Calculations Of Energy Surfaces Research Articles

Emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations.

We present in this work the emle-engine package (https://github.com/chemle/emle-engine)─the implementation of a new machine learning embedding scheme for hybrid machine learning potential/molecular-mechanics (ML/MM) dynamics simulations. The package is based on an embedding scheme that uses a physics-based model of the electronic density and induction with a handful of tunable parameters derived from in vacuo properties of the subsystem to be embedded. This scheme is completely independent of the in vacuo potential and requires only the positions of the atoms of the machine learning subsystem and the positions and partial charges of the molecular mechanics environment. These characteristics allow emle-engine to be employed in existing QM/MM software. We demonstrate that the implemented electrostatic machine learning embedding scheme (named EMLE) is stable in enhanced sampling molecular dynamics simulations. Through the calculation of free energy surfaces of alanine dipeptide in water with two different ML options for the in vacuo potential and three embedding models, we test the performance of EMLE. When compared to the reference DFT/MM surface, the EMLE embedding is clearly superior to the MM one based on fixed partial charges. The configurational dependence of the electronic density and the inclusion of the induction energy introduced by the EMLE model leads to a systematic reduction in the average error of the free energy surface when compared to MM embedding. By enabling the usage of EMLE embedding in practical ML/MM simulations, emle-engine will make it possible to accurately model systems and processes that feature significant variations in the charge distribution of the ML subsystem and/or the interacting environment.

Effects of triaxial deformation on the fission barrier in the Z = 118 − 120 nuclei* *Supported by the National Natural Science Foundation of China (Grant Nos. 12205076 and 12047504), the China Postdoctoral Science Foundation (Grant No. 2020M670012), and the Launching Fund of Henan University of Technology (Grant No. 2021BS047).

By using potential energy surface (PES) calculations in the three-dimensional space (β 2, γ, β 4) within the framework of the macroscopic-microscopic model, the fission trajectory and fission barrier for Z = 118(Og), 119, 120 nuclei has been systematically investigated. The calculated PES includes macroscopic liquid-drop energy, microscopic shell correction and pairing correction. Taking the 294Og176 nucleus as an example, we discuss the next closed shell after Z = 82 and N = 126 with the calculated Woods–Saxon single-particle levels. Then, the results of PES in 294Og is illustrated from the (X, Y) scale to the (β 2, γ) scale. The γ degree of freedom reveals the shape evolution clearly during the fission process. The structure near the minimum and saddle point of the PES in the Z = 118, 119, 120 nuclei is demonstrated simultaneously. Based on the potential energy curves, general trends of the evolution of the fission barrier heights and widths are also studied. The triaxial deformation in these superheavy mass regions plays a vital role in the first fission barrier, showing a significant reduction in both triaxial paths. In addition, the model-dependent fission barriers of proton-rich nuclei 295Og, 296119, and 297120 are analyzed briefly. Our studies could be valuable for synthesizing the superheavy new elements in the forthcoming HIAF and other facilities.

Alloy [FA,Cs]PbI3 perovskite surfaces: The role of surface cesium composition in stability and tolerance to defect formation

Halide-perovskite alloys that include cesium have achieved records of stability and efficiency in solar cells. Controlling the surface composition, defects, and electronic properties guarantees interface stability and improves performance. By using density functional theory and molecular dynamic simulations, we analyzed which surface compositions of the formamidinium (FA) and cesium (Cs) lead iodide perovskite FA1−xCsxPbI3 with 25 and 50 % of Cs become more stable than pure perovskites. Structural and electronic properties and tolerance to defect formation were also evaluated. Surface energy calculations show that only the alloys with 25 % Cs and FAI-enriched surfaces are more stable than pure FAPbI3 ones. The most stable alloy surface shows electronic energy levels similar to the FAPbI3 perovskite, suggesting that this alloy may also be efficient for charge transport in the cell. However, the presence of Cs on the alloy surface, although low, favors the formation of FAI vacancies, which is detrimental to the stability of the perovskite. These results suggest evaluating FA1−xCsxPbI3 alloys with small Cs compositions to mitigate the formation of defects or using a passivation scheme. This study delivers valuable information for efficiency device improvement from the perspective of interface stability.

Acetate Assistance in Regioselective Hydroamination of Allenamides: A Combined Experimental and Density Functional Theory Study.

A key factor in the development of selective nucleophilic addition to allenamides is controlling the reactivity of electrophilic intermediates, which is generally achieved using an electrophilic activator via conjugated iminium intermediates. In this combined experimental and computational study, we show that a general and highly chemoselective hydroamination of allenamides can be accomplished using a combination of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and NaOAc. Experimental mechanistic studies revealed that HFIP mediates proton transfer to activate the allenamide, while the acetate additive significantly contributes to N-selective interception. This strategy enables a general hydroamination of allenamides without the use of metals. We demonstrated that various functionalized 1,3-diamines could be readily synthesized and diversified into value-added structural motifs. Detailed mechanistic investigations using the density functional theory revealed the role of NaOAc in the formation of reactive electrophilic intermediates, which ultimately governed the selective formation of 1,3-diamine products. Critically, calculations of the potential energy surface around the proton-transfer transition state revealed that two different reactive electrophilic intermediates were formed when NaOAc was added.

High-efficiency and low-damage modification of engineering metal materials by oxygen-mixing atmospheric pressure cold plasma jets

Engineering metal materials have been widely developed and applied in aviation, aerospace and biomedicine fields. Wettability improvement of these materials can alleviate problems caused by low adhesion and poor bioactivity, thereby facilitating their practical applications. Compared with other methods, atmospheric pressure cold plasma treatment has better versatility and can efficiently improve wettability without causing serious damages, and has therefore been widely used in polymer hydrophilization. However, when treating metal materials, the cold plasma may induce surface breakdown or have low efficiency. In this paper, we developed a new cold plasma jet by mixing oxygen into working gas to achieve high-efficiency and low-damage modification. When oxygen mixing ratio was 0.4 %, the cold plasma jet could modify TC4 titanium alloy surface to be superhydrophilic within 20 s, which was much more efficient than traditional plasma jet (120 s). We then further investigated the mechanism contributing to higher efficiency, and found that the oxygen-mixing plasma jet did not cause serious damages, while generating more polar groups by higher-concentration active particles, as confirmed by surface energy calculation and optical emission spectra. Besides titanium alloy, the oxygen-mixing plasma jet could also achieve rapid hydrophilization of various engineering metal materials, showing promising application prospects.

Adaptive TiN-Cu/PAO composite lubrication system: The tribocatalysis-induced PAO6 transferring to amorphous carbon

A friendly solid-liquid lubrication system, which is the key to solve the environmental harm caused by phosphorus and sulfur additives in lubricants, has attracted the attention. In this paper, the TiN-Cu/PAO solid-liquid composite system was constructed in situ by tribochemical reaction based on the performance of nitride film and base oil. The results show that when rubbing in PAO, the carbon-based films deriving from PAO will form at the contacting interface. From the perspectives of surface energy, friction products and simulation calculation, the mechanisms of friction and wear reduction of the solid-liquid composite system was systematically investigated. Meanwhile, the degradation process of PAO molecules during friction was revealed from the molecular level, including adsorption, dehydrogenation, C-C bond breaking and reconstruction.

N-H and N-C Bond Dissociation Pathways in Ultraviolet Photodissociation of Dimethylamine.

We investigated the interlinked N-H and N-C photochemistry of primary and secondary amines via the state-resolved detection of vibrationally excited CH3 product and H atom product by 200-235 nm dimethylamine photodissociation using resonance-enhanced multiphoton ionization (REMPI) and velocity map imaging (VMI) techniques. The out-of-plane bending (ν2) vibrationally excited CH3 showed a bimodal translational energy distribution that became unimodal with a near-zero product yield at longer photolysis wavelengths (λphotolysis). In contrast, a unimodal distribution was observed for the C-H stretching (νCH) vibrationally excited CH3 products with an almost constant product yield in the examined λphotolysis region. We ascribed the state-specific energy releases of the CH3 products to two reaction pathways based on calculations of the potential energy surface (PES): the direct N-CH3 dissociation pathway and the indirect N-CH3 dissociation pathway via the N-H bond conical intersection. Meanwhile, the H atom product showed a bimodal energy distribution similar to the ammonia photodissociation model, with an excited-state counterproduct channel that became accessible at a shorter λphotolysis. These results suggest that the N-H and N-C bond dissociations are connected, and these dissociations cause different photochemistry between primary/secondary amines and tertiary amines.

Machine learning accelerated discovery of corrosion-resistant high-entropy alloys

Corrosion has a wide impact on society, causing catastrophic damage to structurally engineered components. An emerging class of corrosion-resistant materials are high-entropy alloys. However, high-entropy alloys live in high-dimensional composition and configuration space, making materials designs via experimental trial-and-error or brute-force ab initio calculations almost impossible. Here we develop a physics-informed machine-learning framework to identify corrosion-resistant high-entropy alloys. Three metrics are used to evaluate the corrosion resistance, including single-phase formability, surface energy and the compactness of oxide films formed on an alloy surface evaluated by Pilling–Bedworth ratios. We used random forest models to predict the single-phase formability, trained on an experimental dataset. Machine learning inter-atomic potentials were employed to calculate surface energies and Pilling–Bedworth ratios, which are trained on first-principles data fast sampled using embedded atom models. A combination of random forest models and high-fidelity machine learning potentials represents the first of its kind to relate chemical compositions to corrosion resistance of high-entropy alloys, paving the way for automatic design of materials with superior corrosion protection. This framework was demonstrated on AlCrFeCoNi high-entropy alloys and we identified composition regions with high corrosion resistance from a wide range of compositions. Machine learning predicted lattice constants and surface energies are consistent with values by first-principles calculations. The predicted single-phase formability and corrosion-resistant compositions of AlCrFeCoNi agree well with experiments. This framework provides a computationally efficient approach to navigate high-dimensional composition space of high-entropy alloys. It is general in its application and applicable to other complex materials, enabling high-throughput screening of material candidates and potentially accelerating the iteration of integrated computational materials engineering.

Nitrogen Plasma Treatment of Composite Materials Based on Polylactic Acid and Hydroxyapatite.

The effect of surface modification by an arc discharge plasma in a nitrogen flow with treatment durations of 5 and 10 min on the physicochemical properties and biocompatibility of the surface of composites based on polylactic acid and hydroxyapatite (PLA/HA) with different mass ratios (80/20, 70/30, 60/40) has been investigated. The aim of this work was to show the correlation between the changes of the physicochemical characteristics (chemical compound, morphology, wettability) of the surface layer of the PLA/HA composites and the cell viability (macrophages) in the presence of the plasma-modified materials. The dependence of alterations of the functional properties (wettability, biocompatibility) on the change in the chemical composition under the plasma exposure has been established. The chemical composition was studied using X-ray photoelectron spectroscopy (XPS), the surface morphology was researched with scanning electron microscopy (SEM), and the wettability of the composite's surface was analyzed by measuring the contact angle and surface energy calculation. In addition, the viability of macrophages was investigated when the macrophages from three donors interacted with a modified PLA/HA surface. It was found that the formation of the new functional groups, -C-N and N-C=O/C=O, improves the wettability of the surface of the composites and promotes the viability of macrophages in the presence of the composite materials. The fundamental principles for obtaining promising materials with the required properties for eliminating bone defects have been created.

Surface energy calculation for some transition metal using the GEAM

The three low index surface energies of fcc metals Cu, Ag, and Au are here calculated using the generalized embedded-atom method (GEAM). The low-index surface energies {, and }, with having the lowest and having the highest energy value. The anticipated values accord well with the experimental values.

Sampling the reciprocal Coulomb potential in finite anisotropic cells.

We present a robust strategy to numerically sample the Coulomb potential in reciprocal space for periodic Born-von Karman cells of general shape. Our approach tackles two common issues of plane-wave based implementations of Coulomb integrals under periodic boundary conditions: the treatment of the singularity at the Brillouin-zone center and discretization errors, which can cause severe convergence problems in anisotropic cells, necessary for the calculation of low-dimensional systems. We apply our strategy to the Hartree-Fock and coupled cluster (CC) theories and discuss the consequences of different sampling strategies on different theories. We show that sampling the Coulomb potential via the widely used probe-charge Ewald method is unsuitable for CC calculations in anisotropic cells. To demonstrate the applicability of our developed approach, we study two representative, low-dimensional use cases: the infinite carbon chain, for which we report the first periodic CCSD(T) potential energy surface, and a surface slab of lithium hydride, for which we demonstrate the impact of different sampling strategies for calculating surface energies. We find that our Coulomb sampling strategy serves as a vital solution, addressing the critical need for improved accuracy in plane-wave based CC calculations for low-dimensional systems.

Hydrodynamic Modeling of Stratification and Mixing in a Shallow, Tropical Floodplain Lake

AbstractFloodplain lakes are widespread and ecologically important throughout tropical river systems, however data are rare that describe how temporal variations in hydrological, meteorological and optical conditions moderate stratification and mixing in these shallow lakes. Using time series measurements of meteorology and water‐column temperatures from 17 several day campaigns spanning two hydrological years in a representative Amazon floodplain lake, we calculated surface energy fluxes and thermal stratification, and applied and evaluated a 3‐dimensional hydrodynamic model. The model successfully simulated diel cycles in thermal structure characterized by buoyancy frequency, depth of the actively mixing layer, and other terms associated with the surface energy budget. Diurnal heating with strong stratification and nocturnal mixing were common; despite considerable heat loss at night, the strong stratification during the day meant that mixing only infrequently extended to the bottom at night. Simulations indicated that the diurnal thermocline up and downwelled creating lake‐wide differences in near‐surface temperatures and mixing depths. Infrequent full mixing creates conditions conducive to anoxia in these shallow lakes given their warm temperatures.

SurfFlow: High-throughput surface energy calculations for arbitrary crystals

We introduce SurfFlow, an open-source high-throughput workflow package designed for automated first-principles calculations of surface energies in arbitrary crystals. Our package offers a comprehensive solution capable of handling multi-element crystals, nonstoichiometric compositions, and asymmetric slabs, for all potential terminations. To streamline the computational process, SurfFlow employs an efficient pre-screening method that discards surfaces with suspected high surface energy before conducting resource-intensive density functional theory computations. The results generated are seamlessly compiled into an optimade-compliant database, ensuring easy access and compatibility. Additionally, a user-friendly web interface facilitates workflow submission and management, provides result visualization, and enables the examination of Wulff shapes. SurfFlow represents a valuable tool for researchers looking to explore surface energies and their implications in a diverse range of systems.

First-principles study of the electronic and catalytic properties of nickel-antimony (Ni-Sb) alloy catalyst for hydrogen evolution reaction

Hydrogen evolution reaction (HER) is a vital half-reaction for water splitting to produce H2. Exploring efficient, affordably priced, and environmentally sustainable HER catalysts is necessary for the development of renewable energy conversion and storage technologies. Here, the HER catalytic activity of hexagonal NiSb(010), hexagonal NiSb(001), hexagonal NiSb(101), cubic Ni3Sb(100), cubic Ni3Sb(010), cubic Ni3Sb(101), orthorhombic Ni3Sb(010), and orthorhombic Ni3Sb(101), is systematically investigated by density functional theory methods. Based on the calculated surface energy, all the studied surfaces are stable. Subsequently, we further evaluate their HER activity by calculating Gibbs free energy of hydrogen adsorption (ΔG*H) and exchange current density (i0). The results show that hexagonal NiSb and orthorhombic Ni3Sb are expected to be promising HER catalysts in Ni-Sb alloys because their ΔG*H values are respectively −0.03 and 0.03 eV, and they have larger i0 values. The synergistic interaction between the metal atoms of Ni and Sb can effectively promote electron transfer between the catalyst and reaction species, which is clearly demonstrated by the electronic structure analysis, which also illustrates that such high catalytic activity can be attributed to it. This work is conducive to guiding the design of this kind of alloy electrocatalysts for HER.

Wulff Constructions for an Equilibrium MFI-Type Zeolite Shape Modelling under Different Conditions

As an MFI-type zeolite, ZSM-5 zeolite has wide applications in industry, such as in the fine chemical, petrochemical, and coal chemical industries. However, shape control of ZSM-5 nanocrystals constitutes one of the major challenges of current nanotechnology. Here, the MFI framework structure was used as the theoretical model of pure silicon ZSM-5 to investigate the surface energy and Wulff shape. The models with different crystal surfaces were simulated by molecular dynamics (MD) with the assistance of machine learning potentials (MLPs). The factors influencing the crystal surface energy, such as temperature, pH, and ionic concentration, have been studied in detail. Depending on the calculated surface energies, the crystal surface morphology and its ratio were obtained by means of the Wulff theorem. The results show that the area in the equilibrium shape of the (110) surface is usually the largest, and its proportion varies with external conditions. A high temperature and high concentration of the aluminum source promoted the growth of the (110) crystal surface, and the theoretical value of the crystal surface ratio was as high as 90%. This study provides theoretical insight into the synthesis of zeolites with different morphologies of all-silicon or low-aluminum.

Inelastic scattering of NO(A2Σ+) + CO2: rotation-rotation pair-correlated differential cross sections.

A crossed beam velocity-map ion-imaging apparatus has been used to determine differential cross sections (DCSs) for the rotationally inelastic scattering of NO(A2Σ+, v = 0, j = 0.5) with CO2, as a function of both NO(A, v = 0, N') final state and the coincident final rotational energy of the CO2. The DCSs are dominated by forward-peaked scattering for all N', with significant rotational excitation of CO2, and a small backward scattered peak is also observed for all final N'. However, no rotational rainbow scattering is observed and there is no evidence for significant product rotational angular momentum polarization. New ab initio potential energy surface calculations at the PNO-CCSD(T)-F12b level of theory report strong attractive forces at long ranges with significant anisotropy relative to both NO and CO2. The absence of rotational rainbow scattering is consistent with removal of low-impact-parameter collisions via electronic quenching, in agreement with the literature quenching rates of NO(A) by CO2 and recent electronic structure calculations. We propose that high-impact-parameter collisions, that do not lead to quenching, experience strong anisotropic attractive forces that lead to significant rotational excitation in both NO and CO2, depolarizing product angular momentum while leading to forward and backward glory scattering.

Theoretical study on the insertion reaction of CH(X2) into the oh bond in n-C4H9OH

CH radicals play an important role in the combustion of hydrocarbon. The insertion mechanism of a CH radical into the O-H bond of n-C4H9OH is investigated theoretically by a detailed potential energy surface calculation at the BHandHLYP/6-311++G(3df,2p) and CCSD(T)/6-311++G(d,p) (single-point) levels. Our results show that the CH radical attacks into the oxygen atom in n-C4H9OH to form a prereaction complex (COMP) to be followed by an insertion of the CH radical into the O-H bond of the n-C4H9OH molecule to form the low-lying intermediate IS1 (CH2OCH2CH2CH2CH3). This intermediate can isomerize to form IS2 (CH3OCH2CHCH2CH3), IS3 (CH3CH2CH2CH2CH2O), and IS4 (CH3CH2CH2CH2CHOH). These intermediates can decompose to yield 9 products (PR1-PR9) in which major ones are PR1 (CH2CH2CH2CH3 + CH2O), PR2 (CH2CHCH2CH3 + CH3O) and PR3 (CH2CHCH2OCH3 + CH3).

Elucidating the Surface Properties of Sr3PbO Inverse‐Perovskite Topological Insulator: A First‐Principles Study

The emergence of robust surface electronic states in topological insulators such as bulk Sr3PbO inverse‐perovskite makes them suitable candidates for spintronic devices and solid‐state quantum computers. Herein, the atomic structure, surface energetics, and electronic properties of Sr3PbO inverse‐perovskite Sr2O (SO)‐terminated and SrPb‐terminated (001) surfaces are examined using density functional theory. A comparison of the computed structural properties of SO‐termianted and SrPb‐terminated (001) surfaces reveals maximum surface rumpling and changes in interlayer distances for the SrPb‐terminated surface of Sr3PbO. However, the calculated surface energies indicate that both SO‐termianted and SrPb‐terminated (001) surfaces of Sr3PbO are energetically feasible, indicating that these surfaces can coexist in a polycrystalline sample of this material. Due to the presence of Pb in Sr3PbO, a comprehensive examination of the electronic structure of bulk and supercell slab structures of Sr3PbO by taking spin–orbit coupling effects into consideration is conducted. Noninsulating nature of electronic structure for the two possible (001) terminations of Sr3PbO is found. The domination of Pb‐6p states at the Fermi energy and the hole screening observed at the SrPb‐terminated surface of Sr3PbO support the p‐type nature observed in the experiment.

Ammonia-Induced FCC Ru Nanocrystals for Efficient Alkaline Hydrogen Electrocatalysis.

The urgent development of effective electrocatalysts for hydrogen evolution and hydrogen oxidation reaction (HER/HOR) is needed due to the sluggish alkaline hydrogen electrocatalysis. Here, an unusualface-centered cubic (fcc) Ru nanocrystal with favorable HER/HOR performance is offered. Guided by the lower calculated surface energy of fcc Ru than that of hcp Ru in NH3, the carbon-supported fcc Ru electrocatalyst is facilely synthesized in the NH3 reducing atmosphere. The specific HOR kinetic current density of fcc Ru can reach 23.4mAcmPGM -2, which is around 20 and 21 times greater than that of hexagonal close-packed (hcp) Ru and Pt/C, respectively. Additionally, the HER specific activity is enhanced more than six times in fcc Ru electrocatalyst when compared to Pt/C. Experimental and theoretical analysis indicate that the phase transition from hcp Ru to fcc Ru can negatively shift the d band center, weaken the interaction between catalysts and key intermediates and therefore enhances the HER/HOR kinetics.

Adsorption and dissociation of CH3SH on FeS surface: A DFT study

Methyl mercaptan (CH3SH) is a common sulfide in oil and natural gas, easily corroded in transportation pipes and storage containers. In this paper, the adsorption and dissociation processes of CH3SH on FeS (0 0 1), (0 1 1), (1 0 0) and (1 1 1) surfaces have been studied by the density functional theory (DFT). And the characteristics of the adsorption and dissociation processes were elucidated. The calculated surface energies show that the order of surface stability is (0 0 1) > (0 1 1) > (1 0 0) > (1 1 1). The stability of CH3SH adsorption is (1 1 1) > (1 0 0) > (0 1 1) > (0 0 1) by the adsorption energy, and the most stable adsorption configurations are obtained. Compared with the changes in electron density and the partial density of states (PDOS) before and after adsorption, there is an obvious electron orbital hybrid phenomenon between CH3SH and FeS (1 0 0), (1 1 1) surface, and its adsorption is stronger than that of the other two surfaces. It can be seen from the calculation of the transition state that the dissociation reaction of CH3SH is endothermic on the (0 0 1) and (0 1 1) surfaces, while the exothermic reaction on the (0 1 1) and (0 0 1) surfaces. CH3SH will dissociate preferentially on the FeS (1 0 0) surface because the reaction of Ea and ΔE on this surface is the smallest. Overall, the adsorption and dissociation processes are exothermic, the increase in temperature makes the crystal surface unstable and susceptible to spontaneous combustion, and the phenomenon occurs first on the FeS (1 0 0) and FeS (1 1 1) surfaces. These findings increase the understanding of the electronic structure and energy of the sulfides' action on the FeS surface and also have a reference value for flame retardant research.