Calculated Energy Barriers Research Articles

Strategies to Control Human Health Risks Arising from Antibiotics in the Environment: Molecular Modification of QNs for Enhanced Plant-Microbial Synergistic Degradation.

In the present work, a comprehensive screening and evaluation system was established to improve the plant–microbial synergistic degradation effects of QNs. The study included the construction of a 3D-QSAR model, the molecular modification, environmental friendliness and functional evaluation of drugs, degradation pathway simulation, and human health risk assessment. Molecular dynamics was applied to quantify the binding capacity of QNs toward the plant degradation enzyme (peroxidase) and microbial degradation enzymes (manganese peroxidase, lignin peroxidase, and laccase). The fuzzy comprehensive evaluation method was used in combination with the weighted average method for normalization and assigning equal weights to the plant and microbial degradation effect values of the QNs. Considering the synergistic degradation effect value as the dependent variable and the molecular information of the QNs as the independent variable, a 3D-QSAR model was constructed for the plant–microbial synergistic degradation effect of QNs. The constructed model was then employed to conduct the molecular modification, environmental friendliness and functional evaluation, degradation pathway simulation, and human health risk assessment of transformation products using pharmacokinetics and toxicokinetics. The results revealed that the synergistic degradation effect 3D-QSAR (CoMSIA) model exhibited good internal and external prediction ability, fitting ability, stability, and no overfitting phenomenon. Norfloxacin (NOR) was used as the target molecule in the molecular modification. A total of 35 NOR derivatives with enhanced plant–microbial synergistic degradation effect (1.32–21.51%) were designed by introducing small-volume, strongly electronegative, and hydrophobic hydrogen bond receptor groups into the active group of the norfloxacin structure. The environment-friendliness and the functionality of NOR were evaluated prior to and after the modification, which revealed seven environment-friendly FQs derivatives exhibiting moderate improvement in stability and bactericidal efficacy. The simulation of the NOR plant and microbial degradation pathways prior to and after the modification and the calculation of the reaction energy barrier revealed Pathway A (D-17 to D-17-2) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in plants and Pathway A (D-17 to D-17-1) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in microorganisms. This demonstrated that the degradation of the modified NOR derivatives was significantly enhanced, with the hydroxylation and piperazine ring substitution reaction playing an important role in the degradation process. Finally, the parameters, including hepatotoxicity, mutagenicity, and rodent carcinogenicity, among others, predicted using the pharmacokinetics and toxicokinetics analyses revealed a significant reduction in the human health risk associated with the modified NOR, along with a considerable reduction in the toxicity of its transformation products, implying that the human health risk associated with the transformation products was reduced remarkably. The present study provides a theoretical basis for novel ideas and evaluation programs for improving the plant–microbial synergistic degradation of the QNs antibiotics for source control and drug design, thereby reducing the residues of these antibiotics and the associated hazard in the complex plant–soil environment, ultimately decreasing the potential risks to human health.

Scandium decorated C24 fullerene as high capacity reversible hydrogen storage material: Insights from density functional theory simulations

Using first principles density functional theory simulations, we have observed that the scandium decorated C24 fullerene can adsorb up to six hydrogen molecules with an average adsorption energy of −0.35 eV per H2 and average desorption temperature of 451 K. The gravimetric wt% of hydrogen for the scandium decorated C24 fullerene system is 13.02%, which is sufficiently higher than the Department of Energy, United States demand. Electronic structure, orbital interactions, and charge transfer mechanisms are explained using the density of states, spatial charge density difference plots, and Bader charge analysis. A total amount of 1.44e charge transfer from the 3d and 4s orbitals of scandium to the 2p carbon orbitals of C24 fullerene. Hydrogen molecules are attached to scandium decorated C24 fullerene by Kubas type of interactions. Diffusion energy barrier calculations predict that the existence of a sufficient energy barrier will prevent metal–metal clustering. Ab-initio molecular dynamics (A.I.M.D.) simulations confirm the solidity of structure at the highest desorption temperature. Therefore, we believe that the scandium decorated C24 fullerene system is a thermodynamically stable, promising reversible high-capacity hydrogen storage device.

Theoretical Insights into the NH3 Decomposition Mechanism on the Cu- and Pt- Embedded Graphene Surfaces: A DFT Approach

Herein, the catalytic activities of Cu-and Pt-embedded graphene surfaces on the sequential decomposition reaction of NH3 molecule were investigated by density functional theory (DFT). Partial charge changes on the surfaces by embedding Cu and Pt atoms on the bare graphene surface were analyzed by the Bader charge analysis and depicted by the electron density difference maps. Grimme-D2 dispersion correction was employed for weak interactions between adsorbates and both graphene surfaces. The most stable geometries of the adsorption of NHx (x = 0 → 3) and H species and their fragmented co-adsorption structures on both graphene surfaces were obtained. The internal energy barrier calculations required for the sequential decomposition of NH3 on both graphene surfaces were calculated by the CINEB method and the results obtained for complete decomposition of NH3 were illustrated by relative energy diagram. The findings revealed that the decomposition of NH3 to NH2, NH, and N on the Cu-embedded graphene surface had relatively lower activation barriers of 1.52 eV, 0.72 eV, and 0.64 eV, respectively, compared to the Pt-embedded graphene surface. The Cu-embedded graphene surface was of high selectivity over the NH3 sequential decomposition reaction. This information may paw the way for different strategies for the development of Cu-based catalysts for NH3 decomposition.

Kinetic Monte Carlo simulation of ZrO2 coating deposited by EB‐PVD

AbstractKinetic Monte Carlo (KMC) simulations have been used for electron beam physical vapor deposition (EB‐PVD) of ZrO2 coatings, with the critical potential function fitted by full first‐principles calculations in the framework of density functional theory, emphasizing the effect of critical processing parameters, for example, the substrate temperature (600–1150 K), deposition rate (0.03–7.5 μm/min), and initial kinetic energy (0–0.5 eV). Here, the interaction between ZrO2 particles is described by coarse grain (CG) model with a numerical non‐bonded potential developed by multi‐iterative boltzmann inversion (multi‐IBI). Overall, the calculated energy barrier by the nudged elastic band (NEB) shows the internal diffusion (3.29–4.80 eV) requires more energy than the surface diffusion (2.90–3.42 eV), because of fewer surrounding particles in the latter. Moreover, the energy barrier of Line Jump is smaller than that of Schwoebel Jump, contributing to the columnar grains rather than a dense coating. Of importance, the simulated morphologies of ZrO2 coatings are well consistent to experiments, with a weaker effect from the substrate temperature, initial kinetic energy to deposition rate. Furthermore, the porosity can be effectively reduced by increasing the temperature and initial kinetic energy, however, with a slight increase when increasing the deposition rate.

Computational insights into the reactivity of chlorpyrifos and chlorpyrifos-methyl toward singlet oxygen.

A complete mechanism for the •OH-initiated atmospheric decomposition of the pesticides chlorpyrifos and chlorpyrifos-methyl is proposed, incorporating additional studies on the competing reaction with singlet oxygen. The computational study is based on density functional theory (DFT) at the double-hybrid functional level to treat static correlation in the calculations of energy barriers. Reaction of the P-bonded intermediate with 1O2 has a small energy barrier of ~ 2kcalmol-1, generating the Oxone compound and the HOSO• radical, with a reaction free energy of - 49.8kcal/mol for the chlorpyrifos reaction pathway. Direct reaction of the pesticides with singlet oxygen is unlikely to happen due to the exceedingly high energy barrier of ~ 52kcal/mol. However, in aqueous solution, the activation energy reduces dramatically and changes the reaction thermodynamics, making it kinetically accessible and thermodynamically viable.

First‐Principles Investigation of the Effect of Vanadium Doping on Hydrogen Incorporation in Tungsten

AbstractUsing the first‐principles method based on the density functional theory, hydrogen diffusion, electron structure, and mechanical properties of hydrogen impurity in W15V structure are investigated in this paper. It is found that in W‐V lattice the single H atom tends to be located in the tetrahedral interstitial site nearest to V atom with the solution energy of 0.614 eV. The calculation of energy barriers shows that the V doping can be helpful to trap H atoms near the V atom. The analysis of the elastic moduli shows that the V‐alloying can decrease the strength and improve the ductility of pure W. In addition, the H impurity further enhances this situation. Besides, the effect of H impurity on pure W is greater than W15V structure. The results of this study offer a useful database for the research of W‐based alloys for plasma facing materials (PFMs).

Noble Gas in a Ring.

We have designed a new type of molecule with a noble gas (Ng = Kr and Xe) atom in a six-membered ring. Their structures and stability have been studied by density functional theory and by correlated electronic structure calculations. The results showed that the six-membered ring is planar with very short Ng–O and Ng–N polar covalent bonds. The calculated energy barriers for all the unimolecular dissociation pathways are higher than 20 and 35 kcal/mol for Ng = Kr and Xe, respectively. The current study suggests that these molecules and their derivatives might be synthesized and observable at cryogenic conditions.

Effect of alloying elements on stacking fault energies and twinnabilities in high‐entropy transition‐metal carbides

AbstractTwinning is a fundamental mechanism behind the simultaneous increase in the strength and ductility of high‐entropy alloys. Similar approaches may contribute to the remarkable improvements of the mechanical properties of high‐entropy ceramics. In this study, the stacking fault energies (SFEs) and twinnabilities of a novel category of ZrNbTa‐based high‐entropy transition‐metal carbides (HETMCs) are investigated in terms of their generalized stacking fault energy curves (γ‐curves) via first‐principle calculations. The γ‐curves show that dislocation nucleation in ZrNbTa‐based HETMCs occurs more easily than that of unary transition metal (TM, TM = Zr, Nb, Ta, Hf, Ti, V) carbides. When a pre‐existing intrinsic stacking fault (ISF) is considered, C‐ vertices (TM‐ mirror) twinning fault (TF) more likely forms and TF may be more stable than ISF. The stable SFEs of C‐ vertices ISF and TF decrease with the addition of Hf, Ti, and V atoms to (ZrNbTa)C owing to the severe local lattice distortion. The calculated barrier energies and twinnabilities further indicate that twinning is possible for the selected ZrNbTa‐based HETMCs. Theoretical twinnabilities (τa) decrease in the following sequence: (ZrNbTa)C > (ZrNbTaHfTi)C > (ZrNbTaHf)C > (ZrNbTaHfTiV)C. Thus, the addition of Hf, Ti, and V atoms to (ZrNbTa)C may decrease the twinning probability. This study may be used as a guide for the design of twinning‐induced plasticity HETMCs with excellent mechanical properties.

Alkali-Rich Antiperovskite M3FCh (M = Li, Na; Ch = S, Se, Te): The Role of Anions in Phase Stability and Ionic Transport.

To improve ionic conductivity, solid-state electrolytes with polarizable anions that weakly interact with mobile ions have received much attention, a recent example being lithium/sodium-rich antiperovskite M3HCh (M = Li, Na; Ch = S, Se, Te). Herein, in order to clarify the role of anions in antiperovskites, the M3FCh family, in which the polarizable H- anion at the octahedral center is replaced by the ionic F- anion, is investigated theoretically and experimentally. We unexpectedly found that the stronger attractive interaction between F- and M+ ions does not slow down the M+ ion diffusion, with the calculated energy barrier being as low as that of M3HCh. This fact suggests that the low-frequency rotational phonon modes of the octahedron of cubic M3FCh (and M3HCh) are intrinsic to facilitate the fast ionic diffusion. A systematic analysis further reveals a correlation between the tolerance factor t and the ionic transport: as t decreases within the cubic phase, the rotational mode becomes softer, resulting in the reduction of the migration energy. The cubic iodine-doped Li3FSe has a room-temperature ionic conductivity of 5 × 10-5 S/cm with a bulk activation energy of 0.18 eV.

Oxidative decomposition and mineralization of caffeine by advanced oxidation processes: The effect of hybridization

The study consists of a detailed investigation of the degradability of the emerging water contaminant-caffeine by homogeneous and heterogeneous Advanced Oxidation Processes (AOP’s), estimation of a synergy index for each hybrid operation thereof, and proposing the most plausible reaction mechanisms that are consistent with the experimental data. It also encompasses evaluation of the effect of the water matrix represented by carbonate species and humic acids, as strong scavengers of hydroxyl radicals. The results showed that single AOP’s such as sonolysis (577 kHz) and photolysis with H2O2 provided complete caffeine elimination, but they were insufficient for the mineralization of the compound. Hybrid AOP’s were considerably more effective, particularly when operated at a heterogeneous mode using commercial TiO2. The most effective hybrid process was UV-H2O2/TiO2, which provided more than 75% TOC decay at the minimum test doses of the reagent and catalyst. While the addition of ultrasound to the process significantly increased the rate of caffeine decomposition, it reduced the overall degradation of the compound to 64% in terms of TOC decay. The antagonistic effect was attributed to the formation of excess H2O2, and the presence of cavity clouds and/or high density layers that inhibited the transmission of UV light. The effect of natural water ingredients was found to reduce the reaction rates, signifying the major contribution of hydroxyl radicals to the destruction of caffeine. The proposed reaction mechanisms based on OH radical attack and the calculated energy barriers were in good agreement with the experimentally detected reaction byproducts.

New Mechanistic Pathways for the Reactions of Formaldehyde with Formic Acid Catalyzed by Sulfuric Acid and Formaldehyde with Sulfuric Acid Catalyzed by Formic Acid: Formation of Potential Secondary Organic Aerosol Precursors

Formaldehyde (HCHO) plays an important role in the formation of secondary organic aerosols. Here, we report new mechanistic pathways for the reactions of formaldehyde with formic acid catalyzed by sulfuric acid and formaldehyde with sulfuric acid catalyzed by formic acid by using quantum chemical methods and reaction rate theory. We have found that sulfuric acid and formic acid have a strong catalytic role in the HCHO···HCOOH + H2SO4 and HCHO···H2SO4 + HCOOH reactions because the calculated energy barriers of the sulfuric acid-catalyzed reaction of formaldehyde with formic acid and formic acid-catalyzed reaction of formaldehyde with sulfuric acid are decreased by 21.17 and 14.81 kcal/mol, respectively. The calculated rates show that the reaction rate of HCHO···HCOOH + H2SO4 is faster than those of HCHO···H2SO4 + HCOOH and HCHO + HCOOH···H2SO4. Moreover, the HCHO + HCOOH + H2SO4 → H2C(OH)OCOH + H2SO4 reaction readily forms the carboxylic acid ester (H2C(OH)OCOH); this is a new mechanistic pathway for the reaction of formaldehyde with formic acid, which is expected to extend to other aldehydes’ reaction with carboxylic acids. Additionally, the present findings also suggest that formic acid-catalyzed formaldehyde and sulfuric acid reaction leads to the formation of an organosulfate as the nucleation precursor. The present results not only help understand the mechanisms for the initial processes of atmospheric nucleation but also are expected to extend other aldehydes and acids in the atmosphere.

Conversion of methane to methanol on C-doped boron nitride: A DFT study

Computational modeling of the methane-to-methanol catalytic conversion reaction on the carbon-boron nitride nanosheet (C-BNN) was reported with the density functional theory. The charge density on C-BNN was displayed with the electron density difference map and investigated with the Bader charge analysis. The reaction mechanism was constituted according to the Eley Rideal model. CH4 → CH3OH conversion reaction were analyzed through the interaction of CH4 with O or O2 on the surface. The calculated energy barrier of the CH4 + O* → CH3OH and CH4 + O2 → CH3OH + O on C-BNN is 0.97 eV and 0.20 eV respectively. Our calculation results showed that the C-BNN surface was a highly active catalyst for the conversion reaction of methane to methanol. This information can provide different strategies for new catalyst researches with low cost and high catalytic activity.

Accurate reaction barriers and rate constants of H-abstraction from primary, secondary, and tertiary amines by H atom determined with the isodesmic reaction method

The H-abstraction reaction kinetics of primary, secondary and tertiary amines with H atom are computed using the isodesmic reaction method. The average unsigned deviation of energy barriers is 12.40 kcal mol−1 at the HF/6-31+G(d) level compared to the CCSD(T)/CBS(D-T-Q) method but reduced to 0.75 kcal mol−1 after corrections. The calculated rate constants of all reactions and corresponding rate rules are also presented. This work solves the accurate energy barrier calculations for larger molecules reaction amines + H at a low level HF method and also provides the accurate reaction kinetics for the critical important H-abstraction reactions of amines combustion modeling.

Toward alcohol synthesis from CO hydrogenation on Cu(111)-supported MoS2 - predictions from DFT+KMC.

In the quest for cheap and efficient catalysts for alcohol synthesis from syngas, a material of interest is single-layer MoS2 owing to its low cost, abundancy, and flexible structure. Because of the inertness of its basal plane, however, it is essential to find ways that make it catalytically active. Herein, by means of density functional theory based calculations of reaction pathways and activation energy barriers and accompanying kinetic Monte Carlo simulations, we show that while S vacancy row structures activate the MoS2 basal plane, further enhancement of chemical activity and selectivity can be achieved by interfacing the MoS2 layer with a metallic support. When defect-laden MoS2 is grown on Cu(111), there is not only an increase in the active region (surface area of active sites) but also charge transfer from Cu to MoS2, resulting in a shift of the Fermi level such that the frontier states (d orbitals of the exposed Mo atoms) appear close to it, making the MoS2/Cu(111) system ready for catalytic activity. Our calculated thermodynamics of reaction pathways lead to the conclusion that the Cu(111) substrate promotes both methanol and ethanol as the products, while kinetic Monte Carlo simulations suggest a high selectivity toward the formation of ethanol.

Heterogeneous photooxidation of 6:2 polyfluoroalkyl phosphoric acid diester on dust mineral components under simulated sunlight and the influence of relative humidity and oxygen

Polyfluoroalkyl phosphoric acid diesters (diPAPs) have been widely and increasingly detected in various environmental mediums. The degradation of diPAPs brings perfluoroalkyl carboxylic acids (PFCAs) concerned of adverse health effects. DiPAPs mainly occur in particulate matter in ambient air and their photo-degradation behaviors have not been investigated. In this study, heterogeneous photo-degradation of 6:2 diPAP was studied on four model mineral components in ambient dust. 6:2 diPAP was found to undergo a fast degradation on titanium dioxide (TiO2) particles as well as on artificial mineral dust containing TiO2 (2.67% in mass) to produce C5–C7 PFCAs and other intermediates. Based on monitored intermediates and further degradation tests on important intermediates, thermodynamic calculation of energy barrier and Gibbs Free Energy was used to explain the observed degradation patterns and accordingly the degradation pathways of diPAPs were proposed. The increase in relative humidity promotes the production of hydroxyl radicals, which enhances the hydrolysis of 6:2 mono- and di-PAPs and the yield of C5 and C7 PFCAs. Oxygen is critical for radical formation, which bypasses the production of fluorotelomer carboxylic acid. Results of this study for the first time demonstrate that diPAP may account for additional PFCA sources in both indoor and outdoor environments and the heterogeneous degradation pathways were different from those of volatile fluorotelomer alcohols.

Mechanistic insight into the hydrogenation of acetylene on the Pd2/g-C3N4 catalyst: effect of Pd clustering on the barrier energy and selectivity

In this work, the hydrogenation of acetylene on the Pd2/g-C3N4 catalyst is investigated by the density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) calculations. The pre-reactant (R), transition states (TSs), and the intermediates (IMs), involved in the hydrogenation process, are characterized from the point of view of energy and structure. The calculated energy barriers for the hydrogen transfer to the acetylene and ethylene are 6.77 and 12.28 kcal/mol, respectively, which shows that the Pd2/g-C3N4 catalyst has good selectivity for the conversion of acetylene to ethylene rather than ethane. Comparing the values of these energy barriers with those of the hydrogenation of acetylene on the Pd/g-C3N4 catalyst (21.53 and 38.88 kcal/mol, respectively) shows that the increase in the number of the Pd atoms decreases the energy barriers of the hydrogenation reaction and increases the selectivity of the catalyst for the ethylene production.

Enlisting Potential Cathode Materials for Rechargeable Ca Batteries

The development of rechargeable batteries based on a Ca metal anode demands the identification of suitable cathode materials. This work investigates the potential application of a variety of compounds, which are selected from the inorganic crystal structural database, considering 3d-transition metal oxysulfides, pyrophosphates, silicates, nitrides, and phosphates with a maximum of four different chemical elements in their composition. Cathode performances of CaFeSO, CaCoSO, CaNiN, Ca3MnN3, Ca2Fe(Si2O7), CaM(P2O7) (M = V, Cr, Mn, Fe, and Co), CaV2(P2O7)2, Ca(VO)2(PO4)2, and α-VOPO4 are evaluated through the calculation of operation voltages, volume changes associated with the redox reaction, and mobility of Ca2+ ions. Some materials exhibit attractive specific capacities and intercalation voltages combined with energy barriers for Ca migration around 1 eV (CaFeSO, Ca2FeSi2O7, and CaV2(P2O7)2). Based on the Density Functional Theory results, αI-VOPO4 is identified as a potential Ca cathode with a maximum theoretical specific capacity of 312 mAh/g, an average intercalation voltage of 2.8 V, and calculated energy barriers for Ca migration below 0.65 eV.

Catalyzed Ethanol Chemical Looping Gasification Mechanism on the Perfect and Reduced Fe2O3 Surfaces

Biomass chemical looping gasification (CLG) is a novel gasification technology for hydrogen production, where the oxygen carrier (OC) transfers lattice oxygen to catalytically oxidize fuel into syngas. However, the OC is gradually reduced, showing different reaction activities in the CLG process. Fully understanding the CLG reaction mechanism of fuel molecules on perfect and reduced OC surfaces is necessary, for which the CLG of ethanol using Fe2O3 as the OC was introduced as the probe reaction to perform density functional theory calculations to reveal the decomposition mechanism of ethanol into the synthesis gas (including H2, CH4, ethylene, formaldehyde, acetaldehyde, and CO) on perfect and reduced Fe2O3(001) surfaces. When Fe2O3(001) is reduced to FeO0.375(001), the calculated barrier energy decreases and then increases again, suggesting that the reduction state around FeO(001) favors the catalytic decomposition of ethanol to produce hydrogen, which proves that the degree of reduction has an important effect on the CLG reaction.

Noncatalytic Bromination of Icosahedral Dicarboranes: The Key Role of Anionic Bromine Clusters Facilitating Br Atom Insertion into the B-H σ-Bond.

The mechanism of the noncatalytic bromination of carboranes was studied experimentally and theoretically. We found that the reactions of o- and m-carboranes 1 and 2 with elemental bromine are first order in the substrate but unusually high (approximately fifth) order in bromine. The calculated energy barriers of these reactions decrease sharply as more bromine molecules are added to the quantum-chemical system. A considerable primary deuterium kinetic isotope effect for the bromination of 2 indicates that the rate-limiting stage is B-H bond breakage. According to quantum-chemical reaction path calculations, the bond breakage proceeds after the intrusion of a bromine atom into the B-H σ-bond. The 9-Br and 9-OH substituents in carborane 1 strongly retard the bromination of the corresponding derivatives. The bromination mechanism of 9-OH-1 is complex and includes neutral, deprotonated, and protonated forms of the carborane. The high experimental kinetic reaction order in bromine, together with quantum chemical modeling, points to a specific mechanism of bromination facilitated by anionic bromine clusters which significantly stabilize the transition state.

A practical way to enhance the synthesis of N8- from an N3- precursor, studied by both computational and experimental methods.

Polymeric nitrogen (PN) belongs to a general family of materials containing all-nitrogen molecules or clusters. Although it is rare and challenging to synthesize PN members, they are attracting increasing scientific attention due to their high energy storage capacity and possible use as a green catalyst. A few theoretical calculations predicted the possible PN phases from N2 gas, but they all require extremely high pressures and temperatures to synthesize. In this work, a practical way to synthesize N8 polymeric nitrogen from an N3- precursor is elucidated using density functional theory calculations. The detailed mechanism, , is determined. The calculated energy barriers indicate that the first step is the rate-limiting step. This result guides us to rationally synthesize N8 under UV (254 nm) irradiation, chosen based on the calculated absorption spectrum for the azide anion. As expected, UV irradiation enhances N8 yields by nearly four times. This provides an interesting route to the scalable synthesis of high energy density N8 compounds.