Density Functional Theory Molecular Dynamics Research Articles

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.

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.

Pore Wall Engineered Polar COFs as Size‐Matched Nanotraps Enable Highly Efficient Capture of Long‐Chain Alkylamines

AbstractLong‐chain alkylamines are widely used as surfactants and inevitably cause environmental pollution. However, there is still a lack of adsorbents that can efficiently remove them due to the scarcity of available binding sites. Herein, this study demonstrates that pore wall‐engineered polar covalent organic frameworks (COFs) with tailored pore size can be used as promising nanotraps for the rapid and highly efficient capture of octadecylamine (ODA, a typical long‐chain alkylamine) from complex practical samples (e.g., salt lake brine). Under the optimized conditions, nitro‐functionalized COFs (TpPa‐NO2 and TpBD‐NO2) show much better ODA adsorption performances than unfunctionalized TpPa, and TpPa‐NO2, whose pore size matches the ODA molecule best, obtained an ODA adsorption capacity as high as 128.5 mg g−1 within 20 min. Density functional theory (DFT) calculations and molecular dynamics (MD) simulations elucidate the underlying adsorption mechanisms, revealing that COFs provide multiple interaction forces, including electrostatic, polar, van der Waals, hydrogen bond, hydrophobic, and C─H σ–π interactions, which synergistically contribute to the highly efficient capture of ODA in the 1D polar nanotraps of TpPa‐NO2. This study provides a theoretical foundation and experimental evidence for utilizing COFs as long‐chain alkylamine adsorbents and offers a strategy for designing functionally tailored COFs for environmental applications.

Formation mechanism of environmentally persistent free radicals during soot aging

Environmentally persistent free radicals (EPFRs) are a newly emerging class of pollutants that are known to be formed on metal oxides (MOs). Recent experimental investigations have suggested that EPFRs may also be formed on soot. However, little is known about the structural and compositional characteristics of soot surfaces conducive to EPFRs formation. Concurrently, the changes in the surface structure and composition of soot indicate its aging process, yet the detailed mechanism underlying EPFRs formation in this process remain obscure. Additionally, it is uncertain whether the formation mechanism of EPFRs on soot differs from that on MOs. In this study, the density functional theory (DFT) and ab initio molecular dynamics (AIMD) were used to investigate EPFRs formation on soot at different stages of aging. The results indicate that EPFRs could be formed on both the complete soot surface with hydroxyl groups and the defective surface. Correspondingly, during the aging process of soot, the formation trend of EPFRs increases in the early stage of the aging process and then decreases over time. Additionally, the formation mechanism on soot is different from that on CuO. On soot, the EPFRs formation is initiated by free hydroxyl radical formed through the desorption process, following the Eley-Rideal mechanism, while on CuO surfaces, its formation involves the surface-bound hydroxyl groups, and thus follows the Langmuir-Hinshelwood mechanism. Furthermore, EPFRs triggered by soot are less stable than those by CuO, due to the easier desorption process of phenoxyl radicals on soot. These findings provide valuable insights into the detailed formation mechanism of EPFRs on soot at different stages of aging, thereby contributing to control EPFRs emissions from a mechanism perspective.

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.

Exploring the photophysics of cinnamoyl-coumarin derivatives in cucurbit [7]uril complexes and assessing phototoxicity in HeLa cells

Cinnamoyl-coumarin derivatives containing 5 or 12 carbon aliphatic chains were evaluated as photosensitizers and their photophysical properties were studied in detail. Moreover, these compounds were encapsulated in cucurbit[7]uril macrocycle with relatively high binding affinities in aqueous media. Fluorescence quantum yields, fluorescence lifetimes and singlet oxygen quantum yields were measured upon encapsulation. Computational DFT calculations and molecular dynamics simulations allowed the visualization of the binding modes of both derivatives inside the macrocycle. In particular, the free energy profiles for the insertion of the molecules into the macrocycle were determined to assess the most probable conformations of the complexes in water. In vitro phototoxicity assays were carried out in HeLa cells showed significant decreases in cell viability upon illumination of the 5 carbon aliphatic chain derivative at 460 nm with an LED source at different concentrations and enhanced by cucurbit[7]uril. However, the one with 12 carbon aliphatic chain did not display any phototoxicity regardless of the presence of cucurbit[7]uril. This behavior is related to the high lipophilicity introduced by a 12 carbon aliphatic chain conditioning its distribution on hydrophobic compartments and decreasing its phototoxicity. The enhanced phototoxicity elicited by cucurbit[7]uril on the 5 carbon aliphatic chain derivative but not in the 12 carbon derivative remark that there is a balance between hydrophobicity of these probes with the carrier properties of cucurbit[7]uril to be reach for effective phototoxicity properties.

The impact of surface functional groups on MXene anode protective layer in aqueous zinc-ion batteries: Understanding the mechanism

The development of energy storage has seen a significant increase in the use of aqueous zinc-ion batteries (AZIBs) with intrinsic safety, which have become an important choice for new high-security energy storage. However, the dendrite growth and hydrogen evolution reaction (HER) on Zn anodes present a significant challenge to the commercialisation of AZIBs. The stability of Zn anodes can be effectively improved by using an anodic interfacial protective layer. The novel two-dimensional (2D) MXene material is capable of effectively inhibiting zinc dendrite growth and the HER reaction when employed as a protective layer for AZIBs anodes due to its readily adjustable properties. The surface functional groups of MXene exhibit different electrochemical properties in different electrolytes, which affects the realization of the protective function. The current understanding of the influence of these surface functional groups on the monolayer MXene as an anodic protective layer for AZIBs is incomplete. A combination of density functional theory calculations and molecular dynamics simulations was employed to investigate the electronic properties, adsorption energies for Zn2+ and H2O, free energies for HER, Zn2+ diffusion energy barriers, Zn2+ diffusion coefficients, and coordination numbers of Zn2+ with water molecules of monolayer MXene (Mo2CTx) with nine different surface functional groups were investigated. The mechanism of the impact of surface functional groups on monolayer Mo2CTx as an anodic protective layer for AZIBs was elucidated. This study will provide guidance for the extensive use of MXene materials in AZIBs to effectively enhance the anode stability and prolong the battery operation life.

Temperature and structure measurements of heavy-ion-heated diamond using in situ X-ray diagnostics

We present in situ measurements of spectrally resolved X-ray scattering and X-ray diffraction from monocrystalline diamond samples heated with an intense pulse of heavy ions. In this way, we determine the samples’ heating dynamics and their microscopic and macroscopic structural integrity over a timespan of several microseconds. Connecting the ratio of elastic to inelastic scattering with state-of-the-art density functional theory molecular dynamics simulations allows the inference of average temperatures around 1300 K, in agreement with predictions from stopping power calculations. The simultaneous diffraction measurements show no hints of any volumetric graphitization of the material, but do indicate the onset of fracture in the diamond sample. Our experiments pave the way for future studies at the Facility for Antiproton and Ion Research, where a substantially increased intensity of the heavy ion beam will be available.

Machine Learning Orchestrating the Materials Discovery and Performance Optimization of Redox Flow Battery

AbstractThis review exploits the crucial role of computational methods in discovering and optimizing materials for redox flow batteries (RFBs). Integration of high‐throughput computational screening (HTCS) and machine learning (ML) accelerates materials discovery, guided by algorithms categorizing RFBs. A collaborative exploration, spanning macroscopic to mesoscopic scales, combines quantum machine learning with reinforcement learning, transfer learning, time series analysis, Bayesian optimization, active learning and various generative models. The collaborative integration of ML with computational techniques and experimental methods, anchored in experimentally validated Density Functional Theory (DFT) calculations and molecular dynamics (MD) simulations, proves indispensable for cost‐effective RFBs. Data collection and feature engineering are explored, emphasizing the integration of optimization goals and precise data collection within the ML framework. Feature analysis importance is highlighted, utilizing methods such as the filter, embedded, wrapper and deep learning methods for efficient energy materials exploration. Computational perspectives on materials features and operating conditions encompass membrane characteristics, fluid dynamics, temperature dependence and pressure sensitivity. Time‐dependent features and ML‐generated insights are crucial for understanding cycling performance intricacies, providing a comprehensive understanding of RFB materials.

Applications of machine‐learning interatomic potentials for modeling ceramics, glass, and electrolytes: A review

AbstractThe emergence of artificial intelligence has provided efficient methodologies to pursue innovative findings in material science. Over the past two decades, machine‐learning potential (MLP) has emerged as an alternative technology to density functional theory (DFT) and classical molecular dynamics (CMD) simulations for computational modeling of materials and estimation of their properties. The MLP offers more efficient computation compared to DFT, while providing higher accuracy compared to CMD. This enables us to conduct more realistic simulations using models with more atoms and for longer simulation times. Indeed, the number of research studies utilizing MLPs has significantly increased since 2015, covering a broad range of materials and their structures, ranging from simple to complex, as well as various chemical and physical phenomena. As a result, there are high expectations for further applications of MLPs in the field of material science and industrial development. This review aims to summarize the applications, particularly in ceramics and glass science, and fundamental theories of MLPs to facilitate future progress and utilization. Finally, we provide a summary and discuss perspectives on the next challenges in the development and application of MLPs.

Dodecanophene: A novel 2D carbon allotrope with untunable metallic behavior under stress

The appeal of 2D carbon allotropes lies in their extraordinary optical and mechanical properties, paving the way for advancements in optoelectronics. This study introduces a novel planar 2D carbon allotrope, Dodecanophene, composed of rings with 3-6-12 atoms. Its mechanical, electronic, and optical characteristics are discussed using density functional theory and ab initio molecular dynamics simulations. This material demonstrates intrinsic metallic behavior with low formation energy, indicating stability under thermal and mechanical stresses. Its band structure reveals one Dirac cone, which is untunable when the material is subjected to moderate and high uniaxial strains. Dodecanophene preserves its Dirac cone even under significant deformation. It also displays mechanical and optical anisotropy (Young’s modulus ranging from 356.98 to 553.81 GPa), with intense optical activity within the infrared, visible, and ultraviolet spectra.

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.

Adsorption studies of isoxazole derivatives as corrosion inhibitors for mild steel in 1M HCl solution: DFT studies and molecular dynamics simulation.

The corrosion of mild steel is a significant issue in various industries, prompting the need for effective corrosion inhibitors. This study focuses on understanding the corrosion inhibition properties of organic compounds derived from isoxazole, namely series Iso(a), Iso(b), Iso(c), Iso(d), Iso(e), Iso(f), Iso(g), and Iso(h), which could have implications for materials science and industrial applications. By investigating the influence of different substitutions on these compounds, valuable insights can be gained into designing better corrosion inhibitors for practical use. Theoretical studies were conducted using density functional theory (DFT) with the B3LYP functional and the 6-31G (d,p) basis set. These calculations enabled the evaluation of various parameters including frontier orbital energies (EHOMO, ELUMO), energy gap (∆E), electronegativity (χ), absolute hardness (η), softness (σ), fraction of transferred electrons (∆N), as well as local properties such as natural atomic populations and Fukui indices. Additionally, molecular dynamics simulations were performed to study the adsorption behavior of the inhibitors on the surface of Fe (110). The simulations were conducted using Materials Studio version 8.0 software package using COMPASS force field to understand the impact of different functional groups on the inhibitors before and after adsorption on the iron surface.

The cage effect of electron beam irradiation damage in cryo-electron microscopy

Electron beam irradiation can cause damage to biological and organic samples, as determined via transmission electron microscopy (TEM). Cryo-electron microscopy (cryo-EM) significantly reduces such damage by quickly freezing the environmental water around organic molecules. However, there are multiple hypotheses about the mechanism of cryo-protection in cryo-EM. A lower temperature can cause less molecular dissociation in the first stage, or frozen water can have a “cage” effect by preventing the dissociated fragments from flying away. In this work, we use real-time time-dependent density functional theory molecular dynamics(rt-TDDFT-MD) simulations to study the related dynamics. We use our recently developed natural orbital branching (NOB) algorithm to describe the molecular dissociation process after the molecule is ionized. We find that despite the difference in surrounding water molecules at different temperatures, the initial dissociation process is similar. On the other hand, the dissociated fragments fly away at room temperature, while they remain in the same cage when frozen water is used. Our results provide direct support for the cage effect mechanism.

Synergistic effect of amino and hydroxyl bifunctional modified h-BN on interfacial thermal conductivity in polydimethylsiloxane matrix: Simulations and experiments

As a widely used thermal conductive matrix material, the interface problem between polydimethylsiloxane (PDMS) and thermal conductive fillers needs to be solved urgently. The interfacial heat transfer mechanism between PDMS and hexagonal boron nitride (h-BN) modified by different groups was studied by combining density functional theory (DFT) simulation and molecular dynamics (MD) simulation. The bi-functionalization of h-BN was achieved by the environmentally friendly 6-aminocaproic acid (ACA) additive-assisted water ball milling process. The h-BN/PDMS composite thermal interface materials were prepared using a simple rolling method. The thermal conductivity of the obtained sample reached 1.256 W m−1 K−1 at a filler loading of 15 wt%. The proposed bifunctional synergistic heat transfer mechanism is expected to provide theoretical guidance for the preparation of high thermal conductivity and insulating PDMS used in electronic communications.

Elucidating the role of polar functional groups in fluorinated polymer artificial interphase for stable lithium anodes

The properties of solid electrolyte interphase (SEI) are pivotal for stable lithium (Li) metal anodes. However, the process of formation and ion transport behavior of lithium fluoride (LiF) through the polar groups of organic fluorinated artificial SEI has not been clearly elucidated. Herein we demonstrate that the key role of polar functional groups in fluorinated polymer artificial SEI (FPASEI) is elucidated by using 2,2,2-trifluoroethylacrylate (TFEA) through radical polymerization. Density functional theory and ab initio molecular dynamics calculations demonstrate that the abundant CO polar groups in TFEA contribute a large number of electrons, thereby facilitating the degradation kinetics of CF bond cleavage in lithium bis(trifluoromethanesulfonyl)imide salt to yield LiF. Moreover, the presence of CF, COC, and CO groups in TFEA facilitate the migration of Li+ towards interchain regions through cation-dipole interaction, leading to dendrite-free Li deposition. The implementation of FPASEI in a Li||Li cell results in 500 h of Li plating/stripping cycling at 1 mA cm−2 and retains a capacity retention rate of 80 % after 265 cycles in Li||LiNi0.8Co0.1Mn0.1O2 cell. This study not only emphasizes the critical role of polar groups in artificial SEI but also presents a promising strategy for achieving stable Li metal batteries.