Lowest Energy Path Research Articles

Theoretical investigations on the growth mode of GaN thin films on an AlN(0001) substrate

The growth modes of GaN thin films on an AlN(0001) substrate are systematically investigated using our macroscopic theory with the aid of empirical interatomic potential and ab initio calculations. Using empirical interatomic potential calculations, we demonstrate that a GaN/AlN(0001) system with misfit dislocation (MD) is stabilized compared with a coherently grown system when the GaN film thickness exceeds six monolayers. According to the calculated results including the surface energy of GaN, the macroscopic free energy calculations for the growth mode imply that the growth of GaN on AlN(0001) proceeds along the lower-energy path from two-dimensional coherent (2D-coherent) to 2D-MD under Ga-rich conditions but from 2D-coherent to three-dimensional coherent with truncated hexagonal pyramid islands consisting of {} facets under N-rich conditions owing to surface energy anisotropy, which depends strongly on the growth conditions. These results suggest that surface energy anisotropy is crucial for the growth of GaN on an AlN(0001) substrate.

Low-energy electron properties: Electron inelastic mean free path, energy loss function and the dielectric function. Recent measurements, applications, and the plasmon-coupling theory

We review new self-consistent models of inelastic electron scattering in condensed matter systems for accurate calculations of low-energy electron inelastic mean free paths (IMFPs) for XAFS and low energy diffraction. The accuracy of theoretical determinations of the electron IMFP at low energies is one of the key limiting factors in current XAFS modeling and Monte Carlo transport. Recent breakthroughs in XAFS analysis show that there exist significant discrepancies between theoretical and experimental IMFP values, and that this can significantly impact upon extraction of other key structural parameters from both XANES and XAFS. Resolution of these discrepancies is required to validate experimental studies of material structures, and is particularly relevant to the characterization of small molecules and organometallic systems for which tabulated electron scattering data is often sparse or highly uncertain.Novel models implement plasmon coupling mechanisms for the first time, in addition to causally-constrained lifetime broadening and high-precision density functional theory, and enables dramatic improvements in the agreement with recent high profile IMFP measurements. We discuss a theoretical approach for IMFP determination linking the optical dielectric function and energy loss spectrum of a material with its electron scattering properties and characteristic plasmon excitations. We review models inclusive of plasmon coupling, allowing us to move beyond the longstanding statistical approximation and explicitly demonstrate the effects of band structure on the detailed behaviour of bulk electron excitations in a solid or small molecule. This interrogates the optical response of the material, which we obtain using density functional theory. We find that new developments dramatically improve agreement with experimental electron scattering results in the low-energy region (30 eV → 200 eV) where plasmon excitations are dominant. Corresponding improvements are therefore made in Low Energy Electron Transport, LEEM, theoretical XAFS spectra and detector modelling.

Low-energy paths for octahedral tilting in inorganic halide perovskites

Instabilities relating to cooperative octahedral tilting is common in materials with perovskite structures, and in particular in the sub class of halide perovskites. In this work, the energetics of octahedral tilting in the inorganic metal halide perovskites CsPbI$_3$ and CsSnI$_3$ are investigated using first-principles density functional theory calculations. Several low energy paths between symmetry equivalent variants of the stable orthorhombic (\textit{Pnma}) perovskite variant are identified and investigated. The results are in favor of the presence of dynamic disorder in the octahedral tilting phase transitions of inorganic halide perovskites. In particular, one specific type of path, corresponding to an out-of-phase "tilt switch", is found to have significantly lower energy barrier than the others, which indicates the existence of a temperature range where the dynamic fluctuations of the octahedra follow only this type of path. This could produce a time averaged structure corresponding to the intermediate tetragonal (\textit{P4/mbm}) structure observed in experiments. Deficiencies of the commonly employed simple one-dimensional "double well" potentials in describing the dynamics of the octahedra are pointed out and discussed.

Method of indoor navigation and collaborative semi-automatic Wi-Fi radiomap construction

Introduction:An important and complicated problem related to the multilateration of Wi-Fi or Bluetooth Low Energy signals as well as Wi-Fi fingerprinting is the procedure of infrastructure adjustment which includes Wi-Fi radio map construction and Wi-Fi or Bluetooth Low Energy radio signal path loss model calibration.Purpose:Developing a method for navigation and Wi-Fi radio map construction, which would provide user’s indoor navigation, Bluetooth Low Energy path loss model calibration and Wi-Fi radio map collaborative semi-automatic construction.Results:The paper presents a collaborative semi-automatic Wi-Fi radio map construction method based on the combination of Bluetooth Low Energy multilateration, Wi-Fi fingerprinting, Wi-Fi radio map collaborative semiautomatic construction procedure and semi-automatic Bluetooth Low Energy path loss model calibration. For the semi-automatic calibration procedure of the Bluetooth Low Energy signal propagation model and for the method of collaborative semi-automatic construction of Wi-Fi radio map and indoor navigation, a calibration algorithm and an algorithm of collaborative semi-automatic construction of Wi-Fi radio map and indoor navigation were proposed, respectively. A mobile application has been developed which implements the proposed algorithms in order to test them and analyze the results.Practical relevance:The proposed method allows you to avoid time-consuming procedures of constructing a map of Wi-Fi radio signals and semi-automatic calibration of Bluetooth Low Energy signal propagation in the offline phase.

Is the Inversion of Phosphorus Trihalides (PF3, PCl3, PBr3, and PI3) a Diradical Process?

This work explores possible reaction paths for the inversion of a series of trigonal pyramidal phosphorus trihalides, PF3, PCl3, PBr3, and PI3, and it especially addresses the question of whether and when the bonding of the lowest-energy species along the inversion paths should be described as a hyper-open-shell diradical. The various paths for inversion are calculated using a single-reference method within the framework of Kohn-Sham density functional theory and also with multireference wave function methods. Our calculated results using both kinds of methods show that, for all the halogens studied (F, Cl, Br, and I), the lowest-energy singlet path for the inversion occurs by the formation of a C2 v transition structure rather than a D3 h transition structure. This geometrical preference agrees with what has been inferred previously based on closed-shell singlet calculations. But in the present study, we examined not only closed-shell singlet transition states but also open-shell singlet states and triplet states for calculating stationary points and inversion paths, and for some of the phosphorus trihalides, we found that paths involving open-shell configurations are lower in energy than those restricted to closed-shell configurations. We analyzed the changes along the paths in terms of hybridization and orientation of the frontier orbitals and in terms of locally avoided crossings, and the extent of the diradical character was quantified by calculating the effective number of unpaired electrons. Even for the singlet inversion path that goes via a D3 h structure, the barrier for PF3, PCl3, and PBr3 is higher for a closed-shell singlet spin state than for the open-shell singlet configuration. Furthermore, the energy of the triplet D3 h structure is below even that of the open-shell D3 h singlet for PCl3, PBr3, and PI3. This necessitates rethinking the role of open-shell states in nominally closed-shell processes.

Collective capacitive and memristive responses in random nanowire networks: Emergence of critical connectivity pathways

Random nanowire networks (NWNs) are promising synthetic architectures for non-volatile memory devices and hardware-based neuromorphic applications due to their history-dependent responses, recurrent connectivity, and neurosynaptic-like behaviors. Such brain-like functions occur due to emergent resistive switching phenomena taking place in the interwire junctions which are viewed as memristive systems; they operate as smart analogue switches whose resistance depends on the history of the input voltage/current. We successfully demonstrated that NWNs made with a particular class of memristive junctions can exhibit a highly-selective conduction mechanism which uses the lowest-energy connectivity path in the network identified as the “winner-takes-all” state. However, these complex networks do not always behave in the same fashion; in the limit of sufficiently low input currents (preceding this selective conduction regime), the system behaves as a leakage capacitive network and its electrical activation is driven by cascades of breakdown-based activation events involving binary capacitive transitions. Understanding these two regimes is crucial to establish the potential of these materials for neuromorphics, and for this, we present two computational modelling schemes designed to describe the capacitive and memristive responses of NWNs interrogated adiabatically by voltage/current sources. Our results are corroborated by experimental evidence that reveal the fine electrical properties of NWN materials in their respective formation (capacitive) and conducting (memristive) stages.

Multipath VTST rate constants for D + methyl formate reactions: Importance of torsional anharmonicity and conformational flexibility for combustion chemistry

The thermal rate constants for the methyl formate hydrogen abstraction reaction by deuterium was investigated by the multipath canonical variational transition state theory with large curvature tunneling (MP-CVT/LCT). The multistructural torsional anharmonicity factor decreases the thermal rate constants for deuterated reaction R1a and increases considerably for R2a. The path-averaged generalized transmission coefficient is dominated by the characteristics of the lowest-energy paths for both reactions. The MP-CVT/LCT rate constants are in excellent agreement with experimental data (T = 1079–1270 K).

Formation mechanism of multivacancies on H-passivated and Si-reconstructed surfaces of 6H–SiC (0001): a DFT calculation

The clarification of formation mechanism of surface vacancies (mono-, di-, and multivacancy) is of great help to the defect and electronic engineering of functional crystalline solids. Herein we use the density functional theory (DFT) calculations to elucidate the formation mechanism and evolution paths of vacancies within the Si–C atomic bilayers on H-passivated (H-P) and () R 30° Si-reconstructed (S-R) 6H–SiC (0001) surfaces. The calculation results of formation energies (Efs) reveal that Si monovacancies (VSi) prefer to form within the first outer Si–C bilayer while two isolated VSi and C monovacancies (VC) are more likely to aggregate into a VSiVC divacancy on both selected surfaces. In particular, Efs of multivacancies (Vns) with different missing Si/C atoms (n = 3 ∼ 10) and spatial configurations were systematically calculated and compared, from which the lowest energy paths (LEPs) of Vns for two kinds of surfaces are clarified. For n ≤ 6, Vns tend to expand within the two-dimensional (2D) first Si–C bilayer but they will expend vertically into the underneath Si–C bilayers when n > 6. The fitted curves of resultant LEPs disclose that the 2D evolution of the multivacancy is the main evolution form with high symmetric Vns being dominant on the 6H–SiC (0001) surfaces.

Emergence of winner-takes-all connectivity paths in random nanowire networks

Nanowire networks are promising memristive architectures for neuromorphic applications due to their connectivity and neurosynaptic-like behaviours. Here, we demonstrate a self-similar scaling of the conductance of networks and the junctions that comprise them. We show this behavior is an emergent property of any junction-dominated network. A particular class of junctions naturally leads to the emergence of conductance plateaus and a “winner-takes-all” conducting path that spans the entire network, and which we show corresponds to the lowest-energy connectivity path. The memory stored in the conductance state is distributed across the network but encoded in specific connectivity pathways, similar to that found in biological systems. These results are expected to have important implications for development of neuromorphic devices based on reservoir computing.

Generating conformational transition paths with low potential-energy barriers for proteins.

The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.

On the Mechanism of Trimethylphosphine-Mediated Reductive Dimerization of Ketones.

High-level single-reference calculations reveal that trimethylphosphine-mediated reductive dimerization of properly substituted (e.g., CF3) ketones proceeds via initial formation of an oxaphosphirane intermediate, with the oxygen atom occupying an equatorial position at phosphorus. In the "oxirane route", this oxaphosphirane intermediate loses a trimethylphosphine oxide unit, thus behaving as a carbene transfer agent toward a second carbonyl molecule and giving rise to a carbonyl ylide that cyclizates to the corresponding oxirane. This in turn transfers the carbene unit to a second phosphine molecule, with loss of acetone, affording a phosphorane. The latter undergoes typical Wittig reaction to the final homocoupling product through the oxaphosphetane intermediate. The alternative direct conversion of oxaphosphirane into phosphorane constitutes the lowest energy path as it skips the highest barrier oxirane → phosphorane conversion. The oxirane route is favored by the use of polar solvents and electron deficient carbonyl components. The lowest barrier most exergonic process from oxaphosphirane is the pericyclic cycloaddition of the acetone C═O bond along the endocyclic P-C bond, furnishing the stable 1,3,2-dioxaphospholane product.

Synergy between Experimental and Theoretical Results of Some Reactions of Annelated 1,3-Azaphospholes.

Computational calculations have been used successfully to explain the reactivity of the >C=P- functionality in pyrido-annelated 1,3-azaphospholes. Theoretical investigation at the Density Functional Theory (DFT) level shows that the lone pair of the bridgehead nitrogen atoms is involved in extended conjugation, due to which electron density increases considerably in the five-membered azaphosphole ring. The electron density in the azaphosphole is further enhanced by the presence of an ester group at the 3-position making the >C=P- functionality electron-rich. Thus, 1,3-azaphospholo[5,1-a]pyridine, i.e., 2-phosphaindolizine having ester group at the 3-position only does not undergo Diels-Alder (DA) reaction with an electron rich diene, such as 2,3-dimethyl-1,3-butadiene (DMB). However, an ester group at 1-position acts as electron-sink, due to which transfer of the electron density to the >C=P- moiety is checked and DA reaction occurs across the >C=P- functionality. The coordination of the Lewis acid to the carbonyl group at the 3-position raises the activation barrier, while it is lowered remarkably when it is coordinated to the P atom. Furthermore, the attack of 1,3-butadiene on the Si face of the P-coordinated (o-menthoxy)aluminum dichloride complex is a lower activation energy path. Fukui functions could be used to explain relative reactivities of indolizine and 2-phosphaindolizine towards electrophilic substitution reactions.

Low-energy electron inelastic mean free paths for liquid water

We improve the Mermin–Penn algorithm (MPA) for determining the energy loss function (ELF) within the dielectric formalism. The present algorithm is applicable not only to real metals, but also to materials that have an energy gap in the excitation spectrum. Applying the improved MPA to liquid water, we show that the present algorithm is able to address the ELF overestimation at the energy gap, and the calculated results are in good agreement with experimental data.

Experimental and Theoretical Investigation of the Reaction of Amines with Methyl Propiolate

AbstractMichael addition of secondary amines, R1R2NH to methyl propiolate occurs with complete stereoselectivity to give trans‐methyl β‐aminoacrylate in 71–91% yields. The reaction with benzylamine, however, leads to the formation of a mixture of the corresponding trans‐ and cis‐isomers in 26:74% respectively as indicated by 1H NMR. A theoretical investigation of the model reactions at the DFT level reveals that the reaction occurs in two steps, the first step leading to the formation of a zwitterionic intermediate being rate determining. Furthermore, formation of an initial reactant‐complex of methyl propiolate with a molecule of amine followed by the nucleophilic attack of the amine is a lower energy path than the one followed by direct reaction between the two reactants. The low activation enthalpies, ▵H# (ca. 12–20 kcal mol−1) in the gas phase are further lowered (ca. 7–15 kcal mol−1) in methylene chloride. The initially formed zwitterionic intermediate undergoes 1,3‐prototropic shift through a bridge established by a molecule of amine between the donor (+NH) and the acceptor (−C2) sites. In the reaction with benzylamine, theoretical calculations indicate the cis‐isomer to be thermodynamically more stable than the trans‐isomer by 0.5 kcal mol−1 which corresponds to 70% of the former. Furthermore, existence of the “enamine‐imine‐enamine” phenomenon is established theoretically, which facilitates trans‐cis isomerization.

Context-dependent responses to turbulence for an anguilliform swimming fish, Pacific lamprey, during passage of an experimental vertical-slot weir

Fish passage systems (fishways) have become the most common mitigation tool for improving the connectivity of migratory fish populations in ecosystems with barriers to movement. Because fishways often have high-velocity and high-turbulence environments, fish should seek low-energy movement paths during passage. We tested this hypothesis by analyzing the swimming paths of 90 adult Pacific lamprey (Entosphenus tridentatus) in response to hydraulic conditions when passing a vertical-slot weir in an experimental fishway. Varying hydraulic conditions were achieved by manipulating three variables: water velocity (1.2, 1.8, 2.4m/s), vertical-slot length (0.33m, 0.66m, 1.00m), and presence or absence of a turbulence-inducing structure. Turbulence parameters, such as turbulent kinetic energy (TKE), were quantified using an Acoustic Doppler Velocimeter (ADV). Pacific lamprey exhibited context-dependent behaviors in response to turbulence whereby lamprey were more likely to move towards areas of lower turbulence along their swimming paths, but only as the surrounding turbulence within the vertical-slot increased. In contrast, when the surrounding turbulence within the vertical-slot was low, Pacific lamprey became more likely to move towards areas of higher turbulence. The ‘turbulence-avoidance’ behaviors likely allowed passage of the hydraulic obstacle by reducing energy expenditure or physiological stress, while the ‘turbulence-attraction’ behaviors may have resulted from lamprey using turbulence as a mechanism for upstream orientation. Overall, our results provide new insight into how fish may use turbulence as an important sensory modality for perceiving the aquatic environment.

Spin-forbidden CO binding to iron–sulfur cluster-free hydrogenase: A density functional study

Spin-forbidden CO binding to the iron–sulfur cluster-free hydrogenase (Hmd) is studied by the DFT calculation. The result shows that the surface of the triplet causes a PHmd–CO minimum and that 3,5MECP is the lowest energy path to PHmd–CO. It is found that this CO binding involves a low barrier of 0.931 kcal/mol because of the need to change from a bound triplet state to the Hmd quintet ground state.

High level potential energy surface and mechanism of Al(CH3)2OCH3-promoted lactone polymerization: initiation and propagation.

Despite increasing experimental interest in aliphatic polyesters as biodegradable and bioassimilable polymers a theoretical description of ring-opening polymerization (ROP) is not yet fully established. We report a detailed theoretical account of the mechanism of the ROP of three lactones (glycolide, 1,5-dioxepan-2-one and ε-caprolactone) using dimethylaluminium methoxide (Al(CH3)2OCH3) as the initiator. Both the initiation and propagation steps of the ROP are investigated using a composite method consisting of explicitly correlated Moller-Plesset (DF-MP2-F12) and explicitly correlated local coupled cluster methods (DF-LCCSD(T)-F12), for an accurate and definitive determination of the transition state and intermediate electronic energies. A hitherto unreported transition state is found in the initiation reaction, which is the highest energy stationary state for all three lactones. Computed reaction free energies suggest a thermodynamically favourable polymerization of the ROP for all three lactones and a "living mechanism" in the cases of glycolide and 1,5-dioxepan-2-one. The intrinsic reaction coordinate analysis for the ROP of glycolide connects the different stationary states and establishes mechanistic differences between the initiation and propagation reactions. The analysis of structural and electronic parameters along the reaction coordinate reveals a decoupling of structural and electronic changes in the initiation reaction, which allows it to proceed over a lower energy path than in the propagation reaction, where no decoupling is found. Finally, the ab initio electronic energies are compared to popular DFT functionals, where it is found that PBE0 performs best among all tested functionals.

Theoretical insights into the sites and mechanisms for base catalyzed esterification and aldol condensation reactions over Cu.

Condensation and esterification are important catalytic routes in the conversion of polyols and oxygenates derived from biomass to fuels and chemical intermediates. Previous experimental studies show that alkanal, alkanol and hydrogen mixtures equilibrate over Cu/SiO2 and form surface alkoxides and alkanals that subsequently promote condensation and esterification reactions. First-principle density functional theory (DFT) calculations were carried out herein to elucidate the elementary paths and the corresponding energetics for the interconversion of propanal + H2 to propanol and the subsequent C-C and C-O bond formation paths involved in aldol condensation and esterification of these mixtures over model Cu surfaces. Propanal and hydrogen readily equilibrate with propanol via C-H and O-H addition steps to form surface propoxide intermediates and equilibrated propanal/propanol mixtures. Surface propoxides readily form via low energy paths involving a hydrogen addition to the electrophilic carbon center of the carbonyl of propanal or via a proton transfer from an adsorbed propanol to a vicinal propanal. The resulting propoxide withdraws electron density from the surface and behaves as a base catalyzing the activation of propanal and subsequent esterification and condensation reactions. These basic propoxides can readily abstract the acidic Cα-H of propanal to produce the CH3CH(-)CH2O* enolate, thus initiating aldol condensation. The enolate can subsequently react with a second adsorbed propanal to form a C-C bond and a β-alkoxide alkanal intermediate. The β-alkoxide alkanal can subsequently undergo facile hydride transfer to form the 2-formyl-3-pentanone intermediate that decarbonylates to give the 3-pentanone product. Cu is unique in that it rapidly catalyzes the decarbonylation of the C2n intermediates to form C2n-1 3-pentanone as the major product with very small yields of C2n products. This is likely due to the absence of Brønsted acid sites, present on metal oxide catalysts, that rapidly catalyze dehydration of the hemiacetal or hemiacetalate over decarbonylation. The basic surface propoxide that forms on Cu can also attack the carbonyl of a surface propanal to form propyl propionate. Theoretical results indicate that the rates for both aldol condensation and esterification are controlled by reactions between surface propoxide and propanal intermediates. In the condensation reaction, the alkoxide abstracts the weakly acidic hydrogen of the Cα-H of the adsorbed alkanal to form the surface enolate whereas in the esterification reaction the alkoxide nucleophilically attacks the carbonyl group of a vicinal bound alkanal. As both condensation and esterification involve reactions between the same two species in the rate-limiting step, they result in the same rate expression which is consistent with experimental results. The theoretical results indicate that the barriers between condensation and esterification are within 3 kJ mol-1 of one another with esterification being slightly more favored. Experimental results also report small differences in the activation barriers but suggest that condensation is slightly preferred.

LEACH–V: A Solution for Intra-Cluster Cooperative Communication in Wireless Sensor Network

Objectives: A Wireless Sensor Network (WSN) plays an important role in the future wireless communication domain because of its properties, which includes intelligence, cheaper and smaller in size. With the wireless interfaces, these can communicate with each other in case of cooperative communication in a single or multiple networks. Methods/Statistical Analysis: As multiple nodes are required for cooperative communication, the Low Energy Adaptive Clustery Hierarchy (LEACH) Protocol is used for cluster formation. Further Vector Quantization (VQ) is used for analysis of low energy path for the nodes and clusters respectively. Findings: The main issue of inter-cluster node communication is carried out in earlier work using LEACH protocol. The proposed technique illustrates the LEACH-Vector Quantization (LEACH-V) protocol for intra-cluster communication in a cooperative communication network. Application/Improvements: As per the application point of view, LEACH-V performs the lowest energy path for intra-cluster communication. LEACH provides the optimum cluster size and their Cluster Head and using VQ, the minimum distance is calculated using Euclidean distance between the multiple cluster heads which creates the shortest path results in energy efficient technique. Further, the spectral distortion of the proposed technique has been analyzed for practical implementation.

Theoretical Investigations for Strain Relaxation and Growth Mode of InAs Thin layers on GaAs(111)A

The growth mode of InAs/GaAs(111)A is systematically investigated using our macroscopic theory with the aid of empirical potential calculations that determine parameter values used in the macroscopic theory. Here, stacking-fault tetrahedron (SFT) found in InAs/GaAs(111)A and misfit dislocation (MD) formations are employed as strain relaxation mechanisms. The calculated results reveal that the MD formation occurs at the layer thickness h about 7 monolayers (MLs). Moreover, we found that the SFT forming at h about 4 MLs makes surface atoms move upward to reduce the strain energy to promote the two dimensional (2D) growth. Therefore, the SFT in addition to the MD plays an important role in strain relaxation in InAs thin layers on GaAs(111)A. The macroscopic free energy calculations for the growth mode imply that the InAs growth on the GaAs(111)A proceeds along the lower energy path from the 2D-coherent (h ≤ 4 MLs) to the 2D-MD (h ≥ 7 MLs) via the 2D-SFT (4 MLs ≤ h ≤ 7 MLs). Consequently, the 2D growth on the InAs/GaAs(111)A results from strain relaxation due to the formation of the SFT near the surface and the subsequent MD formation at the interface.