Bond Energy Analysis Research Articles

Identifying the Degradation Products of Dexamethasone for COVID‐19 Treatment in Mexico City's Wastewater: Theory and Experiments

AbstractQuantum chemistry calculations were performed to elucidate the reaction sites and degradation routes of dexamethasone. Flow Injection Analysis Electrospray Fourier‐Transform Ion Cyclotron Resonance Mass Spectrometry (FIA‐ESI‐FTCIR‐MS) was used to identify dexamethasone and its byproducts in Mexico City's wastewater, guided by results from ab‐initio calculations on the bond energy analysis and thus propose possible degradation routes. Products of hydroxylation/reduction, decarbonylation/formylation and defluorination reactions were identified. The results of this study contribute to the identification of the degradation products of drugs commonly used in the treatment of COVID‐19 in urban areas. Through wastewater analysis and computationally assisted Mass‐Spectrometry techniques, an alternative approach is presented to identify byproducts in complex matrices when analytical standards are unavailable or in case of limited understanding on the stability of the degradation byproducts in aqueous medium.

A guided ion beam investigation of UO2+ thermodynamics and f orbital participation: Reactions of U+ + CO2, UO+ + O2, and UO+ + CO.

A guided ion beam tandem mass spectrometer was employed to study the reactions of U+ + CO2, UO+ + O2, and the reverse of the former, UO+ + CO. Reaction cross sections as a function of kinetic energy over about a three order of magnitude range were studied for all systems. The reaction of U+ + CO2 proceeds to form UO+ + CO with an efficiency of 118% ± 24% as well as generating UO2+ + C and UCO+ + O. The reaction of UO+ + O2 forms UO2+ in an exothermic, barrierless process and also results in the collision-induced dissociation of UO+ to yield U+. In the UO+ + CO reaction, the formation of UO2+ in an endothermic process is the dominant reaction, but minor products of UCO+ + O and U+ + (O + CO) are also observed. Analysis of the kinetic energy dependences observed provides the bond energies, D0(U+-O) = 7.98 ± 0.22 and 8.05 ± 0.14eV, D0(U+-CO) = 0.73 ± 0.13eV, and D0(OU+-O) = 7.56 ± 0.12eV. The values obtained for D0(U+-O) and D0(OU+-O) agree well with the previously reported literature values. To our knowledge, this is the first experimental measurement of D0(U+-CO). An analysis of the oxide bond energies shows that participation of 5f orbitals leads to a substantial increase in the thermodynamic stability of UO2+ relative to ThO2+ and especially transition metal dioxide cations.

Paying Comprehensive Attention to the Temperature-Dependent Dual-Channel Excited-State Intramolecular Proton Transfer Mechanism of Fluorescence Ratio Probe BZ-DAM.

The mechanism of fluorescence detection of diethyl chlorophosphate (DCP) based on 2-substituted benzothiazole (BZ-DAM) was studied by a theoretical calculation method. It should not be ignored that both the BZ-DAM and the detection product BZ-CHO have two excited-state intramolecular proton transfer (ESIPT) channels. Density functional theory (DFT) and time-dependent DFT (TDDFT) theory were used to study the photophysical mechanism of two compounds in two channels in (acetonitrile) ACN solvent, and the temperature dependence of the two channels was given. Channel 1 is more likely to exist at low temperatures and channel 2 is more likely to exist at high temperatures. By theoretical analysis of the constructed potential energy curve, the hydrogen bond energy and electron-hole analysis, we confirmed that both molecules undergo ESIPT and intramolecular charge transfer (ICT) processes in channel 1 and ESIPT and twisted intramolecular charge transfer (TICT) coupling processes in channel 2. The formation of product BZ-CHO molecules led to a significant fluorescence blue-shift phenomenon and inhibited the ICT process, which confirmed that BZ-DAM could be used as a fluorescence probe for fluorescence detection. We sincerely hope that this work will not only help to clarify the excited-state dynamics behavior of the BZ-DAM probe but also provide a new idea for designing and optimizing a new chemical dosimeter.

Molecular dynamics of the ERRγ ligand-binding domain bound with agonist and inverse agonist.

Estrogen-related receptor gamma (ERRγ), the latest member of the ERR family, does not have any known reported natural ligands. Although the crystal structures of the apo, agonist-bound, and inverse agonist-bound ligand-binding domain (LBD) of ERRγ have been solved previously, their dynamic behavior has not been studied. Hence, to explore the intrinsic dynamics of the apo and ligand-bound forms of ERRγ, we applied long-range molecular dynamics (MD) simulations to the crystal structures of the apo and ligand-bound forms of the LBD of ERRγ. Using the MD trajectories, we performed hydrogen bond and binding free energy analysis, which suggested that the agonist displayed more hydrogen bonds with ERRγ than the inverse agonist 4-OHT. However, the binding energy of 4-OHT was higher than that of the agonist GSK4716, indicating that hydrophobic interactions are crucial for the binding of the inverse agonist. From principal component analysis, we observed that the AF-2 helix conformation at the C-terminal domain was similar to the initial structures during simulations, indicating that the AF-2 helix conformation is crucial with respect to the agonist or inverse agonist for further functional activity of ERRγ. In addition, we performed residue network analysis to understand intramolecular signal transduction within the protein. The betweenness centrality suggested that few of the amino acids are important for residue signal transduction in apo and ligand-bound forms. The results from this study may assist in designing better therapeutic compounds against ERRγ associated diseases.

Experimental study on CO2 separation using hydrophobic deep eutectic solvent based supported liquid membranes

Deep eutectic solvents (DESs) have been proposed as a viable and more sustainable solvent for CO2 capture, owing to their low volatility and tunable properties. In this work, polymer membranes were combined with hydrophobic DESs to prepare supported liquid membranes (DES-SLMs), and the potential of using SLMs for CO2/N2 separation was investigated. COSMO-RS model simulations, bond energy analysis as well as stability tests were used to select the polymeric porous support. Hydrophobic polyvinylidene fluoride (PVDF) with a nominal pore size of 0.1 μm was chosen to support three selected hydrophobic DESs. The gas permeabilities through three selected DES-SLMs were experimentally determined, where the thymol-coumarin (1:1) based SLM showed the best performance with a CO2 permeability of 175.0 Barrer and selectivity of 30.2 at room temperature. The separation capability was further improved by mixing the DES with traditional physical absorbents. In addition, the effects of water presence in the gas phase on the DES-SLM were investigated. The membrane was physically stable, but the ideal selectivity of CO2/N2 through the membrane deteriorated with time on steam. By predicting the permeabilities of CO2 and N2 through traditional organic liquid based SLMs, the prospects of developing DESs for SLM applications were demonstrated. Finally, an advanced membrane capture process for a natural gas-fired combined cycle (NGCC) power plant was studied with process simulation and economic analysis, where the SLMs are used to purify the CO2 product.

Modelling G3 gas as an alternative gas for SF6 using COMSOL multiphysics

Sulfur hexafluoride (SF6) gas is the most often gas used in high voltage systems as insulating medium and arc quenching because it has many advantages such as high dielectric strength, low boiling point, low toxicity, and stability for a long period. The 1997 Kyoto protocol recommended the elimination of SF6 gas, because its impact on the atmosphere has global warming potential (GWP) equal to 23,500 and an ozone depletion potential (ODP) equal to 0.08. Kyoto protocol recommended alternatives gases for SF6 gas such as CF3CHCL2, and others. In this paper a new gas called a HeptaFluoro-iso-Butyronitrile+CO2 ([(CF3)2CFCN+CO2]) which is known commercially as green global gas (G3) The dielectric strength for the proposed gas is approximately equal to SF6 gas and excellent arc quenching and achieve Kyoto protocol recommendations about using alternative gases with 98% less impact on GWP than SF6 gas also G3 gas maintain the same dimension and overall footprint which is an important economical factor for utilities. The total bond energy analysis of SF6 and G3 gases has been studied. COMSOL multiphysics was used to simulate the SF6 and G3 gases to show the ability of the G3 gas when working in geographic information system (GIS) equipment.

Atomic-scale insights into the colossal barocaloric effects of neopentyl glycol plastic crystals

Neopentyl glycol has become an important candidate material for solid-state refrigeration in the future because of its environmental protection, high energy efficiency, high stability, and economy. However, the complete micro-dynamic mechanism remains to be established, which restricts its further applications. In this work, we investigate one representative material-plastic crystal neopentyl glycol (NPG) by means of large-scale molecular dynamics simulation. It is found that NPG exhibits colossal barocaloric effects (CBCEs) with high isothermal entropy changes and potentially large adiabatic temperature changes, which closely relates to the reversible order disorder change in NPG's molecular orientation, in which the non-bond interaction between molecules plays a key role. Further analysis of orientational dynamics and hydrogen bond energy during phase transition along with pressure dependent thermal conductivity sheds light on the underlying microscopic mechanism. Our work reveals the molecular mechanism of CBCEs in NPG as a prototypical plastic crystal, providing valuable insight into achieving practical caloric materials in future cooling technology.

Chemical defect-dependent resistive switching characterization in CeO2 thin films

The aim of this study was to characterize the resistive memory switching mechanism of cerium dioxide (CeO2) thin insulating films for different dopants. Three chemical elements (Gd, Zr, and Ca) were used for the doping of 60 nm CeO2 thin films in Pt/CeO2/Pt memory devices. The switching mechanism exhibited unipolar behavior. The results of the electrical measurements for the Gd- and Zr-doping of the Pt/CeO2/Pt device showed a high-resistance ratio of approximately 104, good data retention, which was stable and maintained at approximately 104 s at 25 °C, and reliable endurance over 1500 cycles. However, Ca-doping had the opposite effects. The results suggested that the chemical defects and oxygen vacancies in metallic Gd and Zr were more effective than those of Ca in the CeO2 films. The X-ray photoelectron spectroscopy (XPS) results indicated the important role of oxygen in the doped film composition to generate conductive filaments, which lead to component resistance conversion in the insulating layer. Furthermore, the bond energy analysis of XPS showed that, compared to the undoped components, the Gd- and Zr-doped components had a lower CeO2 bond energy, resulting in a stable configuration conversion, while the Ca-doped components had a higher CeO2 bond energy, resulting in an unstable configuration conversion.

Theoretical exploration of global minima, magnetism, structural stability and growth pattern of holmium‐doped silicon HoSin0/− (n = 10–18) nanoclusters

AbstractThe structural growth pattern of medium‐sized holmium‐doped silicon nanoclusters HoSin0/− (n = 10–18) was systematically probed by means of unbiased structure searches and double‐hybrid density functionals. The identified global minima of the nanoclusters have been confirmed by comparing the calculated spectral properties such as photoelectron spectroscopy, adiabatic electron affinities and vertical detachment energies with the experimental data. The structural evolution reveals Ho‐linked configuration for neutral and anionic nanoclusters (starting from n = 10 and 12, respectively). In this configuration, the linker Ho atom connects two small silicon sub‐clusters. The nanoclusters starting from n = 16 prefer the configuration in which Ho atoms reside in the center of Si‐cluster. The natural population analysis interprets the involvement of 4f electron of Ho atom in bonding. The participation in bonding has been traced by a transition of an electron from 4f to 5d orbital. This also results in larger magnetic moments (4 and 5 μB) than that of an isolated Ho atom. The HoSi16− nanocluster has good thermodynamic and moderate chemical stabilities as corroborated by average bond energy analysis, highest occupied molecular orbital‐lowest unoccupied molecular orbital gap, and chemical bonding, thus suggesting it the most appropriate building block for new functional nanomaterials.

Dynamics of the catalyst deactivation: tutorial experience with formalism of thermodynamics of non-equilibrium processes

The catalytic process, during which the catalyst loses activity, is usually difficult for investigation and industrial application, especially when the life time of the catalyst is relatively long (10 to 104 h). Therefore, experimental studies of the deactivation kinetics are very expensive, and mathematical modeling and simulation of the deactivation mechanisms becomes more significant, even more than models of reaction mechanisms. In this paper we present an approach to developing and analysis of deactivation dynamics models based on formalism of thermodynamics of non-equilibrium processes. The simplest two step sequence mechanism of the target reaction is used for deriving and analyzing models of reversible and irreversible deactivation mechanisms corresponding to poisoning and coking phenomena. Differential equations for dynamics of the key deactivation intermediate and of the target reaction rate, as well as of the catalyst relative activity are derived and solved. It is shown that thermodynamic formalism coupled with classic kinetic consideration is useful for the analysis of optimal bond energy of key intermediate with the catalyst, which can provide low deactivation.

Origin of the Enhanced Binding Capability toward Axial Nitrogen Bases of Ni(II) Porphyrins Bearing Electron-Withdrawing Substituents: An Electronic Structure and Bond Energy Analysis.

Axial coordination to metalloporphyrins is important in many biological and catalytic processes. Experiments found the axial coordination of nitrogenous bases to nickel(II) porphyrins to be strongly favored by electron-withdrawing substituents such as perfluorophenyls at the meso carbon positions. Careful analysis of the electronic structure reveals that the natural explanation in terms of density change of the nickel(II) porphyrin system (in particular the metal), does not apply. Electron density changes, by the assumed inductive or polarizing effects on the metal or on the porphyrin ring system, are slight. The effect is caused by a remarkable through-space electric field effect on the metalloporphyrin system, originating from the charge distribution inside the perfluorphenyl groups (mostly the C-F dipoles).

Development of size and shape dependent model for magnetic properties from bulk to nanoscale

A simple model based on the bond energy analysis is developed. The model is used to compute the size and shape dependence of magnetic properties, viz. Curie temperature TC(D), magnetization MS(D), and Neel temperature TN(D), where D denotes the size of nanoparticles. It is found that TC(D) and MS(D) decrease with a decrease in size. TN(D) is found to increase or decrease with dropping D, depending on the interaction strength at the film/substrate interface. The model predictions have been compared with the available experimental data. There is a reasonably good agreement between model predictions and experimental results. The model may be extended to other nanomaterials in different size and shape, due to its simplicity. The results obtained for corresponding bulk material are also included for comparison purposes.

Strong intramolecular hydrogen bonds and steric effects involving C═S groups: An NMR and computational study.

A number of 5-acyl rhodanines and thiorhodanines with bulky acyl groups (pivaloyl and adamantoyl), not previously available, have been synthesized. The compounds are shown to exist in the enol form. Structures have been calculated using both the MP2 approach and the B3LYP-GD3BJ functional and the 6-311++G(d,p) basis set. Hydrogen bond energies are estimated by subtracting energies of a structure with the OH group turned 180° from those of the intramolecularly hydrogen-bonded one. Properties such as OH chemical shifts, two-bond isotope effects on 13 C chemical shifts, electron densities at the bond critical point from atoms in molecules analysis, and the hydrogen bond energies show that the sterically hindered compounds have stronger hydrogen bonds than methyl or isopropyl derivatives. The combination of oxygen and sulfur derivatives enables a detailed analysis of hydrogen bond energies.

Molecular knot with nine crossings: Structure and electronic properties from density functional theory computation

The electronic structure of a molecule with nine-crossing composite knots 973 link denoted by the Alexander-Briggs notation (complex-1) are studied by means of theoretical methods (DFT). The most interesting feature of this kind of molecules is their capability to capture anion spices inside the cage. Stability and chemical reactivity were evaluated taking advantage of the criteria chemical hardness and chemical potential. The simulation of the infrared spectra is also included and shows the characteristic signal of the molecule in a range 1000–1600 cm−1. The frontier molecular orbitals were also analyzed. Whereas the capability to capture chlorine ion into the cavity of the complex-1 is explored by means the analysis of bond energy. Also, the electron density distribution of the chlorine complex was studied by means the quantum theory of atoms in molecules (QTAIM) formalism in order to stablish its bonding properties as well as the electron transfer between chlorine ion and complex-1 which was approached by the natural bonding orbital (NBO) and Hirshfeld charge. Ours results revels semiconductor behaviors for both compounds.

Impact of doping on bonding energy hierarchy and melting of phase change materials

The impact of doping on the bonding energy hierarchy and melting point of phase change material germanium telluride is studied. The underlying bonding energy decomposition is based on density functional theory calculations. It is shown that doping can influence the bonding energy hierarchy to lower the melting temperature and latent heat of fusion. Conversely, doping slightly increases the specific heat capacity. Nevertheless, doping induces a net reduction in energy consumption for the “reset” operation of phase change memory devices. This bonding energy analysis is three to four orders of magnitude more computationally efficient than the widely used ab initio molecular dynamics simulations. It is expected that this approach could be useful for next-generation high-throughput simulation-based phase change material design and optimization.

A DENSITY FUNCTIONAL THEORY INVESTIGATION OF D8 TRANSITION METAL(II) (NI, PD, PT) CHLORIDE COMPLEXES OF SOME VIC-DIOXIMES DERIVATIVES

Herein, a theoretical study on the stability of some vic-dioxime complexes of Ni(II), Pd(II) and Pt(II) in gas and aqueous phases is reported. The DFT/M06/SDD and DFT/M06/6-31G+(d,p) levels of theory were adopted for the metal ions and for every other element respectively. Structural analyses of investigated complexes have revealed square planar geometries stabilized by two O–H⋯Cl hydrogen bonds. Analysis of hydrogen bond energies calculated via quantum theory of atoms in molecules (QTAIM) and computed chemical hardness values has revealed that the stability of the complexes is determined by the hydrogen bond strength. Natural population analysis has revealed ligand-metal charge transfer in the complexes investigated. A good linear agreement with correlation coefficient 0.992 has been found between calculated and experimental IR vibrational frequencies, indicating the validity of the theoretical method employed herein. Negative binding energies obtained are indicative of the stability of the complexes, thus affirming the use of vic-dioximes ligands as potential d8 transition metal eliminating agents in solution.

Evaluation of SF6-alternative gas C5-PFK based on arc extinguishing performance and electric strength

C5-PFK (C5-perfluoroketone, C5F10O) is under wide consideration as an environmentally-friendly alternative gas to SF6 in high-voltage applications, because of its superior insulation performance. The aim of this work is to study theoretically the arc extinguishing performance and electric strength of C5-PFK.The arc extinguishing performance of C5-PFK was evaluated by analyzing and comparing the thermophysical properties of C5-PFK, SF6, CF4, CO2 and N2 plasmas. It was difficult to obtain the species formed in C5-PFK plasmas because of the complex C5-PFK molecular decomposition process. In this work, the decomposition process of C5-PFK and the related species were analyzed by the bond energy analysis method. For the species for which parameters such as the partition function and the enthalpy of formation were not available, computational chemistry methods were used to obtain the required data. The collision integrals were calculated using the phenomenological potential model. Using these results, the local thermodynamic equilibrium composition at temperatures from 300 to 30 000 K at 1–10 atm of pure C5-PFK was calculated by the method of minimization of the Gibbs free energy, and the corresponding transport coefficients were calculated by Chapman–Enskog method. Through the comparison of the thermophysical properties, it was found that C5-PFK had similar characteristics to SF6, with large peaks in specific heat below 4500 K, indicating potentially good thermal interruption capability. However, the specific heat peak at 7000 K corresponding to CO decomposition may detract from the thermal interruption capability. Specific heat peaks at higher temperatures are associated with the breaking of double or triple bonds, and should be avoided if possible in the new alternative gases.The electric strength of C5-PFK was assessed using the molecular electrostatic potential, which can be accurately calculated or measured, and gives strong insights into important characteristics of the molecule. Based on the analysis of the molecular surface electrostatic potential and electric strength of C5-PFK, SF6, CF4, CO2, and N2, it is found that the positive potential area of the molecular surface has a strong correlation with the electric strength and is expected to be one of the predictors of electric strength. To verify this phenomenon, 36 kinds of particles were used for the correlation analysis. The correlation coefficient between the positive potential area and electric strength is up to 0.9 which means strong correlation.

Computational insights into novel dicobalt polynitrogen: structure, stability, intermolecular interaction, and application

Previous studies have suggested that polynitrogen species are significant as potential candidates for superior energetic material. In this paper, the polynitrogen species of Co2(N5)4 were reasonably designed and studied by the density functional theory (DFT), and five isomers of Co2(N5)4 were selected. These species were explored in detail, including structure, stability, intermolecular interaction, and application. The five isomers, each with its own special structure feature, were stable enough based on the analysis of bond energy, chemical hardness, and aromaticity. Furthermore, the intermolecular interactions suggested the presence of a covalent interaction in the Co–Co and N–N bonds, the electronic delocalization in cyclo-N5, and the ionic feature in the Co–N bond. In addition, all of the title species held high-energy content. Compared with the known high energy density materials of HB(N5)3Be2(N5)3BH, energetic material of nitromethane, and famous nitramine explosive HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane), Co2(N5)4 holds a stronger advantage. The five Co2(N5)4 species were located at 27.8–35.8 kcal/mol per N2 unit, their energy densities were about 2.73 × 104 MJ/kg, and their mass densities were in the range of 2.60–2.74 g/cm3. Significantly, the 4-1 was the most stable, and its density was also the greatest among the five species. Thus, it has the most potential as a high energy density material.

DFT study on the mechanism of the Diels–Alder reactions leading to bicyclo[4.2.0]octenones

The regioselectivity and mechanism of the Diels–Alder reaction (DA) between 2-substituted cyclobut-2-enones and some electron-rich 1,3-butadiene derivatives, were studied using density functional theory (DFT). Four possible reaction pathways, which are related to the formation of bicyclo[4.2.0]oct-3-en-7-ones, were investigated using natural bond orbital analysis, geometrical parameter and energy analysis and also DFT-based reactivity indices. The energy and bond order analyses show that the larger activation energy prevents the formation of meta products. Therefore ortho products are preferred and the process follows an asynchronous concerted mechanism with a polar nature via DA cycloaddition. Moreover, high regio- and stereoselectivity have been seen in the DA reaction of 2-cyanocyclobut-2-enone.

Theoretical insights into the nature of bonding in group 13–group 15 compounds [RE[dbnd]E′R] (E = B–Tl; E′ = N–Bi; R = Me, Ph, Ar): Bonding energy analysis

Molecular geometry, electronic structure and bonding analysis of multiply bonded, monomeric group 13–group 15 compounds [REE′R] (E=B–Tl; E′=N–Bi; R=Me, Ph, Ar=C6H3-2,6-Ph2) were investigated using BP86/TZ2P/ZORA level of theory. The optimized geometrical parameters are in excellent agreement with the experimental values. The Pauling and Mayer bond order of the optimized structures of [REE′R] shows that the EE′ bonds in these compounds are essentially multiple bonds. The electronic structure of the studied compounds, which is obtained by NBO analysis, reveals that the EE′ σ-bonding orbitals consist of nearly sp hybridized orbital at group 13 element (E) while the heavier group 15 elements (E′) have >75% p-orbital contribution to the total atomic orbital contributions. The bending of EE′C bond angles have been discussed in terms of the percentage s character of group 15 elements along EE′ and E′C bonds and a second order Jahn–Teller distortion. The EE′ π-bonding orbitals are highly polarized toward the group 15 atom. The contributions of orbital interactions, ΔEorb, to the EE′ bonds are larger than the electrostatic interactions, ΔEelstat, indicating greater covalent characters of the EE′ bonds than the ionic characters. In all studied compounds, the π-bonding contributions to the total EE′ bonds are smaller (19.5–37.6%) than the corresponding σ-bonding contributions. The absolute values of the interaction energy, as well as bond dissociation energy decreases in the order N>P>As>Sb>Bi and B>Al>Ga>In>Tl.