Molecular Density Functional Theory with AtomisticDipolar Solvent to Study Pressure Effect on a Diels-AlderReaction

We assess the performance of molecular density functional theory (MDFT) to predict hydration free energies of the small drug-like molecules benchmark, FreeSolv. The MDFT in the hypernetted chain approximation (HNC) coupled with a pressure correction predicts experimental hydration free energies of the FreeSolv database within 1 kcal/mol with an average computation time of 2 cpu·min per molecule. This is the same accuracy as for simulation-based free energy calculations that typically require hundreds of cpu·h or tens of gpu·h per molecule.

Molecular dynamics (MD) simulation and density functional theory (DFT) calculations were used to predict the material properties and explore the improvement on the surface corrosion resistance for the Mg66Zn30Ca3Sr1 bulk metallic glass (BMG). The Mg66Zn30Ca4 BMG was also investigated to realize the influence of the addition of Sr element on the material behaviors of Mg66Zn30Ca4. The Mg-Zn-Ca-Sr parameters of the next nearest-neighbor modified embedded atom method (2NN MEAM) potential were first determined by the guaranteed convergence particle swarm optimization (GCPSO) method based on the reference data from the density functional theory (DFT) calculation. Besides, using the 2NN MEAM parameters of the Mg-Zn-Ca-Sr system, the structures of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1 were predicted by the simulated-annealing basin-hopping (SABH) method. The local atomic arrangements of the predicted BMG structures are almost the same as those measured in some related experiments from a comparison with the calculated and experimental X-ray diffraction (XRD) profiles. Furthermore, the HA index analysis shows that the fractions of icosahedra-like local structures are about 72.20% and 72.73% for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1, respectively, indicating that these two BMG structures are entirely amorphous. The uniaxial tensile MD simulation was conducted to obtain the stress-strain relationship as well as the related mechanical properties of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1. Consequently, the predicted Young’s moduli of both BMGs are about 46.4 GPa, which are very close to the experimental values of 48.8 ± 0.2 and 49.1 ± 0.1 GPa for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1, respectively. However, the predicted strengths of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1 are about 850 and 900 MPa, both are slightly higher than the measured experimental values about 747 ± 22 and 848 ± 21 MPa for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1. Regarding the thermal properties, the predicted melting temperature of Mg66Zn30Ca3Sr1 by the square displacement (SD) profile is about 620 K, which is very close to the experimental melting temperature of about 613 K. The self-diffusion coefficients of Mg, Zn, Ca, and Sr elements were also calculated for temperatures near their melting points by means of the Einstein equation. The methodology can determine the diffusion barriers for different elements by utilizing these diffusion coefficients resulting in a fact that the diffusion barriers of Ca and Sr elements of Mg66Zn30Ca3Sr1 are relatively high. For the electronic properties predicted by the DFT calculation, the projected density of states (PDOS) profiles of surface Mg, Zn, Ca, and Sr elements clearly show that the addition of Sr into Mg66Zn30Ca4 effectively reduces the s and p orbital states of surface Mg and Zn elements near the Fermi level, particularly the p orbits, which suppresses the electron transfer as well as increases the surface corrosion resistance of Mg66Zn30Ca4. Consequently, this study has provided excellent 2NN MEAM parameters for the Mg, Zn, Ca, and Sr system by the GCPSO method to predict real BMG structures as well as by means of the DFT calculation to explore the electronic properties. Eventually, through our developed numerical processes the material properties of BMGs with different compositions can be predicted accurately for the new BMG design.

The classical molecular dynamics (MD) method and density functional theory are utilized to study the dynamics and high-pressure behaviors of C20@Tube peapod structure. Results show that the critical and most suitable diameters of the tube for filling the C20 molecule are 9.5 and 10.86 Å, respectively. The mean free path and frequency of collision between the host and guest molecules are analyzed. Competition between the tube’s confinement effect and the temperature on the molecular motion is studied. Two superhard carbon phases with a large bulk modulus are obtained under high pressure. The encapsulated C20 molecule induces a decrease in the band gap under ambient conditions and a lower pressure of closure of band gap. In addition, the application of pressure leads to a redistribution of electric charge between the host and guest molecule. The encapsulation induces a red shift of the vibrational optic modes for both the tube and the C20 molecule.

Epoxy resins are widely used in the coating, adhesive and electronics industries. However, it is a difficult-to-machine polymer owing to its nature of thermal softening and soft-plastic and corrosion resistance characteristics. To overcome these difficulties, surface roughness (Sa) is usually set at more than 4 nm, and material removal rate (MRR) is normally set lower than 2 μm h-1 during traditional chemical mechanical polishing (CMP). Nevertheless, atomic level surface roughness is desired by high-performance devices of epoxy resins. This poses a challenge in conventional CMP. To address this challenge, herein, a novel CMP was developed, and the CMP slurry included ceria, dichloromethane, sodium carboxymethyl cellulose and deionized water. After CMP, an atomic level surface roughness was achieved with an Sa of 0.198 nm, and the MRR was 5.46 μm h-1. To the best of our knowledge, both the surface roughness and MRR are the best values reported in the literature. An atom-molecular dual-scale model was proposed to investigate the dynamically interactive mechanism between dichloromethane and the epoxy resin. Fourier transform infrared and Raman spectroscopies revealed that the conformation of epoxy resin varied and surface swelling occurred during the diffusion of dichloromethane. Hydrogen atoms of dichloromethane were selectively adsorbed onto the oxygen atoms of ether bonds in the epoxy resin, reducing the energy of the chains. The adsorption energy was high, reaching up to -67.3 kcal mol-1, and this conformation was the most stable. During adsorption, 0.012 eV of energy was transferred to dichloromethane from the small crosslinked molecules. Molecular dynamics simulations and density functional theory were used to perform these calculations. Dichloromethane relaxed the resin surface, speeding up the migration rate of chains and reducing their energy of breaking. The combined effect of mechanical shear force, compressive force and relaxation of swelling led to the breakage of C-N bonds with the lowest energy in the chains. The broken short chains were wrapped in dichloromethane, separating from the surface of the resin with the slurry flow. Our results provide new insights into acquiring an atomic level epoxy resin surface with soft-plastic, thermal softening and corrosion resistance characteristics.

Correlations of the shear viscosity of quartz nanofluids with particle concentration, particle size, and temperature were investigated with molecular dynamics simulations and density functional theory (DFT) calculations. A new understanding to the experimentally concluded correlations was addressed in terms of microscopic particle–water interfacial interaction in three aspects. First, the viscosity of quartz nanofluids at different particle concentrations, particle sizes, and temperatures were simulated using the equilibrium molecular dynamics simulations method to reproduce the experimental observations. At the same particle size, the nanofluid viscosity decreases significantly with temperature and increases with nanoparticle volume concentration, and at the same volume concentration, the nanofluid viscosity increases with the decrease of particle size. Second, DFT calculations confirm a stronger particle–water interaction than that among water molecules. The important role of particle–water interaction in the viscosity determination of nanofluids was revealed. Finally, a correlation was proposed to fit the simulated results and compared with earlier two-parameter correlations. One parameter in the correlation is indeed a constant, while the other is a function of SiO2–water interaction energy. Our study proposes a physical basis for the experimentally concluded correlations on the viscosity of nanofluids.

Performance evaluation of waste cooking oil at different stages and rejuvenation effect of aged asphalt through molecular dynamics simulations and density functional theory calculations

Cancer is a complex and life‐threatening disease characterized by uncontrolled tumor cell growth. Targeting the MDM2 protein to reactivate the tumor suppressor p53 presents a promising therapeutic strategy. This study employed an energy‐optimized pharmacophore model to perform a virtual screening of 47,451 compounds from the comprehensive marine natural product database (CMNPD), leveraging the rich diversity of marine‐derived bioactives with high efficacy and low side effects. The screening workflow combined ADMET profiling and molecular docking using HTVS, SP and XP methods to identify potential MDM2 inhibitors. Six top hits exhibited strong binding affinities and favorable interactions compared to standard drugs. Molecular dynamics (MD) simulations and density function theory (DFT) studies were conducted to evaluate the structural stability and electronic properties of the protein–ligand complexes. MM‐GBSA calculations quantified the binding free energies, confirming the stability of these complexes. Specifically, comp‐4 and 6 showed low energy gaps in DFT analysis, indicating strong ligand affinity. Principal component analysis (PCA) and free energy landscape (FEL) evaluations further demonstrated stable conformational behavior throughout the MD simulation trajectories. Collectively, these integrated computational approaches identified potent and stable MDM2 inhibitors, providing promising candidates for experimental validation and further development as anticancer therapeutics.

Introduction: Diabetes mellitus (DM) is a multimodal metabolic disease whose world inci-dence is estimated to reach approximately 366 million by the year 2030, even with the progress being made in biomedical research. The interaction of genetics, lifestyle, and environment complicates its management. Dipeptidyl peptidase IV (DPP-IV) and α-glucosidase inhibition a promising therapies: DPP-IV inhibition increases the effect of incretin and the release of insulin, and α-glucosidase inhibition postpones carbohydrate digestion and glucose absorption. Methods: Molecular docking and density functional theory (DFT) were employed to explore the anti-diabetic effect of stigmasterol, a phytosterol with Glycine max. Docking experiments were conducted to determine the binding affinities and interaction patterns between stigmasterol and DPP-IV and α-glucosidase. DFT analysis was done to obtain global reactivity descriptors and energy band gap, which estimated the electronic stability and reactivity of the molecule. Results: Stigmasterol exhibited high affinity towards the two target enzymes with docking scores of -8.8 kcal/mol to DPP-IV and -8.4 kcal/mol to α-galactosidase. The analysis of the DFT showed that it had a good (moderate) band gap and unaltered electronic configuration, which is indicative of good chemical reactivity and stability. Discussion: The binding affinities and electronic properties indicate that stigmasterol can be a dual DPP-IV and α-glucosidase inhibitor, which can be used synergistically to produce synergistic glycemic control via the regulation of incretin-mediated insulin release and postprandial carbohydrate absorption. The computational findings are in favor of its candidacy as a natural antidiabetic compound, but the weaknesses of in silico studies demand experimental confirmation. Conclusion: Stigmasterol has been suggested as a promising dual DPP-IV and alpha-glucosidase inhib-itor that could be useful in the management of diabetes mellitus. It needs to be further tested in vitro and in vivo to verify its biological efficacy, pharmacokinetics, and safety profile.

Theoretical Study on Reaction Pathways of Methyl Radical with Ethylamine

Molecular integral equations theory in the near critical region of CO2

We present results of molecular dynamics (MD) simulations and density functional theory (DFT) calculations of the diffusion of Cu adatom and dimer on Ag(111). We have used potentials generated by the embedded-atom method for the MD simulations and pseudopotentials derived from the projected-augmented-wave method for the DFT calculations. The MD simulations (at three different temperatures: 300, 500, and 700 K) show that the diffusivity has an Arrhenius behavior. The effective energy barriers obtained from the Arrhenius plots are in excellent agreement with those extracted from scanning tunneling microscopy experiments. While the diffusion barrier for Cu monomers on Ag(111) is higher than that reported (both in experiment and theory) for Cu(111), the reverse holds for dimers [which, for Cu(111), has so far only been theoretically assessed]. In comparing our MD result with those for Cu islets on Cu(111), we conclude that the higher barriers for Cu monomers on Ag(111) results from the comparatively large Ag-Ag bond length, whereas for Cu dimers on Ag(111) the diffusivity is taken over and boosted by the competition in optimization of the Cu-Cu dimer bond and the five nearest-neighbor Cu-Ag bonds. Our DFT calculations confirm the relatively large barriers for the Cu monomer on Ag(111)---69 and 75 meV---compared to those on Cu(111) and hint a rationale for them. In the case of the Cu dimer, the relatively long Ag-Ag bond length makes available a diffusion route whose highest relevant energy barrier is only 72 meV and which is not favorable on Cu(111). This process, together with another involving an energy barrier of 83 meV, establishes the possibility of low-barrier intercell diffusion by purely zigzag mechanisms.

Background: Type 2 diabetes mellitus continues to pose a threat to the existence of the human race. The increasing number of diabetic subjects can be effectively controlled by targeting enzymes responsible for high blood glucose levels. Xanthones are a class of phytochemicals that possesses promising pharmacological potentials. Objective: This study identified fructose 1,6-biphosphatase (FBPase) inhibitors by exploring xanthones isolated from African medicinal plants through ensemble docking, molecular dynamics simulation and density functional theory methods. Methods: The study used ensemble docking, molecular dynamics simulation and density functional theory (B3LYP/6-3G (d,p) basis set) and ADMET methods to select lead compound that may be effective as fructose-I,6-biphosphatase inhibitor. Results: The ensemble docking results identified globulixanthone C (-10.0 kcal/mol), 1-Isomangostin (- 9.0 kcal/mol), laurentixanthone A (-9.0 kcal/mol), bangangxanthone A (-8.9 kcal/mol) and staudtiixanthone B (-8.8 kcal/mol) as potential inhibitors of fructose-1,6-biphosphatase. Molecular dynamics studies showed the xanthones established good binding mode and their binding energy ranged from -74.057 to 53.669 kJ/mol. Also, the electronic and ADMET studies of the xanthones elucidated their excellent pharmacological potential. Conclusion: The study identified xanthones as potential fructose-1,6-biphosphatase inhibitors. The ligands' binding energy and MMPBSA calculations supported their possible inhibitory property. Also, the ADMET properties estimated show the ligands as suitable drug candidates as fructose-1,6-biphosphatase inhibitors. Further in vitro and in vivo investigation of the hit molecules is necessary to develop new FBPase inhibitors.

Study of Mechanism Keto-Enol Tautomerism (isomeric reaction) Structure Cyclohexanone by Using Ab initio Molecular Orbital and Density Functional Theory (DFT) Method with NBO Analysis

Decomposition characteristics of C5F10O/air mixture as substitutes for SF6 to reduce global warming

Crystal structure, theoretical calculations, mechanoluminescence feature and antimicrobial activity based on a double-armed Salamo-type ligand and its trinuclear Cu(Ⅱ) complex