and isotropic islands were formed on clean Si and Ga/Si(100)-2×3 substrates, isotropic islands were dominantly formed on Ga/Si(100)-2×2 substrates at 300°C. The density and size of GaSb islands on 2×2-Ga at 300°C were estimated to be 4.9×1010cm−2 and 29.1nm, respectively. The difference in the GaSb island shapes could be caused by the terrace and step of the substrate surface being changed by step rearrangement due to the deposition of Ga atoms at high temperatures. Above 350°C, the density and size of islands decreased to 2.7×109cm−2 and increased to 62.0nm, respectively. In the initial growth stage, scanning tunneling microscopy results revealed that a Sb/Si(100)-2×1 reconstructed surface was formed above 350°C. The large islands were assumed to aggregate from the surface diffusion of each atom because the Sb-terminated Si surface is inactive against Ga and Sb atoms. The type of the reconstructed surface is also suggested to affect the density and size of the islands.

Rearrangement of Aryl Geranyl Ethers

This article describes the thermal rearrangement reactions of aryl geranyl ethers. These reactions depend on the structure of the aryl moiety of the substrate and the reaction conditions used. The naphthyl ethers underwent a [1,3]-alkyl shift, followed by acid-catalyzed intramolecular cyclization. The microwave-assisted rearrangement of isoquinolinyl ether showed a pattern of an abnormal Claisen rearrangement. The multi step rearrangement of the quinolyl ether afforded a spiro compound. These new reactions were used to synthesize novel heterocyclic compounds.

MBE fabrication of self-assembled Si and metal nanostructures on Si surfaces

Two types of fairly regular distributions of Si nanostructures, of interest as templates to grow spatially controlled ensembles of metal (Co, Fe, Ag, etc.) nanostructures, are presented in this paper. Both of them are achieved by self-assembling processes during Si homoepitaxy. One corresponds to films grown by molecular beam epitaxy (MBE) on Si(0 0 1)-2 × 1 surfaces with low (<1°) miscut angles. In this case, arrays of 3D Si-islands displaying well defined pyramid-like shapes can be obtained, as evidenced by Scanning Force Microscopy (SFM) and Scanning Transmission Electron Microscopy (STEM). Such arrays exhibit strong similarities with those reported for Ge and SiGe islands on Si(0 0 1), and may thus serve as a simpler route to produce ordered distributions of metallic nanodots. On the other hand, on Si(1 1 1)-7 × 7 vicinal substrates misoriented 4° toward the [ 1 1 2 ¯ ] direction, step rearrangement during homoepitaxy permits to produce nanopatterned surfaces, the building-blocks of which are triangular (1 1 1) platforms, with lateral dimensions of hundreds of nanometers, bound by step bunches about 30 nm high. Furthermore, different Ag deposition experiments support this spontaneous patterning on Si(1 1 1) as a promising approach to achieve regular distributions of metallic nanocrystals with an overall homogeneity in sizes, shapes and spacing.

Behavior of Ga atoms on Si(001) surface at high temperature

The growth processes and structures of Ga layers formed on a Si(001) surface have been studied by scanning tunneling microscopy and low-energy electron-diffraction analysis. Si(001) wafers cut at 0.5° toward the [110] direction and showing a double-domain surface structure were used as substrates. Ga atoms from a Knudsen cell were deposited on substrates maintained at 600°C. In a Ga coverage range between 0.15 and 0.30 monolayer (ML), a Si(001)2×3–Ga structure composed of Ga ad-dimers rows was formed. In this coverage range, the ratio of the surface area of the TA terrace to that of the TB terrace (terraces where Si dimer rows run parallel and perpendicular to the step, respectively) was changed by step rearrangement, and biatomic steps were formed partially. Such step rearrangement can be explained by the substitution of Si atoms by Ga atoms at kinks. On the TB terrace, Ga ad-dimer rows along the SA step filled the terrace, while those along the SB step (an SA step where Si dimer rows on the upper terrace run parallel and perpendicular to the SB step) terminated partly. At a Ga coverage of about 0.48 ML, a Si(001)2×2–Ga single-domain structure occupied almost the entire surface (accounts for 97% of the whole surface area). On the terraces on the surface, Ga ad-dimer rows run parallel to step edges. Bright irregular protrusions were observed on biatomic step edges, while small hazy protrusions attributed to adatoms were observed on the ledge and edge of the step.

Identification of a new cluster of T-cell receptor delta recombining elements.

Within the human T-cell receptor delta (TCRD) gene we have identified a new cluster of seven delta recombining elements (deltaRec2.1-2.7), located 2.6-5.2 kilobases downstream of the Vdelta2 gene segment. The deltaRec2 elements are isolated recombining signal sequences (RSS), which were shown to rearrange with the Ddelta3 and Jdelta1 segments of the TCRD gene as well as with the psiJalpha of the TCRA gene. Rearrangements involving the deltaRec2 elements were found in all peripheral blood (PB) samples from 10 healthy individuals, although their frequency was about 100-fold lower than that of classical deltaRec rearrangements. The total frequency of deltaRec2 rearrangements was lower in PB T lymphocytes, as compared with thymocytes, suggesting that they are deleted during T-cell development. The decrease of the frequency of the deltaRec2-Ddelta3 rearrangements was most prominent: 11 times lower in PB T lymphocytes than in thymocytes. Since the deltaRec2-Jdelta1 rearrangements contained the Ddelta3 segment in the junctional region, we assume that they are derived from the deltaRec2-Ddelta3 rearrangements. In contrast, the majority of deltaRec2-psiJalpha rearrangements did not contain the Ddelta3 segment, indicating that they are single step rearrangements. The deltaRec2-Jdelta1 and deltaRec2-psiJalpha rearrangements seem to be T-lineage specific, but the deltaRec2-Ddelta3 rearrangements were also found at very low frequencies in B lymphocytes and natural killer cells. Our results suggest that deltaRec2 rearrangements are transient steps in the recombinatorial process of the TCRAD locus and are probably deleted by subsequent Valpha-Jalpha rearrangements. We hypothesize, that in a similar manner to the classical deltaRec rearrangements, the deltaRec2 rearrangements might also contribute to T-cell differentiation towards the TCR-alphabeta lineage.

1,2 Anionotropic rearrangement of lithium-(1-alkynyl) triorganoborates: semi-empirical analysis of the transition state

The iodine induced rearrangement of lithium alkynylborates yields substituted acetylenes in high yield. Facile control of stereochemistry in these reactions gives them considerable synthetic utility. The product-determining step is a 1,2 migration of an alkyl group from boron to an adjacent carbon. The transition states for both the two step rearrangement and the concerted bimolecular reactions were compared. Free energy differences and partial charges of reactants, products, and transition structures were calculated semi-empirically using the Conductor-like Screening Model for Real Solvents (COSMO) at the AM1 level. These were compared with gas phase results obtained from the same method. We conclude that the concerted iodine induced 1,2 anionotropic migration is energetically more favorable than the analogous two step process by ca. 95 kcal/mol.

Strained islands as step bunches: shape and growth kinetics

We describe the growth of strained heteroepitaxial islands by the motion of atomic steps forming the island surface. The adatom attachment to a step from the down terrace and the detachment to the up terrace provide the mass transport mechanism to the island top. As the island increases in size, the bulk stress concentration at the island edges and the stress relaxation at the island top lead to steeper island sides and a flatter top. This effect is treated as a primary source for the shape transformation from “pyramids” to “domes”, with subsequent faceting by a slight rearrangement of steps.

Step rearrangement on Si(001) surface during diborane exposure

We observed step rearrangement on Si(001) surface during B adsorption by using scanning tunneling microscopy. The coverage of B atoms was varied by exposing the surface to diborane during observation. Our results showed that B atoms adsorbed on Si(001) are responsible for the step rearrangement. Variation of the terrace size was analyzed as a function of diborane dose. Comparing our results with previous reports, we ascribed the dominant factor in terrace narrowing during B adsorption to the reduction of the energies to create S A steps.

Kinetics and Thermodynamics of Surface Steps on Semiconductors

Controls of atomic step arrangement on Si(1 11) surfaces that have been developed in our laboratory are reviewed. The basis of step bunching on vicinal surfaces is first described using the free energies of uniform and hill-and-valley surfaces. Then experimental results of step rearrangement occurring on Si(111) surfaces during the phase transition between ‘1×1’ to 7×7-reconstruction are be discussed on this basis. The surfaces misoriented toward the direction consist of wide terraces and stepped regions. The stepped regions are transformed to (331) facets when the misorientation angle is large. The surfaces misoriented toward the direction are covered with one-layer-high and three-layer-high steps. The misorientation-direc-tion dependence of the step arrangement is interpreted by considering free energies of terrace surfaces and steps and by considering step-step interaction energies. Step motions associated with adatom evaporation at high temperatures can be controlled by using etched patterns and the step arrangement on the patterned surfaces therefore can be artificially positioned. This technique can be used to form ultralarge step-free terraces, which is useful to study step dynamics. Step-flow homoepitaxial growth can also be utilized to control step arrangement. On Si(1 11) surfaces, out-of-phase boundaries of the 7×7 reconstructed domains exist and influence the evolution of step arrangement during growth. In particular cases, ordered networks of step and out-of-phase boundaries patterns are self-organized. These techniques for step arrangement control can be applied to the standard Si processes because similar results are obtained when furnace processing are used. Finally, the impact of the step arrangement controls is discussed. Step observation techniques are summarized in the Appendix.

In-situ study of gold-induced surface structures and step rearrangements on the Si(001) surface by high-temperature STM

The formation of Au-induced surface structures and step arrangements on the Si(001) surface at temperatures between 500 and 700°C were observed in situ by UHV high-temperature STM. At 500–600°C, various kinds of stripe structures with two-fold periodicity along the stripe ([110] direction) were formed after about 1 ML deposition, and their widths depended on the substrate temperature. At 700°C, the stripes were well ordered and a c(18 × 2) structure was formed. Stripes were elongated along the dimer rows of the original substrate surface, independent of the substrate temperature. During the formation of the stripe structure, an array of single-height steps was rearranged to form straight 2 n-height steps parallel to the stripes, and a single-domain structure was formed at high temperatures.

Step arrangement control of vicinal Si(001) by Ag adsorption

Upon adsorption of Ag on 4° vicinal Si(001) the existing double steps form bunches with multiple step heights separated by flat (001) terraces. The step rearrangement is completely reversible and can be controlled by the adsorption temperature. Below 550°C an extremely regular array of 4-fold steps results. At higher temperatures the formation of a mixture of (115)- and (117)-facets, composed of up to 25 double steps has been observed. Using this method a regular series of flat and straight (001) terraces with an temperature controlled width of up to 100 nm could be generated.

REM Studies of Surface Dynamics on Si Surfaces

Recent developments in techniques of real space observations of surfaces are notable. In them reflection electron microscopy (REM) is a unique technique where in-situ real time observations of wide areas of surfaces are possible. In the present paper recent studies of surface dynamic processes on Si surfaces are reviewed. Observed dynamic processes are adsorption induced successive phase transitions, adsorbate induced facet formations and step rearrangements induced by a reversal of specimen heating current direction(so called current effect) and by a reversal of the sign of the surface strain(strain effects).Figure 1 reproduces a series of REM images and RHEED patterns taken during successive phase transition induced by Au deposition on a clean Si(lll) surface at 780°C[l]. (a) shows a REM image taken before Au deposition. Line images with zigzag in shape are atomic steps on the surface. The surface steps up to the right as indicated by a step mark. The corresponding RHEED pattern in (b) shows that the surface has the 7×7 structure.

Step arrangement design and nanostructure self-organization on Si surfaces

A novel technique for wafer-scale rearrangement of atomic steps due to misorientation on the Si(111) surfaces is proposed. The process controls step motion at high temperatures by using patterns formed on the surfaces in advance. With high-temperature annealing, steps originally randomly distributed on the surface are rearranged along the pattern and remain ordered on the surface after the initial pattern has disappeared. During this process, a nanostructure consisting of step-bunched and debunched areas is self-organized and forms a micro-step-network. Another application of this process is the formation of ultralarge-scale step-free surfaces. By controlling step behavior on patterned surfaces, a step spacing as large as 10 μm can be obtained. This paper also compares heating in an ultrahigh vacuum with furnace annealing in hydrogen atmosphere and shows that both techniques can be used for designing step arrangements.

REFLECTION ELECTRON MICROSCOPY OBSERVATION OF THE BEHAVIOR OF MONOATOMIC STEPS ON THE SILICON SURFACES

Ultrahigh vacuum reflection electron microscopy (UHV REM) has been applied to imaging of monoatomic steps on silicon surfaces (111) and (100). The reversible rearrangements of the monoatomic step trains to the step bands and step antibands were found from direct observation of monoatomic step motion during sublimation. The influence of the direction of the electric current heating the specimen was observed. The recent data on atomic mechanisms of step bunching and debunching were reviewed. The monoatomic step behavior on the (100) silicon surface as well as (7×7)-(1×1) phase transition on the (111) surface was described. Direct observations of homoepitaxial processes were carried out. Transition from the step flow growth mode to the nucleation of two-dimensional islands was studied depending on the deposition rate and the substrate temperature. The initial stages of the heteroepitaxial process of germanium, gold and calcium fluorite on the silicon (111) surface were investigated. Finally, the mechanism of step rearrangements during the formation of superstructure domains leading to monoatomic step clustering was discussed.

Crystallographic evidence for the stereospecific synthesis of 4-amino-(D 3)-trishomocubanes: crystal structure of 3-methyl-(D 3)-trishomocubane-4-amine hydrochloride hydrate

Abstract A series of C-3 substituted 4-amino-(D 3)-trishomocubanes with promising antiparkinsonian and antiviral activities has been recently synthesized via a modified Ritter reaction. The crystal structure of one of these compounds, the 3-methyl-(D 3)-trishomocubane-4-amine hydrochloride hydrate (C12H18N+Cl− · H2O) has been determined by X-ray diffraction. The symmetry is monoclinic, space group P21/c with a = 6.500(1) Å, b = 7.038(2) Å, c = 25.686(7) Å, β = 91.51(1)°, Z = 4. The 3S4S/3R4R stereochemistry is in favor of a one step rearrangement mechanism of the SN2 type for the synthesis of (D 3)-trishomocubanes via the Ritter reaction.

Kinetics of atomic-scale fluctuations of steps on Si (001) measured with variable-temperature STM

Using a variable-temperature scanning tunneling microscope (STM) we measure the time evolution of the atomic-scale morphology of steps on Si(001) in equilibrium at temperatures up to 350°C. At temperatures above 230°C, local changes in the atomic arrangement of the steps are observed between successive STM images. The relative rate at which events occur depends on the local configuration of the step. Rearrangement events are more likely to occur at kink sites than at straight sections of the step. The relative rates at which the rearrangement events occur are determined by the configuration energy of the steps as expected from detailed balance. By measuring the event rate as a function of temperature we determine the effective activation energy barrier for step rearrangement, 1.3 ± 0.3 eV.