Isosurface Value Research Articles

Boiling, critical, and freezing temperatures in light of molecular descriptors: correlation and causation.

In the pursuit of tracking some physicochemical properties of fluids down to the molecular level, ab initio molecular surface analyses were performed on 169 molecules. This included electrostatic potential (EP), average local ionization energy (ALIE), and electron localization function (ELF) mapped onto an electron density isosurface value of 0.001 au. Using stepwise linear regression (SLR) analysis, it was found that besides the well-studied EP, ALIE and ELF played important roles in determining the normal boiling and freezing points and critical temperatures of fluids. Apparently, the ALIE and ELF were relevant to the attractive polarization forces and repulsive Pauli forces, respectively, between molecules. To further demonstrate and rationalize this assumption, a localized molecular orbital energy decomposition analysis (LMO-EDA) was carried out. In the LMO-EDA analysis, the complexes of the helium atom, He, and ClCl, ClBr, ClI, OCO, OCS, OCSe, and CO/OC molecules were investigated, where the helium atom faced different molecular sites in each molecule. Fortunately, the results showed that lower the ALIE value on a molecular site, the stronger (i.e., more attractive) the polarization interaction energy. The results also indicated that higher the ELF value on a molecular site, the stronger (i.e., more repulsive) the Pauli interaction. The work is aimed to present novel molecular-based rationales to physical chemists, chemical engineers, and materials scientists.

Theoretical investigation on switchable [3 + 3] cycloaddition of vinyl sulfoxonnium ylide with cyclopropenone for divergent synthesis of phenol

The mechanism is investigated for regioselective [3 + 3] cycloaddition of vinyl sulfoxonnium ylide with cyclopropenone in switchable mode. For reaction catalyzed by NHC-Cu, the coordination with vinyl sulfoxonnium ylide produces copper carbene after releasing of Cl and DMSO. The annulation is realized via bonding sequence of first C1-C6 then C3-C4 leading to 2,3,4,5-tetrasubstituted phenol as major product. The outcome turns to be another tetrasubstituted phenol conformer under metal-free condition with a bonding sequence of first C3-C6 then C1-C4. Both of the two cases are featured by vinyl sulfoxonnium ylide as C3-synthon not C2-synthon involving ring transformation. Based on comparison between two possible paths, the regioselectivity of dominant product is kinetically controlled. The positive solvation effect was suggested by decreased relative and activation energies in dioxane and TFE solution. These results are supported by Frontier MO analysis on specific TSs, ELF isosurface, DI and MBO value of vital bonding, breaking.

Solvothermal self-assembly of a novel metal-organic square grid complex using a biscarbohydrazone ligand building block: Crystal structures, Hirshfeld and void surface analyses, band gap calculations and DFT studies

Here we report the solvothermal self-assembly of a novel metal–organic square complex [Zn(HL)]4Cl2·ZnCl4·16H2O (1) using 1,5-bis(2-benzoylpyridine) carbohydrazone (H2L) ligand building block. Single-crystal X-ray diffraction (SCXRD) study confirm the structure of the complex, which is characterized by other physicochemical methods. The crystal study reveals the presence of a tetrahedral ZnCl42- counter anion also. The DFT quantum chemical calculations and analysis of the square grid cation are explored first time and are compared with the crystal structure and DFT calculations of the ligand building block H2L also. The solid-state band gap (Eg) of the ligand and the square grid complex are determined experimentally using the Kubelka-Munk model and are found to be 3.22 and 1.74 eV respectively. Hirshfeld surface (HS) analyses of both the building block and the complex were also explored to quantify the intermolecular interactions in their crystal lattices. The molecular packing of the complex and the ligand were found to be dominated by isotropic H···H contacts. However, strong H···Cl contacts are contributing the most in the crystal structure cohesion of the complex, while the C···H interactions are the dominating anisotropic forces contributing to the overall Hirshfeld surface in the ligand lattice. The theoretical void space calculations of the complex [Zn(HL)]4Cl2·ZnCl4 (1a) were then carried out. The close packing in the crystal lattice possesses small voids and cavities and an isosurface value of 0.0008 au was found suitable for crystal void calculation, in agreement with PLATON calculations. The corresponding pore volume and the surface area per unit cell were found to be 940.58 Å3 and 1656.04 Å2 respectively.

BiO 2-x Nanosheets with Surface Electron Localizations for Efficient Electrocatalytic CO 2 Reduction to Formate

BiO _2-x Nanosheets with Surface Electron Localizations for Efficient Electrocatalytic CO ₂ Reduction to Formate

Silver Ion-Induced Formation of Unprecedented Thorium Nonamer Clusters via Lacuna-Construction Strategy

Silver Ion-Induced Formation of Unprecedented Thorium Nonamer Clusters via Lacuna-Construction Strategy

A DFT-Based Descriptor to Predict the Water Vapor Corrosion Resistance of Rare-Earth Monosilicates.

Rare-earth monosilicates are used as environmental barrier coatings (EBCs) due to their excellent water vapor corrosion resistance. However, existing experimental studies on the water vapor corrosion behavior of rare-earth monosilicates are discrepant and even contradictory. Previous theoretical investigations on water vapor corrosion resistance mainly focus on a Mulliken analysis of Si-O bonds in the monosilicates. In this study, the structural and electronic properties of rare-earth monosilicates have been studied by density functional theory (DFT) calculations, and a descriptor correlated to the corrosion resistance has been developed. The maximum isosurface value of the valence band maximum (VBMFmax) can be used to predict the water vapor corrosion resistance of RE2SiO5. The results show that RE2SiO5 with a smaller VBMFmax may have better water vapor corrosion resistance.

Superatomic Signature and Reactivity of Silver Clusters with Oxygen: Double Magic Ag 17 – with Geometric and Electronic Shell Closure

Understanding the stability and reactivity of silver clusters toward oxygen provides insights to design new materials of coinage metals with atomic precision. Herein, we report a systematic study o...

Engineering Electronic Structure of Single-Atom Pd Site on Ti 0.87 O 2 Nanosheet via Charge Transfer Enables C–Br Cleavage for Room-Temperature Suzuki Coupling

The palladium (Pd)-catalyzed Suzuki reaction is widely applied in the pharmaceutical industry, where constructing highly active and low-cost Pd sites are impendent. Here, we report the fabrication ...

Electron transfer study between hydrogen molecules and graphene surface

Electron transfer studies on the interaction of graphene surface and hydrogen (H2) molecules have been carried out. The calculations were based on the Density Functional Theory (DFT) with a basis set of Generalized-Gradient-Corrected PBE method approach (Perdew-Burke-Ernzerhof). The results showed that the optimum distance (lowest potential energy) between hydrogen molecules on the surface of the graphene was 3.2 Å, and the partial density of state (PDOS) calculation showed that the hydrogen-graphene system band gap was 2.51 eV. The electron transfer shown by the isosurface value indicates that the electron transfer from the p sub orbitals from the surface of the graphene to the hydrogen molecular orbitals was +0.3603 e/Å.

On the kinematics of scalar iso-surfaces in decaying homogeneous, isotropic turbulence

ABSTRACTScalar iso-surfaces have been used to describe many interface problems in turbulence, such as flame surfaces in turbulent reacting flows and turbulent/non-turbulent interfaces. In this paper we report on direct numerical simulations of the behaviour of iso-surfaces of two differently initialised conserved scalars evolving in isotropic turbulence. The terms in the equation for the iso-surface area density, along with the area density itself, are evaluated for a wide range of iso-surface values using a novel numerical method for evaluating surface integrals. Specifically, we quantify the behaviour of the iso-surface area density production term, related to the strain-rate, and the destruction term, related to iso-surface curvature and molecular diffusion. We find that production of iso-surface area density is not affected by the initial conditions, but it does have a small dependence on the iso-surface value. The destruction term depends not only on the iso-surface value, but also on the initial conditions.

Structure and Properties of the α-Cs2Mo2−xWxO7 Solid Solution

The tungsten substitution for molybdenum in cesium dimolybdate Cs2Mo2O7 with the formation of an α-Cs2Mo2−xWxO7 solid solution is studied, and its homogeneity region at 540 °C is found to reach 0 ≤ x ≤ 0.6. It is established that the volume of the monoclinic (pseudo-orthorhombic) unit cell and the solid solution melting point monotonically increase with increasing tungsten content, whereas the phase transition temperature to the orthorhombic phase remains practically constant and is ∼390 °C. The crystals of solid solutions with several compositions are obtained, their structure is determined, and the tungsten atoms are found to be mainly located in octahedral positions of the α-Cs2Mo2O7 structure. As a result of the phase transition at 390 °C the electrical conductivity of Cs2Mo2O7 increases approximately by two orders of magnitude reaching 1.2·10−4S/cm at 460 °C. Due to a large size of Cs+ ions and a high charge of molybdenum cations it is supposed that the charge carriers are oxygen anions. The calculation of bond valence sum (BVS) maps for possible positions of oxygen atoms in the α-Cs2Mo2O7 cell shows the formation of a 3D system of oxygen conductivity channels at boundary BVS isosurface values ≥ 2.13.

The Influence of Isoconcentration Surface Selection in Quantitative Outputs from Proximity Histograms.

Isoconcentration surfaces are commonly used to delineate phases in atom probe datasets. These surfaces then provide the spatial and compositional reference for proximity histograms, the number density of particles, and the volume fraction of particles within a multiphase system. This paper discusses the influence of the isoconcentration surface selection value on these quantitative outputs, using a simple oxide dispersive strengthened alloy, Fe91Ni8Zr1, as the case system. Zirconium reacted with intrinsic oxygen impurities in a consolidated ball-milled powder to precipitate nanoscale zirconia particles. The zirconia particles were identified by varying the Zr-isoconcentration values as well as by the maximum separation data mining method. The associated outputs mentioned above are elaborated upon in reference to the variation in this Zr isosurface value. Considering the dataset as a whole, a 10.5 at.% Zr isosurface provided a compositional inflection point for Zr between the particles and matrix on the proximity histogram; however, this value was unable to delineate all of the secondary oxide particles identified using the maximum separation method. Consequently, variations in the number density and volume fraction were observed as the Zr isovalue was changed to capture these particles resulting in a loss of the compositional accuracy. This highlighted the need for particle-by-particle analysis.

Corrigendum: DFT Study on the Hydrogen Evolution Reaction for Different Facets of Co2P

The authors found a technical error in their manuscript, whereby they used the gamma k-point for structure optimization of the surface of H adsorbed for (001), (010), (101), (112), and (113) facets, as described in the Methods section. However, after publication of the paper, the authors found that the gamma k-point is good for the (010), (112), and (113) facets of Co2P, but is not appropriate for (001) and (101), which both need 2×3×1 k-point, even though the gamma k-point has been used in previous studies of surface analysis.1 With this setup of k-point, the authors have redone the DFT calculations of the (001) and (101) facets and would like to update the corresponding results. Although there are some changes of the data, the main conclusions of the paper still hold. The key changes are summarized here: 1. As shown in the updated version of Figure 1, the order of ΔGH* is now (113) L1 ≈ (101) L1 < (112) L1 < (001) L1 < (010) L4, whereas it was previously (113) L1 ≈ (001) L1< (112) L1< (101) L5< (010) L4. The (113) facet still has the best hydrogen evolution reaction (HER) activity, which remains one of the key conclusions. 2. As shown in the updated version of Figure 3, the mean absolute error and R-square of the multiple linear regression between the H−Co bond distribution and ΔGH* become 0.0777 eV and 0.818, respectively (previously, 0.0756 eV and 0.814). From the updated versions of Figures 3 and S12, the P atoms show relatively fewer effects on ΔGH* than the Co atoms, which is also reasonable because the P ratio on the surface is lower than the Co ratio. Despite these major changes, changes to other details (i.e. the optimized structures, H−Co bond distribution, and atomic charge) are small, even trivial, but further information can be obtained upon request from the corresponding author. Updated versions of Figures 2–4 as well as Tables 1 and 2 are provided below and a revised Supporting Information file can be found at https://doi.org/10.1002/celc.201801630. The Gibbs free energy of H* (ΔGH*) on the best adsorption site of these five facets: (001), (010), (101), (112), and (113). The local structures with H* atom on a) (112) L2, b) (001) L1, c) (113) L3, d) (112) L5, e) (101) L2, and f) (113) L4. Co: blue, P: pink, H: red. The black double-arrow in (a) shows an example for the vertical distance between Co and H. The free-energy values of DFT calculation are compared with the fitted ΔGH* from the multiple linear regression. The black dashed line means DFT results equal to the fitted results. The dots correspond to different Co sites and the filled color corresponds to the absolute error (unit: eV) between the DFT calculated ΔGH* and regression-fitted ΔGH* values. a–d) The differential charge density of the (010) L4 site, (101) L1 site, (112) L1 site, and (113) L1 site, respectively. The yellow and cyan regions represent electron flow in and flow out, respectively. The isosurface value is 0.0017 e-/bohr3. e–h) The local structures of the red dashed box in (a)–(d), respectively. The inserts in (e)–(h) are the corresponding side views. The azure arrows in (e)–(h) and the inserts represent the main direction of electron transfer. Adsorption site CoS CoM CoL N L̄ [Å] D̄ [Å] N L̄ [Å] D̄ [Å] N L̄ [Å] D̄ [Å] (112) L2 1 1.503 1.501 (001) L1 1 1.559 0.844 2 2.351 1.406 (113) L3 2 1.680 1.005 1 2.645 1.111 (112) L5 3 1.775 0.797 (101) L2 1 1.807 0.205 3 2.138 1.050 (113) L4 3 1.774 0.789 Co81 Co33 P9 P10 H (101) L1 L [Å] 1.510 2.815 2.921 2.921 / Q [e] 0.217 0.330 −0.358 −0.358 −0.225 Co160 Co58 P18 P80 H (112) L1 L [Å] 1.660 1.825 2.590 2.601 / Q [e] 0.242 0.290 −0.427 −0.411 −0.286 The authors apologize for the mistake. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

A quantitative tool to establish magic number clusters, ε3, applied in small silicon clusters, Si2-11.

The present work focuses on establishing a function to rank the stability of small silicon clusters to characterize their magic numbers. This function is composed by a thermodynamic descriptor, the atomization Gibbs free energy, and indirect kinetic descriptors, the highest occupied molecular orbital energy and the lowest excitation energy of each system. The silicon clusters geometries were optimized using density functional theory within a hybrid meta-GGA approximation (M06), while the electronic energy was corrected by single-point calculation using CASPT2 level of theory to obtain the molecular properties. Both methodologies were combined with polarized diffused triple zeta, 6-311++G(3df,3pd), basis set for all atoms. Some molecular properties and their combinations were considered to create the aforementioned function to represent the clusters chemical stability and their magic numbers. The chosen stability ranking function, called ε3, presents results in agreement with the previous mass spectrometry experimental data identifying 4, 6, 7 and 10 as magic numbers for small silicon clusters. We believe this stability ranking function can be useful to study other intramolecular atomic and molecular clusters. Graphical abstract Stability ranking function,ε31, applied on Sin (n = 2 - 11) clusters showing Fukui's functions for the Sin (n = 2 - 11) obtained by the electronic density difference through CASPT2//M06/6-311++G(3df,3pd) with an isosurface value equal to 0.003.

High-Speed 3d Modelling from Premium Rebuilding of Solid State Models

Objectives: We execute a work in a 3D setting and make projections from solid builders for 3D representations of 3D scenery to transition from 2D displays to 3D models. Methods: Constructional work of area-laying is the 3D model-driven real-world object modelling that starts from the acquisition of data in range format and passing to the transfer of them for transition modelling. Ranging-depth is the key-factor in the factorization of the depth-maps to the iso-surface values. Factorizing to building factors of 3D formation concerns settings of 3D rebuilding. Mid-depth ranging is a key factor in the factorization of iso-value/surface depth mapping. Findings: The dimension exchange transit passes through three axe-transitive passage build-up ranged frames. Multiple dimensions are entered to make a variety of reforms across a 3D overlay created by hand during state change transition.Having factorized to its building-blocks in 3-D, the only left matter to-do in our reform is to regulate the whole worlds of the 3-Dimensional rebuilding. With the state changes that fitting out in time varying mode, we could be able to fully rig-out the complete surface ground.The state change fits the surroundings in the time varying mode with skinning. Directed mapping produces a detailed 3D model of a surface domain area. The 3D modeling of solid objects cannot be finalized until it is made more efficient. Our proposed design approach is adaptively refining also the higher-order multi-variate problems with specially-recreation ways under certain boundary constraints for exceeding the status of former that is passed by our series of proposed techniques in multiphase structured solid work tests. Applications: The speed of reincarnation is in turn altered. This processing lasts shorter period of time at last and it will improve outcomes by transferring triangular structuring tiles faster through refined procedures.

Detection of Buried Roman Wall Remains in Ground‐penetrating Radar Data using Template Matching

AbstractWhereas in the last decades the acquisition and processing of archaeological ground‐penetrating radar (GPR) data have become mature, the interpretation is still challenging. Manual delineation in three dimensions is time consuming, and often the determination of an isosurface value is not straightforward. This paper presents a method designed specifically for the extraction of buried linear features such as wall foundations, based on template matching. First, the three‐dimensional (3D) GPR data cube is synthesized into a two‐dimensional (2D) slice. To achieve this, an energy slice based on a sufficiently large time window may often be appropriate, although in this study a combination with other attributes, for example based on phase symmetry, made weak anomalies more distinct. In the next step, we compute the 2D normalized cross‐correlation of the composite 2D slice and a number of templates with dimensions similar to the walls in the data set. Of the resulting correlation matrices, the highest correlation coefficient is kept for each pixel, if it exceeds a certain threshold. In this way, wall foundations are successfully mapped, but also many false detections are produced. The latter are greatly reduced in number by using a size threshold and discarding isolated features. The remaining regions are enclosed in bounding boxes, which after vertical extrusion can be used as a simplified 3D representation of the wall structures, and for the creation of a filtered isosurface. For the evaluation of our results, a manual interpretation was used. In the 2D case (i.e. when comparing the total area of the automatically mapped structures versus the manually delineated ones), both the detection rate and the correctness were ~77%. Slightly lower rates (~71%) were obtained in the 3D case (i.e. comparing volumes). Our method was applied to the GPR survey of a Roman villa in Kent, UK. Copyright © 2016 John Wiley &amp; Sons, Ltd.

Oxygen vacancy effects in HfO2-based resistive switching memory: First principle study

The work investigated the shape and orientation of oxygen vacancy clusters in HfO2-base resistive random access memory (ReRAM) by using the first-principle method based on the density functional theory. Firstly, the formation energy of different local Vo clusters was calculated in four established orientation systems. Then, the optimized orientation and charger conductor shape were identified by comparing the isosurface plots of partial charge density, formation energy, and the highest isosurface value of oxygen vacancy. The calculated results revealed that the [010] orientation was the optimal migration path of Vo, and the shape of system D4 was the best charge conductor in HfO2, which effectively influenced the SET voltage, formation voltage and the ON/OFF ratio of the device. Afterwards, the PDOS of Hf near Vo and total density of states of the system D4_010 were obtained, revealing the composition of charge conductor was oxygen vacancy instead of metal Hf. Furthermore, the migration barriers of the Vo hopping between neighboring unit cells were calculated along four different orientations. The motion was proved along [010] orientation. The optimal circulation path for Vo migration in the HfO2 super-cell was obtained.

Gauge-Origin Independent Calculations of the Anisotropy of the Magnetically Induced Current Densities.

Gauge-origin independent current density susceptibility tensors have been computed using the gauge-including magnetically induced current (GIMIC) method. The anisotropy of the magnetically induced current density (ACID) functions constructed from the current density susceptibility tensors are therefore gauge-origin independent. The ability of the gauge-origin independent ACID function to provide quantitative information about the current flow along chemical bonds has been assessed by integrating the cross-section area of the ACID function in the middle of chemical bonds. Analogously, the current strength susceptibility passing a given plane through the molecule is obtained by numerical integration of the current flow parallel to the normal vector of the integration plane. The cross-section area of the ACID function is found to be strongly dependent on the exact location of the integration plane, which is in sheer contrast to the calculated ring-current strength susceptibilities that are practically independent of the chosen position of the integration plane. The gauge-origin independent ACID functions plotted for different isosurface values show that a visual assessment of the current flow and degree of aromaticity depends on the chosen isosurface. The present study shows that ACID functions are not an unambiguous means to estimate the degree of molecular aromaticity according to the magnetic criterion and to determine the current pathway of complex molecular rings.

Orientation and concentration of Ag conductive filament in HfO2-based resistive random access memory: first-principles study

HfO2-based resistive random access memory takes advantage of metal dopants defects in its principle of operation. Then, it is significantly important to study the performance of metal dopants in the formation of conductive filament. Except for the effects of the applied voltage, the orientation and concentration mechanism of the Ag dopants are investigated based on the first principle. First, five possible models of Ag in HfO2 are established in [001], [010], [100], [-111] and [110] directions, in each of which adequate and equal dopants of Ag are ensured. The isosurface plots of partial charge density, formation energy, highest isosurface value and migration barrier of Ag dopants are calculated and compared to investigate the promising formation direction of Ag in the five established orientation systems. The formations of conductive filament are observed in [100], [010], [001] and [-111] directions in the unit cell structure from the isosurface plots of partial charge density. But no filament is formed in [110] direction. And the highest isosurface value of Ag dopant is largest in [-111] direction. This indicates that the most favorable conductive filament formation takes place in this direction. The formation energy of Ag in the different direction is different, and the values in [-111] and [100] direction are minimum and close to each other, which shows that it is easy to form conductive filaments in these two directions. In addition, the smallest migration barrier of Ag in [-111] direction reveals that the [-111] orientation is the optimal conductive path of Ag in HfO2, which will effectively influence the SET voltage, formation voltage and the ON/OFF ratio of the device. Next, based on the results of orientation dependence, four different concentration models (HfAgxO2, x=2, 3, 4, 5) are established along the [-111] crystal orientation. The isosurface plots of partial charge density about those concentration models are compared, showing that the resistive switching phenomenon cannot be observed for the samples deposited in a mixture with less than 4.00 at.% of Ag content (HfAg4O2). The RS behavior is improved with Ag content increasing from 4.00 at. % to 4.95 at.%. However, the formation energy and highest isosurface value are calculated and it is found that the conductive filaments cannot be switched into a stable state when Ag content becomes greater than 4.00 at.%. Then, the total electron density of states and the projected electron density of states are also calculated for the two models. It indirectly shows that the conductive filament is mainly comprised of Ag atoms, rather than Hf atoms or oxygen vacancy. Also, it is not helpful to improve the ON/OFF ratio of the device when the Ag dopant concentration is higher than 4.00 at.%. Therefore, the best doping concentration of Ag is 4.00 at.% and it is more advantageous to change the resistance memory storage features. This work may provide a theoretical guidance for improving the performances of HfO2-based resistive random access memory.

First principle simulations on the effects of oxygen vacancy in HfO2-based RRAM

HfO2-based resistive random access memory (RRAM) takes advantage of oxygen vacancy (V o) defects in its principle of operation. Since the change in resistivity of the material is controlled by the level of oxygen deficiency in the material, it is significantly important to study the performance of oxygen vacancies in formation of conductive filament. Excluding effects of the applied voltage, the Vienna ab initio simulation package (VASP) is used to investigate the orientation and concentration mechanism of the oxygen vacancies based on the first principle. The optimal value of crystal orientation [010] is identified by means of the calculated isosurface plots of partial charge density, formation energy, highest isosurface value, migration barrier, and energy band of oxygen vacancy in ten established orientation systems. It will effectively influence the SET voltage, forming voltage, and the ON/OFF ratio of the device. Based on the results of orientation dependence, different concentration models are established along crystal orientation [010]. The performance of proposed concentration models is evaluated and analyzed in this paper. The film is weakly conductive for the samples deposited in a mixture with less than 4.167at.% of V o contents, and the resistive switching (RS) phenomenon cannot be observed in this case. The RS behavior improves with an increase in the V o contents from 4.167at.% to 6.25at.%; nonetheless, it is found difficult to switch to a stable state. However, a higher V o concentration shows a more favorable uniformity and stability for HfO2-based RRAM.