Van Der Waals Energy Research Articles

Effect of oxidation kinetic aging on the adhesion behaviour of asphalt-aggregate interfaces from molecular view

ABSTRACT Asphalt oxidation kinetic aging effect on the adhesion behavior of asphalt-aggregate interfaces at atomistic scale was investigated in this study. The asphalts were aged at different aging durations. The sulfoxide and carbonyl functional group content as well as SARA fractions of the asphalts at different aging times were studied through the tests of Fourier Transform Infrared Spectroscopy (FTIR) and Saturate, Aromatic, Resin and Asphaltene (SARA) fractions. Asphalt molecular models of virgin, rapid-rate aged, slow-rate aged and full-aged were established based on SARA fractions and FTIR results, to construct asphalt quartz and asphalt-calcite interface systems at different aging stages. The simulation results showed that the nanostructure of asphalt is influenced by the aggregate type and asphalt oxidative aging. The growth rates of adhesion energy of asphalt-quartz and asphalt-calcite systems increase rapidly first and then slowly with aging time, but the growth rates are different. Meanwhile, the Van der Waals energy is the major energy source of adhesion energy, and the contribution of van der Waals and electrostatic energy to adhesion energy is different. The aging of asphaltene and resin promotes the adhesion ability to quartz or calcite, while the aging of aromatic components is not conducive and the saturate has almost no effect.

Potential Mechanisms of Casein Hexapeptide YPVEPF on Stress-Induced Anxiety and Insomnia Mice and Its Molecular Effects and Key Active Structure.

The hexapeptide YPVEPF with strong sleep-enhancing effects could be detected in rat brain after a single oral administration as we previously proved. In this study, the mechanism and molecular effects of YPVEPF in the targeted stress-induced anxiety mice were first investigated, and its key active structure was further explored. The results showed that YPVEPF could significantly prolong sleep duration and improve the anxiety indexes, including prolonging the time spent in the open arms and in the center. Meanwhile, YPVEPF showed strong sleep-enhancing effects by significantly increasing the level of the GABA/Glu ratio, 5-HT, and dopamine in brain and serum and regulating the anabolism of multiple targets, but the effects could be blocked by bicuculline and WAY100135. Moreover, the molecular simulation results showed that YPVEPF could stably bind to the vital GABAA and 5-HT1A receptors due to the vital structure of Tyr-Pro-Xaa-Xaa-Pro-, and the electrostatic and van der Waals energy played dominant roles in stabilizing the conformation. Therefore, YPVEPF displayed sleep-enhancing and anxiolytic effects by regulating the GABA-Glu metabolic pathway and serotoninergic system depending on distinctive self-folding structures with Tyr and two Pro repeats.

Investigation on Combustion Characteristics and Molecular Structures of Heiyanquan Mining Area, Xinjiang, China.

In order to comprehend the molecular composition of coal and better understand the process of coal combustion, this study involved the development of a molecular structure model for Heiyanquan coal in Xinjiang, as well as the optimization and annealing dynamics simulation of the model. Thermogravimetric analysis (TG), Fourier transform infrared spectroscopy (FTIR), and high-resolution transmission electron microscopy (HRTEM) were utilized to investigate the spontaneous combustion characteristics of coal at different temperatures (room temperature, 50-500 °C with 50 °C interval). The findings revealed that the coal primarily consists of aromatic carbon, with the aromatic structure mainly comprising naphthalene, anthracene, and phenanthrene, and the aliphatic carbon mainly consisting of CH2 and CH, along with a small quantity of minerals. The empirical molecular formula of Heiyanquan coal was determined to be C175H125O21N3. After the optimization, the total energy of the model was significantly reduced, and the aromatic layers tended to align in a regular parallel manner, with van der Waals energy playing a crucial role in maintaining structural stability. As the temperature increased, the activation energy of the three stages also increased, with the combustion stage exhibiting the highest activation energy. The presence of hydroxyl groups and oxygen-containing functional groups was found to mainly participate in the reaction, while the content of aromatic hydrocarbons remained relatively stable, C=C exhibited a decreasing trend, and C-O displayed an increasing trend. Moreover, it was observed that 1 × 1 and 2 × 2 were the predominant aromatic stripes in the coal samples, accounting for more than 90% of the total stripes.

Effect of mixed collector on the LRC flotation: an experimental and molecular dynamics simulation study

ABSTRACT To investigate the mechanism underlying the effect of mixed collector (MC) composed of diesel and span-80 on LRC flotation, a combination of experimental and molecular simulation approaches was employed. The flotation results demonstrated that the use of MC yielded superior flotation performance compared to diesel alone. The ratio of diesel to span-80 emerged as a key factor influencing the performance of MC collection. Furthermore, molecular dynamics (MD) simulations were employed to investigate the adsorption processes of dodecane and MC molecules on the LRC surface in the LRC/dodecane/water and LRC/MC/water systems, respectively. The analysis encompassed microstructure, dynamic properties, interaction energy, and hydrogen bonding. The findings indicated that the presence of span-80 molecules facilitated the direct entry of dodecane molecules in MC into “microscopic cavities,” thereby enhancing the adsorption of MC on the LRC surface. The analysis of interaction energy revealed a stronger interaction between MC molecules and the coal surface, with van der Waals energy playing a major role in the adsorption process. Additionally, span-80 molecules induced hydrogen bonding adsorption on the LRC surface.

Potential anti-obesity effect of saponin metabolites from adzuki beans: A computational approach.

In contrast to its widespread traditional and popular culinary use to reduce weight, Vigna angularis (adzuki beans) was not subjected to sufficient scientific scrutiny. Particularly, its saponins whose role was never investigated before to unveil the beans' antidiabetic and anti-obesity effects. Four vital pancreatic and intestinal carbohydrate enzymes were selected to assess the potency of the triterpenoidal saponins of V. angularis to bind and activate these proteins through high-precision molecular modeling and dynamics mechanisms with accurate molecular mechanics Generalized Born Surface Area (MMGBSA) energy calculations; thus, recognizing their anti-obesity potential. Our results showed that adzukisaponin VI and adzukisaponin IV were the best compounds in the α-amylase and α-glucosidase enzymatic grooves, respectively. Adzukisaponin VI and angulasaponin C were the best fitting in the N-termini of sucrase-isomaltose (SI) enzyme, and angulasaponin C was the best scoring compound in maltase-glucoamylase C-termini. All of them outperformed the standard drug acarbose. These compounds in their protein complexes were selected to undergo molecular simulations of the drug-bound protein compared to the apo-protein through 100 ns, which confirmed the consistency of binding to the key amino acid residues in the four enzyme pockets with the least propensity of unfolding. Detailed analysis is given of the different polar and hydrophobic binding interactions of docked compounds. While maltase-adzukisaponin VI complex scored the lowest MMGBSA free energy of -67.77 Kcal/mol, α-amylase complex with angulasaponin B revealed the free binding energy of -74.18 Kcal/mol with a dominance of van der Waals energy (ΔEVDW) and the least change from the start to the end of the simulation time. This study will direct researchers to the significance of isolating the pure adzuki saponin components to conduct future invitro and invivo experimental works and even clinical trials.

Study on the Effect of Cations on the Surface Energy of Nano-SiO2 Particles for Oil/Gas Exploration and Development Based on the Density Functional Theory.

Although nano SiO2 exhibits excellent application potential in the field of oil and gas exploration and development, such as drilling fluid, enhanced oil/gas recovery, etc., it is prone to agglomeration and loses its effectiveness due to the action of cations in saline environments of oil and gas reservoirs. Therefore, it is crucial to study the mechanism of the change in energy between nano SiO2 and cations for its industrial application. In this paper, the effect of cations (Na+, K+, Ca2+, and Mg2+) on the surface energy of nano SiO2 particles is investigated from the perspective of molecular motion and electronic change by density functional theory. The results are as follows: Due to the electrostatic interactions, cations can migrate towards the surface of nano SiO2 particles. During the migration process, monovalent cations are almost unaffected by water molecules, and they can be directly adsorbed on the surface by nano SiO2 particles. However, when divalent cations migrate from a distance to the surface of nano SiO2 particles, they can combine with water molecules to create an energy barrier, which can prevent them from moving forward. When divalent cations break through the energy barrier, the electronic kinetic energy between them and nano SiO2 particles changes more strongly, and the electrons carried by them are more likely to break through the edge of the atomic nucleus and undergo charge exchange with nano SiO2 particles. The change in interaction energy is more intense, which can further disrupt the configuration stability of nano SiO2. The interaction energy between cations and nano SiO2 particles mainly comes from electrostatic energy, followed by Van der Waals energy. From the degree of influence of four cations on nano SiO2 particles, the order from small to large is as follows: K+ < Na+ < Mg2+ < Ca2+. The research results can provide a theoretical understanding of the interaction between nano SiO2 particles and cations during the application of nano SiO2 in the field of oil and gas exploration and development.

Potential Inhibitors from Natural Compounds against SARS‐CoV‐2 Main Protease: A Systematic Molecular Modelling Approach

AbstractThe COVID‐19 outbreak poses a significant threat to the world‘s human population in 2020. Finding new drugs rapidly during this pandemic is quite challenging. Thus, in silico drug screening experiments may provide effective therapeutic alternatives for better assessing natural remedies in preventing and treating COVID‐19. The main protease (Mpro) is an important drug target that is essential and ubiquitous for the survival of SARS‐CoV‐2. In this study, we performed in silico high‐throughput virtual screening to identify potential hits employing a database of 3 million natural compounds (supernatural‐II database). The initially obtained top 100 virtual hits were subjected to a standard SP and XP docking protocol, achieving the top 30 hits. Compounds SN00340755 (glide score: −16.0 kcal/mol and ΔGbind: −134.29 kcal/mol) and SN00213037 (glide score: −13.30 kcal/mol and ΔGbind: −81.18 kcal/mol) exhibited significant binding energy against Mpro (PDB ID: 6XQS). The ligands SN00340755 and SN00213037 formed multiple hydrogen bonds with the catalytic residues, especially with the functionally important residue GLU166, which plays a significant role in protomer dimerization. Further post‐docking minimization studies (MM‐GBSA) were performed to estimate the ligand‐protein affinity. From MM‐GBSA studies, it was observed that Coulombic (−140.70 to −37.66 kcal/mol) and van der Waals (−79.32 to −20.59 kcal/mol) energies, favoring the binding of ligands to the Mpro target protein. The ADMET properties were predicted using Qikprop, Chem Axon, and Data Warrior tools, demonstrating the beneficial pharmacokinetic parameters of these natural compounds. The 100 ns molecular dynamics simulation study revealed minor protein fluctuations, indicating the stability of the protein‐ligand complex.

Adsorption Characteristics of CO2/CH4/H2S Mixtures in Calcite Nanopores with the Implications for CO2 Sequestration

Summary Injecting CO2 into reservoirs for storage and enhanced oil recovery (EOR) is a practical and cost-effective strategy for reducing carbon emissions. Commonly, CO2-rich industrial waste gas is used as the CO2 source, whereas contaminants such as H2S may severely impact carbon storage and EOR via competitive adsorption. Hence, the adsorption behavior of CH4, CO2, and H2S in calcite (CaCO3) micropores and the impact of H2S on CO2 sequestration and methane recovery are specifically investigated. The Grand Canonical Monte Carlo (GCMC) simulations were applied to study the adsorption characteristics of pure CO2, CH4, and H2S, and their multicomponent mixtures were also investigated in CaCO3 nanopores to reveal the impact of H2S on CO2 storage. The effects of pressure (0–20 MPa), temperature (293.15–383.15 K), pore width, buried depth, and gas mole fraction on the adsorption behaviors are simulated. Molecular dynamics (MD) simulations were performed to explore the diffusion characteristics of the three gases and their mixes. The amount of adsorbed CH4, CO2, and H2S enhances with rising pressure and declines with rising temperature. The order of adsorption quantity in CaCO3 nanopores is H2S &amp;gt; CO2 &amp;gt; CH4 based on the adsorption isotherm. At 10 MPa and 323.15 K, the interaction energies of CaCO3 with CO2, H2S, and CH4 are −2166.40 kcal/mol, −2076.93 kcal/mol, and −174.57 kcal/mol, respectively, which implies that the order of adsorption strength between the three gases and CaCO3 is CO2 &amp;gt; H2S &amp;gt; CH4. The CH4-CaCO3 and H2S-CaCO3 interaction energies are determined by van der Waals energy, whereas electrostatic energy predominates in the CO2-CaCO3 system. The adsorption loading of CH4 and CO2 are lowered by approximately 59.47% and 24.82% when the mole fraction of H2S is 20% at 323.15 K, reflecting the weakening of CH4 and CO2 adsorption by H2S due to competitive adsorption. The diffusivities of three pure gases in CaCO3 nanopore are listed in the following order: CH4 &amp;gt; H2S ≈ CO2. The presence of H2S in the ternary mixtures will limit diffusion and outflow of the system and each single gas, with CH4 being the gas most affected by H2S. Concerning carbon storage in CaCO3 nanopores, the CO2/CH4 binary mixture is suitable for burial in shallower formations (around 1000 m) to maximize the storage amount, while the CO2/CH4/H2S ternary mixture should be buried as deep as possible to minimize the adverse effects of H2S. The effects of H2S on CO2 sequestration and CH4 recovery in CaCO3 nanopores are clarified, which provides theoretical assistance for CO2 storage and EOR projects in carbonate formation.

Mechanical strength changes of combustible municipal solid waste components during their early pyrolysis stage and mechanism analysis.

Implementation of municipal solid waste (MSW) source segregation leads to a more convenient recycle of combustible MSW components. Textiles, plastics and papers are commonly available combustible components in MSW. Their shredding is conducive to resources recovery. But these components usually have high tensile strengths and are difficult to shred. To understand their mechanical strength changes in their early pyrolysis stage will help to address this problem. In this study, a universal electronic testing machine was used to determine the breaking strengths of the materials including cotton towel, polyethylene glycol terephthalate (PET), ivory board (IB), kraft paper (KP) and wool scarf in the temperature range of 30-250°C under N2 atmosphere, and the mechanisms of their strength changes were explored. The reaction force field molecular dynamics (ReaxFF-MD) simulation was used to explain the decomposition behaviours of different sugar groups of hemicellulose in cotton and paper and the change of van der Waals energy of wool during their early pyrolysis stages. The results showed that breaking strengths of all the combustible MSW components reduced as the temperature increased. The breaking strength of PET was found to have the highest descent rate with increasing temperature, then the descent rates of wool and cotton came as the second and third, respectively. Compared with cotton, the breaking strengths of KP and IB decreased more slowly. As the temperature increased, the breaking strength of cotton reduced mainly due to the decomposition of the glucuronic acid in hemicellulose, and the reduction was characterized by CO2 release. The breaking strength reduction of PET was caused by its molecular chain being relaxed. The breaking strength reduction of wool was firstly caused by the decrease in the van der Waals energy between its molecules, and then caused by molecular chain breaking. In addition, in order to understand the influence of material size on the breaking strength change during thermal treatment, the breaking strengths of cotton yarn bundles were correlated with their yarn number and temperature. This study lays the foundation for understanding changes in mechanical strengths of combustible MSW components during their early pyrolysis stage.

Docking for Molecules That Bind in a Symmetric Stack with SymDOCK.

Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of great current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures, the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein's symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand's docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural-network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in a prospective study, SymDOCK predicted the structure of the PET tracer MK-6240 bound in a symmetrical stack to AD PHF tau before that structure was determined; the docked pose was used to determine how MK-6240 fit the cryo-EM density. In proof-of-concept studies, SymDOCK enriched known ligands over property-matched decoys in retrospective screens without sacrificing docking speed and can address large library screens that seek new symmetrical stackers. Future applications of this approach will be considered.

Adsorption of toremifene on carboxylic acid functionalized N/B-doped coronene: DFT, AIM, solvation, docking and MD analyses

The adsorption of toremifene (TOR) on coronene (GG) and carboxylic acid-functionalized coronene (COOHGG) and doped with boron/nitrogen (BBGG/NNGG) has been researched using DFT and TD-DFT simulations. The chemical properties, AIM, and SERS were all considered when conducting this investigation. Intermolecular interactions emphasizing on reactive zones result from graphene acting as an electron acceptor and nucleophilic part of TOR acting as an electron-donor. All of the TOR-complexes had negative Gibbs free energy changes due to TOR adsorption. Enthalpy modifications also differ greatly across the doped complexes (-26.39 to −86.97 kJ/mol lin air and −65.39 to −86.97 kJ/mol in water) and GG complex (-2.55 kJ/mol in air and −40.58 kJ/mol in water). Our results show that the TOR with BBGG doped complex, with a binding energy of −55.73 kJ/mol in air, while in water adsorption with NNGG gives −90.92 kJ/mol, are the most stable complexes among the various systems under study. The GG complex has the lowest energy, followed by other doped complexes. After adsorption multiple modes of TOR have higher Raman intensities, and this is because of an amplification process brought on by the SERS effect. The presence of substituted COOHGG, BBGG and NNGG cages has a higher tendency to interact with the drug molecule than GG. From MD simulations, TOR had van der Waals energy of −147.293+/–22.370 kJ/mol, an electrostatic energy of −53.749 +/–33.825 kJ/mol, polar solvation energy of 112.531+/−30.651 kJ/mol, and a binding energy of −70.130+/–23.290 kJ/mol.

Molecular dynamics simulation on the intelligent repair behavior of microencapsulated resin matrix composites

Microencapsulated resin matrix composites have attracted wide attention for their ability to intelligently detect and repair microcracks, whereas the interaction mechanism between the repair agent and resin after the microcapsules crack has not been well understood. To reveal the repair mechanism of composites containing linseed oil microcapsules, the molecular model consisting of the oxidized linseed oil, microcracks, and cross-linked resin was established based on the molecular dynamics (MD) technique. The intelligent repair process of the models was analyzed. The repairing performance was evaluated by means of elastic modulus, adhesion energy, and interfacial thickness. The influence of temperature and the type of repair agent on repairing performance was studied. The results show that the increased temperature can significantly enhance the diffusion rate of the repair agent molecules and shorten the time for them to reach the crack surface. The changing rate of mechanical properties dramatically increases after 100 ps, and van der Waals energy has a great contribution to the repairing efficiency. The adhesion energy and the interfacial thickness between the components show a trend towards increasing and then decreasing as the temperature increases, and the oxidized linseed oil has a stronger twisting effect with the resin matrix compared with pure resin and cross-linked resin. These findings help understand the intelligent repair behavior of composites on the atomic scale, providing a reference for the design of intelligent composites.

Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach

Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1–S6) displayed a glide score (G-score) within the range of −9.013 to −7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTS E.coli is a common cause of urinary tract infections. E.coli MurD enzyme is a suitable target for drug development. Novel inhibitors against E.coli MurD enzyme were identified. Molecular dynamics studies identified in-silico potential of identified compound. ADMET predictions and Lipinski’s rule of five studies showed promising results. Communicated by Ramaswamy H. Sarma

Identification of potential drug molecules against fibroblast growth factor receptor 3 (FGFR3) by multi-stage computational-biophysics correlate

The fibroblast growth factor receptor 3 (FGFR3) is warranted as a promising therapeutic target in bladder cancer as it is described in 75% of papillary bladder tumors. Considering this, the present study was conducted to use different approaches of computer-aided drug discovery (CADD) to identify the best binding compounds against the active pocket of FGFR3. Compared to control pyrimidine derivative, the study identified three promising lead structures; BDC_24037121, BDC_21200852, and BDC_21206757 with binding energy value of −14.80 kcal/mol, −12.22 kcal/mol, and −11.67 kcal/mol, respectively. The control molecule binding energy score was −9.85 kcal/mol. The compounds achieved deep pocket binding and produced balanced interactions of hydrogen bonds and van der Waals. The FGFR3 enzyme residues such as Leu478, Lys508, Glu556, Asn562, Asn622, and Asp635. The molecular dynamic (MD) simulation studies additionally validated the docked conformation stability with respect to FGFR3 with a mean root mean square deviation (RMSD) value of < 3 Å. The root mean square fluctuation (RMSF) complements the complexes structural stability and the residues showed less fluctuation in the presence of compounds. The Poisson–Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods revalidated compounds better binding and highlighted van der Waals energy to dominate the overall net energy. The docked stability was additionally confirmed by WaterSwap and AMBER normal mode entropy energy analyses. In a nutshell, the compounds shortlisted in this study are promising in term of theoretical binding affinity for FGFR3 but experimental validation is needed.Communicated by Ramaswamy H. Sarma

Adsorption Efficiency of Carbon Materials for the Removal of Organic Pollutants: DDT from Aqueous Solution.

Carbon nanotubes (CNTs) are widely used to adsorb organic pollutants from wastewater due to their porous structure, large specific surface area, and unique physical and chemical properties. Examining the interactions between pollutant molecules and carbon nanotubes is an important topic in the applications of nanotubes for the removal of pollutants. In this study, molecular dynamics (MD) and metadynamics simulations were used to investigate the adsorption mechanism of Dichlorodiphenyltrichloroethane (DDT) pollutants on carbon nanotubes. Obtained results revealed that functionalized CNTs (f-CNTs) with active groups exhibited significantly enhanced performance compared to pristine CNTs. The adsorption isotherms were analyzed at different DDT concentrations, and it was found that increasing the concentration of DDT molecules led to a decrease in system energy and increased stability. The presence of biosurfactants as functional groups on the CNTs enhanced the interaction between DDT molecules and the nanotubes. In CNT, the addition of DDT increases the van der Waals energy from -176.83 kJ/mol for 3 DDT molecules to -2237.88 kJ/mol for 50 DDT molecules. In the case of f-CNT, the van der Waals energy in the system with 50 DDT molecules is about 2061.05 kJ/mol more negative than the system with 3 DDT molecules. The number of contacts between the adsorbent and DDT molecules increased over time, indicating increased adsorption interaction. The radial distribution functions (RDF) of DDT molecules around CNTs and f-CNTs showed the highest probability of finding DDT molecules at a distance of about 0.5 nm from the adsorbent surface. The study provided valuable insights into the adsorption process and can guide future experimental studies.

Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical burden is high. New therapeutics are needed to treat multidrug-resistant Acinetobacter baumannii infections and reduce transmission. The study used computer-integrated drug discovery approaches including pharmacophore modelling, molecular docking, and molecular dynamics simulation to screen potential inhibitors against the enoyl-acyl carrier protein reductase—FabI protein of Acinetobacter baumannii. The top three potential inhibitors: 21272541 > 89795992 > 89792657 showed favourable binding free energies including coulombic energy, van der Waals energy, and polar and non-polar energies. Furthermore, all three complexes were extremely stable and compact with reduced fluctuations during the simulations period. Inhibitor 21272541 exhibited the highest binding affinity against the Acinetobacter baumannii FabI protein. This is similar to our recent report, which also identified 21272541 as the lead inhibitor against Klebsiella pneumoniae infections. Future clinical studies evaluating drug effectiveness should prioritise inhibitor 21272541 which could be effective in treating infections caused by Gram-negative organisms.

Level dyeing property and aggregation morphology of reactive black 5 on cotton fabric in a salt-free and less-water dyeing system

In a traditional water-based dyeing system, large amounts of salts and water are consumed. However, a non-aqueous media dyeing system achieves salt-free and less-water dyeing. In a non-aqueous media dyeing system, a small amount of water is used, which may affect the aggregation morphology of the dyes. The molecular dynamics of reactive dyes on the surface of cotton fibers were investigated. The results showed that the color depth of dyed cotton fabric did not change much when the dosage of salt was below 5.2% o.w.f. However, continuing to increase the amount of salt could influence the dyeing level of dyed fabric. The diffusion coefficient of dye was 0.3044 × 10−5 cm−2/s when there was no salt in dyeing system. But it was decreased by 14.03% and 16.62% when the salt concentration was increased from zero to 5.2% and 13% o.w.f., respectively. When the concentration of sodium sulfate was zero, the dye molecules in the solution displayed in the form of unimolecular molecules and dimers. However, reactive dyes mainly existed in the form of trimers and polymers when the concentration of sodium sulfate was above 5.2%. When there was no salt in the less-water dyeing system, the van der Waal energy between fiber and dye was 131.29 kJ/mol, but it was increased to 382.92 kJ/mol when the dosage of sodium sulfate was 5.2%. Therefore, with the increase of sodium sulfate dosage, the color depth of the dyed fabric changed little, but the level of dyeing property became poorer.

Exploring the inhibitory effect of H2O on CO2/CH4 adsorption in coal: Insights from experimental and simulation approaches

To investigate the inhibitory effect of H2O on the adsorption of CH4/CO2 in coal, the anthracite was selected for physical adsorption experiments on CH4/CO2 gases in this study. Combined with Materials Studio software, the effect of moisture on the isothermal adsorption characteristics of CH4/CO2 in coal was investigated by using density functional theory and giant canonical Monte Carlo simulation. The intermolecular interaction energies were obtained, as well as the effects of electrostatic potentials, adsorption sites, and hydrogen bonding of oxygen-containing functional groups. The results show that: ①According to the CH4/CO2 isothermal adsorption experiments, it was found that moisture significantly inhibited the adsorption of CH4/CO2 by coal. For CH4, the relationship between adsorption constants a/b and moisture content can be expressed by the equations y = 43.447-3.348x and y = 3.225-0.751x. For CO2, adsorption constant a follows a power function relationship with moisture content, expressed as y = 29.114x-0.063, while adsorption constant b is represented by the polynomial fitting equation y = 1.672+0.508x+0.083x2. ② The findings have revealed correlations between the moisture influence coefficient and moisture content. The exponential functional equation η = exp(-0.188ω) was found to be more accurate for coal adsorbing CH4, whereas the linear functional equation η = 1/(1 + 0.243ω) was considered more appropriate for CO2. ③ The van der Waals and electrostatic energies between coal and CH4/CO2 decreased with an increase in moisture content, whereas the van der Waals and electrostatic energies between coal and H2O increased. ④ The orders of hydrogen bond formation ability between CH4/CO2 and functional groups were as follows: –CHO > –COOH > –OH > –CH3 and –OH > –COOH > –CHO > –CH3. The ability of H2O to form hydrogen bonds with –COOH, –OH, –CHO, and –CH3 is as follows: –COOH > –OH > –CHO> –CH3. This study provides a theoretical basis for the integrated use of hydraulic fracturing techniques and coalbed gas injection and replacement.

Investigation of the Multimechanism Laser Cleaning Dynamics for Rough Fused Silica Surfaces with Organic Contaminants: A Computational Simulation and Atomic Analysis.

The detrimental impact of organic contaminants on optical components poses a significant obstacle to high-energy laser systems. However, irregularities or defects on the surface of optical components during manufacturing can affect the process of organic contaminant removal. Thus, a comprehensive understanding of the intricate interplay among surface roughness, contaminant absorption, and ablation is essential to effectively address the challenges of laser-induced damage. In this study, a molecular dynamics approach was employed to investigate the interaction between laser-fused silica and contaminants and to analyze the influence of surface roughness on the removal of contaminants from fused silica. Research findings demonstrate that during laser irradiation, organic contaminants on the surface of mechanical components diffuse into the optical elements. As the laser flux increases, the contaminants gradually decompose into smaller molecular clusters. Additionally, the phenomenon of contaminant ablation is observed to consist of two distinct phases: the "Thermal expansion phase" and the "Thermal ablation phase." The study examines the impact of substrate roughness on the contaminant removal in these two phases. It is found that a higher surface roughness leads to stronger thermal expansion and vaporization of contaminants. With increasing roughness of the fused silica substrate, the corresponding van der Waals energy and pressure decrease under the same laser fluence, making the removal of contaminants easier. These results provide valuable insights into the interaction between laser irradiation and organic contaminants.

New 2,4-dihydro-1H-1,2,4-triazole-3-selones and 3,3′-di(4H-1,2,4-triazolyl)diselenides. Synthesis, biological evaluation, and in silico studies as antibacterial and fungicidal agents

The reaction of aromatic ring-substituted isoselenocyanates with 2-thiopheacetic and 4-pyridinecarboxylic acid hydrazides yielded selenosemicarbazides which were further converted into previously unknown 1,2,4-triazole-3-selones and 3,3′-di(4H-1, 2,4-triazolyl)diselenides. The structures of the obtained compounds were studied by NMR spectroscopy, IR spectroscopy, and high-resolution mass spectroscopy (HR-MS). The bactericidal and fungicidal activity of some obtained compounds was evaluated in molecular modeling studies such as docking and simulation studies. The compound 3ba was reported as the most promising compound to show robust binding energy with different antibacterial and antifungal compounds. The compounds were observed in strong hydrophilic and hydrophobic interactions and remained in stable binding conformation with the receptor enzymes. Furthermore, the interatomic interaction energies were dominated by Van der Waals and electrostatic energies indicating the formation of stable complexes.