Comment on “Ideal strength and phonon instability in single-layerMoS2”

Helium behavior in oxide nuclear fuels: First principles modeling

Interatomic potentials and defect properties of Fe–Cr–Al alloys

We have investigated the importance of polarization by the enzyme dihydrofolate reductase (DHFR) on its substrates, folate and dihydrofolate, using a series of quantum mechanical (QM) techniques (Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2), local density approximation (LDA) and generalized gradient approximation (GGA) density functional theory (DFT) calculations) in which the bulk enzyme is included in the calculations as point charges. Polarization, in terms of both charges on components (residues) of the folate and dihydrofolate molecules and changes in the electron density, particularly of the pterin ring of the substrates, and the implications for the catalytic reduction are discussed. Significant differences in polarization behavior are observed for the different theoretical methods employed. The consequences of this, particularly for choosing an appropriate model for quantum mechanical/molecular mechanical (QM/MM) calculations, are pointed out. The HF and MP2 QM methods show small polarizations (approximately 0.04 electrons) of the pterin ring but quite large polarizations with both LDA and GGA DFT methods (0.3-0.5 electrons). This large difference in polarization for both folate and dihydrofolate arises as a result of substantial differences between the charge distributions for the gasphase DFT and HF calculations, specifically the charges on the dianionic glutamate side chain. Some recent literature reports of incorrect representation of anionic systems by DFT methods are noted. The DFT results are similar to the previously reported LDA DFT results of Bajorath et al. predicting a large polarization of the pterin ring of folate (Proteins 9:217-224, 1991) and dihydrofolate (PNAS 88:6423-6426, 1991) of approximately 0.5-0.6 electrons.

Analyses of the local crystal and electronic structure in the vicinity of Fe3+ centers in perovskite KMgF3 crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe3+ centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe3+ centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe3+ center case), FeF5O cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe3+ centers in KMgF3.

The core structure of -type screw dislocations in hexagonal close packed titanium is investigated computationally using periodic supercells with quadrupolar configurations in combination with density functional theory (DFT) and a modified embedded atom method (MEAM) classical potential. Two arrangements of the quadrupolar supercell configurations are examined, and within each arrangement two initial dislocation positions are compared. (Meta)stable pyramidal and prismatic dislocation core structures exist within both DFT and MEAM methods, and the relaxed structure from a given configuration resulting from our anisotropic elasticity theory solution depends only on the assumed initial dislocation positions. Within DFT we find the ground state core structure to be spread on the pyramidal plane. We find that it is necessary to include the semi-core 3p electrons as valence states in the DFT calculations in order to converge the ground state dislocation core configuration and difference in energy between structures. In terms of k-point sampling, it is found that at least a k-point mesh is necessary to converge the dislocation core structure for a supercell one Burgers vector deep. Use of higher k-point densities or inclusion of additional semi-core electronic states as valence electrons results in the same core structure. With the MEAM potential considered in this work, we find the ground state core configuration to be spread predominantly on the prismatic plane, in contrast with the DFT results.

Modeling palladium surfaces with density functional theory, neural networks and molecular dynamics

Quantum-mechanical DFT calculation supported Raman spectroscopic study of some amino acids in bovine insulin

A DFT-based microkinetic theory for Fe2O3 reduction by CO in chemical looping

Atomistic study of the effect of crystallographic orientation on the twinning and detwinning behavior of NiTi shape memory alloys

In this work, a dataset including structural and mechanical properties of refractory multicomponent alloys was developed by fusing computations of phase diagram (CALPHAD) and density functional theory (DFT). The refractory multicomponent alloys, also named refractory complex concentrated alloys (CCAs) which contain 2–5 types of refractory elements were constructed based on Special Quasi-random Structure (SQS). The phase of alloys was predicted using CALPHAD and the mechanical property of alloys with stable and single body-centered cubic (BCC) at high temperature (over 1,500°C) was investigated using DFT-based simulation. As a result, a dataset with 393 refractory alloys and 12 features, including volume, melting temperature, density, energy, elastic constants, mechanical moduli, and hardness, were produced. To test the capability of the dataset on supporting machine learning (ML) study to investigate the property of CCAs, CALPHAD, and DFT calculations were compared with principal components analysis (PCA) technique and rule of mixture (ROM), respectively. It is demonstrated that the CALPHAD and DFT results are more in line with experimental observations for the alloy phase, structural and mechanical properties. Furthermore, the data were utilized to train a verity of ML models to predict the performance of certain CCAs with advanced mechanical properties, highlighting the usefulness of the dataset for ML technique on CCA property prediction.

Plato: A localised orbital based density functional theory code

A density functional theory is proposed for an inhomogeneous hard-core Yukawa (HCY) fluid based on Rosenfeld's perturbative method. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the hard-core repulsion and a quadratic functional Taylor expansion for the long-ranged attractive or repulsive interactions. To test the established theory, grand canonical ensemble Monte Carlo simulations are carried out to simulate the density profiles of attractive and repulsive HCY fluid near a wall. Comparison with the results from the Monte Carlo simulations shows that the present density functional theory gives accurate density profiles for both attractive and repulsive HCY fluid near a wall. Both the present theory and simulations suggest that there is depletion for attractive HCY fluid at low temperature, but no depletion is found for repulsive HCY fluid. The calculated results indicate that the present density functional theory is better than those of the modified version of the Lovett-Mou-Buff-Wertheim and other density functional theories. The present theory is simple in form and computationally efficient. It predicts accurate radial distribution functions of both attractive and repulsive HCY fluid except for the repulsive case at high density, where the theory overestimates the radial distribution function in the vicinity of contact.

To consider whether existing molecular force fields can adequately reproduce cation−π interactions without adding special interaction terms, theoretical calculations with geometry optimization were performed on three configurations of tetramethylammonium (TMA) interacting via one, two, or three N-methyl groups with a benzene ring, by use of density-functional theory (DFT) methods B3LYP/6-31G* and B3LYP/6-311G**, ab initio method MP2/6-31G*, and molecular mechanic methods EFF, Tinker's Amber and MM3. Only the first configuration was found to be stable from the DFT and MP2 results, and its geometry was found to be highly flexible. ESP CHELPG charges estimated from the DFT and MP2 calculations were used to modify the atomic charges of the force fields employed in the molecular mechanics calculations to improve agreement with the BSSE-corrected binding energies deduced from the DFT and MP2 results. After this modification, the molecular mechanics results were found to be in good agreement with those obtained by DFT and MP2, without a requirement to add any additional terms to the force fields. This was confirmed by comparing the energy profiles of the complex as benzene was moved away from TMA in 0.2 Å intervals. Hence it is possible to use existing force fields to represent cation−π interactions by a simple adjustment of certain partial atomic charge parameters. In this context, we discuss the high flexibility of the cation−π interactions in the framework of molecular recognition in biological systems.

Finnis–Sinclair-type potential for atomistic simulation of defects behaviour in V-Ti-Ta ternary system

High-entropy alloys (HEAs) hold promise as candidate structural materials in future nuclear energy systems. Body-centred cubic V-Ti-Ta-Nb HEAs have received extensive attention due to their excellent mechanical properties. In this work, the Finnis-Sinclair interatomic potential for quaternary V-Ti-Ta-Nb HEAs has been fitted based on the defect properties obtained with the density functional theory (DFT) calculations. The new potential for Nb accurately reproduces the vacancy formation energy, vacancy migration energy and interstitial formation energy. The typical radiation defect properties predicted by the alloy potential were consistent with the DFT results, including the binding energies between substitutional solute atoms, the binding energy between substitutional atoms and vacancies, and the formation energy of interstitial solute atoms. In addition, the mixing enthalpies of the alloys were also consistent with the DFT results. The present potential can also describe reasonably the collision cascade process of quaternary V-Ti-Ta-Nb HEAs.