First-principles and classical molecular dynamics simulation of shocked polymers

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

We present an overview of the current status of experimental, theoretical, molecular dynamics (MD), and density functional theory (DFT) studies of argon vapor-to-liquid nucleation. Since the experimental temperature-supersaturation domain does not overlap with the corresponding MD and DFT domains, separate comparisons have been made: theory versus experiment and theory versus MD and DFT. Three general theoretical models are discussed: Classical nucleation theory (CNT), mean-field kinetic nucleation theory (MKNT), and extended modified liquid drop model-dynamical nucleation theory (EMLD-DNT). The comparisons are carried out for the area below the MKNT pseudospinodal line. The agreement for the nucleation rate between the nonclassical models and the MD simulations is very good--within 1-2 orders of magnitude--while the CNT deviates from simulations by about 3-5 orders of magnitude. Perfect agreement is demonstrated between DFT results and predictions of MKNT (within one order of magnitude), whereas CNT and EMLD-DNT show approximately the same deviation of about 3-5 orders of magnitude. At the same time the agreement between all theoretical models and experiment remains poor--4-8 orders of magnitude for MKNT, 12-14 orders for EMLD-DNT, and up to 26 orders for CNT. We discuss possible reasons for this discrepancy and the ways to carry out experiment and simulations within the common temperature-supersaturation domain in order to produce a unified picture of argon nucleation.

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

The liquid waste is the major source of waste, which usually generated from academic laboratories and industry during the extraction, separation, chemical synthesis, and pretreatment processes. These chemical and engineering processes require more solvents. In this regard, there is a need to develop more environmentally friendly, cheaper, non-toxic solvents that are harmless to humans and the environment. In this regard, deep eutectic solvents (DES) and their derivatives so-called natural deep eutectic solvents (NADES) are a new field in the search for green alternative solvents. In our work, the formation of choline chloride-based NADESs using density functional theory (DFT) calculations, and classical all-atom molecular dynamics (MD) simulation was studied in detail using Gaussian09 and Gromacs software's. Next, the ground state geometry optimizations were performed in the gas phase using DFT B3LYP 6-31 + G(d) level of theory. Moreover, classical all-atom MD simulations were implemented using Gromos force field. After the modeling and simulations, the DFT calculation results revealed the formation of NADESs via formation (creation) of binding between chlorine and choline, and chlorine and glucose. At the same time, the results of classical all-atom MD simulations, based on the time average of the equilibrated production run of MD simulations, stated that the nitrogen atom of choline ion and chloride ion has greater interactions, while chloride ion has also greater interaction with glucose during formation of NADES. The outcomes of both DFT and classical all-atom MD simulations are in good agreements.

In the Comment by S\oderlind et al. [Phys. Rev. B 90, 157101 (2014)], the authors argue that (1) density functional theory (DFT), especially with all-electron methods, already models U metal and U-Zr alloy accurately; and (2) $\mathrm{DFT}+U$ results calculated at ${U}_{\mathrm{eff}}=1.24$ for volume, enthalpy, and magnetic moments that they select from our study [Phys. Rev. B 88, 235128 (2013)] suggest adding the Hubbard $U$ potential in $\mathrm{DFT}+U$ reduces accuracy compared to DFT. With respect to argument (1) by S\oderlind et al., we argue that previously neglected and very recent experimental data suggest that DFT in S\oderlind's full-potential linear muffin-tin orbital calculations [Phys. Rev. B 66, 085113 (2002)] still models the bulk modulus and elastic constants of \ensuremath{\alpha}U with errors considerably larger than other related elements, e.g., most transition metals. In addition, we demonstrate that the assertion by S\oderlind et al. that our DFT results are not satisfactory because deficiency exists in our projector augmented wave calculation is unfounded. With respect to argument (2) by S\oderlind et al., we argue that they have inappropriately focused on just one phase [the bcc phase \ensuremath{\gamma}(U,Zr)], neglecting the other phases which represent the majority of our evidence; made overgeneralizations based on results at only one ${U}_{\mathrm{eff}}$ value of 1.24 eV; and supported their argument with inaccurate assertions that $\mathrm{DFT}+U$ predicts for \ensuremath{\gamma}(U,Zr) an unprecedentedly large positive volume of mixing and an enthalpy of mixing that is inconsistent with the experimental miscibility gap. We therefore hold to our original conclusion that the accuracy of DFT for modeling U and U-Zr has room for improvement and $\mathrm{DFT}+U$ is a good candidate.

Comparative density functional theory and density functional tight binding study of 2-anthroic acid on TiO2

Density Functional Theory (DFT) calculation at B3LYP level of theory and 6-31G* basis set was applied on some triazole derivatives of pyrimidine which led to the optimization of their structures, generation of electronic and other important Quantum chemical descriptors such as the energy of the highest occupied molecular orbital (EHOMO), the energy of the lowest unoccupied molecular orbital (ELUMO), energy band gap (ΔE), Dipole Moment (μ), chemical hardness (η), chemical softness (σ), global electronegativity() and number of transferred electrons () using SPARTAN’14 Software. The obtained results shows a good correlation between the chemical structures of the inhibitors and their experimental inhibition efficiencies (%IEs). The ranking of these efficiencies (%IEs) nicely matched with the order of a good number of the generated descriptors but with a varying degree of correlation as majority of the descriptors indicates that I-4 is the best inhibitor among the data set. Furthermore, molecular dynamic (MD) simulations were carried out to search the best adsorption configuration of the inhibitor on the steel (1 1 0) surface using Material Studio 8.0. The obtained results of MD simulations suggest that the interaction was as a results of the chemical adsorption on the steel surface, since the binding energy > 100 Kcalmol-1 for all the inhibitors and the best adsorption energy was found to be -488.07 Kcalmol-1 (I-4). This observation are in good agreement with the DFT results and the experiment findings. Thus; this study provides a valuable approach and new direction to novel steel corrosion inhibitor discovery.

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

A computational method to evaluate fracture toughness of single-and multilayered coatings using first-principles density functional theory (DFT) calculations was proposed.This method was first applied to calculate elastic properties and fracture toughness K IC of single crystalline TiC and several transition metal nitrides with cubic structure, such as TiN, CrN, ZrN, VN and HfN.After comparison with known experimental data and other DFT results, the reliability of present calculations was favourably confirmed.Next, DFT was applied to calculate the ideal work of adhesion W ad , Young's modulus E and interfacial fracture toughness K IC Int for bi-layer combinations of five transition metal nitrides in ( 100) and (110) surface orientations.For the analyzed coatings, the following trends were observed: E(100) > E(110), W ad (100) < W ad (110) and K IC Int (100) < K IC Int (110), demonstrating that it is the W ad that plays a decisive role in determining interfacial fracture toughness of these materials.All interfaces formed with TiN in the (110) orientation showed the best combination of adhesion and interfacial fracture toughness.

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

Li's paper [Phys. Rev. B 85, 235407 (2012)] presents density functional theory (DFT) results of stress as a function of different strain states. The work of Cooper et al. [Phys. Rev. B 87, 035423 (2013)] performs the same DFT calculations as part of an investigation into the nonlinear elastic properties of ${\mathrm{MoS}}_{2}$. Some of the DFT results of Li are substantially different from our recently published paper, Cooper et al. [Phys. Rev. B 87, 035423 (2013)]. Although both papers agree on states of equibiaxial stress, there is substantial disagreement on states of uniaxial tensile stress. In this Comment we show that our DFT computations are properly executed and consistent across three different DFT codes, including the one used by Li.

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.

Molecular density profiles and charge distributions determined by density functional theory (DFT) are used in conjunction with the continuum Navier-Stokes equations to compute electro-osmotic flows in nanoscale channels. The ion species of the electrolyte are represented as centrally charged hard spheres, and the solvent is treated as a dense fluid of neutral hard spheres having a uniform dielectric constant. The model explicitly accounts for Lennard-Jones interactions among fluid and wall molecules, hard sphere repulsions, and short range electrical interactions, as well as long range Coulombic interactions. Only the last of these interactions is included in classical Poisson-Boltzmann (PB) modeling of the electric field. Although the proposed DFT approach is quite general, the sample calculations presented here are limited to symmetric monovalent electrolytes. For a prescribed surface charge, this DFT model predicts larger counterion concentrations near charged channel walls, relative to classical PB modeling, and hence smaller concentrations in the channel center. This shifting of counterions toward the walls reduces the effective thickness of the Debye layer and reduces electro-osmotic velocities as compared to classical PB modeling. Zeta potentials and fluid speeds computed by the DFT model are as much as two or three times smaller than corresponding PB results. This disparity generally increases with increasing electrolyte concentration, increasing surface charge density and decreasing channel width. The DFT results are found to be comparable to those obtained by molecular dynamics simulation, but require considerably less computing time.

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.

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.