Energies Of Different Species Research Articles

Theoretical investigation of d-orbitals involvement in catalytic activity by incorporation of bimetallic on adjacent position

Numerous articles on M-N-C-based materials have been extensively studied for their catalytic activity in various reaction perspectives, such as CO oxidation, CO2 reduction, oxygen reduction, and oxygen/hydrogen evaluation. However, the understanding of the involvement of d-orbitals of transition metal atoms and the tunability of their electronic structure for different catalytic species is under observation. Herein we have suggested bimetallic iron-doped nitrogen-based graphene FeN4-MN4/Gr (M= Co, Ni, Cu, Zn) and single-atom iron-doped nitrogen-based graphene for comparative study. The effect of bimetallic atoms on iron on the adjacent position was studied by Bader charge, adsorption energy for different species, and the strengthening of iron nitrogen codoped graphene Fe-N4/Gr. Moving from Co to Zn, the number of outermost electrons is increasing, creating steric hindrances effect and torsional strain, affecting Bader charge and formation energy and changing the bond length between nitrogen and iron. Similarly, steric hindrance also has a prominent effect on the d-orbital, as moving from Co to Zn, the availability of finding of d-orbital on z-direction are increasing which is confirmed by adsorption energy of different species like Co, O2, and H+ + e−. Our finding reveals that not only d-orbitals along the z-direction can play a vital role in catalytic activity, but the d-band center and magnetic moment also have a projecting role in boosting catalytic activity.

Formation and stability of the early stage solute and defect clusters in Cu-free ferritic steels during irradiation

• The mechanism of the role of specific element species in the local stability of the Mn-Ni-Si quartet clusters are investigated by DFT. • The interaction of Mn with the dumbbell interstitials is stronger than other solutes. and this is favorable for formation of the cluster. • Si can stabilize solute clusters because it forms stable covalent bonds with other solutes at 1nn. Irradiation induced significant volume fractions of Mn-Ni-Si clusters have been characterized as severe cause for the matrix embrittlement in low-Cu reactor pressure vessel steels (RPV) at high flux. The formation mechanism of these clusters is still unclear, especially when the RPV does not contain Cu. In this work, we perform density functional theory (DFT) calculations to examine the mechanism of the role of specific element species in the local stability of clusters in Fe-Mn-Ni-Si system. The binding energy of different species or configurations for quartets including Mn, Ni, Si, vacancies, and interstitial atoms is presented. Based on the DFT data, we found that point defects are more likely to promote cluster formation, and when Mn is present near the dumbbell interstitials, is favorable for formation of the cluster. Si also plays an important role by forming stable covalent bonds at 1nn to other solutes, but Si atoms cannot be close to each other because this would interfere with the magnetic properties of the surrounding Fe atoms to the extent of reducing the stability of the clusters. These results are helpful for a better understanding of the cluster formation mechanism and can provide fundamental parameters for the solute-cluster evolution with larger scale simulations.

QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II)

Phenolic and polyphenolic compounds are distributed in plant tissues as a secondary metabolite which are compromised in multiple and imperative physiological phenomena. Herein, inhibition mechanism of human carbonic anhydrase isoform II, hCAII, with seven phenolic compounds including phenol, catechol, resorcinol, 4-methyl catechol, vanillic acid, trans-cinnamic acid and ortho-coumaric acid has been investigated using quantum mechanical and ONIOM calculations. B3LYP-D3/6–311++G** method has been employed to calculate the electronic structure and electronic energy of different species through the reaction mechanism path. The model system of hCAVII has been used that includes the core of the catalytic center, Zn2+, binds to three histidine residues and a hydroxide ion or water molecule forming a first coordination shell. Thr199 and Glu106 were considered as neighboring residues to the ones binding zinc. All thermodynamic functions through the reaction path are evaluated in different phases. The calculated results indicate that all phenolic inhibitors do not directly interact with the zinc ion in the CA active center, and the presence of aromatic moieties was associated with more effective inhibition. In addition, the implicit and explicit solvent effect has been considered for water solvent using QM and ONIOM (QM/MM) calculations.

The study of structure and interactions of glucose-based natural deep eutectic solvents by molecular dynamics simulation

In the current study, molecular dynamics simulations were conducted to investigate the structural and dynamical properties of glucose-based Deep Eutectic Solvents (DESs) at different molar ratios (the mixture of glucose and choline chloride with the molar ratios of 1:3, 1:1 and 3:1). Accordingly, the interaction energies of different species and structural properties such as atom–atom radial distribution functions (RDFs), the hydrogen-bonding network between species, and spatial distribution functions (SDFs) were computed to understand effective interactions in the eutectic mixture formation. It was found that the insertion of glucose molecules reduced the accumulation of chloride anions around choline cations, eventually decreasing the interaction between the choline chloride ion pairs. Moreover, the possible explanations for the thermos-physical properties of DESs, such as the shear viscosity and density, have been provided. Dynamical properties of DES were evaluated by calculating the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of the mass of the ions and glucose molecules. MSD analysis results were then used to calculate the self-diffusion parameter by applying the Einstein relation. The simulation results indicated that increasing the temperature led to easing the migration of the molecules and decreasing the dependence of the movement of the molecules on each other. This growing trend of migration may lead to an increase in the self-diffusion coefficient of molecules. Structural analysis revealed that a ratio of 1:1 of glucose: choline chloride could provide the best condition to maintain the low melting point of the mixture due to the strong hydrogen-bonded network between the two species.

Insights into the mechanism of lead species adsorption over Al2O3 sorbent

Al2O3 is regarded as an effective sorbent to capture lead from flue gas. The adsorption behaviors of different species of lead (Pb, PbO, PbCl and PbCl2) on the Al2O3 surfaces were explored based on density functional theory. The results show that the chemisorption mechanism is responsible for the adsorption of lead species on the Al2O3 surface. The high reactivity of Pb adsorption on the α-Al2O3 (110) surface is mainly attributed to the existence of unsaturated Al atoms. The Al hollow sites are identified as the effectively active sites for Pb adsorption on the (110) surface. The adsorption energies of different species of lead on the Al-terminated (110) surface are in the range of − 4.20 to − 6.30 eV. PbO adsorption at the Al hollow site of the Al-terminated (110) surface shows the highest adsorption energy (− 6.30 eV), suggesting that Al2O3 prefers to capture PbO among different species of lead. The strong interactions of PbO, PbCl and PbCl2 molecules with the unsaturated Al atoms of the α-Al2O3 (110) surface are responsible for PbO, PbCl and PbCl2 capture by Al2O3. Al2O3 has a good ability to capture different species of lead, and the adsorption capacity follows the order: PbO > Pb > PbCl > PbCl2.

Molecular modeling insights in the extraction of benzene from hydrocarbon stream using deep eutectic solvent

The present study aims to elucidate the molecular insights into the extraction of benzene from hydrocarbon mixture using a phosphonium based deep eutectic solvent (DES). The prepared DES consists of the hydrogen bond acceptor (HBA; methyltriphenylphosphonium bromide, MTPB) and hydrogen bond donor (HBD; ethylene glycol) at a molar ratio of 1:4. The atomic-level classical molecular dynamic (MD) simulation technique is then employed to investigate the equilibrium phase behaviour of the DES + benzene + hexane ternary system with respect to solvent rich and hydrocarbon-rich phases. To observe the effect of feed concentration, three different concentrations were considered from the reported experimental runs, which gave high selectivity and distribution coefficient values. The non-bonded interaction energies of different species and the structural properties such as radial distribution functions, spatial distribution functions (SDFs), and the average number of hydrogen bonds are then computed. It is found that the cation within the HBA, namely, MTP, initiates interactions with benzene when compared to HBD or its anion (Br). MTP and ethylene glycol both are seen to contribute to the hydrogen bonding with benzene, which results in a higher experimental solubility value. The calculations of SDFs further reveal the fact that the benzene molecules are evenly distributed around the active sites of the MTP molecule, whereas hexane molecules are found to be distributed around the non-active sites of the DES. In order to validate the simulation procedure, the concentration in both the phases was compared with the existing LLE experimental results. In the penultimate part, 2D 1H-13C Heteronuclear Multiple Bond Correlation (HMBC) NMR is performed for investigating and confirming the hydrogen bonding interactions among components of DES and benzene.

First-Principles Modeling of the Repassivation of Corrosion Resistant Alloys: Part II. Surface Adsorption Isotherms for Alloys and the Chloride Susceptibility Index

Quantitatively predicting the corrosion resistance of alloys is vital to the design and application of the next generation of superior corrosion resistant alloys (CRAs). Here, the Chloride Susceptibility Index (CSI), a scientifically based quantitative descriptor for repassivation tendency of CRAs, is proposed as a metric constructed through combining atomistically resolved information regarding adsorption and alloy surface composition with environmental conditions such as applied potential, temperature, pH, and Cl− concentration. Using this method, the response of CRAs to relevant environments can be predicted. CSI is determined by: (1) estimation of thermoequilibrium surface coverages of O and Cl by a Langmuir isotherm model using adsorption energies of different species (O, Cl, OH, H2O) obtained from DFT. (2) determination of CSI by integrating Cl surface coverage over a realistic window of applied potentials, thereby incorporating the effect of Cl surface coverage and electrochemical environment simultaneously. A series of Ni-Cr-X alloys was used as an example to develop and validate the method through studying the effect of different alloy solutes X on chloride resistance. The trends and relations predicted by CSI are in qualitative agreements with experimental observations. Moreover, a quantitative correlation is found between CSI and the repassivation potential.

Energy transfer and electron energization in collisionless magnetic reconnection for different guide-field intensities

Electron dynamics and energization are one of the key components of magnetic field dissipation in collisionless reconnection. In 2D numerical simulations of magnetic reconnection, the main mechanism that limits the current density and provides an effective dissipation is most probably the electron pressure tensor term, which has been shown to break the frozen-in condition at the x-point. In addition, the electron-meandering-orbit scale controls the width of the electron dissipation region, where the electron temperature has been observed to increase both in recent Magnetospheric Multiple-Scale (MMS) observations and in laboratory experiments, such as the Magnetic Reconnection Experiment (MRX). By means of two-dimensional full-particle simulations in an open system, we investigate how the energy conversion and particle energization depend on the guide field intensity. We study the energy transfer from the magnetic field to the plasma in the vicinity of the x-point and close downstream regions, and E·J and the threshold guide field separating two regimes where either the parallel component, E||J||, or the perpendicular component, E⊥·J⊥, dominate the energy transfer, confirming recent MRX results and also consistent with MMS observations. We calculate the energy partition between fields and kinetic and thermal energies of different species, from electron to ion scales, showing that there is no significant variation for different guide field configurations. Finally, we study possible mechanisms for electron perpendicular heating by examining electron distribution functions and self-consistently evolved particle orbits in high guide field configurations.

Molecular Dynamic Simulations for the Extraction of Quinoline from Heptane in the Presence of a Low-Cost Phosphonium-Based Deep Eutectic Solvent.

The present study aims at the extraction of a polyaromatic hydrocarbon from fuel oils using a novel low-cost deep eutectic solvent (DES). The DES is prepared by mixing the hydrogen bond acceptor (HBA; methyltriphenylphosphonium bromide, MTPB) and hydrogen bond donor (HBD; ethylene glycol) at a molar ratio of 1:4. The liquid-liquid equilibrium is then measured at ambient condition. The classical molecular dynamic (MD) simulation technique is then employed to investigate and compare the experimental phase behavior of a DES-quinoline-heptane ternary system. For performing the MD simulations, two experimental feed points are considered which gave high selectivity and distribution coefficient values. The interaction energies of different species and the structural properties such as radial distribution functions, average number of hydrogen bonds, and spatial distribution functions (SDFs) are then computed. It is found that the cation within the HBA, namely, MTP, possesses favorable interactions with quinoline when compared to HBD or anion (Br). MTP here acts as a HBA and contributes to the hydrogen bonding with quinoline, which results in higher experimental selectivity values. The calculations of SDFs further reveal the fact that the DES molecules are evenly distributed around the active sites of the quinoline molecule, whereas heptane molecules are found to be distributed around the nonactive sites of the aromatic ring.

Cavitation of tumoral basement membrane as onset of cancer invasion and metastasis: physics of oncogenic homeorhesis via nonlinear mechano-metabolomics

We investigate the catalytic reactions model used in cell modeling. The reaction kinetics is defined through the energies of different species of molecules following a random independent distribution. The related statistical physics model has three phases and these three phases emerge in the dynamics: fast dynamics phase, slow dynamic phase and ultra-slow dynamic phase. The phenomenon we found is rather general, and does not depend on the details of the model. We assume as a hypothesis that the transition among these phases (glassiness degrees) is related to cancer. The imbalance in the rate of processes between key aspects of the cell (gene regulation, protein-protein interaction, metabolical networks) creates a change in the fine tuning among these key aspects, affects the logics of the cell and initiates cancer. It is probable that cancer is a change of phase resulting from increased and deregulated metabolic reactions. Copyright c © EPLA, 2012 Introduction. – When observing the life on the ground of statistical physics of complex systems we see a hierarchial level of organization and modularity. How can we describe the “good, natural” relations between different parts of complex system? In statistical physics we describe different systems through different order parameters, and in equilibrium different parts of the system have the same temperature. For the stability of the system, it is reasonable to assume the similarity of order parameters at different hierarchy levels and parts (modules) of the system. There is a good similarity with the no-arbitrage condition in financial markets [1] where different stocks that can fluctuate in equilibrium have only identical order parameters, defined as a ratio of driven and diffusion motions. The Random Energy Model (REM) [2] and related complexity (replica symmetry breaking) order parameters [3] work starting from the proteins [4] till quantum chromo-dynamics and strings; therefore we assume that the cell organization and cancer should not be exclusions, and there is a possibility that REM-related ideas can work there. Using the known results of REM, we will prove that the phase structure of (a)E-mail: saakian@yerphi.am the chemical reaction network kinetics is related with the probabilistic distributions of different chemicals in the steady-state distribution. Then we will speculate about the origin of the cancer using similar complexity ideas. One of the main ideas for cell modeling is to consider the dynamical models with network structure [5–7]. One can realize this program studying the network of catalytic reactions, identifying the phenotype of the cell with the attractor of the nonlinear system of differential equations. While constructing the kinetic constants, it is advantageous to have a detailed balance condition. The density of different chemical components change according to the kinetic constants, and the latter are defined through the energies of that components. We are following [8]. There are M chemical components. The transformation between chemicals Xi and Xj is catalyzed by some component xc, so it has a rate ki,jxcxi Thus, we can write a set of equations [8]:

On the electrochemical properties of platinum stepped surfaces vicinal to the (100) pole. A computational study

DFT studies on platinum stepped surfaces have been carried out in order to understand the differences in the electrochemical behavior between the surfaces with (111) and (100) terraces. Thus, adsorption energies of different species on selected surfaces have been computed. For the adsorption of Bi and Cu on the Pt(553) and Pt(711) surfaces, it has been found that the adsorption energy on the site corresponding to the step decoration for the Pt(553) surface is ca. 0.5eV higher than that calculated on the (111) terrace sites. On the other hand, there is no preferential adsorption site for Cu or Bi on the Pt(711) surface, since the energy differences between the different sites on this stepped surface with (100) terraces are very small. CO and OH adsorption on the surfaces with (100) terraces, namely the Pt(100), the Pt(711) and the Pt(510) surfaces, has been also investigated. The energy differences between step sites and terrace sites for the surfaces are very small, ca. 0.2eV for OH adsorption and <0.1eV for CO adsorption. For OH, the preferred adsorption mode is a bridge mode, whereas the adsorption energy for the on top and bridge configurations of CO are similar on those surfaces. The comparison with previous DFT calculations indicates that the perturbation created by the step on the (100) terrace is significantly smaller than that created on the (111) terraces. Thus, the modification of the electrochemical properties produced by the presence of a step in the (100) terrace is minor, in agreement with the experimental results.

The three different phases in the dynamics of chemical reaction networks and their relationship to cancer

We investigate the catalytic reactions model used in cell modeling. The reaction kinetics is defined through the energies of different species of molecules following a random independent distribution. The related statistical physics model has three phases and these three phases emerge in the dynamics: fast dynamics phase, slow dynamic phase and ultra-slow dynamic phase. The phenomenon we found is rather general, and does not depend on the details of the model. We assume as a hypothesis that the transition among these phases (glassiness degrees) is related to cancer. The imbalance in the rate of processes between key aspects of the cell (gene regulation, protein-protein interaction, metabolical networks) creates a change in the fine tuning among these key aspects, affects the logics of the cell and initiates cancer. It is probable that cancer is a change of phase resulting from increased and deregulated metabolic reactions.

Molten salt synthesis of single phase CoFe2O4 powders

CoFe2O4 powders were synthesised at low temperature by a molten salt method using Fe2O3 and Co3O4 as raw materials. The crystal structure and morphology of the powder were characterised by X-ray diffraction (XRD) and scanning electron microscope (SEM). X-ray diffraction (XRD) reveals that single phase CoFe2O4 powder can be obtained at 700°C, and SEM images show that the powder is well developed and dispersed. The effect of processing parameter on phase formation and particle size was investigated. The particle growth mechanism is briefly discussed and the activation energies of different species of salts are calculated and compared. The magnetic properties of the powder were also characterised.

Theoretical Investigation of the Neutral/Zwitterionic Equilibrium of γ-Aminobutyric Acid (GABA) Conformers in Aqueous Solution

Since γ-aminobutyric acid does not form a stable zwitterionic species in the gas phase, as calculated at the HF/6-311++G** level, the GABA·2H2O system was optimized for several neutral and zwitterionic GABA tautomers/conformers. The obtained molecular geometries and vibrational frequencies determined for the dihydrates reflect structural changes for GABA due to close and strongly bound water molecules. By use of GABA geometries optimized in the dihydrates, relative free energies of different species in aqueous solution were calculated. MP2/6-311++G**//HF/6-311++G** energy values show that the neutral form is strongly preferred over the zwitterionic one for the isolated GABA species. The neutral tautomer, which is most stable in the gas phase, is only marginally changed by hydration; it is without an intramolecular hydrogen bond and has nearly gauche−gauche arrangements, 54 and −83°, for the NCCC and the CCCC torsion angles, respectively, as determined in the dihydrate. In aqueous solution the zwitterionic...

Diels-Alder dimerization of 1,3-butadiene: an ab initio CASSCF study of the concerted and stepwise mechanisms and butadiene-ethylene revisited

Ab initio CASSCF calculations with the 3-21G basis set have been fixed to locate transition structures for concerted and stepwise mechanisms of the Diels-Alder and [2+2] dimerizations of 1,3-butadiene. The butadiene-ethylene reaction was also studied with six-orbital/six-electron CASSCF calculations and the 3-21G and 6-31G * basis sets. The CASSCF calculations appear to slightly overestimate the stabilities of biradicals relative to concerted mechanisms, based upon comparisons with experimerital data and expectations about correlation energies of different species. Energies were also evaluated with QCISD(T)/6-31G * calculations