Density Functional Theory Molecular Dynamics Research Articles

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.

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.

Computational Insights into Chromene/pyran Derivatives: Molecular Docking, ADMET Studies, DFT Calculations, and MD Simulations as Promising Candidates for Parkinson's Disease.

Parkinson's disease (PD) is a neurodegenerative condition characterized by both motor and non-motor symptoms. Although PD is commonly associated with a decline of dopaminergic neurons in the substantia nigra, other diagnostic criteria and biomarkers also exist. In the search for novel therapeutic agents, chromene and pyran derivatives have shown potential due to their diverse pharmacological activities. This study utilizes a comprehensive computational approach to investigate the viability of chromene/pyran compounds as potential treatments for PD. The drug-likeness characteristics of these molecules were analyzed using ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) studies. Molecular docking was performed against PDB ID: 2V5Z. The best three molecules chosen were compound 7, compound 24, and compound 67 have a binding energy of -6.7, -8.6, and -10.9 kcal/mol. Molecules demonstrating positive blood-brain barrier permeability, good solubility, and favorable binding affinity were further evaluated using Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations to assess their electronic structure and stability. DFT calculations indicated that molecule 82 has a dipole moment of 15.70 D. RMSD and RMSF results confirmed the stability of the complexes over a 100 ns simulation, with a maximum of 3 hydrogen bonds formed.

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.

Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness.

Expanding the functions and applications of DNA by integrating noncanonical bases and structures into biopolymers is a continuous scientific effort. An adenine-rich strand (A-strand) is introduced as functional scaffold revealing, in the presence of the low-molecular-weight cofactor cyanuric acid (CA, pKa 6.9), supramolecular hydrogel-forming efficacies demonstrating multiple pH-responsiveness. At pH 1.2, the A-strand transforms into a parallel A-motif duplex hydrogel cross-linked by AH+-H+A units due to the protonation of adenine (pKa 3.5). At pH 5.2, and in the presence of coadded CA, a helicene-like configuration is formed between adenine and protonated CA, generating a parallel A-CA triplex cross-linked hydrogel. At pH 8.0, the hydrogel undergoes transition into a liquid state by deprotonation of CA cofactor units and disassembly of A-CA triplex into its constituent components. Density functional theory calculations and molecular dynamics simulations, supporting the structural reconfigurations of A-strand in the presence of CA, are performed. The sequential pH-stimulated hydrogel states are rheometrically characterized. The hydrogel framework is loaded with fluorescein-labeled insulin, and the pH-stimulated release of insulin from the hydrogel across the pH barriers present in the gastrointestinal tract is demonstrated. The results provide principles for future application of the hydrogel for oral insulin administration for diabetes.

Exploring the inhibitory action of betulinic acid on key digestive enzymes linked to diabetes via in vitro and computational models: approaches to anti-diabetic mechanisms

ABSTRACT Phytochemicals are now increasingly exploited as remedial agents for the management of diabetes due to side effects attributable to commercial antidiabetic agents. This study investigated the structural and molecular mechanisms by which betulinic acid exhibits its antidiabetic effect via in vitro and computational techniques. In vitro antidiabetic potential was analysed via on α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin inhibitory assays. Its structural and molecular inhibitory mechanisms were investigated using Density Functional Theory (DFT) analysis, molecular docking and molecular dynamics (MD) simulation. Betulinic acid significantly (p < 0.05) inhibited α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin enzymes with IC50 of 70.02 μg/mL, 0.27 μg/mL, 1.70 μg/mL and 8.44 μg/mL, respectively. According to DFT studies, betulinic acid possesses similar reaction in gaseous phase and water due to close values observed for highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) and the chemical descriptors. The dipole moment indicates that betulinic acid has high polarity. Molecular electrostatic potential surface revealed the electrophilic and nucleophilic attack-prone atoms of the molecule. Molecular dynamic studies revealed a stable complex between betulinic acid and α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin. The study elucidated the potent antidiabetic properties of betulinic acid by revealing its conformational inhibitory mode of action on enzymes involved in the onset of diabetes.

Modulating Thermal Conductivity via Targeted Phonon Excitation.

Thermal conductivity is a critical material property in numerous applications, such as those related to thermoelectric devices and heat dissipation. Effectively modulating thermal conductivity has become a great concern in the field of heat conduction. Here, a quantum modulation strategy is proposed to modulate the thermal conductivity/heat flux by exciting targeted phonons. It shows that the thermal conductivity of graphene can be tailored in the range of 1559 W m-1 K-1 (decreased to 49%) to 4093 W m-1 K-1 (increased to 128%), compared with the intrinsic value of 3189 W m-1 K-1. The effects are also observed for graphene nanoribbons and bulk silicon. The results are obtained through both density functional theory calculations and molecular dynamics simulations. This novel modulation strategy may pave the way for quantum heat conduction.