Combination Of DFT Calculations Research Articles

Chemical Orderings in CuCo Nanoparticles: Topological Modeling Using DFT Calculations

The orderings of atoms in bimetallic 1.6–2.1 nm-large CuCo nanoparticles, important as catalytic and magnetic materials, were studied using a combination of DFT calculations with a topological approach. The structure and magnetism of Cu50Co151, Cu101Co100, Cu151Co50, and Cu303Co102 nanoparticles; their resistance to disintegrating into separate Cu and Co species; as well as the exposed surface sites, were quantified and analyzed, showing a clear preference for Cu atoms to occupy surface positions while the Co atoms tended to form a compact cluster in the interior of the nanoparticles. The surface segregation of Co atoms that are encapsulated by less-active Cu atoms, induced by the adsorption of CO molecules, was already enabled at a low coverage of adsorbed CO, providing the energy required to displace the entire compact Co species inside the Cu matrices due to a notable adsorption preference of CO for the Co sites over the Cu ones. The calculated adsorption energies and vibrational frequencies of adsorbed CO should be helpful indicators for experimentally monitoring the nature of the surface sites of CuCo nanoparticles, especially in the case of active Co surface sites emerging in the presence of CO.

Ammonia monooxygenase-mediated cometabolic biotransformation of volatile 4-chlorophenol in nitrifying counter-diffused biofilms: A combined molecular dynamics simulation, DFT calculation and experimental study

Ammonia monooxygenase (AMO)-mediated cometabolism of organic pollutants has been widely observed in biological nitrogen removal process. However, its molecular mechanism remains unclear, hindering its practical application. Furthermore, conventional nitrification systems encounter significant challenges such as air pollution and the loss of ammonia-oxidizing bacteria, when dealing with wastewater containing volatile organic pollutants. This study developed a nitrifying membrane-aerated biofilm reactor (MABR) to enhance the biodegradation of volatile 4-chlorophenol (4-CP). Results showed that 4-CP was primarily removed via Nitrosomonas nitrosa-mediated cometabolism in the presence of NH4+-N, supported by the increased nicotinamide adenine dinucleotide (NADH) and adenosine triphosphate (ATP) content, AMO activity and the related genes abundance. Hydroquinone, detected for the first time and produced via oxidative dechlorination, as well as 4-chlorocatechol was primary transformation products of 4-CP. Nitrosomonas nitrosa AMO structural model was constructed for the first time using homology modeling. Molecular dynamics simulation suggested that the ortho-carbon in the benzene ring of 4-CP was more prone to metabolismcompared to the ipso-carbon. Density functional theory calculation revealed that 4-CP was metabolized by AMO via H-abstraction-OH-rebound reaction, with a significantly higher rebound barrier at the ipso-carbon (16.37 kcal·mol-1) as compared to the ortho-carbon (6.7 kcal·mol-1). This study fills the knowledge gap on the molecular mechanism of AMO-mediated cometabolism of organic pollutants, providing practical and theoretical foundations for improving volatile organic pollutants removal through nitrifying MABR.

Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach.

An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.

Adsorption differences of xanthate, dithiophosphate and dithiocarbamate on stibnite (010) surface with Cu2+ activated: Combined DFT calculations and experiments

Antimony is an important strategic metal resource. Stibnite as one of the main sources of antimony resources, efficiently recycling stibnite has always been a topic of interest. Currently, there is a scarcity of research examining the adsorption differences of butyl xanthate (BX), sodium diethyldithiocarbamate (DDTC) and ammonium dibutyl dithiophosphate (ADD) on the stibnite (010) surface with Cu2+ activated based on atomic scale. This study investigates the adsorption differences of BX, DDTC and ADD on the stibnite (010) surface with Cu2+ activated, combining density functional theory with experiments. DFT calculations showed that there are five adsorption sites of Cu2+ on the stibnite surface, analysis of partial density of states (PDOS) indicated that the difference in hybridization strength between Cu 3d and S 3p orbitals caused discrepancy in adsorption sites performance. Analysis of PDOS, Mulliken population and electron density difference, it can be concluded that the collector interaction strongly with the stibnite surface with Cu2+ activated and the difference of charge transferred by S atoms during the interaction process is the main reason for the differences in adsorption performance and the varying stability of CuS bonds in adsorption models. Under comprehensive comparison the flotation experiments and adsorption tests showed that with Cu2+ activation, the recovery rate of stibnite was significantly improved with DDTC and the adsorption effect was optimal. Finally, the adsorption performance sequence on Cu2+ activated stibnite surface for the three collectors is as follows: DDTC > ADD > BX. This study combining experimental and DFT calculations, provides guidance for the development of efficient collectors for stibnite flotation in the future.

Revealing the interaction forms between Hg(II) and group types (–Cl, –CN, –NH2, –OH, –COOH) in functionalized Poly(pyrrole methane)s for efficient mercury removal

To explore the impact of different functional groups on Hg(II) adsorption, a range of poly(pyrrole methane)s functionalized by –Cl, –CN, –NH2, –OH and –COOH were synthesized and applied to reveal the interaction between different functional groups and mercury ions in water, and the adsorption mechanism was revealed through combined FT-IR, XPS, and DFT calculations. The adsorption performance can be improved to varying degrees by the incorporation of functional groups. Among them, the oxygen-containing functional groups (–OH and –COOH) exhibit stronger affinity for Hg(II) and can increase the adsorption capacity from 180 mg g−1 to more than 1400 mg g−1 at 318 K, with distribution coefficient (Kd) exceeding 105 mL g−1. The variations in the capture and immobilization capabilities of functionalized poly(pyrrole methane)s predominantly stem from the unique interactions between their functional groups and mercury ions. In particular, oxygen-containing –OH and –COOH effectively capture Hg(OH)2 through hydrogen bonding, and further deprotonate to form the –O–Hg–OH and –COO–Hg–OH complexes which are more stable than those obtained from other functionalized groups. Finally, the ecological safety has been fully demonstrated through bactericidal and bacteriostatic experiments to prove the functionalized poly(pyrrole methane)s can be as an environmentally friendly adsorbent for purifying contaminated water.

Enhanced piezo-catalytic performance of BaTiO3 nanorods combining highly exposed active crystalline facets and superior deformation capability: Water purification and activation mechanism

Using piezoelectric materials for advanced oxidation is a green and viable means of water purification and environmental restoration. However, unmodified piezoelectric catalysts exhibited unsatisfactory catalytic performance, which had become a bottleneck for the practical application of piezoelectric catalysis. In this work, piezoelectric responsiveness and exposed active crystal surface area were rationally coordinated by synthesizing one-dimensional BaTiO3 nanorods (BTO NRs). Enhanced piezo-responsivity enables faster free charge carriers transfer, while the highly exposed area of the (001) facets provides more active sites for piezo-catalytic reactions. Consequently, BTO NRs degraded RHB (Rhodamine B) and TC (Tetracycline) with first-order rate constants of 0.018 min−1 and 0.012 min−1, respectively, 5 times higher than BaTiO3 nanoparticles. The specific active sites on the (001) crystal plane were further investigated through a combination of DFT calculations, free radical trapping experiments, and XPS analysis. Ti4+ adsorbs and activates water molecules to generate Ti3+ and •OH, in the catalytic reaction. Afterward, Ti3+ is oxidized to Ti4+ by piezo-holes (holes driven by piezoelectric potential), while •OH is desorbed and involved in the degradation of pollutants. This research not only provides an approach to modify piezoelectric catalysts with high catalytic activity but also presents new insights into the mechanism of piezoelectric catalysis from the viewpoint of the atom level.

Metal-Oxo Electronic Tuning via In Situ CO Decoration for Promoting Methane Conversion to Oxygenates over Single-Atom Catalysts.

Direct methane conversion (DMC) to oxygenates at low temperature is of great value but remains challenging due to the high energy barrier for C-H bond activation. Here, we report that in situ decoration of Pd1-ZSM-5 single atom catalyst (SAC) by CO molecules significantly promoted the DMC reaction, giving the highest turnover frequency of 207 h-1 ever reported at room temperature and ~100 % oxygenates selectivity with H2O2 as oxidant. Combined characterizations and DFT calculations illustrate that the C-atom of CO prefers to coordinate with Pd1, which donates electrons to the Pd1-O active center (L-Pd1-O, L=CO) generated by H2O2 oxidation. The correspondingly improved electron density over Pd-O pair renders a favorable heterolytic dissociation of C-H bond with low energy barrier of 0.48 eV. Applying CO decoration strategy to M1-ZSM-5 (M=Pd, Rh, Ru, Fe) enables improvement of oxygenates productivity by 3.2-11.3 times, highlighting the generalizability of this method in tuning metal-oxo electronic structure of SACs for efficient DMC process.

Metal‐Oxo Electronic Tuning via In Situ CO Decoration for Promoting Methane Conversion to Oxygenates over Single‐Atom Catalysts

AbstractDirect methane conversion (DMC) to oxygenates at low temperature is of great value but remains challenging due to the high energy barrier for C−H bond activation. Here, we report that in situ decoration of Pd1‐ZSM‐5 single atom catalyst (SAC) by CO molecules significantly promoted the DMC reaction, giving the highest turnover frequency of 207 h−1 ever reported at room temperature and ~100 % oxygenates selectivity with H2O2 as oxidant. Combined characterizations and DFT calculations illustrate that the C‐atom of CO prefers to coordinate with Pd1, which donates electrons to the Pd1−O active center (L−Pd1−O, L=CO) generated by H2O2 oxidation. The correspondingly improved electron density over Pd−O pair renders a favorable heterolytic dissociation of C−H bond with low energy barrier of 0.48 eV. Applying CO decoration strategy to M1‐ZSM‐5 (M=Pd, Rh, Ru, Fe) enables improvement of oxygenates productivity by 3.2–11.3 times, highlighting the generalizability of this method in tuning metal‐oxo electronic structure of SACs for efficient DMC process.

The First Example of the Friedel-Crafts Cyclization Leading to (10-Hydroxy-9,10-dihydroanthr-9-yl)phosphonium Salts without the Expected Bradsher Dehydration.

The reaction of (ortho-acetalaryl)arylmethanols with various phosphines PR1R2R3 (R1 = R2 = R3 = Ph; R1 = R2 = Ph, R3 = Me and R1 = R2 = Me, R3 = Ph) under acidic conditions (e.g., HCl, HBF4, TsOH) unexpectedly led to the formation of (10-hydroxy-9,10-dihydroanthr-9-yl)phosphonium salts instead of the corresponding anthryl phosphonium salts. The cyclization occurred according to the Friedel-Crafts mechanism but without the usually observed Bradsher dehydration, giving cyclic products in the form of cis/trans isomers and their conformers. In case of electron-rich and less-hindered dimethylphenylphosphine, all four stereoisomers were recorded in 31P{1H} NMR spectra, while for the other phosphines, only the two most stable cis/trans stereoisomers were detected. This study was supported by DFT and NCI calculations in combination with FT-IR analysis.

Computational screening and experimental fabrication of MoSe2/3d–TMOS heterojunction for room-temperature gas sensor

Heterogeneous engineering is an efficient method to overcome the poor adsorption performance of MoSe2 materials. In this work, the screening process for a suitable transition metal oxide semiconductor with 3d orbital (3d–TMOS) was performed based on the work of adhesion and band edges positions with reference to the MoSe2 material. Then, the gas sensor performance of the suitable composite system was further tested and discussed. The results show that the Cr2O3, Fe2O3 and Co3O4 surface present good interfacial binding strength with MoSe2 compared with other 3d–TMOSs. And the MoSe2/Co3O4 system was selected considering the suitable band edges positions. The as-fabricated MoSe2/0.5–Co3O4 nanocomposite exhibits excellent sensitivity to NO2 at room temperature. Moreover, the MoSe2/0.5–Co3O4 nanocomposite exhibits excellent linear response (R2 = 0.985), selectivity, repeatability, and long–term stability to NO2. The improvement mechanism of gas sensor performance can be mainly attributed to the fast charge extraction rate of type-II heterojunction and greatly sensitive of built-in potential barrier to the carrier density in the MoSe2/0.5–Co3O4 nanocomposite. This research provides a promising method to select the candidates for gas sensor using the combined DFT calculations and experiments.

Highly dense passivation enhanced corrosion resistance of Ti2AlC MAX phase coating in 3.5 wt.% NaCl solution

This study aimed to investigate the dependence of electrochemical behavior upon the microstructural evolution of Ti2AlC MAX phase coating in 3.5 wt.% NaCl solution. The results showed that high-purity Ti2AlC coating with unique equiaxed nanocrystals exhibited remarkably higher impedance and lower current densities compared to those of uncoated Ti-6Al-4V substrate, which was attributed to the formed highly dense and continuously amorphous Al2O3 passive film on the coating surface. According to the combined DFT calculations, both the large diffusivity of Al atoms and the robust stability of Ti2AlxC with Al vacancies exceeding 50% contributed to the unusual achievement of electrochemical passivation characteristics, enabling the significant enhancement of anti-corrosion capability for Ti2AlC coating.

Discovery of new tetrazines for bioorthogonal reactions with strained alkenes via computational chemistry.

Tetrazines are widely employed reagents in bioorthogonal chemistry, as they react readily with strained alkenes in inverse electron demand Diels-Alder reactions, allowing for selective labeling of biomacromolecules. For optimal performance, tetrazine reagents have to react readily with strained alkenes, while remaining inert against nucleophiles like thiols. Balancing these conditions is a challenge, as reactivity towards strained alkenes and nucleophiles is governed by the same factor - the energy of unoccupied orbitals of tetrazine. Herein, we utilize computational chemistry to screen a set of tetrazine derivatives, aiming to identify structural elements responsible for a better ratio of reactivity with strained alkenes vs. stability against nucleophiles. This advantageous trait is present in sulfone- and sulfoxide-substituted tetrazines. In the end, the distortion/interaction model helped us to identify that the reason behind this enhanced reactivity profile is a secondary orbital interaction between the strained alkene and sulfone-/sulfoxide-substituted tetrazine. This insight can be used to design new tetrazines for bioorthogonal chemistry with improved reactivity/stability profiles.

Origins of Selectivity in Glycosylation Reactions with Saccharosamine Donors.

A combination of DFT calculations and experiments is used to describe how the selection of a promoter can control the stereochemical outcome of glycosylation reactions with the deoxy sugar saccharosamine. Depending on the promoter, either α- or β-linked reactive intermediates are formed. These studies show that differential modes of activation lead to the formation of distinct intermediates that undergo highly selective reactions through an SN2-like mechanism.

Migration pathway and solidification mechanism of heavy metal Pb during the conversion of municipal solid waste incineration fly ash into ettringite and simultaneously purification of chloride salts solution process

The solidification/stabilization of heavy metals and valuable component recovery from municipal solid waste incineration (MSWI) fly ash are of great significance for its safe disposal. In this study, MSWI fly ash was transformed into a new solid phase mainly composed of ettringite, achieving the solidification of excessive heavy metal Pb while obtaining a mixed solution of sodium chloride and potassium chloride with extremely low impurity content, which can be recovered by evaporation-crystallization respectively. The solidification mechanism of heavy metal Pb by ettringite was investigated through a combination of DFT calculations and experiments. The results indicate that a high conversion rate of calcium ions (99.68%), separation rate of chloride (95.99%), and conversion rate of heavy metal Pb (99.42%) can be achieved by controlling the ions ratio of the MSWI fly ash reaction system to n(Ca2+):n(Al3+):n(SO42−) = 6:2:3. DFT calculations show that the reaction pathway of the formation of a vacancy-Pb entering the vacancy at the Ca-2 site of ettringite is more likely to occur. The substitution of heavy metal Pb at the Ca-2 site leads to an increase in the unit cell volume, redistribution of charges, and a decrease in the thermal stability of the ettringite. The solidified body of ettringite presents a promising potential for application in cement-based materials due to its negligible risk of heavy metals leaching and low chloride content.

Computational assessment of the reactivity and pharmaceutical potential of novel triazole derivatives: An approach combining DFT calculations, molecular dynamics simulations, and molecular docking

The worldwide prevalence of cancer and its increasing frequency make it a key research area in drug discovery programs. The current research paper describes the development of QSAR models based on the in vitro against topoisomerase II, which identified the structural origin of anticancer activity for derivatives of triazole moieties linked to mansonone E. The models PLS regression QSARs validated by LOO showed an R2 of 0.92, 0.89 and 0.99 and a Q2 of 0.75, 0.62 and 0.88 for CoMFA, CoMSIA and HQSAR respectively. External validation criteria were used to validate the reliability of the models. These results show the impact of electrostatic and steric fields and of the hydrogen bond donor on the activity of the compounds studied. Based on these results, seven novel inhibitors with high activity were designed, which successfully passed Lipinski's rule of five for oral bioavailability. The evaluations of ADME/Tox parameters and synthetic accessibility for chemical synthesis showed acceptable results. Ligand interactions in binding site protein were assessed using molecular docking. The results show the correct conformational pose of the designed compounds especially the compound T1 where it forms hydrogen and hydrophobic interactions with the main binding site residues. The stability of the complexes was confirmed by the MD study and the calculation of the free binding energy. The T1 synthesis reaction was carried out according to the 1,3 cycloaddition reaction. The study of the local and global reactivity and the energy of activation of this reaction have shown the predicted of the regioselectivity of compound T1. Also we have described the state of transition of two isomers T1,4 and T1.5. Finally, this study would be interesting to help identify and optimize avenues for early discovery of anticancer drugs.

Highly efficient hydrogenation of carbamates catalyzed by pincer ruthenium complexes

The [fac-PNN]RuH(PPh3)(CO) complex (Ru1) has been identified as a highly efficient catalyst for the hydrogenation of a broad spectrum of arylcarbamates and their derivatives (49 examples). The hydrogenation reaction occurs smoothly via CN bond cleavage, affording the desired amines and alcohols or diols at a low catalyst loading of 0.25 mol% in tert-amyl alcohol. Most importantly, this catalytic system offers a promising route for the sustainable depolymerization and recycling of polyurethanes (PUs). Moreover, a detailed mechanism for the hydrogenation of carbamates has been established through combined DFT calculations and control experiments, which suggests that Ru-hydride pathways involve three cycles, with the rate-determining step most likely being the dissociation of the CN bond in the key intermediate H(CO)NHPh. These results have far-reaching implications for the development of more effective and eco-friendly catalytic systems for carbamate transformation and their potential industrial application on a large scale.

Enhancing the selectivity of CO2-to-HCOOH conversion by constructing tensile-strained Cu catalyst

Heterogeneous interface engineering endows catalyst with the possibility to enhance the activity and tune the selectivity of electrochemical CO2 reduction reaction (CO2RR) by induced surface strain and interfacial charges transfer. Herein, a novel In2O3/Cu heterojunction catalyst with 3D succulents-like morphology significantly enhance the selectivity and activity for electrochemical CO2-to-HCOOH conversion as compared to the In2O3 and Cu counterparts, achieving a maximum faraday efficiency (FE) of 87.5 % at −1.1 V vs RHE with corresponding formate partial current density of −70 mA cm−2 at −1.4 V vs RHE. The combined DFT calculation and experimental studies revealed that electrons transfer from interfacial In to Cu via O bridge preserves the metallic state of Cu, which facilitates the capture and activation of CO2 molecules. Furthermore, the surface tensile strain together with interfacial electronic interaction lowers the energy barrier for the formation of *HCOO intermediate, thus boosting the selectivity for HCOOH production. This work demonstrates a feasible strategy for advanced catalyst design by implanted heterogeneous interfaces to manipulate the lattice strain and electronic coupling.

(Invited) Computational Modelling of Super-Reduced Polyoxometalates for Energy Storage

It is well know that polyoxometalates can be reduced at relatively potentials and can act as reservoir of electrons. Very recently, it has been reported that polyoxometalates clusters like Li6[P2W18O62] can achieve very high proton–electron storage capacities in aqueous solution. DFT calculations in combination with classical MD and CPMD simulations were able to substantiate that the physical properties of classical polyoxotungstates, like those of the prototypical Dawson anion [P2W18O62]6-, strongly depend on the presence of collective forces associated to POM concentration, pH and countercation nature. At low POM concentration and neutral pH only four electrons are reversibly incorporated to the POM. However, in acidic media, the POM framework begins to protonate after the third electron reduction. The salt concentration is also very relevant, since it favours the POM aggregation, which induces an additional stabilization of molecular orbitals. These and another features of reduced polyoxometales will be discussed in the present communication.

Anion regulation strategy of lithium-aluminum layered double hydroxides for strengthening resistance to deactivation in lithium recovery from brines

Lithium aluminum layered double hydroxides (LiAl-LDHs) have emerged as the most promising adsorbent for lithium extraction from salt lake brines. However, the development of LiAl-LDHs is impeded by their susceptibility to structural collapse and deactivation during desorption process. Herein, an interlayer anion regulation strategy was proposed to endow LiAl-LDHs with superior resistance to deactivation induced by excessive Li+ deintercalation through strengthening the interlayer interactions. Consequently, a novel LiAl-LDH with interlayer Cl− partially replaced by PO43− (LiAl-LDH-P) was synthesized by coupling PO43− intercalation with Li+ insertion during co-precipitation. Combining DFT calculations and elution strength experiments, it was revealed that the intercalated PO43− could anchor Li+ into the vacancies of Al-O octahedron via high interlayer binding energy and strong electrostatic interaction, which imparted LiAl-LDH-P with an excellent anti-elution deactivation ability. Moreover, LiAl-LDH-P presented distinctly advanced compared to commercialized and reported LiAl-LDHs, with extraordinary Li+ adsorption capacity (9.35 mg/g), selectivity (separation factors of 270.3, 450.3, 453.7 for Li+/Na+, Li+/K+, Li+/Mg2+, respectively), and reusability in Lop Nor brine, even at the ultra-high eluent consumption. Furthermore, the physicochemical properties and Li+-extraction mechanism of the LiAl-LDH-P were investigated as well. This work provides a promising strategy to solve the current deactivation of LiAl-LDHs and offers a prospective adsorbent for Li+ extraction from brine.

Combined First-Principles and Experimental Study on the Microstructure and Mechanical Characteristics of the Multicomponent Additive-Manufactured Ti-35Nb-7Zr-5Ta Alloy.

New β-stabilized Ti-based alloys are highly promising for bone implants, thanks in part to their low elasticity. The nature of this elasticity, however, is as yet unknown. We here present combined first-principles DFT calculations and experiments on the microstructure, structural stability, mechanical characteristics, and electronic structure to elucidate this origin. Our results suggest that the studied β Ti-35Nb-7Zr-5Ta wt % (TNZT) alloy manufactured by the electron-beam powder bed fusion (E-PBF) method has homogeneous mechanical properties (H = 2.01 ± 0.22 GPa and E = 69.48 ± 0.03 GPa) along the building direction, which is dictated by the crystallographic texture and microstructure morphologies. The analysis of the structural and electronic properties, as the main factors dominating the chemical bonding mechanism, indicates that TNZT has a mixture of strong metallic and weak covalent bonding. Our calculations demonstrate that the softening in the Cauchy pressure (C' = 98.00 GPa) and elastic constant C̅44 = 23.84 GPa is the origin of the low elasticity of TNZT. Moreover, the nature of this softening phenomenon can be related to the weakness of the second and third neighbor bonds in comparison with the first neighbor bonds in the TNZT. Thus, the obtained results indicate that a carefully designed TNZT alloy can be an excellent candidate for the manufacturing of orthopedic internal fixation devices. In addition, the current findings can be used as guidance not only for predicting the mechanical properties but also the nature of elastic characteristics of the newly developed alloys with yet unknown properties.