Principles Molecular Dynamics Research Articles

Hydrogenation of calcite and change in chemical bonding at high pressure: Diamond formation above 100 GPa

Synchrotron X-ray diffraction (XRD) and Raman spectroscopy in laser heated diamond anvil cells and first principles molecular dynamics (FPMD) calculations have been used to investigate the reactivity of calcite and molecular hydrogen (H2) at high pressures up to 120 GPa. We find that hydrogen reacts with calcite starting below 0.5 GPa at room temperature forming chemical bonds with carbon and oxygen. This results in the unit cell volume expansion; the hydrogenation level is much higher for powdered samples. Single-crystal XRD measurements at 8–24 GPa reveal the presence of previously reported III, IIIb, and VI calcite phases; some crystallites show up to 4% expansion, which is consistent with the incorporation of ≤ 1 hydrogen atom per formula unit. At 40–102 GPa XRD patterns of hydrogenated calcite demonstrate broadened features consistent with the calcite VI structure with incorporated hydrogen atoms. Above 80 GPa, the CO stretching mode of calcite splits suggesting a change in the coordination of CO bonds. Laser heating at 110 GPa results in the formation of CC bonds manifested in the crystallization of diamond recorded by in situ XRD at 300 K and 110 GPa and by Raman spectroscopy on recovered samples commenced with C13 calcite. We explored several theoretical models, which show that incorporation of atomic hydrogen results in local distortions of CO3 groups, formation of corner-shared CO polyhedra, and chemical bonding of H to C and O, which leads to the lattice expansion and vibrational features consistent with the experiments. The experimental and theoretical results support recent reports on tetrahedral C coordination in high-pressure carbonate glasses and suggest a possible source of the origin of ultradeep diamonds.

Effects of liquefied gas temperature and negative pressure on the microstructural characteristics of oxide Mg2SiO4 using molecular dynamics simulation method

Our study focused on examining the behavior of oxide Mg2SiO4 under various liquefied gas temperatures, including 4.22 K (Helium), 77 K (Nitrogen), 83.88 K (Argon), 90 K (Oxygen), 194.3 K (Carbon), and 300 K (room temperature), while maintaining a pressure of 0 GPa. Additionally, we explored the effects of pressures ranging from 0 to −6 GPa at a temperature of 77 K using first principles molecular dynamics simulations. Our findings indicate significant variations in the system’s size, energy, and the lengths of Si-Si, Si-O, O-O, Si-Mg, Mg-O, and Mg-Mg bonds with decreasing temperature at 0 GPa and decreasing pressure at a temperature of 77 K. Moreover, substantial variations were observed in the average coordination number of bonds, the quantity of SiOx, MgOy structural units (where x = 4, 5 and y = 3, 4, 5, 6, 7), and bond angles of Si-O-Si, and Mg-O-Mg under negative pressure while remaining relatively constant across liquefied gas temperatures. Furthermore, we successfully established a linear relationship between temperature, pressure, and the total energy of the system. These insights into the behavior of oxide Mg2SiO4 serve as valuable groundwork for future experimental investigations, particularly in leveraging the material’s potential applications in advanced technological fields.

Numerical validation of Yukawa fluid excitations within the quasilocalized charge approximation (QLCA) theory

AbstractA first principle molecular dynamics (MD) simulation study on the nonlinear excitations in a quasi‐localized state of a Yukawa system is presented to validate the findings of the nonlinear quasi‐localized charge approximation (QLCA) model. Unlike solids or gases, quasi‐localized states lack certain simplifying features, such as the ability to assume a fixed shape or volume, and they combine large displacements with strong interactions, further complicating the theoretical underpinnings of their behavior. In a recent paper [P. Kumar and D. Sharma, Physics of Plasmas 30 (2023)], the nonlinear QLCA model was applied to characterize the nonlinear excitations in a quasi‐localized state of a Yukawa system, as existing continuum models have shown limited success in this regime. The simulation data presented with the screening and coupling parameters show a close agreement with the QLCA model findings. The MD simulations validate the prediction made by the QLCA model that the properties of a soliton remain unaffected by variations in the coupling parameter. The prediction made by QLCA regarding the formation of multiple solitons at higher screening parameter values has also been confirmed by the MD simulation data. The possibility of the formation of rarefactive solitons at relatively high screening parameter values within the QLCA model is also discussed.

Pockets, jumps and filaments: classifying ionic motion and determining the role of structure in electrochemical properties of 2Li2S-GeS2 superionic glasses

The structural properties of a typical solid electrolyte system (2Li2S-GeS2) is investigated from First principles molecular dynamics simulations. Results reveal that depolymerization of the base GeS2 network by alkali additives takes place but appears reduced with respect to the corresponding sodium analog glass. Experimental structure functions are reproduced and reveal that the network is dominated by GeS 4/2 tetrahedra that are connected by edges (four-membered rings) and corners and disrupted by the addition of lithium, albeit a non-negligible fraction of connecting tetrahedra (Q 2 units) are still present in the glass structure. Dynamic and electric properties are also studied and emphasize that the size of the migrating cation (Li) is essential for ensuring a good level of ionic conductivity as it displays increased values with respect to the parent Na-bearing system. On the atomic (picosecond) timescale, different typical Li trajectories are identified and their distribution calculated: reduced cage-like motion in pockets constrained by the surrounding (Ge,S) network, back and forth jump motions with short transition states and long-range filamentary motion.

First-principles molecular dynamics compression of small metallic nanoparticles

Whether the strength of materials keeps increasing, saturates or decreases when characteristic dimensions are reduced down to the nanometer scale remains an open question. To bring new insights, first principles molecular dynamics calculations are performed to model the compression of 1–2 nm aluminum nanoparticles with different shapes. We find that the plastic deformation occurs at high strains and stresses by a mechanism combining diffusive and displacive atomic displacements. This deformation mode is characterized by a slow dynamic and the partial or even complete recovery of crystalline order. The strength depends on the nanoparticles shape, and is in all cases significantly higher than the theoretical bulk strength. It is however substantially lower than values extrapolated using reported classical molecular dynamics investigations. Our results suggest that the strength saturates at low scales.

Engineering the formation of spin-defects from first principles

The full realization of spin qubits for quantum technologies relies on the ability to control and design the formation processes of spin defects in semiconductors and insulators. We present a computational protocol to investigate the synthesis of point-defects at the atomistic level, and we apply it to the study of a promising spin-qubit in silicon carbide, the divacancy (VV). Our strategy combines electronic structure calculations based on density functional theory and enhanced sampling techniques coupled with first principles molecular dynamics. We predict the optimal annealing temperatures for the formation of VVs at high temperature and show how to engineer the Fermi level of the material to optimize the defect’s yield for several polytypes of silicon carbide. Our results are in excellent agreement with available experimental data and provide novel atomistic insights into point defect formation and annihilation processes as a function of temperature.

Absorption and fluorescence spectra of new pyrrolo[3,4‐b]quinolizines in condensed phases: A joint experimental and computational study

AbstractNewly synthesized pyrrolo[3,4‐b]quinolizines, blue‐green to orange‐red in fluorescent dye in solutions and yellow to red fluorescent dyes in solid states, were experimentally and computationally investigated for the electronic and fluorescence spectra in solution as well as in solid state. The solvent effects on the absorption and emission spectra were theoretically investigated by the snapshots‐averaged spectra obtained by the first principle molecular dynamics combined with polarizable continuum model (PCM). Alternatively, the solute–solvent interaction effect on the spectra was examined by fragment molecular orbital‐time dependent density functional theory (FMO‐TDDFT) which considered the explicit solute–solvent interactions. The results indicate that the quantitative prediction limitations of PCM and that the solvatochromic shifts in dichloromethane and ethanol were correctly reproduced by FMO‐TDDFT. The luminescence quantum yields of the compounds were analyzed on the excited state potential surface via the S0/S1‐conical intersections.

Changes in nitrate binding with lanthanides in BLPhen complexes

Preorganized ligands such as bis-lactam-1,10-phenanthroline (BLPhen) offer unique selectivity trends in solvent extraction of rare-earth ions, particularly from aqueous nitrate solutions. However, due to the ligand’s lipophilicity it is experimentally challenging to obtain crystal structures of the corresponding lanthanide (Ln):ligand complexes to describe the local structure of the first coordination shell and the role of the nitrate ions in the organic phase. Herein, we report first principles molecular dynamics (FPMD) simulations of the complexation of trivalent lanthanide ions (La, Nd, and Eu) with the BLPhen ligand in the presence of nitrate ions in the dichloroethane (DCE) solvent. We find that two nitrate anions are present in the first solvation shell and the third nitrate anion is far from the first solvation shell in all three [Ln(BLPhen)2]3+ complexes examined. Moving along the lanthanide series from La to Nd to Eu, the binding pocket formed by the two BLPhen ligands shrinks in size; as a result, the two nitrate configuration changes from one-monodentate/one-bidentate binding mode for La and Nd to all monodentate for Eu. Meanwhile, the total coordination number drops from 11 for La and Nd to 10 for Eu. More interestingly, the bidentate binding in [La(BLPhen)2]3+ and [Nd(BLPhen)2]3+ complexes is highly dynamic, frequently switching to monodentate and back. The FPMD insights into the differing modes and dynamics of nitrates in the first coordination shell will be useful for further atomistic understanding of the complex structure, formation, and stability in the organic phase.

Local structure and transport properties of MgCl2 molten salt with impurity water based on first principles molecular dynamics simulations

Electrolysis of molten anhydrous magnesium chloride is an efficient way to prepare magnesium. Nowadays, it is still an attractive issue to reduce the production cost of anhydrous magnesium chloride in preparing magnesium process by electrolysis. This work focused on the local structure and transport properties of MgCl2 molten salt with impurity water system under various temperature conditions based on the first principles molecular dynamics simulations. The radial distribution function, coordination number distribution, angular distribution function, static structure factor, and self-diffusion coefficient in the temperature range from 1000 K to 1400 K, were compared with of pure MgCl2 to elucidate the microscopic interaction mechanism of impurity water. Besides, this study indicated that the first principles molecular dynamics simulation can serve as an effective and promising tool for the theoretical study of more complex molten salts and provide basic guidance for the experiment to fill in the gaps.

Electrochemical behavior of Sm(III)/Sm(II) and extraction of Sm on reactive electrode from molten LiF-BeF2

The electrochemical behavior of Sm(III)/Sm(II) in 2LiF-BeF2 (FLiBe) molten salt is studied by cyclic voltammetry (CV), square wave voltammetry (SWV), chrono amperometry (CA) and Tafel method in the temperature range of 773 to 973 K. The coexistence of Sm(III) and Sm(II) and the concentration ratio of Sm(III)/Sm(II) are determined by SWV test. The redox reaction of Sm(III)/Sm(II) couple on an inert tungsten electrode is demonstrated to be a quasi-reversible process with diffusion controlled mass transfer. The diffusion coefficients of Sm(III) and Sm(II) determined by chrono amperometry are in the range of 1.17 × 10-6 to 1.09 × 10-5 cm2 s−1 for Sm(III) and 2.49 × 10-6 to 3.90 × 10-5 cm2 s−1 for Sm(II) at 773 K to 973 K and the diffusion activation energy is 8.63 and 10.1 kJ mol−1 for Sm(III) and Sm(II) respectively. The coordination and transport characteristics of the Sm(III)-F and Sm(II)-F are also studied by the first principles molecular dynamics simulations. The Gibbs free energy of the SmF2 is calculated to be −1004.4 kJ mol−1 at 873 K by experimental data, and the standard reduction potential of E0SmF2/Sm is about −0.583 V vs E0BeF2/Be at 873 K. Thermodynamic evaluation and experimental results indicates that the metallic Sm could be extracted as M−rich SmxMy intermetallics (M = Cu, Ni, Al) from FLiBe based molten salts.

Liquid Structures and Ion Dynamics of Ionic Liquids Viewed from Intermolecular Interactions.

The elucidation of the factors determining liquid structures and transport properties of ionic liquids is important for the design and development of ionic liquid electrolytes. This personal account introduces the importance of computational methods for studying ionic liquids. Molecular dynamics simulations provide detailed information on liquid structures of ionic liquid such as the structures of solvated cation complexes in equimolar mixtures of glymes and Li[TFSA] and the effects of the charges of electrode on liquid structure near the electrode. Ab initio calculations reveal that the magnitude of the attraction between ions and conformational flexibility ions play important roles in determining transport properties of ionic liquids. First principle molecular dynamics simulations elucidate why solvated cation complex is stable in the equimolar mixtures, although the Li+ -[TFSA]- interaction is greater than Li+ -glyme interaction.

Fascinating Electrocatalysts with Dispersed Di-Metals in MN3 -M'N4 Moiety as Two Active Sites Separately for N2 and CO2 Reduction Reactions and Jointly for CN Coupling and Urea Production.

The idealized urea electrocatalyst is crucial to boost the CN coupling reaction and simultaneously suppress their isolated reduction process after adsorbing N2 and CO2 molecules. Therefore, the dispersed MN3 -M'N4 moiety is investigated systematically, including 26 homonuclear and 650 heteronuclear di-metal systems. After, 205 stable systems are selected using lowest-energy principle and ab initio molecular dynamics simulations. According to three possible pathways, NCON, CO, and OCOH to produce urea, a five-step high-throughput screening method for excellent catalytic activity and a five-aspect high-throughput screening strategy for outstanding catalytic selectivity are proposed, respectively. The potential determined steps and the limiting potential through three pathways are identified. The data indicates both CO pathway and OCOH pathway are more competitive at lower Gibbs free energy. Significantly, the most favorite RuN3 -CoN4 combination possesses an extremely low limiting potential of -0.80V for urea production, meanwhile it exists a strong foundation for experimental preparation. This work not only broadens electrocatalytic potentiality of developing di-metals as two active sites, but also provides a feasible high-throughput screening recipe for urea production.

Novel Benzimidazole Derived Imine Ligand and Its Co(III) and Cu(II) Complexes as Anticancer Agents: Chemical Synthesis, DFT Studies, In Vitro and In Vivo Biological Investigations

The emerging interest in the field of coordination chemistry and their biological applications has created a novel impact in the field of chemical biology. With this motivation, in this work we have synthesized a novel benzimidazole derived imine ligand, 2-((E)-((1H-benzo[d]-2-yl)methylimino)methyl)-4-fluorophenol (HBMF) and its Co(III) and Cu(II) complexes. The metal complexes (C1-C4) were synthesized in 2:1 (HBMF: metal ion) and 1:1:1 (HBMF: metal ion: 1,10-phen) ratios. Structural elucidations of all the synthesized compounds were performed using FT-IR, UV-Visible, NMR, Mass spectroscopy and elemental analysis techniques. A combination of first principles calculations and molecular dynamics simulations was applied to computationally investigate the structural, reactive, and spectroscopic properties of the newly synthesized HBMF ligand and its complexes with copper and cobalt metal ions. Quantum-mechanical calculations in this study were based on the density functional theory (DFT), while molecular dynamics (MD) simulations were based on the OPLS4 force field. The DFT calculations were used to obtain the reactive and spectroscopic properties of the ligand and its complexes, while molecular dynamics (MD) simulations were used to address the ligand's reactivity with water. Further, the in vitro anti-proliferative activity of the compounds was tested against the A549, Ehrlich-Lettre ascites carcinoma (EAC), SIHA and NIH3T3 cell lines. The biological results depicted that the compound C4, with molecular formula C27H23Cl2CoFN5O3 exhibited profound anti-proliferative activity against the EAC cell line with a significant IC50 value of 10 µm when compared to its parent ligand and other remaining metal complexes under study. Various assays of hematological parameters (alkaline phosphate, creatinine, urea, RBC and WBC) were performed, and significant results were obtained from the experiments. Furthermore, the effect of C4 on neovascularization was evaluated by stimulating the angiogenesis with rVEGF165, which was compared with non-tumor models. The EAC cells were cultured in vivo and administrated with 50 and 75 mg/kg of two doses and tumor parameters were evaluated.

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.

First principles insights into stability of defected MXenes in water.

Two-dimensional transition metal carbides and nitrides, known as MXenes, have demonstrated remarkable performance in electrochemical energy storage and various other applications. Despite their potential, MXenes exhibit instability in aqueous solutions, and the role of defects in their aqueous stability is unclear. In this study, we report on the interfacial chemistry between water and defected Ti3C2O2 MXene at room temperature using first principles molecular dynamics simulations. We investigate how defects such as O vacancy, Ti vacancy, F terminal groups, and Ti-O vacancy pair influence the chemical interaction of water molecules with the basal plane of Ti3C2O2. Our results show that water molecules can repair the surface O vacancies, by dissociating to hydroxide and hydronium. On the other hand, F terminal groups cannot effectively block water chemisorption on the surface Ti, while Ti vacancies behave as a spectator species on the surface with respect to interaction with water. Ti3C2O2 with a Ti-O vacancy pair is found to behave like Ti3C2O2 with an O vacancy where a water molecule dissociates and refills the vacancy. These findings enrich our understanding of water interaction with defects on the MXene surfaces.

Exciton Nature of Plasma Phase Transition in Warm Dense Fluid Hydrogen: ROKS Simulation.

The transition of warm dense fluid hydrogen from an insulator to a conducting state at pressures of about 20-400 GPa and temperatures of 500-5000 K has been the subject of active scientific research over the past few decades. However, various experimental and theoretical methods do not provide consistent results. In this work, we have applied the restricted open-shell Kohn-Sham (ROKS) method for first principles molecular dynamics of dense hydrogen after thermal excitation to the first singlet excited state. The Wannier localization method has allowed us to analyze the exciton dynamics in this system. The model shows that a key mechanism of the transition is associated with the dissociation of electron-hole pairs, which allows explaining several stages of the transition of fluid H2 from molecular state to plasma. This mechanism is able to give a quantitative description of several experimental results as well as to resolve the discrepancies between experimental studies.

First principles molecular dynamics study of proton disorder in [formula omitted] phase of H2 hydrate

The proton-disordered and -ordered crystal structures proposed based on X-ray diffraction experiments for the C1′ phase of H2 hydrate were investigated using first-principles (FP) path-integral ring-polymer molecular dynamics (RPMD) simulations. Our simulated Raman spectra obtained from the FP-RPMD trajectories provide unambiguous evidence for static orientational disorder of H2O molecules forming stacked H-bonded rings. This feature is essential to reproduce the characteristics of the observed Raman spectra. Furthermore, the present study shows that van der Waals interactions need to be treated carefully to achieve satisfactory computational results. The findings of this study can help for better understanding of icy materials.

Structures and transport properties of supercritical SiO2-H2O and NaAlSi3O8-H2O fluids

Abstract Speciation and transport properties of supercritical fluids is critical for understanding their behavior in the Earth’s interior. Here, we report a systematic first principles molecular dynamics simulation study of the structure, speciation, self-diffusivity (D), and viscosity (η) of SiO2 melt, NaAlSi3O8 melt, SiO2-H2O and NaAlSi3O8-H2O fluids at 2000–3500 K with 0–70 wt% H2O. Our calculations show that as the water content increases, the proportion of Q0 species (Qn species, where n is the number of bridging oxygens in an individual Si/Al-O polyhedra) increases while Q4 decreases. The proportions of Q1, Q2, and Q3 species first increase and then decrease with increasing water content. The diffusivity sequence for the supercritical SiO2-H2O fluids is DH >DO >DSi, and for the supercritical NaAlSi3O8-H2O fluids, on the whole, is DNa ≈ DH >DO >DAl ≈ DSi. The viscosities of the two systems decrease drastically at the beginning of the increase in water content, and then decrease slowly. We demonstrate that the exponential decrease in the viscosity of polymerized silicate melt with increasing water content is due to a sharp decrease in the proportion of Q4 species and increase in Si-O-H. The typical structural feature of supercritical fluid is that it contains a large amount of easy-to-flow partially polymerized or depolymerized protonated silicate units, which leads to a low viscosity while being enriched in silicate. This feature provides supercritical fluids the potential to transport elements that are hard to migrate in aqueous fluids or hydrous silicate melts, such as high field strength elements.

Short-range ordering heredity in eutectic high entropy alloys: A new model based on pseudo-ternary eutectics

Eutectic high entropy alloys (EHEAs) have garnered wide attention in the metal community due to their excellent castability and unique microstructures. However, the formation mechanisms of these eutectic microstructures and their compositional design remain puzzling. In this paper, we have developed a simple yet unified pseudo-ternary model to unravel the puzzle of multiple eutectics in Ni-Al-containing high entropy alloys (HEAs) deploying a combination of the chemical similarity/dissimilarity coefficient concept, CALPHAD technique and first principle molecular dynamics simulation. Using the chemical similarity/dissimilarity parameters derived from CALPHAD model parameters and the eutectic valleys of Ni-Al-Cr, we reproduce the multiple eutectic patterns in the Ni-Al-containing HEAs and present a general approach for pinpointing the composition of eutectic HEA (EHEA) in the vast temperature-composition space. Aided by the first principle molecular dynamics calculation, we have shown that although the eutectic structures of Ni-Al containing EHEAs are different, the formation mechanism of the eutectic structure is similar, which stems from the short-range-ordering (SRO) heredity of EHEA liquid from the eutectic valleys of the pseudo Ni-Al-Cr ternary. Two EHEAs, EHEA 1 (Al16.95Cr16.95Fe19.1Ni47) with L12+B2 eutectic structures and EHEA 2 (Al33.5Cr33Co4Ni29.5) with BCC+B2 eutectic structures were designed using the model and experimentally verified. This unified Ni-Al-Cr ternary model, validated by experimental data in both literature and our fabricated EHEAs, presents a compelling solution to the long-debated grouping strategy in EHEA design and offers a new paradigm to map the complicated but intriguing eutectic microstructures in EHEAs and conventional alloys.

Formation of the structure-II gas hydrate from low-concentration propane mixed with methane

It has been recognized that a small amount of propane mixed with methane can change greatly in not only the thermodynamics but also the structural properties of gas hydrate. However, its mechanism is still not well understood yet. In this research, structure-II (sII) hydrate is synthesized using a methane-propane gas mixture with an initial mole ratio of 99:1, and it is found that large (51264) cages are co-occupied by multiple gases based on the rigid structure analysis of neutron diffraction data. The first principles calculation and molecular dynamics simulation are conducted to uncover the molecular mechanism for sII methane-propane hydrate formation, revealing that the presence of propane inhibits the formation of structure-I (sI) hydrate but promotes sII hydrate formation. The results help to understand the accumulation mechanism of natural gas hydrate and benefit to optimize the condition for gas storage and transportation in hydrate form.