Density Functional Theory Molecular Dynamics Research Articles

High‐Voltage Single‐Ion Covalent Organic Framework Electrolytes Enabled by Nitrile Migration Ladders for Lithium Metal Batteries

The poor electrochemical stability window and low ionic conductivity in solid‐state electrolytes hinder the development of safe, high‐voltage, and energy‐dense lithium metal batteries. Herein, taking advantage of the unique electronic effect of nitrile groups, we designed a novel azanide‐based single‐ion covalent organic framework (CN‐iCOF) structure that possesses effective Li+ transport and high‐voltage stability in lithium metal batteries. Density functional theory (DFT) calculations and molecular dynamics (MD) revealed that electron‐withdrawing nitrile groups not only resulted in an ultralow HOMO energy orbital but also enhanced Li+ dissociation through charge delocalization, leading to a high tLi+ of 0.93 and remarkable oxidative stability up to 5.6 V (vs. Li+/Li) simultaneously. Moreover, cyanation leveraging Strecker reaction transformed reversible imine‐linkage to a stable sp3‐carbon‐containing azanide anion, which facilitated contorted alignment of transport “ladders” along the one‐dimensional anionic channels and the ionic conductivity could reach 1.33 × 10−5 S cm−1 at ambient temperature without any additives. As a result, CN‐iCOF allowed operation of solid‐state lithium metal batteries with high‐voltage cathodes such as LiNi0.8Mn0.1Co0.1O2 (NCM811), demonstrating stable lithium deposition up to 1,100 h and reversible battery cycling at ambient temperature up to 4.5 V, shedding light on the importance of discovering new functionality for forthcoming high‐performance batteries.

High-Voltage Single-Ion Covalent Organic Framework Electrolytes Enabled by Nitrile Migration Ladders for Lithium Metal Batteries.

The poor electrochemical stability window and low ionic conductivity in solid-state electrolytes hinder the development of safe, high-voltage, and energy-dense lithium metal batteries. Herein, taking advantage of the unique electronic effect of nitrile groups, we designed a novel azanide-based single-ion covalent organic framework (CN-iCOF) structure that possesses effective Li+ transport and high-voltage stability in lithium metal batteries. Density functional theory (DFT) calculations and molecular dynamics (MD) revealed that electron-withdrawing nitrile groups not only resulted in an ultralow HOMO energy orbital but also enhanced Li+ dissociation through charge delocalization, leading to a high tLi+ of 0.93 and remarkable oxidative stability up to 5.6 V (vs. Li+/Li) simultaneously. Moreover, cyanation leveraging Strecker reaction transformed reversible imine-linkage to a stable sp3-carbon-containing azanide anion, which facilitated contorted alignment of transport "ladders" along the one-dimensional anionic channels and the ionic conductivity could reach 1.33 × 10-5 S cm-1 at ambient temperature without any additives. As a result, CN-iCOF allowed operation of solid-state lithium metal batteries with high-voltage cathodes such as LiNi0.8Mn0.1Co0.1O2 (NCM811), demonstrating stable lithium deposition up to 1,100 h and reversible battery cycling at ambient temperature up to 4.5 V, shedding light on the importance of discovering new functionality for forthcoming high-performance batteries.

Ab Initio Molecular Dynamics Insight to Structural Phase Transition and Thermal Decomposition of InN

Extensive ab initio density functional theory molecular dynamics calculations were used to evaluate stability conditions for relevant phases of InN. In particular, the p-T conditions of the thermal decomposition of InN and pressure-induced wurtzite–rocksalt solid–solid phase transition were established. The comparison of the simulation results with the available experimental data allowed for a critical evaluation of the capabilities and limitations of the proposed simulation method. It is shown that ab initio molecular dynamics can be used as an efficient tool for simulations of phase transformations of InN, including solid–solid structural transition and thermal decomposition with formation of N2 molecules. It is of high interest, because InN is an important component of epitaxial quantum structures, but it has not been obtained as a bulk single crystal. This makes it difficult to determine its basic physical properties to develop new applications.

High ionic conductivity materials Li3YBr6andLi3LaBr6for solid-state batteries: First-principles calculations.

High ionic conductivity solid-state electrolytes are essential for powerful solid-state lithium-ion batteries. With density functional theory and ab initio molecular dynamics simulations, we investigated the crystal structures of Li3YBr6and Li3LaBr6. The lowest energy configurations with uniform distribution of lithium ions were identified. Both materials have wide electrochemical stability windows (ESW): 2.64 V and 2.57 V, respectively. The experimental ESW for Li3YBr6is 2.50 V. Through extrapolating various temperature diffusion results, the conductivity of Li3YBr6was obtained at room temperature, approximately 3.9 mS/cm, which is comparable to the experimental value 3.3 mS/cm. Li3LaBr6has a higher conductivity, a 100% increase compared with Li3YBr6. The activation energies of Li3YBr6and Li3LaBr6through the Arrhenius plot are 0.26 eV and 0.24 eV, respectively, which is also close to the experimental value of 0.30 eV for Li3YBr6. This research explored high ionic conductivity halide materials and will contribute to developing solid-state lithium-ion batteries.

Collision of rare-gas atoms on helium nanodroplets: Theoretical evidence for an efficient coagulation of heavy rare-gas atoms.

The coagulation of rare-gas atoms (RG = Ne, Ar, Kr, Xe, and Rn) in helium nanodroplets (HNDs) composed of 1000 atoms is investigated by zero-point averaged dynamics where a He-He pseudopotential is used to make the droplet liquid with proper energies. This method reproduces the qualitative abundances of embedded Arn+1 structures obtained by Time-Dependent Density Functional Theory and Ring Polymer Molecular Dynamics for Ar + ArnHe1000 collisions at realistic projectile speeds and impact parameters. More generally, coagulation is found to be much more efficient for heavy rare-gases (Xe and Rn) than for light ones (Ne and Ar), a behavior mainly attributed to a slower energy dissipation of the projectile in the HND. When coagulation does not occur, the projectile maintains a speed of 10-30m s-1 within the HND, but its velocity vector is rarely oriented toward the dopant, and the projectile roams in a limited region of the droplet. The structure of embedded RGn+1 clusters does not systematically match their gas-phase global minimum structure, and more than 30% of RGn-RG unbound structures are due to one He atom located in between the projectile and a dopant atom.

Probing Self-Assembly of Ammeline in Chloroform and Aqueous Media: Interplay Between Hydrogen Bonding Diversity and Dimerization.

Ammeline (AM) is a molecule with a very low reputation in the field of supramolecular community, but with a recently proven potential both experimentally and theoretically. In this work, dispersion-corrected density functional theory (DFT-D) computations and molecular dynamics (MD) simulations were employed to understand the aggregation mechanism of AM in chloroform and water media. Our DFT-D and MD analyzes show that the most important interactions are those formed by the amine groups (-NH2) with both the pyridine-type nitrogen atoms and the carbonyl groups (C=O). In the more polar solvent, the interactions between water molecules and the C=O group prevent the AM from forming more interactions with itself. Nevertheless, four types of dimers involving N-H∙∙∙O interactions were found to exist in water solutions. The overlooked tetrel bond between endocyclic N and C atoms can also stabilize dimers in solution. Moreover, while most AM dimers are enthalpy-driven, our results indicate that the unique DD-AA dimer (D=donor, A=acceptor) that originates cyclic rosettes is entropy-driven.

Understanding and controlling chemical clogging in drip irrigation: Integrating experimental methods, density functional theory calculations and molecular dynamics simulations

AbstractThe chemical clogging of water drips is the main obstacle to the adoption and spread of microirrigation technology. The aim of this research is to understand the scaling phenomenon by identifying the substances responsible for emitter clogging using a combination of different methods of characterization and to investigate the effectiveness of a new product ‘Melacide P/2’ as a calcium carbonate scale inhibitor. A non‐electrochemical method from the Laboratory of Chemistry and Genie of the Environment (LCGE) was employed to investigate the effect of the inhibitor against calcium carbonate precipitation at 25°C. X‐ray diffraction (XRD) and scanning electron microscopy (SEM) were used to study the effect of Melacide P/2 on the scale morphology and crystalline phases. Density functional theory (DFT) and Monte Carlo (MC) simulations were performed to support the experimental results. Characterization techniques revealed that the scale recovered from the drips consisted mainly of calcium carbonate, a variety of calcite. The experimental data indicate the likelihood of preventing calcium carbonate precipitation after the addition of a very small amount (0.30 mg L⁻¹) of Melacide P/2 under the conditions of the experiment. XRD and SEM revealed that the inhibitor tested has the potential to disrupt or block regular CaCO3 crystal growth and transform a more stable and adherent scale of calcite to aragonite, which is easy to eliminate. The theoretical approach adopted supports the experimental findings. Therefore, Melacide P/2 could be used as a cost‐effective green‐scale inhibitor to protect microirrigation systems from unwanted scale formation.

A-Site Cations Impact on Nonradiative Recombination, Mobility, and Defect Dynamics in Sn-Based Perovskites.

Sn-based perovskites with different cations in the A-site exhibit distinct electronic structures and dynamic properties. By utilizing time-dependent density functional theory and nonadiabatic molecular dynamics, we demonstrate that larger FA cations decrease wave function overlap between initial and final states and slow down nuclear motion. In the case of FASnI3, this alteration decreases the nonadiabatic coupling and increases the nonradiative electron-hole recombination time by 130% and 76%, respectively, compared to CsSnI3 and MASnI3 (CH3NH3SnI3). Furthermore, A-site modification significantly improves electron mobility and changes the properties of defects in FASnI3 (HC(NH2)2SnI3), which achieves higher electron mobility through a polar optical phonon-dominated scattering mechanism and exhibits higher defect formation energy and migration barriers of A-site cations due to increased steric hindrance, relative to CsSnI3 and MASnI3. These results emphasize the critical function of A-site cation substitution in controlling nonradiative recombination dynamics, electron mobility, and defect characteristics in Sn-based perovskites and provide theoretical insights for the advancement of novel lead-free perovskite materials.

First-Principles Computational Screening of Two-Dimensional Polar Materials for Photocatalytic Water Splitting.

The band gap constraint of the photocatalyst for overall water splitting limits the utilization of solar energy. A strategy to broaden the range of light absorption is employing a two-dimensional (2D) polar material as photocatalyst, benefiting from the deflection of the energy level due to their intrinsic internal electric field. Here, by using first-principles computational screening, we search for 2D polar semiconductors for photocatalytic water splitting from both ground- and excited-state perspectives. Applying a unique electronic structure model of polar materials, there are 13 photocatalyst candidates for the hydrogen evolution reaction (HER) and 8 candidates for the oxygen evolution reaction (OER) without barrier energies from the perspective of the ground-state free energy variation calculation. In particular, Cu2As4Cl2S3 and Cu2As4Br2S3 can catalyze HER and OER simultaneously, becoming promising photocatalysts for overall water splitting. Furthermore, by combining ground-state band structure calculations with excited-state charge distribution and transfer calculated by linear-response time-dependent density functional theory (LR-TDDFT) and time-dependent ab initio nonadiabatic molecular dynamics (NAMD), respectively, the rationality of the 2D polar material model has been manifested. The intrinsic built-in electric field promotes the separation of charge carriers while suppressing their recombination. Therefore, our computational work provides a high-throughput method to design high-performance photocatalysts for water splitting.

Modeling bicarbonate formation in an alkaline solution with multi-level quantum mechanics/molecular dynamics simulations

Understanding carbonate speciation and how it may be modulated is essential for the advancement of carbon dioxide (CO2) capture and storage technologies, which often rely on the transformation of CO2 into carbonate, e.g. via the formation of carbonate minerals. To date, few atomic-level, quantum-mechanics-based simulations have been carried out to characterize how carbonic acid (H2CO3) and bicarbonate ( HCO 3 − ) form in aqueous solution, and how pH affects this process. Recently, Martirez and Carter utilized rare-event sampling density functional theory molecular dynamics simulations in combination with multi-level embedded correlated wavefunction theory, thus accounting for both solvent dynamics and electron correlation accurately, to elucidate the mechanism of H2CO3 formation in neutral solution (J. Am. Chem. Soc., 145, 12561, 2023). Here, we perform a complementary simulation using the same method to map out the energetics of HCO 3 − formation from dissolved CO2 in basic solution. We find that, as in H2CO3 formation, including water dynamics is important to obtain an accurate prediction of the energetics for the aforementioned reaction. Furthermore, only with MD did we identify the correct pathway for the reaction, in which water – not hydroxide – acts as the initial nucleophile and only at the transition state does it lose a proton.

AlC3 monolayer: Highly responsive and selective gas sensing material for SF6 decomposed gases (SOF2, SO2F2 and SO2)

Sulfur hexafluoride (SF6) is widely employed in industrial applications due to its interesting insulating properties. However, under electrical discharge conditions, it can undergo decomposition, yielding hazardous gases such as SOF2, SO2F2, and SO2, which can pose significant risks due to their increased toxicity and corrosive nature, affecting human health, the environment, and equipments. In this investigation, we employed density functional theory and ab-initio molecular dynamics to evaluate the stability of AlC3 monolayer and investigate its sensing capabilities. The findings establish the AlC3 monolayer as a champion material for detecting SF6 decomposition gases, specifically SOF2, SO2F2, and SO2. Importantly, the AlC3 monolayer exhibited low sensitivity to humidity and other gases, including CO2, CO, HF, H2, HCN, and H2S, highlighting its exceptional selectivity. SO2F2 exhibited the substantial adsorption energy of −1.36 eV, a work function of 5.2 eV, and a −0.69e charge transfer. Similarly, SO2 and SOF2 displayed significant adsorption energy (-1.19 eV and −1.08 eV, respectively), work functions (4.55 eV and 4.81 eV), and charge transfers (-0.61e and 0.78e). The significant variation in work function upon SO2F2 adsorption indicates the AlC3 monolayer's potential selectivity for SO2F2 over SO2 and SOF2, making it a promising material for surface work function modulated transistors. Ab-initio molecular dynamics simulations confirm AlC3 monolayer stability after adsorption at 300 K, validating predicted positions by density functional theory.

Pb Segregation in SnPb eutectic solder alloy induced by gamma irradiation

Pb segregated and formed a Pb segregation area in SnPb eutectic solder joint after 100 h of gamma irradiation. With the irradiation time increased to 150 h, Pb segregating stopped. The Pb segregation was attributed to the oxidation of β-Sn to SnO2 induced by the gamma irradiation. The Pb element content in the segregation area predicted by the segregation heat formulas is 53.5 %, which is consistent with the experimental result of 49.11 %. Density functional theory (DFT) calculation and Molecular dynamics (MD) simulation results were used to prove that the Pb segregation is caused by the oxidation of β-Sn.

Unveiling Moroccan Nature's Arsenal: A Computational Molecular Docking, Density Functional Theory, and Molecular Dynamics Study of Natural Compounds against Drug-Resistant Fungal Infections.

Candida albicans and Aspergillus fumigatus are recognized as significant fungal pathogens, responsible for various human infections. The rapid emergence of drug-resistant strains among these fungi requires the identification and development of innovative antifungal therapies. We undertook a comprehensive screening of 297 naturally occurring compounds to address this challenge. Using computational docking techniques, we systematically analyzed the binding affinity of each compound to key proteins from Candida albicans (PDB ID: 1EAG) and Aspergillus fumigatus (PDB ID: 3DJE). This rigorous in silico examination aimed to unveil compounds that could potentially inhibit the activity of these fungal infections. This was followed by an ADMET analysis of the top-ranked compound, providing valuable insights into the pharmacokinetic properties and potential toxicological profiles. To further validate our findings, the molecular reactivity and stability were computed using the DFT calculation and molecular dynamics simulation, providing a deeper understanding of the stability and behavior of the top-ranking compounds in a biological environment. The outcomes of our study identified a subset of natural compounds that, based on our analysis, demonstrate notable potential as antifungal candidates. With further experimental validation, these compounds could pave the way for new therapeutic strategies against drug-resistant fungal pathogens.

Virtual screening, molecular docking, MD simulation studies, DFT calculations, ADMET, and drug likeness of Diaza-adamantane as potential MAPKERK inhibitors.

Introduction: Multiple sclerosis (MS) is an autoimmune and inflammatory disease that destroys the protective coating of central nervous system (CNS) nerve fibers and affects over 2.8 million people worldwide. Despite several studies on new therapeutic targets and lead compounds, MS disease has limited treatment options. This condition may be caused by a complicated interaction of environmental and genetic variables. Studies showed that MS-associated microglial cells' increased MAPKERK activity may cause CNS inflammation and oligodendrocyte damage. Thus, screening for lead compounds that inhibit MAPKERK may protect brain cells and slow disease progression. Methods: The study aims to discover compounds that may inhibit MAPKERK as a novel approach for protecting the nervous system in managing MS. The study includes in silico methods, such as virtual screening, molecular docking, Density-functional theory (DFT) investigations (using the B3LYP/6-31++G(d,p) basis set in a gas phase environment), drug likeness scores, and molecular dynamic (MD) simulations. Results and Discussion:During the docking process with the MAPKERK protein, it was shown that the ligand L12 receptor had the best binding affinity, with a docking score of -6.18kcal/mol. To investigate the stability of the binding, a 100ns MD simulation was performed on the complex formed by the MAPKERK protein and L12. The receptor-ligand combination exhibited significant stability throughout the duration of the MD simulation. Additionally, the pharmacokinetic and drug-likeness properties of these ligands suggest that they have the potential to be considered viable candidates for future development in MS management.

Is Ortho-Terphenyl a Rigid Glass Former?

Ortho-terphenyl (OTP) has long been used as a model system to study the glass transition due to its apparent simplicity and a widespread assumption that it is a rigid molecule. Here, we employ terahertz time-domain spectroscopy and low-frequency Raman spectroscopy to investigate the rigidity of OTP by direct observation of the low-frequency vibrational dynamics. These terahertz phonons involve complex large-amplitude atomic motions where intramolecular and intermolecular displacements are often mixed. Comparison of experimental results with density functional theory and ab initio molecular dynamics simulations shows that the assumption of rigidity neglects important implications for the glass transition and must be revisited. These results highlight the significance of terahertz modes on elasticity, which will be even more critical in more complex systems such as biomolecules.

Atomic oxygen erosion mechanism of polyimide via reactive molecular dynamics simulation and density functional theory calculation

Atomic oxygen (AO) causes serious oxidative degradation on polymeric materials in the space environment, yet understanding its reaction mechanism is a challenging task. Herein, we primarily investigate the reaction sites and reaction paths of pure polyimide material to AO erosion and propose a modification strategy involving electron-withdrawing groups to enhance the material's resistance to AO with density functional theory (DFT) and reactive force field molecular dynamics (ReaxFF MD). DFT calculations reveal that AO erosion is an electrophilic reaction, which preferentially interacts on the benzene ring with pronounced electron density distribution on the third part of the polyimide molecule. ReaxFF MD simulations validate this finding and provide additional reaction pathways that are divided into the early-stage reactions and later secondary reactions. In the early stage, only small number of AOs take part in the reactions that include the formation of CO bonds and ring opening processes. These reactions are relatively slow and majorly determine the AO resistance of the material. In the subsequent stage, AO predominantly reacts with reactive species and radicals generated from earlier reactions, leading to fast degradation. With these findings, we propose a strategy to enhance the AO resistance by introducing electron-withdrawing functional groups in the polyimides. As exemplified, the polyimide with -CF3 group shows 21.1% lower erosion yield than unmodified polymer. The present study gives a deep insight for the mechanism of AO erosion on polyimide by exploring its reaction sites and provides valuable theoretical guidance for improving the material's resistance to erosion.

Atomistic Insight on Effect of Silica Fume on Intermolecular Interactions between Poly(carboxylate) Superplasticizer and Calcium Ions in Concrete.

Understanding how poly(carboxylate)s of chemical admixtures interact with calcium ions in cement pore solutions in the presence of silica fume is fundamental to developing better chemical admixtures for concrete production. In this work, the intermolecular interactions of calcium ions with a poly(carboxylate) superplasticizer type of chemical admixture was investigated via classical all-atom molecular dynamics (MD) simulations and Density Functional Theory (DFT) calculation methods in the presence of silica fume. The classical all-atom MD simulation and DFT calculation results indicate that calcium ions are interacting with oxygen atoms of the carboxylate group of PCE. The better interaction energy could mean an improved adsorption of the PCE segment with calcium ions. In this regard, it can be noted that the ester-based PCE segment could have a better adsorption onto calcium ions in comparison with the ether-based PCE segment. Moreover, the presence of silicon dioxide could improve the adsorption of the PCE segment onto calcium ions.

Comparison of combustion and interaction mechanisms of mixed working fluids R152a and R1270: A theoretical and experimental study

In the background of global efforts to reduce carbon emissions, mixed working fluids could mitigate flammability concerns of low global warming potential (GWP) working fluids for organic Rankine cycles (ORCs) and compression refrigeration cycles. In this study, the combustion and interaction mechanisms of R152a/R1216 and R1270/R1216 were investigated. Density functional theory (DFT) and ReaxFF molecular dynamics (MD) methods were employed to analyze the combustion processes of the two binary working fluids and the formation pathways of the toxic substance HF. Additionally, the influence of R1216 on the combustion of R152a and R1270 was evaluated and compared at different reaction temperatures and component ratios. The results showed that, R1216 did not inhibit but rather promoted the consumption of R152a and R1270. Corresponding experiments demonstrate that the combustion of R152a and R1270 becomes more complete and occurs more quickly after the addition of low proportions of R1216. Subsequently, the flammability limits of the two binary working fluids were determined through experiments at different ambient temperatures. The experimental results indicated that the rise in ambient temperature expands the flammability limit ranges of both binary working fluids, and the higher the proportion of R1216, the more sensitive the flammability is to changes in ambient temperature.

Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach.

An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.

Exploring the mechanism of nerve agent (Tabun and Sarin) adsorption on carbon nanocones: Computational insights

Carbon NanoCones (CNCs), distinguished by their conical shape and large surface area, are evaluated for their potential application in nerve gas [tabun (GA) and sarin (GB)] adsorption. Density Functional Theory (DFT) calculations, Molecular Dynamics (MD), and Monte Carlo (MC) simulations are employed to investigate this phenomenon comprehensively. The study findings indicate that tabun (GA) and sarin (GB) undergo spontaneous adsorption, characterized by significant negative energy values. Density Functional Theory (DFT) calculations indicate electron donation tendencies of nerve agents to CNC surfaces. Computational analysis shows higher adsorption efficiency in the inner portion (P1) of CNCs. Molecular Dynamics (MD) and Monte Carlo (MC) simulations confirm planar adsorption configurations parallel to CNC surfaces. The DFT calculations show that GA has a far greater adsorption energy on a Carbon Nanocone compared to GB (−44.96 kcal/mol for GA, whereas GB has an adsorption energy of −35.95 kcal/mol). Furthermore, the analysis reveals significant differences between Sarin and Tabun nerve agents. Sarin exhibits higher global hardness, indicating increased stability, while Tabun shows higher overall softness, suggesting greater reactivity. Despite similar electronegativities, Sarin’s greater ionization energy and electron affinity imply enhanced stability and reactivity. Differences in HOMO and LUMO energies highlight unique reactivity profiles, with Sarin being more susceptible to nucleophilic attacks and Tabun to electrophilic attack. Sarin’s larger energy gap between HOMO and LUMO orbitals signifies its superior stability under electronic disturbances.