Functional Theory Simulations Research Articles

Framework for Laplacian-Level Noninteracting Free-Energy Density Functionals.

A framework for orbital-free Laplacian-level meta-generalized-gradient approximation (meta-GGA) for the noninteracting free-energy-density functionals based upon analysis of the fourth-order gradient expansion is developed. The framework presented here provides a new tool for developing advanced orbital-free thermal functionals at the meta-GGA level of theory. A nonempirical meta-GGA functional, which in the slowly varying density limit correctly reduces to the finite-temperature fourth-order gradient expansion for the noninteracting free energy, is constructed. Application to warm dense helium demonstrates that the developed meta-GGA functional drastically increases the accuracy of orbital-free-density functional theory simulations at temperatures below 40 eV as compared to the lower Thomas-Fermi and GGA rungs.

Modulation of Cerium Carbonate Crystal Growth by Polyvinylpyrrolidone using Density Functional Theory.

Cerium carbonate crystal morphology is predicted using density functional theory (DFT) simulations in this paper. In the nucleation phase, the ketone group in polyvinylpyrrolidone (PVP) will preferentially bind to Ce3+ to form complexes and provide heterogeneous nucleation sites for the system, prompting the nucleation of cerium carbonate crystals. In the growth stage, due to the adsorption of PVP, the probability of (120) crystal plane appearing in the equilibrium state is the greatest, resulting in the formation of hexagonal flake cerium carbonate crystals with (120) crystal plane as the oblique edge. Experimentally, hexagonal sheet cerium carbonate crystals were successfully prepared using PVP as a template agent. Therefore, DFT can be used to predict the morphology of cerium carbonate crystals, which not only elucidates the growth mechanism of cerium carbonate crystals, but also greatly reduces the experimental cost.

Multiscale simulation approach to investigate the binder distribution in catalyst layers of high-temperature polymer electrolyte membrane fuel cells

A multiscale approach involving both density functional theory (DFT) and molecular dynamics (MD) simulations was used to deduce an appropriate binder for Pt/C in the catalyst layers of high-temperature polymer electrolyte membrane fuel cells. The DFT calculations showed that the sulfonic acid (SO3−) group has higher adsorption energy than the other functional groups of the binders, as indicated by its normalized adsorption area on Pt (− 0.1078 eV/Å2) and carbon (− 0.0608 eV/Å2) surfaces. Consequently, MD simulations were performed with Nafion binders as well as polytetrafluoroethylene (PTFE) binders at binder contents ranging from 14.2 to 25.0 wt% on a Pt/C model with H3PO4 at room temperature (298.15 K) and operating temperature (433.15 K). The pair correlation function analysis showed that the intensity of phosphorus atoms in phosphoric acid around Pt ({rho }_{mathrm{P}}{g}_{mathrm{Pt}-mathrm{P}}left(rright)) increased with increasing temperature because of the greater mobility and miscibility of H3PO4 at 433.15 K than at 298.15 K. The coordination numbers (CNs) of Pt–P(H3PO4) gradually decreased with increasing ratio of the Nafion binders until the Nafion binder ratio reached 50%, indicating that the adsorption of H3PO4 onto the Pt surface decreased because of the high adsorption energy of SO3− groups with Pt. However, the CNs of Pt–P(H3PO4) gradually increased when the Nafion binder ratio was greater than 50% because excess Nafion binder agglomerated with itself via its SO3− groups. Surface coverage analysis showed that the carbon surface coverage by H3PO4 decreased as the overall binder content was increased to 20.0 wt% at both 298.15 and 433.15 K. The Pt surface coverage by H3PO4 at 433.15 K reached its lowest value when the PTFE and Nafion binders were present in equal ratios and at an overall binder content of 25.0 wt%. At the Pt (lower part) surface covered by H3PO4 at 433.15 K, an overall binder content of at least 20.0 wt% and equal proportions of PTFE and Nafion binder are needed to minimize H3PO4 contact with the Pt.

On the Investigation of Effective Factors on Electronic Structure Properties of Transition Metal Complexes: Robust Modeling Using GPR Approach

Materials discovery is usually done using high-throughput computational screening. The use of costly and complex direct density functional theory (DFT) simulation methods has been commonly used to determine subtle trends in spin-state ordering and inorganic bonding of inorganic materials and, in general, to predict the electronic structure properties of transition metal complexes. A Gaussian process regression (GPR) framework consisting of four kernel functions is introduced for spin-state splitting estimation through inorganic chemistry-appropriate empirical inputs. To this end, the present study reviewed an extensive range of data values from earlier works. According to statistical analysis, the GPR model showed very good performance. The coefficients of determination were calculated to be 0.986 for the exponential and Matern kernel functions, suggesting the highest predictive power of these methods. Moreover, the sensitivity of output to inputs was measured. Artificial intelligence (AI) helped accurately predict the target values through various input ranges.

Applications of Data Driven Methods in Computational Materials Design

In today’s digitized world, large amounts of data are becoming available at rates never seen before. This holds true also for materials science where high-throughput simulations and experiments continuously produce new data. Data driven methods are required which can make best use of the information stored in large data repositories. In the present article, two of such data driven methods are presented. First, we apply machine learning to generalize and extend the results obtained from computationally intense density functional theory (DFT) simulations. We show how grain boundary segregation energies can be trained with gradient boosting regression and extended to many more positions in the grain boundary for a complete description. The second method relies on Bayesian inference, which can be used to calibrate models to give data and quantification of the model uncertainty. The method is applied to calibrate parameters in thermodynamic models of the Gibbs energy of Ti-W alloys. The uncertainty of the model parameters is quantified and propagated to the phase boundaries of the Ti-W system.

Comparative Atomic-Level Analysis of Sorption and Diffusion Properties of Membrane Materials on the Base of Polymer and Its Prepolymer: A Case Study of Polyheteroarylenes.

The sorption properties of polymers and the mobility of penetrants are the main factors which determine the trans-membrane processes. Other factors concern the membrane material structure and chemical nature. In this paper, we consider the case of polymers with similar structure units, namely a polymer and its pre-polymer (polybenzoxazinoneimide and imide-containing polyamic acid). The available experimental data show a great difference in the pervaporation process using these two polymeric membranes. Some explanation of this difference can be found at the atomic-level study. A comparative analysis of the diffusion of water and isopropanol molecules was carried out using the density functional theory and molecular dynamics simulations

First-principles study on the electronic and magnetic properties of ThMnAsN and ThMnPN

The ZrCuSiAs materials have many interesting physical properties and have been extensively studied in recent decades. Recently, two Mn-based ZrCuSiAs-type pnictides, i.e. ThMnAsN and ThMnPN, have been synthesized in the experiment, which shows the anti-ferromagnetic properties. Motived by the experiment, we here perform a comprehensive investigation on their elastic, electronic, and magnetic properties by the density functional theory and Monte Carlo simulations. Our calculations show that ThMnAsN and ThMnPN are both antiferromagnetic semiconductors. The magnetic ground state of both materials is the [Formula: see text]-type anti-ferromagnetism and their bandgaps are about 0.47 eV and 0.61 eV for ThMnAsN and ThMnPN, respectively. The Monte Carlo simulated Néel temperatures of ThMnAsN and ThMnPN are 57 K and 55 K, respectively. These results are well consistent with the experimental results. Our work not only reveals the physical essence of the two newly synthesized materials but also could help to the understanding of the magnetic behaviors of other ZrCuSiAs-type compounds.

Investigation of structural, electronic, magnetic, elastic and thermodynamic properties of Mn3GaN antiperovskite by first principle and Monte Carlo simulations

ABSTRACT Structural, electronic, magnetic, elastic and thermodynamic properties of anti-perovskite have been studied using the first-principles calculations based on density functional theory (DFT) and Monte Carlo simulations within the Ising model. The structural investigation exposes the antiferromagnetic configuration stability of the compound. Also, the density of states (DOS) and band structure calculations show a metallic behaviour of . The computed elastic constants, phonon dispersion and density phonon states calculations demonstrate that the compound is mechanically and dynamically stable. The calculated results of Poisson's ratio, Pugh's ratio and Cauchy pressure show that the is ductile material with a metallic bond. The thermodynamic parameters like heat capacity, Debye and melting temperature have also been calculated. The exchange coupling of has been calculated to obtain the critical temperature () from Monte Carlo calculations. The obtained value of (288 K) is in good agreement with other experimental and theoretical works.

A Grüneisen tensor for rutile and its application to host-inclusion systems

Abstract Rutile is often found as inclusions in garnet, quartz, and several other rock-forming minerals, and it is also a common accessory phase in high-pressure metamorphic rocks. Its relatively simple structure, chemistry, broad P-T stability field, and its wide occurrence in nature makes it a candidate for the application of elastic geobarometry. However, thermodynamic studies coupled with observations on natural samples predict that rutile inclusions in garnets should exhibit zero residual pressure. This implies that the rutile inclusions are detached from the inclusion walls in the host garnet after entrapment. We determined the elastic and vibrational properties of rutile via ab initio hybrid Hartree-Fock/Density Functional Theory simulations under different strain states. Our results confirmed the thermodynamic behavior of rutile in garnet and allowed us to determine for the first time the components of the phonon-mode Grüneisen tensors of rutile. We demonstrated that pure rutile inclusions in garnets from metamorphic rocks exhibit no residual strain or stress, consistent with thermodynamic modeling. Nevertheless, there are rutile inclusions in garnet surrounded by optical birefringence haloes, which are indicative of residual inclusion pressures. Careful examination of these show that they contain significant amounts of amphibole, which reduce the elastic moduli of the composite inclusion to less than that of the garnet hosts. A calculation method for the residual pressures of multi-phase inclusions is described.

Adhesion and Interface Properties of Polydopamine and Polytetrafluoroethylene Thin Films

Abstract Polytetrafluoroethylene (PTFE) has been studied as a low friction surface coating since its discovery. The high wear-rate of PTFE reduces the usefulness of the polymer for mechanical purposes; however, combining PTFE with polydopamine (PDA) has been shown to greatly reduce the film wear-rate. During rubbing tests involving PDA/PTFE thin films, a tenacious layer of PTFE remains intact after substantial testing even though pure PTFE film layers are destroyed quickly. Understanding the interface mechanics that allow PTFE and PDA to adhere so well during experimental rubbing tests is necessary to improve the wear-rate of PDA/PTFE thin films. In this study, we use density functional theory (DFT) and molecular dynamics (MD) simulations to investigate the adhesive properties and interface deformation mechanisms between PDA and PTFE molecules. Steered molecular dynamics (SMD) is then performed on isolated pairs of PDA and PTFE molecules to investigate different modes of deformation from equilibrium. PDA trimer oligomers were identified as the most adhesive to PTFE and selected to use in a PDA/PTFE thin film, where nano-indentation and scratch tests are performed. Our results indicate that a combination of the unique deformation mechanisms of PDA molecules and the penetration of PTFE molecules into the PDA substrate provide the PTFE/PDA interface with its wear resistance.

Molecular insights into the loading and dynamics of anticancer drugs on silicene and folic acid-conjugated silicene nanosheets: DFT calculation and MD simulation

The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at the M06-2X/6–31G** level to characterize the optimized geometry properties of the designed complexes. The calculated adsorption energies are in the range from −65.59 to −144.23 kJ/mol, indicating the drug absorption on the surface of SNS and FA-SNS is exergonic. The π-π interaction between the drugs and SNS surface is the main driving force in the formation of drug-carriers complexes. The quantum theory of atoms in molecule (QTAIM) results reveal that the interaction of SNS and FA-SNS with both drugs has a non-covalent nature. The natural bond orbital (NBO) analysis shows that the charge is transferred from the drug molecules to carrier in all of the investigated complexes. Furthermore, MD simulations reveal that the contribution of van der Waals energy in drug-carrier interactions is more than electrostatic energy. Also, the obtained results demonstrate that the movement of drug molecules toward the carriers is spontaneous. Our study provides insights into the drug delivery capability of SNS and FA-SNS for the delivery of two drugs (ANA and MEL). Communicated by Ramaswamy H. Sarma

Cavity-trapped electrons: lithium doped tetracyano-2,6-naphthoquinodimethane (TNAP) systems

The interesting features in the lithium based electride motived us to explore new species with electride properties. To achieve this goal, the tetracyano-2,6-naphthoquinodimethane (TNAP) species has been used as backbone to investigate systematic addition of lithium atoms to the TNAP backbone (Lin@TNAP (n = 1-4) species) through density functional theory (DFT) simulation. After finding the most stable geometries for each Lin@TNAP (n = 1-4) species by full optimization process, we show their electronic-structural features in this work. In the next step, the properties of electron-density-laplacian (∇2ρ(r)), non-linear-optical (NLO), non-nuclear-attractor (NNA), and electron-localization-function (ELF) have been studied to incorporate the reported Lin@TNAP (n = 1-4) species in two different categories, salt or electride. The obtained outcomes present that the Li1@TNAP and the Li2@TNAP molecules are the lithium-salt. In contrast, the Li3@TNAP and the Li4@TNAP molecules are lithium-based electrides along with the isolated electrons in the molecular structure.

Binding interactions between pepsin and 3,3′,4,4′,5-pentachlorobiphenyl

One member of the polychlorinated biphenyls that is linked to a number of human diseases is 3,3′,4,4′,5-pentachlorobiphenyl. Here, density functional theory calculation, molecular simulations and multi-spectroscopic techniques were utilized to evaluate the interaction mechanism of 3,3′,4,4′,5-pentachlorobiphenyl with the pepsin, the digestive enzyme. The results of density functional theory and molecular simulations demonstrated that 3,3′,4,4′,5-pentachlorobiphenyl could be a good candidate for its availability toward pepsin with a frontier orbital gap of 0.18109 eV, and bound to the hydrophobic cavity of pepsin. The steady-state fluorescence and time-resolved fluorescence revealed that the quenching was initiated by complexation of pepsin and 3,3′,4,4′,5-pentachlorobiphenyl with the binding constant of 105 order. The UV-absorption, synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy, circular dichroism spectroscopy, and three-dimensional fluorescence data further confirmed that the changes in the secondary structure of pepsin were induced on the presence of 3,3′,4,4′,5-pentachlorobiphenyl, and a quantitative analysis of the secondary structure elements in pepsin was obtained.

Tracking the Acceleration of Hydration of β-C2S Due to Nanosilica Incorporation Using THz Spectroscopy

β-dicalcium silicate (β-C2S), the second most prevalent constituent of Ordinary Portland Cement (OPC), reacts slowly during the early stage of hydration but is responsible for long-term strength development of concrete. To accelerate the hydration during this stage, nanomaterials are incorporated in the β-C2S matrix which results in pozzolanic reactions. In this work, nanosilica has been added in different percentages, and the acceleration in hydration has been tracked by employing Terahertz spectroscopy for a period of 100 days. This study clearly demonstrates that nanosilica incorporation accelerates the early-stage hydration of β-C2S as seen by the reduction in intensity of the resonances between 500 and 520 cm−1. Density functional theory (DFT) simulations of β-C2S confirm these resonances to be due to SiO4 and CaO bending modes. The prominence of the resonance around 455 cm−1 for the nanosilica-incorporated β-C2S indicates early-stage formation of the key hydration product, calcium silicate hydrate (C–S–H). Furthermore, sharpening of the resonance around 283 cm−1 during hydration could possibly indicate the formation of more ordered structures of the hydration products. By tracking the shift of these resonances, it can be inferred that the degree of polymerization of silicates during C–S–H formation is different compared to cement and C3S. To track the structural changes during hydration, scanning electron microscopy (SEM) has been carried out which shows the formation of fiber-like morphologies, indicative of early-stage formation of C–S–H for the nanosilica-incorporated samples. This study could potentially help to engineer β-C2S-rich cement matrix with nanomaterials which could aid in reducing CO2 emission during cement manufacturing.

Investigating the preservation of π-conjugation in covalently functionalized carbon nanotubes through first principles simulations.

We performed a theoretical investigation of single-walled carbon nanotubes (CNTs) functionalized with triazine molecules. Upon adsorption, the influence of the molecule orientation on the CNTs' electronic properties is examined by combining first-principles density functional theory calculations and simulations of X-ray Absorption Near-Edge Structure (XANES) at the C K-edge. Our calculations show that the electronic properties of functionalized CNTs can preserve the same features of pristine CNTs, for both semiconductor and metallic CNTs, depending on the orientation of the covalently bonded molecule. For that configuration, we observe a breakage of the CNT C-C bond at the molecule adsorption site. Moreover, the XANES spectra reveal that sp2 bonding hybridization is preserved along the CNT network. On the other hand, the electronic properties of pristine CNTs are no longer preserved for adsorbed molecule orientations resulting in intact C-C bond at the adsorption site. In this case, the XANES spectra indicate that the molecule-CNT interactions result in sp3 hybridization. Our findings help to elucidate whether π-conjugation is preserved in functionalized CNTs, demonstrating that calculations of XANES spectra are a powerful tool to resolve such systems.

Alkane Cyclization: A DFT Study on the Effect of Chlorinated γ-Alumina

The effect of a chlorinated γ-alumina (Cl/γ-alumina) surface on the cyclization and/or isomerization of hexane was elucidated based on the thermochemistry determined via first-principles density functional theory (DFT) simulations. The character of chlorine as a Lewis acid dopant on a γ-alumina surface was explored at the atomic scale. The most promising site for the chlorine atom on the (110) surface of γ-alumina resulted from direct adsorption. The binding energy between chlorine and the alumina surface was determined to be –2.11 eV. The binding energy was also measured by BSSE correction, and the result showed that this correction significantly affects the calculated binding energy of the Cl/γ-alumina system. Finally, we performed ab initio molecular dynamics simulations at the temperature of the reforming process (485°C) to determine the configuration of hexane, as a sample alkane, to detect of the role of the acidity of chlorine in the isomerization and/or cyclization process. The investigation of the effect of a chlorine atom on the γ-alumina showed that under vacuum conditions, the cyclization of hexane was strongly promoted over isomerization. This work exploits the power of recent developments in computational modeling and quantum mechanical calculations to elucidate hexane activation and its transformations over Cl/γ-alumina.

Insight into the Mechanism of the OH-induced Reaction of Ketoprofen: A Combined DFT Simulation and Experimental Study

The OH-induced reactions are the most important reactions for the degradation of pharmaceutical and personal care proucts (PPCPs) in advanced oxidation process (AOP) systems. In this work, the transformation mechanisms of a typical PPCP, ketprofen (KP), are investigated in detail by combined density functional theory (DFT) simulations and laboratory experiments. We find that Habstraction pathways are preferred in the OH-initiated reactions, and the influence of the hydrogen bond between the OH radical and the carboxyl group cannot be neglected. The subsequent decarboxylation and decomposition reactions are likely to occur. In addition, under highly acidic condition, the protonation of the carbonyl group in KP or in other benzophenone-like compounds might inhibit the decomposition reactions. Meanwhile, the simulation results are well supported by the Fenton experiments.

Simulation study on CO2 diffusion and adsorption in zeolitic imidazolate framework-8 and -90: influence of different functional groups

Global climate change or global warming due to carbon dioxide (CO2) emissions from humanity activities are believed to be one of the biggest challenges in twenty-first century, where more than 30 billion tons of this gas are released to the atmosphere annually. Among many technical procedures which can be employed to carbon capture from the flue gas stream after combustion, adsorption process utilizing advanced adsorbent materials such as highly porous Metal-Organic Frameworks (MOFs) has gained many attentions thank to many techno-economical and environmental benefits. In this paper, to enhance diffusion and adsorption capacity of CO2 inside two types of the most stable zeolitic imidazolate frameworks namely the ZIF-8 and ZIF-90, subset of MOF materials, ligand functionalization using various functional groups is accomplished through Density functional theory (DFT) and Grand Canonical Monte Carlo (GCMC) simulation. To this purpose, at first the structure of four hypothetical functionalized-ZIF-8 and -90 by NO2 (nitro group), NH2 (amino group), OH (hydroxyl group) and Li is designed using DFT calculations. Afterwards, CO2 adsorption capacity and diffusion in all functionalized-ZIFs are evaluated by GCMC simulation and molecular dynamic calculation, respectively. The accuracy of the calculated results is also evaluated by comparison with experimental data in literatures. Obtained results from simulation study revealed that in both ZIF-8 and -90 structures, Li functional group has the highest influence on the adsorption capacity for CO2 owing to high polarity of Li cations. It is believed that lithium ions create very strong negative charge centers at oxygen atoms that attack to the positive center of carbon in the CO2 molecule during adsorption.

Investigations on Detecting Potential Nuclear Material Diversion from a Pyroprocessing Facility

Under normal operating conditions, a pyroprocessing facility removes highly radioactive and nonradioactive fission product waste from used nuclear reactor fuel to recycle the remaining uranium (U), plutonium (Pu), and other actinides contained in it. The products from this facility are separate ingots of U and mixed transuranic elements (TRUs)–uranium (TRU-U). Uranium in both ingots will be depleted U with 235U enrichment less than 1%. The TRU-U ingot will contain neptunium, Pu, americium (Am), and curium (Cm) mixed with U with an approximate TRU:U ratio of 1:1. Four scenarios of nuclear material diversion by potential misuse of the pyroprocessing facility operations are analyzed and compared with the scenario of normal operating condition when the electrowinning process or the TRU-U ingot manufacturing process is misused. These diversion scenario analyses are carried out to understand the proliferation potential and to recommend safeguards measures. The four scenarios of nuclear material diversion analyzed are (1) 50 g Pu, (2) 100 g Pu, (3) 200 g Pu, and (4) all Pu, i.e., 452 g in the 1-kg TRU-U ingot. Plutonium cannot be diverted by itself because other TRUs (Am and Cm) will be simultaneously extracted with Pu. This is because the reduction potentials of those actinides are not distinguishably different from that of Pu on a liquid cadmium cathode of the electrowinning step of the pyroprocess. Hence, in addition to Pu, simultaneous diversion of respective amounts of Am and Cm for the four diversion scenarios are considered. The diversion scenario analysis also considered the concealment of Pu and Cm removal from the TRU-U ingot by adding an equivalent amount of 252Cf to replenish the neutron source emissions. These five scenarios (four nuclear material diversion scenarios and one normal operation scenario) are modeled and simulated using the Monte Carlo N-Particle (MCNP6) radiation transport computer code by incorporating the model of a NaI gamma radiation detection system. The results show that the presence and absence of Pu in the TRU-U ingot can be confirmed by the NaI gamma radiation detection system. However, identifying the presence of U in the TRU-U ingot is difficult using the NaI gamma radiation detection system due to interference from TRU gamma radiation. To identify the U presence in the TRU-U ingot, an application of nuclear magnetic resonance (NMR) is studied. The NMR technology employs a numerical calculation approach based on density functional theory (DFT) simulation. The DFT calculation results show that the detection of U in a pyroprocess is feasible by NMR technology. In addition, these four nuclear material diversion scenarios are analyzed through MCNP6 simulations by incorporating the model of a coincidence neutron detection system. To conceal the nuclear material diversion, the simulations are performed by replacing the diverted Pu and Cm by an appropriate mass of 252Cf neutron source that is equivalent to the neutron source strengths of the diverted mass. Simulation results show that this concealment (misuse) results in a deceived Pu mass estimate in the TRU-U ingot if the Pu-to-244Cm–ratio method (proposed method in the literature) is used.

On the Use of GPUs in Density Functional Theory Atomistic Simulations: A Case of Acceleration Success

The use of density functional theory (DFT) simulations has proved to be a powerful tool in the Earth and Environmental Sciences. However, these calculations require a large computational power and are limited to ~1000 atoms in big supercomputers. An alternative to parallelize DFT codes in CPU supercomputers is the use of GPU cards. These contain a large number of threads that can accelerate codes which are properly programmed for parallel calculations. In this mini-review we have evaluated which factors are crucial to obtain an appropriate acceleration in the process of moving CPU codes to their GPU version: memory transfer, work flows and CPU/GPU ratio. Accelerations up to 20-40 times the pure CPU version of the DFT code have been achieved. This makes that the additional cost of GPUs cards is less than the price/performance obtained.