First-principles Molecular Dynamics Research Articles

Al-modified environmental barrier coatings for protection against water vapor corrosion

High-temperature water vapor corrosion is a great challenge for long lifetime of Si/mullite/Yb2SiO5 Environmental Barrier Coatings. In this work, the Yb3Al5O12 modified layer was in-situ synthesized on the surface of Yb2SiO5 layer to improve the steam resistance. The reaction mechanism of the Al-modified layer was explored. The steam corrosion experimental results indicated that the defects in Yb2SiO5 layer healed, and the oxidation rate of Si-bonded coating was slowed down under the protection of modified layer. Additionally, the calculation results of first-principle molecular dynamics confirmed that Yb3Al5O12 has excellent steam corrosion resistance.

First-principles simulations of liquid iron-heavy element alloys at high pressure

Iron-rich metallic liquid in the Earth's outer core is thought to contain many elements. While the incorporation of light elements in liquid iron has been widely studied, liquid iron-heavy element mixtures, particularly considering Co, Mo, and W which are relevant in constraining core-forming conditions need more studies. Here we investigate the thermodynamic and structural behavior of these siderophile elements and Ni dissolved in liquid iron in the amount of 2.67 atom% using first-principles molecular dynamics over the pressure range of the entire Earth's interior at temperatures 4000 to 7000 K. The calculated pressure-volume-temperature results of these iron-rich alloys are accurately described by adding the appropriative terms to the equation of state of pure iron liquid to account for the effects of temperature and impurity. The calculated mean iron coordination number of Mo and W is somewhat larger than that of Ni and Co and host iron atoms thus implying substitutional incorporation mechanism. The lack of clustering activity among the impurity atoms means that each of these impurity elements is soluble in liquid iron. Our analysis also shows that Mo and W increase the liquid density much more than Ni and Co mainly for mass reason while the bulk modulus remains essentially unaffected in all cases. The presence of heavy elements widens the apparent density gap between iron-rich liquid and the outer core so additional amounts of lighter impurity elements should be considered when constraining the core composition.

Thermodynamics, Kinetics, and Optical Properties of Rotaxane: A First-Principles Molecular Dynamics Study.

Through molecular mechanics using the force field along with the quantum dynamical aspect of mechanically interlocked compounds, rotaxanes (defined as macromolecular rings that are threaded on a dumbbell-shaped axle molecule) are investigated with advanced quantum mechanical methods, including the atom-centered density matrix propagation simulation technique, at different temperatures like 300, 500, 700, 900, 2000, and 2500 K for 1.2 ps. Ab initio molecular dynamics simulation is carried out. In addition to, we investigate the noncovalent interaction present in the rotaxane compound 2R-D-2PF6 with the help of reduced density gradient, average reduced density gradient, density overlap region indicator, and interaction region indicator as well as Hirshfeld surface analyses. Furthermore, the stability of 2R-D-2PF6 at room temperature and higher temperatures is elucidated by analyzing the thermal fluctuation index through a dynamic process. In order to check the optical behavior of our selected rotaxane compound, an evaluation of the electronic dipole moment, static and frequency-dependent average polarizability, and first- and second-order hyperpolarizability is carried out. The rotaxane compound shows very promising linear and nonlinear optical responses, which indicates its utility as a very good optical material. The calculation of the time-dependent density-functional theory highlights the broad absorption band of rotaxane spanning the UV-visible domain. Therefore, we also unravel that this can tap into solar radiation or harnessing of solar energy.

Hydration Mechanisms of Tungsten Trioxide Revealed by Water Adsorption Isotherms and First-Principles Molecular Dynamics Simulations

WO3 is one of the most interesting materials for photocatalysis due to its optical absorption in UV–vis, good charge carrier transport, and stability against photocorrosion. A detailed knowledge of the hydration state of WO3 is indispensable to gain more precise mechanistic insights into its photocatalytic activity. To the best of our knowledge, the hydration process of WO3 has been scarcely studied so far and only from a theoretical point of view, mostly by means of static density functional theory calculations. Here, we use manometric gas sorption experiments combined with extensive ab initio molecular dynamics simulations to investigate the hydration mechanisms of WO3 at room temperature. We demonstrate that water adsorbs molecularly in a two-step mechanism: the first water sublayer interacts with the under-coordinated surface tungsten atoms through electrostatic interactions, and, in a second step, a full layer is formed through hydrogen bonds established with the pre-adsorbed water molecules and with the under-coordinated surface oxygen atoms. The computed value of −90 kJ·mol–1 for the isosteric enthalpy of adsorption of the first water molecules is in excellent agreement with the experimental value estimated using the Clausius–Clapeyron approach from the experimental adsorption isotherms. The isosteric enthalpy of adsorption steadily decreases in absolute value when the surface coverage is increased to tend toward the enthalpy of condensation of water after three adsorption layers.

Atomistic simulations of thermal conductivity in novel GeC channel materials from first-principles molecular dynamics calculations

Silicon carbide (SiC) has emerged as a candidate material for next-generation power devices to replace traditional silicon power devices. They feature smaller size, faster switching speed, simpler cooling, and greater reliability than Si-MOSFETs. To date, however, the thermal conductance of GeC-based power MOSFETs is unclear. This work explains the heat transfer of GeC by simulating the thermal conductivity through molecular dynamics (MD) and proposes a potential 4H-GeC power MOSFET with wide bandgap and high thermal conductivity to replace Si-MOSFETs.

Performance evaluation and assessment of the corrosion inhibition mechanism of carbon steel in HCl medium by a new hydrazone compound: Insights from experimental, DFT and first-principles DFT simulations

In the present work, a new hydrazone compound, namely N'-[(Z)-(4-chlorophenyl)methylidene]-2-(5-methoxy-2-methyl-1H-indol-3-yl)acetohydrazide, noted HTH, was selected to protect carbon steel against corrosion in 1.0 mol/L HCl. Different chemical, electrochemical, and surface characterization techniques such as scanning electron microscope coupled with X-ray energy dispersion (SEM/EDX) were used to investigate the corrosion inhibition performance. Electrochemical data showed that the effectiveness of the inhibitor improved with increasing concentration, reaching 98% at the optimal concentration of 10-3 mol/L. The results of potentiodynamic polarization measurements showed that hydrazone acted as a mixed-type inhibitor. The EIS results showed an increase in polarization resistance accompanied by a noticeable decrease in Ceff,dl values. In the temperature range of 303 K-333 K, hydrazone protected carbon steel by 89%, showing high resistance to temperature effect. The analysis of the steel surface by SEM/EDX confirmed that the effectiveness of the hydrazone was attributed to the formation of a protective layer on the surface of the metal. Quantum chemical calculations revealed insights into the chemical reactivity of the tested hydrazone while first-principles density functional theory (DFT) and molecular dynamics (MD) simulation supported the experimental conclusions and showed outstanding adsorption ability of HTH on the Fe(110) surface. First-principles DFT simulations showed that the HTH molecule was more stable in a parallel adsorption mode.

Impact of the local atomic structure on the thermal conductivity of amorphous Ge2Sb2Te5.

Thermal properties are expected to be sensitive to the network topology, and however, no clearcut information is available on how the thermal conductivity of amorphous systems is affected by details of the atomic structure. To address this issue, we use as a target system a phase-change amorphous material (i.e., Ge2Sb2Te5) simulated by first-principles molecular dynamics combined with the approach-to-equilibrium molecular dynamics technique to access the thermal conductivity. Within the density-functional theory, we employed two models sharing the same exchange-correlation functional but differing in the pseudopotential (PP) implementation [namely, Trouiller-Martins (TM) and Goedecker, Teter, and Hutter (GTH)]. They are both compatible with experimental data, and however, the TM PP construction results in a Ge tetrahedral environment largely predominant over the octahedral one, although the proportion of tetrahedra is considerably smaller when the GTH PP is used. We show that the difference in the local structure between TM and GTH models impacts the vibrational density of states while the thermal conductivity does not feature any appreciable sensitivity to such details. This behavior is rationalized in terms of extended vibrational modes.

Understanding native defect induced photoluminescence in Zn2SnO4

Simulation of photoluminescence spectroscopy from first principles provides a powerful approach for predicting the experimental spectrum and understanding the origin of the luminescence of materials. We show here that the use of the hybrid-exchange correlation functional combined with first-principles molecular dynamics can simulate the defect-induced photoluminescence spectrum of zinc stannate $({\mathrm{Zn}}_{2}{\mathrm{SnO}}_{4})$ in good agreement with the experiment. The calculations were carried out for 12 different point defects of ${\mathrm{Zn}}_{2}{\mathrm{SnO}}_{4}$, and show that the green-to-red photoluminescence emissions obtained in the experiment are mainly contributed by the oxygen vacancy defects. These defect states play the roles of deep donors and radiative recombination centers during the photoluminescence mechanism. In particular, their electronic properties are significantly affected by temperature, which is related to the strong fluctuation of the nearest-neighbor Sn atoms relative to the vacancy center.

Path-integral molecular dynamics predictions of equilibrium H and O isotope fractionations between brucite and water

Precise prediction of hydrogen (H) isotope fractionations among different substances is a long-standing challenge in isotope geochemistry, as it needs treatments beyond the harmonic approximation. Path-integral molecular dynamics (PIMD) simulations have recently been proved to be valid in predicting equilibrium isotope fractionations for light elements. However, the lack of reliable force fields hinders the application of PIMD to the condensed phases. In this work, the deep potential models trained on the first-principles molecular dynamics (FPMD) data are applied to PIMD simulations to determine the D/H and 18O/16O isotope fractionation factors between brucite and water. To quantitatively assess the influence of quantum effects, the D/H and 18O/16O isotope fractionations between brucite and water are also determined under the framework of harmonic approximation.By comparing the results of the PIMD and those of harmonic calculations, we find that H and O atoms in brucite and water are strongly affected by the anharmonic effects. The accuracy of the harmonic isotope fractionations mainly depends on the cancellation percentage of the anharmonic effects on the reduced partition function ratios (RPFRs) of the two substances. The isotope fractionations predicted by PIMD simulations are close to the experimental results at high temperatures. However, at low temperatures, the predicted isotope fractionations are different from those of experiments. The discrepancies are attributed to the approximations in the density functional theory (DFT) functionals used in this work, i.e., the inaccuracy in predicting the proton positions in brucite and water. Moreover, we find that the H isotope fractionations are extremely sensitive to the change of pressure. The direction of H isotope fractionation between brucite and water (at 300 K) will be even inversed as the pressure increases to more than 3 GPa. This strong pressure sensitivity may be a common characteristic of hydrous minerals and water systems. Therefore, the extrapolated H isotope fractionations used in the studies of dehydration of subducting slabs or deep Earth H distribution based on the isotope fractionations under low pressures may need to be rechecked.

An ab initio study of catechol sensing in pristine and transition metal decorated γ-graphyne

Catechol is a toxic biomolecule due to its low degradability to the ecosystem and unpredictable impact on human health. In this work, we have investigated the catechol sensing properties of pristine and transition metal (Ag, Au, Pd, and Ti) decorated γ-graphyne (GY) systems by employing the density functional theory and first-principles molecular dynamics approach. Simulation results revealed that Pd and Ti atom is more suitable than Ag and Au atom for the decoration of the GY structure with a large charge transfer of 0.29e and 1.54e from valence d-orbitals of the Pd/Ti atom to the carbon-2p orbitals of GY. The GY + Ti system offers excellent electrochemical sensing towards catechol with charge donation of 0.14e from catechol O-p orbitals to Ti-d orbitals, while the catechol molecule is physisorbed to pristine GY with only 0.04e of charge transfer. There exists an energy barrier of 5.19 eV for the diffusion of the Ti atom, which prevents the system from metal–metal clustering. To verify the thermal stability of the sensing material, we have conducted the molecular dynamics simulations at 300 K. We have reported feasible recovery times of 2.05 × 10−5 s and 4.7 × 102 s for sensing substrate GY + Pd and GY + Ti, respectively, at 500 K of UV light.

All-Electron Plane-Wave Electronic Structure Calculations.

We demonstrate the use of the plane wave basis for all-electron electronic structure calculations. The approach relies on the definition of an analytic, norm-conserving, regularized Coulomb potential, and a scalable implementation of the plane wave method capable of handling large energy cutoffs (up to 80 kRy in the examples shown). The method is applied to the computation of electronic properties of isolated atoms as well as the diamond and silicon crystals, MgO, solid argon, and a configuration of 64 water molecules extracted from a first-principles molecular dynamics simulation. The computed energies, band gaps, ionic forces, and stress tensors provide reference results for the validation of pseudopotentials and/or localized basis sets. A calculation of the all-electron band structure of diamond and silicon using the SCAN meta-GGA density functional allows for a validation of calculations based on pseudopotentials derived using the PBE exchange-correlation functional. In the case of (H2O)64, the computed ionic forces provide a reference from which the errors incurred in pseudopotential calculations and in localized Gaussian basis sets calculations can be estimated.

Engineering of Hydrogenated (6,0) Single-Walled Carbon Nanotube under Applied Uniaxial Stress: A DFT-1/2 and Molecular Dynamics Study.

Herein, we systematically studied the electronic, optical, and mechanical properties of a hydrogenated (6,0) single-walled carbon nanotube [(6,0) h-SWCNT] under applied uniaxial stress from first-principles density functional theory (DFT) and molecular dynamics (MD) simulation. We have applied the uniaxial stress range from -18 to 22 GPa on the (6,0) h-SWCNT (- sign indicates compressive and + indicates tensile stress) along the tube axes. Our system was found to be an indirect semiconductor (Γ-Δ), with a band gap value of ∼0.77 eV within the linear combination of atomic orbitals (LCAO) method using a GGA-1/2 exchange-correlation approximation. The band gap for (6,0) h-SWCNT significantly varies with the application of stress. The indirect to direct band gap transition was observed under compressive stress (-14 GPa). The strained (6,0) h-SWCNT showed a strong optical absorption in the infrared region. Application of external stress enhanced the optically active region from infrared to Vis with maximum intensity within the Vis-IR region, making it a promising candidate for optoelectronic devices. Ab initio molecular dynamics (AIMD) simulation has been used to study the elastic properties of the (6,0) h-SWCNT which has a strong influence under applied stress.

First‐Principles Molecular Dynamics Study on Ionic Structure and Transport Properties of NaCl‐MgCl2‐CaCl2 Ternary Molten Salt System

AbstractThe carbochlorination in molten salt is an effective method for titanium extraction form low‐grade titanium slag with a high calcium and magnesium content. However, in industrial practice, the fluidity of molten salt will gradually decrease with the increase of CaCl2 content. It is important to elucidate the influencing mechanism of CaCl2 content on the microstructure and diffusion properties of molten salt for the rational selection of a molten salt system and clean utilization of titanium slag. In this study, the densities of molten salt systems with different CaCl2 contents are measured according to the Archimedes principle. Then, using the first‐principles molecular dynamics (FPMD) method, the ionic structure and transport properties of NaCl‐MgCl2‐CaCl2 ternary molten salt systems under different CaCl2 contents are qualitatively and quantitatively described by determining the partial radial distribution functions (PRDF), coordination number (CN), angular distribution functions (ADF), and diffusion coefficient (DC). The results show that with the addition of CaCl2, Ca2+ ion complexed with Cl− ion to form larger ionic clusters, which reduced the proportion of free Cl− ion and restricted the diffusion of Cl− ion.

The electronic structure of genome editors from the first principles

Ab-initio molecular dynamics enables following the dynamics of biological systems from the first principles, describing the electronic structure and offering the opportunity to “watch” the evolution of biochemical processes with unique resolution, beyond the capabilities of state-of-the-art experimental techniques. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 genome editing revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to establish the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods—i.e., thermodynamic integration and metadynamics—to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues’ protonation states. Overall, first-principles methods are shown to unravel the electronic structure and reveal the catalytic mechanism of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.

First-principles thermal equation of state of fcc iridium

The thermal equation of states for fcc iridium (Ir) is obtained from first-principles molecular dynamics up to 3000 K and 540 GPa. The equation of state (EoS) is globally fitted to a simplified free-energy model and various parameters are derived. The theoretical principal Hugoniot is compared with shock wave experiments, where discrepancy suggests formation of new Ir phases. A few representative EoS parameters, such as bulk modulus ${K}_{T}$, thermal expansivity $\ensuremath{\alpha}$, Gr\"uneisen parameter $\ensuremath{\gamma}$, constant pressure capacity ${C}_{P}$, and Debye temperature ${\mathrm{\ensuremath{\Theta}}}_{\mathrm{D}}$, are computed to compare with experimental data.

Understanding surface complexation of antimony on Mg(OH)2: Insights from first-principles molecular dynamics

Sorption processes at the mineral–water interface are of great importance in dominating the fate and availability of metalloid contaminants in natural environment. Aiming at a thorough understanding of the complexation of antimony (Sb) on metal hydroxide, we conducted first-principles molecular dynamic (FPMD) simulations and batch adsorption experiments to elucidate the quantitative mechanism of Sb complexation on Mg(OH)2. Batch experiments showed the sorption of Sb(III) is nearly pH-independent, while increasing pH markedly weakened Sb(V) sorption; the measured sorption isotherm curves were well fitted by Langmuir model. Subsequently, molecular-level mechanism of Sb(V)/Sb(III) on brucite basal and edge surfaces were revealed by FPMD, including microscopic surface reactive sites, local complexing structures and coordination geometries, and complexing free energies. Results showed that Sb(III)/Sb(V) can form outer-sphere complexation on basal surface by hydrogen bonding. On edge surface, Sb(III)/Sb(V) formed stable inner-sphere mononuclear monodentate and binuclear bidentate complexes. The calculated free energies indicated that the binuclear bidentate complexing was more favorable than monodentate structure, and the complexation of Sb(III) was more stable than Sb(V). Accordingly, reaction pathway of the ligand exchange and thermodynamic stability of the different inner-sphere complexes were clarified. This study provides theoretical basis for evaluating the environmental risk of Sb and improving the engineering efficiency of Sb-contaminated water management.

Electrostatics and Chemical Reactivity at the Air–Water Interface

It has been recently discovered that chemical reactions at aqueous interfaces can be orders of magnitude faster compared to conventional bulk phase reactions, but despite its wide-ranging implications, which extend from atmospheric to synthetic chemistry or technological applications, the phenomenon is still incompletely understood. The role of strong electric fields due to space asymmetry and the accumulation of ions at the interface has been claimed as a possible cause from some experiments, but the reorganization of the solvent around the reactive system should provide even greater additional electrostatic contributions that have not yet been analyzed. In this study, with the help of first-principles molecular dynamics simulations, we go deeper into this issue by a careful assessment of solvation electrostatics at the air-water interface. Our simulations confirm that electrostatic forces can indeed be a key factor in rate acceleration compared to bulk solution. Remarkably, the study reveals that the effect cannot simply be attributed to the magnitude of the local electric field and that the fluctuations of the full electrostatic potential resulting from unique dynamical behavior of the solvation shells at the interface must be accounted for. This finding paves the way for future applications of the phenomenon in organic synthesis, especially for charge transfer or redox reactions in thin films and microdroplets.

Probing the low friction mechanism of hydrogen-free DLC film in oxygen and nitrogen environments by first-principles calculations and molecular dynamics simulation

We try to compare the interfacial bonding behavior of hydrogen-free DLC films in nitrogen or nitrogen atoms environment by first principle calculation and molecular dynamics (MD) simulation, so as to provide an atomic view of the friction behavior in oxygen and nitrogen environments. The results show that hydrogen-free DLC films will form CN bonds and CO bonds when the coverage of nitrogen or oxygen is not higher than 0.75, but will be completely passivated when the coverage of nitrogen or oxygen is higher than 0.75. The lower CO bond strength and higher repulsion force at the friction interface of DLC films in oxygen atmosphere suggest that the friction coefficient is less than that in nitrogen environment. Moreover, the results of molecular dynamics simulation further show that a lower friction of DLC film in the oxygen atmosphere may be due to the smoother friction interface and less interfacial bonds.

Exciton diffusion in poly(3-hexylthiophene) by first-principles molecular dynamics.

Poly(3-hexylthiophene) (P3HT) is a polymer used in organic solar cells as a light absorber and an electron donor. Photogenerated excitons diffuse and dissociate into free charge carriers provided they reach the absorber boundaries. The device efficiency is therefore dependent on the exciton diffusion. Although measurements can be performed for example by time-resolved photoluminescence, a quantitative modeling is highly desirable to get an insight into the relationship between the atomic structure at finite temperature and the diffusion coefficient of the exciton. This is the objective of the present work, achieved by resorting to first-principles molecular dynamics in combination with the restricted open-shell approach to model the singlet excited state. The maximally localized Wannier functions and their centers are used to monitor and localize the electron and the hole along the dynamics. The resulting diffusion coefficient is in close agreement with available measurements.

Unveiling the structure and ion dynamics of amorphous Na3−xOHxCl antiperovskite electrolytes by first-principles molecular dynamics

Amorphous antiperovskites show potential as solid-state electrolytes due to their versatile properties. Using first-principles molecular dynamics, we reveal the Na3−xOHxCl system's structural complexities, Na ion dynamics, H atom role, and ionic conductivity mechanisms.