Energies Of Different Configurations Research Articles

Activated biochar derived from Enteromorpha with high specific surface area for efficient removal of phenanthrene: Experiments, mechanism and DFT calculations

Conversion of solid marine waste into innovative nanomaterials has been successfully developed for removing organic pollutants from aqueous solutions. In this study, activated biochar (HTST) was successfully synthesized using a straightforward three-step method involving pretreatment, carbonization, and chemical regulation. Multiple characterization techniques revealed the presence of abundant three-dimensional hierarchical porous structures in the samples, along with amorphous and active functional group structures such as –COOH, –OH, –NHR, –CC, and C–O. Notably, the prepared sample exhibited a remarkable specific surface area (SBET) of 3284.52 m2/g, which was close to 1700 times larger than that of the raw biomass. Additionally, the highest removal efficiency could reach approximately 100% under neutral condition, while the adsorption capacity even achieved up to 782.37 mg/g within 2 h at room temperature. Calculations simulation not only highlighted the significance of the π–π conjugation between sample and pollutant molecules, but deeply explored the bonding interaction of active functional groups on the surface, whereas adsorption energies of different configurations had the following order: ΔE(-NHR) = 0.75194674 eV > ΔE(-OH) = 0.72502369 > ΔE(-COOH) = 0.71488135 > ΔE(-CC-) = 0.53852269 eV. Moreover, the adsorption activities for the optimized configuration were further analyzed based on the LUMO-HOMO energy gap and electric distribution. This work presents a viable synthesis method for low-cost nanomaterials and offers new insights into the exceptional adsorption properties of advanced adsorbents for wastewater treatment.

Adapting UFF4MOF for Heterometallic Rare-Earth Metal-Organic Frameworks.

Heterometallic metal-organic frameworks based on rare-earth metals (RE-MOFs) have potential in a number of applications where energy transfer between nearby metal atoms is required. This observation implies that it is important to understand the level of local mixing that is achieved between metals of different types during synthesis of RE-MOFs. Density functional theory calculations can give quantitative information on the relative energy of different configurations of RE-MOFs, but these calculations cannot be applied to the full range of medium- and long-range orderings that are possible in heterometallic materials. This limitation can be overcome using force field (FF)-based calculations if appropriate FFs are available. We show that an existing generic FF for MOFs, UFF4MOF, does not accurately predict energies of mixing in heterometallic Nd/Yb MOFs and introduce a modified FF to address this shortcoming. The resulting FF is used to explore metal orderings in large simulation volumes for a Nd/Yb MOF, illustrating the complexities that can arise in the structure of heterometallic RE-MOFs.

Effect of Embedded Thin-Plies on the Charpy Impact Properties of CFRP Composites.

In this study, different configurations of epoxy composite laminates that contained thin plies were prepared and characterised for sudden impact load bearing applications. The primary aim of this investigation was to develop a hybrid epoxy-based thin ply composite for aerospace and automotive applications that would be tolerant of high impacts. The impact properties of the selected configurations were investigated both experimentally and numerically under low-velocity Charpy impact loading conditions. Furthermore, any damage to the laminates was evaluated with an emphasis on the identification of dominant damage mechanisms and locations. This included a comparison between the laminates that were made from traditional plies and the thin ply laminates in terms of their absorbed energy and failure modes. The results revealed that the integration of thin plies into normal ply had a major effect on the amount of absorbed energy under flatwise conditions: up to 8.7 J at a cut-off angle of 90°. However, edgewise conditions produced a maximum observed energy of 10.0 J for the thin plies that were surrounded by normal plies (Plate 3). The damage assessments showed the increased damage resistance of the hybrid thin ply composites due to their uniform stress distribution. The traditional ply composites incurred large deformations from the impact loads. Moreover, it was noted that delamination formed in the middle regions of the traditional plies. The FEM model analysis revealed that it was capable of accurately predicting the absorbed energy for different configurations of composites, which were prepared and analysed experimentally. Both the experimental and numerical values were very similar to each other. These impact damage assessments improved the thin ply composites so that they could be used as working materials for applications that are prone to high loads, such as the aerospace, defence, automotive and structural industries.

Stress relaxation in III-V nitrides: Investigation of metallic atoms interaction with the N-vacancy

Molecular dynamics simulations have been carried out to study the interaction between two point defects in III-nitride materials (AlN, GaN and InN): a substitutional metal atom (indium, aluminum, gallium) and the N-vacancy. The Stillinger-Weber (S-W) empirical potential is used. By calculating the potential energies of different configurations with these two defects, it is shown that the indium atom in AlN and GaN or aluminum and gallium in InN are stable in the immediate vicinity of the N-vacancy. In contrast, the gallium atom in AlN and the aluminum atom in GaN may be difficult to bring near the N-vacancy. This behavior is related to the stress relaxation in the presence of these point defects. In AlN, the stability of indium atoms around the N-vacancy is the highest, indicating a good probability of aggregation, which may constitute a first explanation for the reported phase segregation during the growth of InAlN alloys.

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs.

Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.

Thermodynamics of boron incorporation in BGaN

We study the thermodynamics of boron (B) incorporation into gallium nitride (GaN) using first-principles calculations. In the dilute limit, we have calculated the formation energies of different configurations of the B impurity in GaN and found that substitution on the cation site is favored over substitution on the anion site. Under $p$-type conditions, interstitial boron can become the more favorable configuration and will ultimately limit the $p$-type conductivity. At higher B concentrations we use the generalized quasi-chemical approximation to elucidate the thermodynamic stability of boron gallium nitride (BGaN) alloys. We also investigate the effects of strain, which will be present if BGaN alloys are grown pseudomorphically on a GaN substrate. Without strain, B incorporation at typical growth conditions is limited to about 1.4% at $800{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$. Pseudomorphic strain raises the limit to 3.0% at the same temperature, close to experimentally observed levels of B incorporation.

Indentation and bifurcation of inflated membranes

We study pneumatically inflated membranes indented by rigid indenters of different sizes and shapes. When the volume of the inflated membrane is beyond a critical value, a symmetric deformation mode becomes unstable and the system follows a path of asymmetric deformation. This bifurcation is analysed analytically for a two-dimensional membrane with either a line or plane indenter for which the stable deformation path is determined by computing the total system potential energy of different configurations. An axisymmetric membrane with indenters of different shapes and sizes is further investigated numerically. In this case, a cylindrical indenter can always trigger bifurcation while a small spherical indenter tends to be encapsulated rather than induce an asymmetric deformation mode. This result suggests that the observed bifurcation behaviour can be actively tuned and even triggered selectively by tuning indenter shape and size. We also demonstrate the effects of friction and biased bifurcation analytically through the example of a two-dimensional membrane with a line indenter.

Optimised cost of wind energy using MRWT

In this paper, an effort has been made to compare the cost of energy of different configurations of multi-rotor wind turbines (MRWT). Three different optimisation techniques, i.e., genetic algorithm (GA), particle swarm optimisation (PSO) and pigeon inspired optimisation (PIO) have been employed to find out the most suitable rotor configuration for the minimum cost of wind power generation. Power, energy and cost models as proposed are used to determine the annual energy yield and economics of multi-rotor turbines. Simulation results using three optimisation algorithms give the same rotor configuration for minimum cost of energy.

An analytical method to connect open curves for modeling protein-bound DNA minicircles

We introduce an analytical method to generate the pathway of a closed protein-bound DNA minicircle. We develop an analytical equation to connect two open curves smoothly and use the derived expressions to join the ends of two helical pathways and form models of nucleosome-decorated DNA minicircles. We find that the simplest smooth connector which satisfies the boundary conditions at the end points and the length requirement for such connections to be a quartic function on the xy-plane and linear along the z-direction. This is a general method which can be used to connect any two open curves with well defined mathematical definitions as well as pairs of discrete systems found experimentally. We used this method to describe the configurations of torsionally relaxed, 360-base pair DNA rings with two evenly-spaced, ideal nucleosomes. We considered superhelical nucleosomal pathways with different levels of DNA wrapping and allowed for different inter-nucleosome orientations. We completed the DNA circles with the smooth connectors and studied the associated bending and electrostatic energies for different configurations in the absence and presence of salt. The predicted stable states bear close resemblance to reconstituted minicircles observed under low and high salt conditions.

Atomistic simulations of Epoxy/Water/Aluminum systems using the ReaxFF method

The molecular dynamics (MD) method can be a reliable tool for studying of organic coating/metallic substrate systems, however its accuracy is limited to the force field governing the dynamics of systems. These systems can be divided into three parts: (i) organic phase, (ii) substrate, (iii) interface between the organic phase and substrate. In this work, three recent ReaxFF descriptions were selected. A set of complex experimental data and density functional calculations was selected as the reference point. The density and structural analysis of a wide range of crystalline organic compounds were studied. The density, structural analysis, and self-diffusion constant of water at room temperature were obtained. The glass transition temperature of three different cross-linked epoxy were obtained and compared with the reported experimental results. The interaction energies of different configurations of epoxy and water over an alumina substrate were studied. Additionally, the reaction of water with aluminum was studied. The accuracy of these ReaxFF descriptions in reproducing the reference data was assessed. The results show there is a single ReaxFF description for accurate simulation of C/H/N/O/Al systems, which enables atomistic simulations of complex epoxy coatings/aluminum substrates systems.

Analysis of adsorption properties of SF6 decomposed gases (SOF2, SO2F2, SF4, CF4, and HF) on Fe-doped SWCNT: A DFT study

In order to develop a potential material for monitoring of SF6 decomposed gases online in insulated equipment, the Fe-doped single-walled carbon nanotube (Fe-SWCNT) was proposed and its gas sensing properties to five SF6 decomposed gases were investigated with DFT method. The adsorption structures, charge transfers, density of states (DOS), and frontier molecular orbital theory analysis have been performed. Calculations show that the doping of Fe enhances the conductivity of SWCNT and Fe acts as the active center for adsorption. The conductivity of zigzag Fe-(8, 0) SWCNT is increased with SOF2 adsorption. While the adsorption of SF4 distinctly decreases the conductivity of the system. For SO2F2 adsorption, the difference in adsorption energy of different configurations is small, but the HOMO-LUMO energy gaps vary widely. The adsorption of SO2F2 is weaker than that of SOF2 and SF4. For adsorption of CF4 and HF, the little electron transfer and the low adsorption energy indicate the weak interaction. The negligible decreases of conductivity confirms that the Fe-(8, 0) SWCNT is insensitivity for CF4 and HF detection. After SO2F2, SF4, CF4, and HF adsorbed onto armchair Fe-(5, 5) SWCNT, the conductivity of system is also changed.

Mechanisms of supramolecular ordering of water-soluble derivatives of fullerenes in aqueous media

Fullerenols C60(OH)X and C70(OH)X (X ∼ 30) have been studied in aqueous solutions at the concentrations 0.05–22wt% by X-ray and neutron scattering and using modeling hydroxyls’ arrangements on carbon cages to explain the molecular assembly defined by hydrophobic and hydrophilic interactions of molecules. In the case of C60 quantum chemical calculations minimizing molecular energy for different configurations of OH-groups on the carbon cages showed their preferred localization at C60 spheroids’ equatorial zone and at the opposite poles. However, less symmetric hydroxyls’ localization on C70 molecules was found since hydroxyls do not create closed chains on them. As a result, the molecules C60(OH)X are associated into primary chain-like aggregates (∼20 units, few nanometers in size) more likely in water than the fullerenols C70(OH)X forming similar groups of lower aggregation degree. For C60(OH)X and C70(OH)X the peculiarities in hydroxyls’ grafting affected a coordination of primary groups integrated into secondary and tertiary structures at the distances R ∼ 5 nm and R ∼ 30 nm at the concentrations C > 5wt% and C > 10wt%, respectively. The discovered mechanism of fullerenols’ assembly in water will facilitate their use in chemistry and biomedicine.

Site preference and magnetic properties of Zn-Sn-substituted strontium hexaferrite

The site preference and magnetic properties of Zn, Sn, and Zn-Sn substituted M-type strontium hexaferrite (SrFe12O19) have been investigated using first-principles total-energy calculations based on density-functional theory. The site occupancy of substituted atoms was estimated by calculating the substitution energies of different configurations. The distribution of different configurations during the annealing process at high temperature was determined using the formation probabilities of configurations to calculate magnetic properties of substituted strontium hexaferrite. We found that the magnetization and magnetocrystalline anisotropy are closely related to the distributions of Zn-Sn ions on the five Fe sites. Our calculation shows that in SrFe11.5Zn0.5O19, Zn atoms prefer to occupy 4f1, 12k, and 2a sites with occupation probabilities of 78%, 19%, and 3%, respectively, while in SrFe11.5SnO19, Sn atoms occupy the 12k and 4f2 sites with occupation probabilities of 54% and 46%, respectively. We also found that in SrFe11Zn0.5Sn0.5O19, (Zn,Sn) atom pairs prefer to occupy the (4f1, 4f2), (4f1, 12k), and (12k, 12k) sites with occupation probabilities of 82%, 8%, and 6%, respectively. Our calculation shows that the increase of magnetization and the reduction of magnetic anisotropy in Zn-Sn substituted M-type strontium hexaferrite as observed experimentally are due to the occupation of (Zn,Sn) pairs at the (4f1, 4f2) sites.

Characterizing modulated structures with first-principles calculations: a unified superspace scheme of ordering in mullite.

The benefit of computational methods applying density functional theory for the description and understanding of modulated crystal structures is investigated. A method is presented which allows one to establish, improve and test superspace models including displacive and occupational modulation functions from first-principles calculations on commensurate structures. The total energies of different configurations allow one to distinguish stable and less stable structure models. The study is based on a series of geometrically optimized superstructures of mullite (Al4+2xSi2-2xO10-x) derived from the superspace group Pbam(α0½)0ss. Despite the disordered and structurally complex nature of mullite, the calculations on ordered superstructures are very useful for determining the ideal Al/Si ordering in mullite, extracting atomic modulation functions as well as understanding the SiO2-Al2O3 phase diagram. The results are compared with experimentally established models which confirm the validity and utility of the presented method.

Theoretical and experimental approach to the investigation of hyperpolarizability and charge transfer characteristics of NLO active 2′,3,4,4′,5-pentamethoxy chalcone with silver atoms adsorbed

Organic crystals of 2′,3,4,4′,5-pentamethoxy chalcone (PMC), grown by slow evaporation technique, are subjected to spectroscopic and nonlinear optical analyses. The experimental and theoretical vibrational spectra confirm that the charge-transfer interaction between the methoxy group and phenyl ring through the ethylenic bridge of the PMC molecule must be responsible for the simultaneous IR and Raman activation of C=C stretching and ring modes. The Natural Bond Orbital (NBO) and Atoms In Molecules (AIM) calculations verify the presence of intramolecular hydrogen bonding in the molecule. The large NLO efficiency predicted for PMC is confirmed for the first time by powder SHG efficiency experiment by Kurtz and Perry, while the third order nonlinearity is measured by means of open-aperture Z-scan technique. From the results, the use of PMC for nonlinear optical applications is suggested. The Surface Enhanced Raman Scattering (SERS) spectral investigations have been performed to obtain the adsorption geometry of PMC on the silver surface. Density functional theory at B3LYP/SDD level has been used to compute energies of different configurations of silver adsorbed-PMC to find their stability, optimized geometry of the most stable configuration, and for characterizations including vibrational, NBO and hyperpolarizability analyses.

A dispersion-corrected DFT insight into the structural, electronic and CH4 adsorption properties of small tin-oxide clusters

The main goal of this paper is to investigate the structural and electronic properties of small tin-oxide clusters, SnxOy (x = 2–6), before and after methane (CH4) physisorption. To this end, we employ the dispersion-corrected density functional theory (DFT-D2). At first, we demonstrate the relative binding stability of SnxOy clusters with a fixed number of tin atoms via analysis of their binding energy per atom and second-order energy differences. Our results show that the highest relative stability occurs at y = 2, y = 3, y = 4, y = 6 and y = 8 for Sn2Oy, Sn3Oy, Sn4Oy, Sn5Oy and Sn6Oy clusters, respectively. Furthermore, with the cluster size increasing, the ring-shape to cube-like structural crossover is occurred. The higher average coordination and total number of bonds in cube-like clusters make their interatomic bonds weaker and longer. On the other hand, the cube-like clusters, in comparison with ring-shape ones, possess higher chemical potential and lower chemical hardness that lead to their more chemical reactivity. We then proceed to study the CH4 adsorption properties of the resulted most stable clusters. The lowest-energy structures of CH4-adsorbed clusters have been found by comparing the adsorption energy of different configurations. It is found that Van der Waals interactions lead to exothermic physisorption of CH4 on each tin-oxide cluster with the adsorption energy ranging from −101 to −191 meV. In addition, upon CH4 adsorption on SnxOy clusters, the energy gap is decreased which shows an enhancement in the conductivity of the clusters. As a result, the CH4 physisorption ability of these small studied tin-oxide clusters provides their application feasibility as the low-temperature CH4 gas sensors.

Effect of ionic substitutions on the magnetic properties of strontium hexaferrite: A first principles study

We investigated the effect of substitution of various ions at the Fe sites on magnetic properties of strontium hexaferrite (SrFe12O19) using first principles method based on density functional theory. The site occupancies of substituted atoms were estimated by calculating the substitution energies of different configurations. The formation probabilities of configurations were used to calculate magnetic properties of substituted strontium hexaferrite. A total of 21 elements (M) were screened for their possible substitution in strontium hexaferrite, SrFe12−xMxO19 with x = 0.5. In each case the site preference of the substituted atom and the magnetic properties were calculated. We found that Bi, Sb, Sn, and Sc can effectively increase the magnetization and P, Co, Al, Ga, and Ti can enhance the anisotropy field when substituted into strontium hexaferrite.

First principle characterization of graphene shielding of the late transition metals: The role of coverage

Employing the first principle calculation, we investigate oxygen adsorption and incorporation into the subsurface of the graphene-coated Cu(111) considering various oxygen coverages. The obtained binding energies for different configurations reflect the fact that addition of graphene monolayer in both adsorptive and incorporative sites remarkably weakens the nature of binding, thus results in lower probability for oxygen permeation which is sensitive to the coverage. Additionally, comparison of potential averages of different mid-layer and over-layer graphene configurations confirms that graphene coating strongly increases the corrosion resistance of Cu surface in good agreement with available electrochemical measurements. Our results might be generalized and validated to designing new anti-corrosion coatings for other transition metal surfaces.

Study of Stranski–Krastanov growth using kinetic Monte Carlo simulations with an atomistic model of elasticity

We have analyzed the Stranski–Krastanov growth mode in heteroepitaxial thin films using lattice-based kinetic Monte Carlo simulations with an atomistic model of elasticity. In this growth mode, elastic effects due to the lattice mismatch between the film and the substrate cause a transition from two-dimensional layer-by-layer growth to three-dimensional island growth. In our simulations on a simple cubic lattice model in a 3-dimensional system with nearest neighbor interactions only, we see very little tendency towards islanding. On modifying the anisotropy using next-to-nearest and next-to-next-to-nearest neighbor interactions, the system shows a greater tendency towards islanding. When the calculations are carried out in a 2-dimensional system, islanding is fairly pronounced. To gain insights into the possible reasons for these observations, we evaluate the elastic energy and bond energy of different configurations in a 2-dimensional system. Our calculations show that island growth in 2-dimensions also involves a significant nucleation barrier. This suggests that the barrier for island formation is more easily overcome in a 2-dimensional system as compared to a 3-dimensional system.

Structural defects induced by Fe-ion implantation in TiO2

X-ray photoelectron spectroscopy and resonant x-ray emission spectroscopy measurements of pellet and thin film forms of TiO2 with implanted Fe ions are presented and discussed. The findings indicate that Fe-implantation in a TiO2 pellet sample induces heterovalent cation substitution (Fe2+ → Ti4+) beneath the surface region. But in thin film samples, the clustering of Fe atoms is primarily detected. In addition to this, significant amounts of secondary phases of Fe3+ are detected on the surface of all doped samples due to oxygen exposure. These experimental findings are compared with density functional theory calculations of formation energies for different configurations of structural defects in the implanted TiO2:Fe system. According to our calculations, the clustering of Fe-atoms in TiO2:Fe thin films can be attributed to the formation of combined substitutional and interstitial defects. Further, the differences due to Fe doping in pellet and thin film samples can ultimately be attributed to different surface to volume ratios.