B-COPNA resin formation from ethylene tar light fractions:Process development and mechanical exploration by molecular simulation

An efficient utilization strategy of ethylene tar(ET),the main by-product of the ethylene cracking unit,is urgently required to meet demands for modern petrochemical industry.On the other hand,condensed polynuclear aromatic resin of moderate condensation degree(B-COPNA)is a widely used carbon material due to its superb processability,the production of which is,however,seriously limited by the high cost of raw materials.Under such context,an interesting strategy was proposed in this study for producing B-COPNA resin using crosslinked light fractions of ethylene tar(ETLF,boiling point<260℃)facilitated by molecular simulation.1,4-Benzenedimethanol(PXG)was first selected as the crosslinking agent according to the findings of molecular simulation.The effects of operating conditions,including reactions temperature,crosslinking agent,and catalyst content on the softening point and yield of B-COPNA resin products were then investigated to optimize the process.The reaction mechanism of resin production was studied by analyzing the molecular structure and transition state of ETLF and crosslinking agents.It was shown that PXG exhibited a superior capacity of withdrawing electrons and a higher electrophilic reactivity than other crosslinking agents.In addition to the highest yield and greatest heat properties,PXG-prepared resin contained the most condensed aromatics.The corresponding optimized conditions of resin preparation were 180℃,1:1.9(PXG:ETLF),and 3%(mass)of catalyst content with a resin yield of 78.57%.It was the electrophilic substitution reaction that occurred between the ETLF and crosslinking agent molecules that were responsible for the resin formation,according to the experimental characterization and molecular simulation.Hence,it was confirmed that the proposed strategy and demonstrated process can achieve a clean and high value-added utilization of ETLF via B-COPNA resin preparation,bringing huge economic value to the current petrochemical industry.

Molecular simulation study on the evolution process of hydrate residual structures into hydrate

The clathrate hydrate memory effect is a fascinating phenomenon with potential applications in carbon capture,utilization and storage(CCUS),gas separation,and gas storage as it can accelerate the secondary formation of clathrate hydrate.However,the underlying mechanism of this effect remains unclear.To gain a better understanding of the mechanism,we conducted molecular dynamic simulations to simulate the initial formation and reformation processes of methane hydrate.In this work,we showed the evolution process of hydrate residual structures into hydrate cages.The simulation results indicate that the residual structures are closely related to the existence of hydrate memory effect,and the higher the contribution of hydrate dissociated water to the hydrate nucleation process,the faster the hydrate nucleation.After hydrate dissociation,the locally ordered structures still exist after hydrate dissociation and can promote the formation of cluster structures,thus accelerating hydrate nucleation.Additionally,the nucleation process of hydrate and the formation process of clusters are inseparable.The size of clusters composed of cup-cage structures is critical for hydrate nucleation.The residence time at high temperature after hydrate decomposition will affect the strength of the hydrate memory effect.Our simulation results provide microscopic insights into the occurrence of the hydrate memory effect and shed light on the hydrate reformation process at the molecular scale.

Recent advances in protein conformation sampling by combining machine learning with molecular simulation

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

Effects of Different Concentrations of Sulfate Ions on Carbonate Crude Oil Desorption:Experimental Analysis and Molecular Simulation

Low salinity water containing sulfate ions can significantly alter the surface wettability of carbonate rocks.Nevertheless,the impact of sulfate concentration on the desorption of oil film on the surface of carbonate rock is still unknown.This study examines the variations in the wettability of the surface of carbonate rocks in solutions containing varying amounts of sodium sulfate and pure water.The problem is addressed in the framework of molecular dynamics simulation(Material Studio software)and experiments.The experiment’s findings demonstrate that sodium sulfate can increase the rate at which oil moisture is turned into water moisture.The final contact angle is smaller than that of pure water.The results of the simulations show that many water molecules travel down the water channel under the influence of several powerful forces,including the electrostatic force,the van der Waals force and hydrogen bond,crowding out the oil molecules on the calcite’s surface and causing the oil film to separate.The relative concentration curve of water and oil molecules indicates that the separation rate of the oil film on the surface of calcite increases with the number of sulfate ions.

Molecular simulation study of the stabilization process of NEPE propellant

In this reported study, the density functional theory(DFT) was used at the(U)B3LYP/6-311G(d,p) level to investigate the stabilization process of the nitrate ester plasticized polyether propellant(NEPE). Molecular simulations were conducted of the reaction that generates NO_(2), the autocatalytic and aging reaction triggered by the NO_(2), and the nitrogen dioxide absorption reaction of the stabilizers during the propellent stabilization process. These simulations were derived using the transition-state theory(TST)and variational transition-state theory(VTST). The simulation results suggested that the stabilization of the NEPE propellant consisted of three stages. First, heat and NO_(2) were generated during the denitrification reaction of nitroglycerine(NG) and 1,2,4-butanetriol trinitrate(BTTN) in the NEPE propellant.Second, nitroso products were generated by the reactions of N-Methyl-4-nitroaniline(MNA) and 2-nitrodiphenylamine(2NDPA) with NO_(2). Third, the stabilizers were exhausted and the autocatalytic reaction of NG and BTTN and the aging reaction of polyethylene glycol(PEG) were triggered by the heat and NO_(2)generated in the first stage. By comparing the energy barriers of the various reactions, it was found that the NO_(2)generated from the denitrification reaction significantly reduced the reaction energy barrier to 105.56-126.32 kJ/mol, also increased the reaction rate constant, and decreased the thermal stability and energetic properties of the NEPE propellant. In addition, the NO_(2)also weakened the mechanical properties of the NEPE propellant by attacking the-CH2groups and the O atoms in the PEG molecular chain. The energy barriers of the reactions of MNA and 2NDPA with NO_(2)(94.61-133.61 k J/mol) were lower than those of the autocatalytic and decomposition reactions of NG, BTTN, and the aging reactions of PEG(160.30-279.46 kJ/mol). This indicated that, by eliminating NO_(2), the stabilizer in the NEPE propellant can effectively prevent NO_(2)from reacting with the NG, BTTN, and PEG in the NEPE propellant. Consequently, this would help maintain the energy and mechanical properties of the NEPE propellant, thereby improving its thermal stability.

Dissolution behavior,thermodynamic and kinetic analysis of malonamide by experimental measurement and molecular simulation

In this study,the solid structure,dissolution behavior,thermodynamic properties and nucleation kinetics of malonamide were explored.Firstly,the Hirshfeld surface analysis and molecular electrostatic potential surface were plotted to reveal the percentage contribution of various intermolecular contacts and location of the strongest hydrogen bond.Next,the solubility of malonamide in 12 solvents was determined by dynamic method at temperatures from 278.15 K to 318.15 K.Four thermodynamic models were applied to analyze solubility results.In addition,the thermodynamic properties were calculated to further analyze and discuss the dissolution behavior of malonamide.Moreover,the physicochemical properties of solvents were explored to express the solvent effects.The results illustrate“like dissolves like”,“mass transfer”and“solvent–solute interaction”rules play the synergistic effects on the dissolution process.The molecular dynamic simulation,including radial distribution function analysis and solvent free energy,was used to further explain the dissolution behavior.At last,the nucleation rate and effective interfacial energy in methanol solvent was measured and calculated to reveal the nucleation behaviour.

Molecular Simulation of Methane Adsorption in Different Micro Porous Activated Carbons at Different Temperatures

We employed the previously developed micro porous activated carbon models of different pore sizes ranges of 9-11?,10-12?,and 13-16?that were constructed by molecular simulation method based on a random packing of platelets of carbon sheets,functionalized with oxygen containing groups,to study the adsorption behavior of methane molecules.In studying methane adsorption behavior,we used Grand Canonical Monte Carlo and Molecular Dynamics methods at different temperatures of 273.15,298.15 and303.15 K.Adsorption isotherms,isosteric heats of adsorption,adsorption energy distributions and porosity changes of the models during adsorption process were analyzed and discussed.Furthermore,radial distribution Functions,relative distribution and diffusion coefficients of methane molecules in activated carbon models at different temperatures were studied.After the analysis,the main results indicated that large micro pores activated carbons were favorable for storing methane at lower temperatures and small micro pores were the most favorable for adsorbing methane molecules at higher temperatures.Interestingly,the developed model structures showed high capacities to store methane molecule at ambient temperatures and low pressure.

Molecular basis of cross-interactions between Aβ and Tau protofibrils probed by molecular simulations

Amyloid β-protein(Aβ) and Tau, two common pathogenic proteins associated with Alzheimer’s disease(AD), cross-interact, and thus co-assemble into hybrid aggregates. However, molecular mechanism of the cross-interactions remains unclear. To explore the issue, docking and molecular dynamics(MD) simulations were coupled to study the cross-interactions between Aβ pentamer and Tau pentamer. Four stable hybrid decamer conformations including double layer, single layer, block, and part-in were obtained by protein-protein docking software HADDOCK 2.2. Then, MD simulations were used to explore the molecular mechanism of cross-interactions between Aβ pentamer and Tau pentamer. The results of MD simulations showed that the part-in structure was the most stable among all the above four representative ones. The binding energy between Aβ and Tau was about-759.77 kJ·mol-1in the part-in structure. Moreover, the part-in conformation would undergo conformational transition, which would improve its hydrophobicity and make the structure more compact. This work offers a structural understanding of cross-interactions between Aβ and Tau linked to AD.

Molecular Simulations of the Effect of Hydrated Montmorillonite on the Viscosity of Polyacrylamide under Confined Shear

Our researches are based on the fact that the systems composed of polyacrylamide and montmorillonite under a kind of shear state often appear in some important practical processes like drilling well etc. The viscosity of polyacrylamide is usually the most important one among the characteristics to decide if the practical processes succeed or not. Therefore, we studied the effect of hydrated montmorillonite on the viscosities of polyacrylamide with temperature and shear rate varying under confined shear by molecular simulation method. Adopting the condition of confined shear in the research could make our simulations and the practical processes as similar as possible. First, the model of one polyacrylamide polymer chain with 20 monomers linearly linking surrounded by water molecules between two of montmorillonite layers was constructed. Then canonical ensemble （NVT） MD simulations were carried out for the built model at different temperatures and shear rates. From the gained simulation results, we calculated the polymer＇s structural property-radius of gyration, which was directly related to the viscosity property of polyacrylamide polymer. It was found that the viscosity of the polyacrylamide polymer between hydrated clay layers decreased with the temperature increasing from 298 to 343 K under the condition of confined shear. The variation trend of viscosity from simulation results was also confirmed by our experiments. Besides, the viscosity of the polyacrylamide between hydrated clay layers decreased with the shear rate increasing within the range of higher shear rates.

Molecular simulations of charged complex fluids: A review

Molecular simulation plays an increasingly important role in studying the properties of complex fluid systems containing charges,such as ions,piezoelectric materials,ionic liquids,ionic surfactants,polyelectrolytes,zwitterionic materials,nucleic acids,proteins,biomembranes and etc.,where the electrostatic interactions are of special significance.Several methods have been available for treating the electrostatic interactions in explicit and implicit solvent models.Accurate and efficient treatment of such interactions has therefore always been one of the most challenging issues in classical molecular dynamics simulations due to their inhomogeneity and long-range characteristics.Currently,two major challenges remain in the application field of electrostatic interactions in molecular simulations;(i)improving the representation of electrostatic interactions while reducing the computational costs in molecular simulations;(ii)revealing the role of electrostatic interactions in regulating the specific properties of complex fluids.In this review,the calculation methods of electrostatic interactions,including basic principles,applicable conditions,advantages and disadvantages are summarized and compared.Subsequently,the specific role of electrostatic interactions in governing the properties and behaviors of different complex fluids is emphasized and explained.Finally,challenges and perspective on the computational study of charged systems are given.

Molecular Simulation of Transesterification of Ethylene Carbonate and Methanol Catalyzed by Ionic Liquids

Four ionic liquids [BMIM]OH, [BMIM]IM, [BMIM]Br, and [BMIM]PF6 were synthesized and characterized by infrared spectroscopy. Then the effects of ionic liquids(ILs), cocatalysts, and reaction temperature on the catalytic performance for transesterification of ethylene carbonate and methanol were investigated with orthogonal experiments. The influence of cations and anions of ILs on catalytic activity was revealed by the density functional theory(DFT). The reaction mechanism was proposed based on the experimental results and DFT. The results demonstrated that the optimal catalyst was [Bmim]PF6/CaO, which exhibited the advantages of high activity, excellent stability, and easy recycling. Under the optimized conditions covering a catalytic temperature of 130 °C, an ionic liquid/cocatalyst mass ratio of 5:1, and a catalyst dosage of 4.0%, the conversion rate could reach 65.23% with a dimethyl carbonate selectivity of 98.95%. No significant loss of catalyst activity was detected after 7 recycle times.

Molecular simulation studies on natural gas hydrates nucleation and growth:A review

How natural gas hydrates nucleate and grow is a crucial scientific question.The research on it will help solve practical problems encountered in hydrate accumulation,development,and utilization of hydrate related technology.Due to its limitations on both spatial and temporal dimensions,experiment cannot fully explain this issue on a micro-scale.With the development of computer technology,molecular simulation has been widely used in the study of hydrate formation because it can observe the nucleation and growth process of hydrates at the molecular level.This review will assess the recent progresses in molecular dynamics simulation of hydrate nucleation and growth,as well as the enlightening significance of these developments in hydrate applications.At the same time,combined with the problems encountered in recent hydrate trial mining and applications,some potential directions for molecular simulation in the research of hydrate nucleation and growth are proposed,and the future of molecular simulation research on hydrate nucleation and growth is prospected.

MOLECULAR SIMULATION TECHNIQUE ON POLYMERIC MATERIALS

Molecular simulation, or molecular modeling, is recently fast emergingas an important technique of both the research in polymer science and thedesign of polymeric materials. Not only single chain behavior but also bulkproperties of amorphous, crystalline, and liquid crystalline poly-mers can be investigated by this technique. In other fields of science such

Displacement of shale gas confined in illite shale by flue gas: A molecular simulation study

The shale gas is an unconventional supplementary energy to traditional fossil energy,and is stored in layered rocks with low permeability and porosity,which leads to the difficulty for exploration of shale gas.Therefore,using CO_(2) gas to displace shale gas has become an important topic.In this work,we use molecular simulations to study the displacement of shale gas by flue gas rather than CO_(2),in which flue gas is modeled as a binary mixture of CO_(2) and N_(2) and the shale model is represented by inorganic Illite and organic methylnaphthalene.CH_(4) is used as a shale gas model.Compared to the pure CO_(2),flue gas is easily available and the cost of displacement by flue gas would become lower.Results indicate that the pore size of shale is an important factor in the process of displacing shale gas and simultaneously sequestrating flue gas,while the flue gas N_(2)-CO_(2) ratio shows a small effect on the process of CH_(4) displacement,because the high partial pressure of flue gas is the main driving force for displacement of shale gas.Moreover,the geological condition also has a significant effect on the process of CH_(4) displacement by flue gas.Therefore,we suggest that the burial depth of 1 km is suitable operation condition for shale gas displacement.It is expected that this work provides a useful guidance for exploitation of shale gas and sequestration of greenhouse gas.

Molecular simulation studies of hydrocarbon and carbon dioxide adsorption on coal

Sorption isotherms of hydrocarbon and carbon dioxide （CO2） provide crucial information for designing processes to sequester CO2 and recover natural gas from unmineable coal beds. Methane （CH4）, ethane （C2H6）, and CO2 adsorption isotherms on dry coal and the temperature effect on their maximum sorption capacity have been studied by performing combined Monte Carlo （MC） and molecular dynamics （MD） simulations at temperatures of 308 and 370 K （35 and 97 ~C） and at pressures up to 10 MPa. Simulation results demonstrate that absolute sorption （expressed as a mass basis） divided by bulk gas density has negligible temperature effect on CH4, C2H6, and CO2 sorption on dry coal when pressure is over 6 MPa. CO2 is more closely packed due to stronger interaction with coal and the stronger interaction between CO2 mole- cules compared, respectively, with the interactions between hydrocarbons and coal and between hydrocarbons. The results of this work suggest that the ＂a＂ constant （pro- portional to TcPc） in the Peng-Robinson equation of state is an important factor affecting the sorption behavior of hydrocarbons. CO2 injection pressures of lower than 8 MPa may be desirable for CH4 recovery and CO2 sequestration. This study provides a quantitative under- standing of the effects of temperature on coal sorptioncapacity for CH4, C2H6, and CO2 from a microscopic perspective.

Diffusion and Adsorption of Tetralin Hydrocracking Reaction on Different Zeolites by Molecular Simulation

Three different zeolite catalysts with different pore sizes(MFI-type,BEA-type,and FAU-type zeolites)have been prepared.The influence of different zeolite catalysts on reactivity and product shape selectivity of tetralin is investigated.Clear differences are observed in the reactivity of tetralin and distribution of products achieved by different catalysts.The diffusion and adsorption behavior of the reactant tetralin and its intermediates,n-butylbenzene and 1-methylindane under the reaction conditions are simulated using molecular simulation methods.Upon combining simulation results and experimental observations,it is shown that the difference in diffusion coefficient and competitive adsorption capacity can explain the reactivity of tetralin and the selectivity of products.The steric hindrance of the MFI-type zeolite mainly limits the key step of ring opening of tetralin,leading to lower selectivity of ring-opening products.n-Butylbenzene molecules can diffuse sufficiently fast in the large pores of FAU-type zeolite and the weak adsorption capacity of n-butylbenzene leads to its insufficient cracking.In addition,it also explains the reason that the BEA-type zeolite has the best BTX selectivity,because it can satisfy both good ring-opening activity and sufficient butylbenzene cracking depth.

The application of molecular simulation in ash chemistry of coal

One of the crucial issues in modern ash chemistry is the realization of efficient and clean coal conversion.Industrially,large-scale coal gasification technology is well known as the foundation to improve the atom economy.In practice,the coal ash fusibility is a critical factor to determine steady operation standards of the gasifier,which is also the significant criterion to coal species selection for gasification.Since coal behaviors are resultant from various evolutions in different scales,the multi-scale understanding of the ash chemistry is of significance to guide the fusibility adjustment for coal gasification.Considering important roles of molecular simulation in exploring ash chemistry,this paper reviews the recent studies and developments on modeling of molecular systems for fusibility related ash chemistry for the first time.The discussions are emphasized on those performed by quantum mechanics and molecular mechanics,the two major simulation methods for microscopic systems,which may provide various insights into fusibility mechanism.This review article is expected to present comprehensive information for recent molecular simulations of coal chemistry so that new clues to find strategies controlling the ash fusion behavior can be obtained.

Molecular Simulations in Tin Droplet Spreading on Different Surface of Copper Plate

Molecular simulations using MEAM(Modified Embedded Atom Method) potentials have been applied to research the interfacial properties of the different(hkl) Cu substrate in the soldering.In the simulation,the surface energies and the process of Sn spreading on the different(hkl) copper plate surface were simulated,and the results show that the different(hkl) plane substrates have few effects to the soldering spreading process,the solid-liquid interfacial energy is still the dominant ingredient practically in the wetting process.

Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Here,we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations.The results demonstrated strong salt concentration dependence of the diffusion mechanisms.At low salt concentrations,the one-dimensional diffusion with rotational coupling is the dominant mechanism.At high salt concentrations,the diffusion by three-dimensional mechanism becomes more probable.At wide range of salt concentrations,the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature.This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions.In addition,we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA,which increases the exposure extent of the sites for the binding of other repair proteins.

Molecular Simulation study of Alkyl Monolayers on Si(III) Surface

The structure of eight-carbon monolayers on the H-terminated Si(III) surface was investigated by molecular simulation method. The best substitution percent 50% for octene or octyne-derived monolayer can be obtained using molecular mechanics calculation. And the densely packed, well-ordered monolayer on Si(III) surface can be shown through energy minimization in the suitable-size simulation cell.