Energy Density Functional Theory Research Articles

Gas adsorption and framework flexibility of CALF-20 explored via experiments and simulations

In 2021, Svante, in collaboration with BASF, reported successful scale up of CALF-20 production, a stable MOF with high capacity for post-combustion CO2 capture which exhibits remarkable stability towards water. CALF-20’s success story in the MOF commercialisation space provides new thinking about appropriate structural and adsorptive metrics important for CO2 capture. Here, we combine atomistic-level simulations with experiments to study adsorptive properties of CALF-20 and shed light on its flexible crystal structure. We compare measured and predicted CO2 and water adsorption isotherms and explain the role of water-framework interactions and hydrogen bonding networks in CALF-20’s hydrophobic behaviour. Furthermore, regular and enhanced sampling molecular dynamics simulations are performed with both density-functional theory (DFT) and machine learning potentials (MLPs) trained to DFT energies and forces. From these simulations, the effects of adsorption-induced flexibility in CALF-20 are uncovered. We envisage this work would encourage development of other MOF materials useful for CO2 capture applications in humid conditions.

The atomic configuration and metallic state of extrinsic defects in Nb-doped BiFeO3 thin films

Defects in ferroelectric materials can cause microscopic strain and electron doping, which opens up new possibilities for unique physical properties in nanoelectronics. However, comprehending the relationship between these deep-buried defect configurations and the resulting physical properties is a long-term challenge. Here, utilizing the integrated differential phase imaging technique equipped in scanning transmission electron microscopy combined with energy dispersive X-ray spectroscopy, we show the full element-resolved atomic configuration of characteristic extrinsic defects in Nb-doped epitaxial BiFeO3 thin films. Atomic-resolution characterization reveals that the Nb doping substitutes Fe at the center of an oxygen octahedron and creates Fe vacancies near the defect core, leading to the formation of one perovskite cell-wide BiNbO3 chain that is expanded by 19 % in perovskite cell volume and rotated by 45° relative to the matrix lattice. Further quantitative analysis of the defect demonstrates that the ferroelectric polarization distribution around the dopant-induced defects displays a “head-to-head” configuration, indicating the accumulation of negative charges. Supported by electron energy loss spectroscopy and density functional theory calculations, the linear defect leads to one-dimensional metallic channels embedded within the ferroelectric BiFeO3 matrix. These atomic-scale findings establish the structure-functionality relationship of extrinsic defect in Nb-doped BiFeO3 thin films, providing new insight into their fundamental understanding and potential use in low-dimensional nanoelectronics devices.

Bond-selective effect for the dissociative chemisorption of HOD on the Ni(100) surface revealed at the full-dimensional quantum dynamical level.

We present a comprehensive investigation into the dissociative chemisorption of HOD on a rigid Ni(100) surface using an approximate full-dimensional (9D) quantum dynamics approach, which was based on the time-dependent wave-packet calculations on a full-dimensional potential energy surface obtained through neural network fitting to density functional theory energy points. The approximate-9D probabilities were computed by averaging the seven-dimensional (7D) site-specific dissociation probabilities across six impact sites with appropriate relative weights. Our results uncover a distinctive bond-selective effect, demonstrating that the vibrational excitation of a specific bond substantially enhances the cleavage of that excited bond. The product branching ratios are substantially influenced by which bond undergoes excitation, exhibiting a clear preference for the product formed through the cleavage of the excited bond over the alternative product.

Comparative study of alpha scattering from various nuclei at 130 MeV: Microscopic potentials and coupled channel calculations

The angular distributions of the elastic and inelastic scattering cross sections of alpha projectiles on different heavy ion target nuclei including 12C, 16O, 24Mg, 28Si and 40Ca at energy of 130 MeV have been studied using two different microscopic real potentials generated by the energy density functional (EDF) theory, and single folding cluster model as well as phenomenological Woods-Saxon potentials. A new parameterization was considered for the first time by EDF and to make the normalization coefficient tend to unity, it is necessary to consider correction to the calculated real potential. Coupled channel calculations for various low-lying states were performed, and the best fit values for the deformation length with the above models were extracted by fitting the inelastic scattering cross section and compared to previous work values. The total reaction cross section, as well as the real and imaginary volume integrals, have been studied.

Heterostructure CoSe2/Sb2Se3 Nanocrystals Embedded into Nanocage-in-Nanofiber Carbon Framework for Ultralong-Life Sodium-Ion Batteries

Transition metal selenides are considered as one of the most promising anode materials for sodium-ion batteries (SIBs) on account of their high theoretical specific capacity. However, the poor conductivity, sluggish kinetics and volume expansion during the (de)sodiation process hinder its application. Herein, a novel heterostructure of CoSe2/Sb2Se3 nanocrystals embedded into nanocage-in-nanofiber carbon framework is designed and constructed via electrospinning, carbonization, ion exchange and selenization processes. In this structure, bimetallic selenide heterostructure accelerates electron/ion transfer kinetics and Na+ adsorption capacity, carbon nanocages structure alleviates the volume expansion and maintains structural integrity during the (de)sodiation process, and carbon nanofibers connect the nanocages in series to shorten the electron transmission path and enhance electrical conductivity. As a self-supporting anode for SIBs, as-synthesized CoSe2/Sb2Se3@C@CNF shows a high reversible capacity of 406 mAh g-1 at 0.2Ag-1 after 200 cycles and displays excellent rate capability. More remarkably, the CoSe2/Sb2Se3@C@CNF anode manifests an outstanding cycling stability for over 2000 and 12,000 cycles at 1 and 5Ag-1, with the capacity retention being 97% and 103% respectively. Meanwhile, the excellent sodium storage performance is revealed by kinetic analysis, energy level analysis and density functional theory calculations.

Unraveling the Tandem Effect of Nitrogen Configuration Promoting Oxygen Reduction Reaction in Alkaline Seawater

AbstractDeveloping seawater‐based high‐performance oxygen reduction reaction (ORR) electrocatalysts is meaningful to renewable energy storage and conversion, and the Fe‐based derivatives encapsulated by nitrogen (N) doped carbon are the typical representative. Nevertheless, unrevealing the mechanism of N configuration to ORR activity and chlorine resistance is still a great challenge. In this work, a feasible strategy is developed to prepare controllable pyridinic/pyrrolic‐N doped carbon‐coated Fe‐based electrocatalysts (FexN‐NC). Drawing support from the H3PO4 blocking based in situ Fourier transform infrared spectroscopy (FTIR) test and density‐functional theory (DFT) calculation, the tandem effect of pyridinic‐N and pyrrolic‐N on ORR is proved. Additionally, the low hydrogen peroxide (H2O2) yield and 4e− pathway of FexN‐NC demonstrate that N doping effectively reduces the adsorption of Cl−, which is consistent with the low Cl− adsorption energy of DFT. The half‐wave potential (E1/2) of FexN‐NC for ORR reaches 0.874 V in alkaline seawater, and ZABs assembled with FexN‐NC as the air cathode deliver a remarkable power density (162 mW cm−2), along with excellent long‐term durability (>400 h).

Global properties of nuclei at finite-temperature within the covariant energy density functional theory

Global properties of nuclei at finite-temperature within the covariant energy density functional theory

Anion-Bridged Dual Hydrogen Bond Enabled Concerted Addition of Phenol to Glycal.

A noncovalent organocatalytic concerted addition of phenol to glycal is developed for the stereoselective and regioselective construction of biologically important phenolic 2-deoxyglycosides, featuring wide substrate tolerance. The method relies on an anion-bridged dual hydrogen bond interaction which is experimentally proved by Nuclear Magnetic Resonance (NMR), Ultraviolet and visible (UV-vis), and fluorescence analysis. Experimental evidence including kinetic analysis, Kinetic Isotope Effect (KIE) studies, linear free energy relationship, Hammett plot, and density functional theory (DFT) calculations is provided for a concerted mechanism where a high-energy oxocarbenium ion is not formed. In addition, the potential utility of this method is further demonstrated by the synthesis of biologically active glycosylated flavones. The benchmarking studies demonstrate significant advances in this newly developed method compared to previous approaches.

Heterojunction construction via Fe-doped Ni0.85Se coupled with g-C3N4 for enhancing oxygen evolution reaction performance

Comprehensive previous studies on electrocatalysts have found that increasing the active area of the catalyst as well as increasing the conductivity are effective methods to enhance the catalytic activity of oxygen evolution reaction (OER). In this work, we hydrothermally synthesized an innovative coral-acicular core-shell heterojunction nanomaterial with an overpotential of ∼150 mV and a Tafel slope of ∼78.6 mV dec−1 at a current density of 10 mA cm−2 by doping appropriate amounts of Fe and coupling g-C3N4. It is found that the specific surface area is 13 times higher than that of precursor Ni0.85Se, and the catalytic performance is increased by 200 %. The heterostructure of this material is demonstrated to improve the electron transport properties through energy band analysis and density functional theory (DFT) simulations, and it is found to have the best theoretical overpotential. The coral-acicular core-shell heterostructure in this work provides a valuable theoretical and practical basis for the design and development of efficient catalysts in terms of morphology and structure.

Six-dimensional quantum dynamics study for the dissociative chemisorption of H2 on pure and alloyed AgAu surfaces.

The 6D time-dependent wave packet calculations were performed to explore H2 dissociation on Ag, Au, and two AgAu alloy surfaces, using four newly fitted potential energy surfaces based on the neural network fitting to density functional theory energy points. The ligand effect resulting from the Ag-Au interaction causes a reduction in the barrier height for H2+Ag/Au(111) compared to H2+Ag(111). However, the scenario is reversed for H2+Au/Ag(111) and H2+Au(111). The 6D dissociation probabilities of H2 on Ag/Au(111) surfaces are significantly higher than those on the pure Ag(111) surface, but the corresponding results for H2 on Au/Ag(111) surfaces are substantially lower than those on the pure Au(111) surface. The reactivity of H2 on Au(111) is larger than that on Ag(111), despite Ag(111) having a slightly lower static barrier height. This can be attributed to the exceptionally small dissociation probabilities at the hcp and fcc regions, which are at least 100 times smaller compared to those at the bridge or top site for H2+Ag(111). Due to the late barrier being more pronounced, the vibrational excitation of H2 on Ag(111) is more effective in promoting the reaction than on Au(111). Moreover, a high degree of alignment dependence is detected for the four reactions, where the H2 dissociation has the highest probability at the helicopter alignment, as opposed to the cartwheel alignment.

Design, Synthesis, and Spectral Properties of Novel 2-Mercaptobenzothiazole Derivatives.

This paper is focused on the optimalization of methods for the synthesis, isolation, and purification of 2-mercaptobenzothiazole-based acrylic and methacrylic monomers. The structures of the newly synthesized compounds were confirmed through infrared (IR) and nuclear magnetic resonance spectroscopy (NMR). Spectroscopic properties of the resulting 2-mercaptobenzothiazole derivatives were determined based on their absorption spectra and molar absorption coefficients in solvents with varying polarities. A correlation was established between the calculated density functional theory (DFT) energies and Frontier Molecular Orbitals and the experimental observations, confirming their consistency. The practical utility of the synthesized compounds, particularly in future polymerization processes, hinges on a thorough understanding of these properties.

Nuclear reactions as a tool to study the microscopic structure of pygmy and giant resonances

An advanced microscopic approach based on energy-density functional theory and the quasiparticle-phonon model has been used to study nuclear excitations up to giant dipole resonance energies. In addition, our nuclear structure model has been extended to include reaction theory. The theoretical spectral distributions compared with experimental data performed with different probes and techniques are able to provide us with information about the microscopic structure of the pygmy dipole resonance as well as its collectivity. Evaluations of electric dipole (E1) transition strengths and branching ratios at low energy reveal different properties of the nuclear excitations and the effect of quasi-continuum coupling. The present studies will support above-neutronthreshold γ experiments at ELI-NP targeting γ decays of giant and pygmy resonances, as well as studies on multi-step γ decays by low-lying states.

Dissociative chemisorption of O2 on Al(111): dynamics on a potential energy surface computed with a non-self-consistent screened hybrid density functional approach.

Density functional theory (DFT) at the generalized gradient approximation (GGA) level is often considered the best compromise between feasibility and accuracy for reactions of molecules on metal surfaces. Recent work, however, strongly suggests that density functionals (DFs) based on GGA exchange are not able to describe molecule-metal surface reactions for which the work function of the metal surface minus the electron affinity of the molecule is less than 7 eV. Systems for which this is true exhibit an increased charge transfer from the metal to the molecule at the transition state, increasing the delocalisation of the electron density. This enlarged delocalisation can cause GGA-DFT to underestimate energy values relative to the gas-phase and thus underestimate the barrier height, similar to what has been observed for several gas-phase reactions. An example of such a molecule-metal surface system is O2 + Al(111). Following a similar strategy as for gas-phase reactions, previous work showed results of increased accuracy when using a screened hybrid DF for O2 + Al(111). However, even screened hybrid DFs are computationally expensive to use for metal surfaces. To resolve this, we test a non-self-consistent field (NSCF) screened hybrid DF approach. This approach computes screened hybrid DFT energies based on self-consistent-field (SCF) GGA electronic densities. Here, we explore the accuracy of the NSCF screened hybrid DF approach by implementing the NSCF HSE03-1/3x@RPBE DF for O2 + Al(111). We compute and analyse molecular beam sticking probabilities as well as a set of sticking probabilities for rotationally aligned O2. Our results show that the NSCF approach results in reaction probability curves that reproduce SCF results with near-chemical accuracy, suggesting that the NSCF approach can be used advantageously for exploratory purposes. An analysis of the potential energy surface and the barriers gives insight into the cause of the disagreement between the SCF and NSCF reaction probabilities and into the changes needed in theoretical modelling to further improve the description of the O2 + Al(111) system. Finally, the hole model yields fair agreement with dynamics results for the reaction probability curve, but results in an increased slope of the reaction probability curve compared to the molecular dynamics, with a shift to lower or higher energies depending on whether the vibrational energy of the molecule is included in the initial energy of the molecule or not.

The effect of structural changes on the self-assembly of novel green pyridinium-carboxylate gemini surfactants in Langmuir and Langmuir-Blodgett films.

Engineered molecules with tailored molecular structures have the potential to advance various disciplines by enhancing the properties of biological membranes. In this study, we investigated the fundamental interfacial behavior of newly synthesized, water insoluble, cationic pyridinium-carboxylate based gemini surfactants (GSs) using picolinic acid (PA), nicotinic acid (NA), and isonicotinic acid (INA) and their interactions with dipalmitoylphosphatidylcholine (DPPC) in Langmuir and Langmuir-Blodgett (LB) films. Two synthetic methodologies were employed: (a) connecting two alkyl pyridinecarboxylates through the nitrogen atoms with a xylenyl spacer, namely, PAGS, NAGS1, and INAGS; and (b) dimerizing two nicotinic acid molecules through ester linkages with 1,4-benzenedimethanol, and then quaternizing the pyridine nitrogens with hexadecyl chains to yield NAGS2. A combination of Brewster angle microscopy (BAM) and atomic force microscopy (AFM) imaging techniques yielded valuable insights into the morphology of the GS films and their mixtures with DPPC. Density functional theory (DFT) calculations were used to gain further information on the GSs structures and understand their assembly. The results indicate that the film of INAGS is the most hydrophobic film, and its monolayer is the least compressible. When the nitrogen atom and a carboxylate group of the headgroup are positioned closer to each other, the GS molecules tend to form aggregates instead of a continuous film which is observed for the INAGS surfactant. This observation is consistent with the DFT energy values of pair interactions, indicating that both PAGS and NAGS1 have closely packed conformations with high stabilization energy.

Hydrogen irradiation-driven computational surface chemistry of lithium oxide and hydroxide.

We have investigated, using molecular dynamics, the surface chemistry of hydrogen incident on the amorphous and crystalline lithium oxide and lithium hydroxide surfaces upon being slowed down by a collision cascade and retained in the amorphous surface of either Li2O or LiOH. We looked for the bonding of H to the resident structures in the surface to understand a possible chain of chemical reactions that can lead to surface transformation upon H atom impact. Our findings, using Density-Functional Theory (DFT) trained ReaxFF force field/electronegativity equalization method potentials, stress the importance of inclusion of polarization in the dynamics of a Li-O-H system, which is also illustrated by DFT energy minimization and quantum-classical molecular dynamics using tight binding DFT. The resulting polar-covalent chemistry of the studied systems is complex and very sensitive to the instantaneous positions of all atoms as well as the ratio of concentrations of various resident atoms in the surface.

Hexadecanoic acid analogs as potential CviR-mediated quorum sensing inhibitors in Chromobacterium violaceum: an in silico study

Chromobacterium violaceum is a Gram-negative, rod-shaped and opportunistic human pathogen. C. violaceum is resistant to various antibiotics due to the production of quorum sensing (QS)-controlled virulence factor and biofilm formation. Hence, we need to find alternative strategies to overcome the antimicrobial resistance and biofilm formation in Gram-negative bacteria. QS is a mechanism in which bacteria’s ability to regulate the virulence factors and biofilm formations leads to disease progression. Previously, hexadecanoic acid was identified as a CviR-mediated quorum-sensing inhibitor. In this study, we aimed to discover potential analogs of hexadecanoic acid as a CviR-mediated quorum-sensing inhibitor against C. violaceum by using ADME/T prediction, density functional theory, molecular docking, molecular dynamics and free energy binding calculations. ADME/T properties predicted for analogs were acceptable for human oral absorption and feasibility. The highest occupied molecular orbitals and lowest unoccupied molecular orbitals gap energies predicted and found oleic acid with –0.3748 energies. Docosatrienoic acid exhibited the highest binding affinity −8.15 Kcal/mol and strong and stable interactions with the amino acid residues on the active site of the CviR protein. These compounds on MD simulations for 100 ns show strong hydrogen-bonding interactions with the protein and remain stable inside the active site. Our results suggest hexadecanoic acid analogs could serve as anti-QS and anti-biofilm molecules for treating C. violaceum infections. However, further validation and investigation of these inhibitors against CviR are needed to claim their candidacy for clinical trials. Communicated by Ramaswamy H. Sarma

Revealing the mechanism of manganese doping in sulphoaluminate cement clinker

The production of cement clinker from solid waste generated by industrial development is a valid way to reduce the exploitation of natural resources and protect the environment. This paper reports the doping behavior of manganese (Mn) ions in sulphoaluminate cement (SAC) clinker. Results from energy dispersive spectrometer (EDS), X-ray diffraction (XRD), and density functional theory (DFT) simulations indicate that Mn ions enter C4AF by replacing Fe ions, and rarely incorporate into the other two minerals, C4A3S‾ and C2S. Further analysis of the partial density of states (PDOS) and electron density difference (EDD) indicates that the Mn doping mechanism can be ascribed to the comparable electronic contributions of the host and guest ions. These insights into the doping behavior of Mn ions will provide meaningful information to guide the utilization of Mn-containing solid waste as an alternative raw material for the synthesis of SAC clinker.

TurboGenius: Python suite for high-throughput calculations of ab initio quantum Monte Carlo methods

TurboGenius is an open-source Python package designed to fully control ab initio quantum Monte Carlo (QMC) jobs using a Python script, which allows one to perform high-throughput calculations combined with TurboRVB [Nakano et al. J. Phys. Chem. 152, 204121 (2020)]. This paper provides an overview of the TurboGenius package and showcases several results obtained in a high-throughput mode. For the purpose of performing high-throughput calculations with TurboGenius, we implemented another open-source Python package, TurboWorkflows, that enables one to construct simple workflows using TurboGenius. We demonstrate its effectiveness by performing (1) validations of density functional theory (DFT) and QMC drivers as implemented in the TurboRVB package and (2) benchmarks of Diffusion Monte Carlo (DMC) calculations for several datasets. For (1), we checked inter-package consistencies between TurboRVB and other established quantum chemistry packages. By doing so, we confirmed that DFT energies obtained by PySCF are consistent with those obtained by TurboRVB within the local density approximation (LDA) and that Hartree–Fock (HF) energies obtained by PySCF and Quantum Package are consistent with variational Monte Carlo energies obtained by TurboRVB with the HF wavefunctions. These validation tests constitute a further reliability check of the TurboRVB package. For (2), we benchmarked the atomization energies of the Gaussian-2 set, the binding energies of the S22, A24, and SCAI sets, and the equilibrium lattice parameters of 12 cubic crystals using DMC calculations. We found that, for all compounds analyzed here, the DMC calculations with the LDA nodal surface give satisfactory results, i.e., consistent either with high-level computational or with experimental reference values.

Synergetic assembly of a molybdenum disulfide/carbon quantum dot heterojunction with enhanced light absorption and electron transfer di-functional properties for photocatalysis

Cocatalysts play important roles in enhanced efficiency of heterojunctions that their selection and synthesis are essential. Carbon quantum dots (CQDs), as one of important cocatalysts, often suffer from complicated synthesis, low functionality, and low photocatalytic efficiency issues that need to be solved effectively. In this study, we constructed a new molybdenum disulfide/N,S-doped carbon quantum dots (MoS2/N,S-CQDs) heterojunction with enhanced light absorption and electrons transfer di-functional properties via a facile one-pot hydrothermal method. The MoS2/N,S-CQDs simultaneously degraded 99.8% of methylene blue (MB) and 95.1% of malachite green (MG) in an actual water system (Tianjin Lake) under simulated sunlight irradiation for 120 min. The heterojunction showed obvious efficiencies under both infrared light (degraded 83.8% of MG after 120 min) and visible light (90.1% MG after 120 min) irradiation. According to energy level and density functional theory (DFT) analyses, the electrons in MoS2/N,S-CQDs were demonstrated that transferred from N,S-CQDs to MoS2 interfaces, and the light-absorption range of the composites was effectively extended to near-infrared ranges owing to excellent up-conversion fluorescence property of the N,S-CQDs. We believe that the facile synthetic technique and effective multifunctional properties of composite have the potential for further research on CQDs-based heterojunctions and their industrial applications.

Surface reconstruction and cleavage of phyllosilicate clay edge by density functional theory

Phyllosilicate materials (e.g., smectite) have been proposed to act as a waste barrier within long-term deep geological repositories. Aside from longevity, these clay materials must also limit the mobility of radionuclides, which is achieved through intermolecular interaction involving clay basal planes and edge surfaces. We aim to contribute to the fundamental knowledge of clay edges by investigating surface reconstruction in a dehydrated context. Using density functional theory, surface reconstruction, charge redistribution, and formation energies have been explored for pyrophyllite edges resulting from thirteen terminations. Three primary reconstruction mechanisms were identified: (1) the displacement of Al into the tetrahedral layer, (2) proton shift, and (3) sub-surface reconstruction involving sub-surface -OH or apical O and surface Si. Reduction in overall relative bond deficiency and charge redistribution to becoming more bulk-like were found to be the main driving force for reconstruction. Formation energies were also determined with dispersion correction for dehydrated and hydrated surfaces. The presence of water terminating agents reduced energetic costs by approximately one order of magnitude and the inclusion of dispersion correction resulted in indistinguishable formation energies between different hydrated surfaces. Linear regression models were also explored to predict surface formation energies based on relative bond deficiency and charge. These models were able to identify the key contributions to the surface energy; however, due to the small dataset they were not found to be predictive.