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...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.展开更多
Silicon-containing aryl acetylene resin(PSA)is a new type of high-temperature resistant resin with excellent oxidation resistance,whereas antioxidant reaction mechanism of PSA resin under ultra-high temperatures still...Silicon-containing aryl acetylene resin(PSA)is a new type of high-temperature resistant resin with excellent oxidation resistance,whereas antioxidant reaction mechanism of PSA resin under ultra-high temperatures still remains unclear.Herein,the oxidation behavior and mechanisms of PSA resin are systematically investigated combining kinetic analysis and Reax FF molecular dynamics(MD)simulations.Thermogravimetric analysis indicates that the oxidation process of PSA resin undergoes two main steps:oxidative mass gain and oxidative degradation.The distributed activation energy model(DAEM)is employed for describing oxidation processes and the best-fit one is obtained using genetic algorithms and differential evolution.DAEM model demonstrates that the oxidative weight gain stage is dominated by two virtual reactants and the oxidative degradation stage consists of three virtual reactants.Correspondingly,the observation of MD reaction pathways indicates that oxygen oxidation of unsaturated structures occurs in the initial stage,which results in the formation of PSA resin oxides.Furthermore,cracked pieces react with O_(2)to generate CO and other chemicals in the second step.The resin matrix's great antioxidation resilience is illustrated by the formation of SiO_(2).The analysis based on MD simulations exhibits an efficient computational proof with the experiments and DAEM methods.Based on the results,a two-stage reaction mechanism is proposed,which provides important theoretical support for the subsequent study of the oxidation behavior of silica-based resins.展开更多
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 simu...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.展开更多
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 plat...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.展开更多
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 ...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.展开更多
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-interact...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.展开更多
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,zw...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.展开更多
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 tetral...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.展开更多
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 catalyti...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.展开更多
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 eco...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.展开更多
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.Therefo...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.展开更多
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.Her...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.展开更多
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 tech...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.展开更多
Chain initiation reactions in the oxidation process of lubricant base stock molecules were studied by molecular simulations.Two ways to initiate lubricant oxidation were investigated.They included the dissociation of ...Chain initiation reactions in the oxidation process of lubricant base stock molecules were studied by molecular simulations.Two ways to initiate lubricant oxidation were investigated.They included the dissociation of chemical bonds in base stock molecules and the reaction between base stock molecules and oxygen(O_(2)),respectively.Reaction activation energy of above methods was calculated.The results show that C‒C bonds are more likely to break than C‒H bonds to generate free radicals by the pyrolysis of chemical bonds.The C‒C bonds with tertiary carbon atoms are preferential positions to crack.However,their bond dissociation energy is above 360 kJ/mol,which is difficult to occur under lubricant working conditions.The chain initiation is more likely to occur by the way that O_(2) attacks the two atoms in C‒H bonds at the same time,and is then embedded into the C‒H bond to produce hydrocarbon peroxides.And then,the O‒O bond is cracked to form hydroxyl radicals and alkoxy radicals.The C‒H bonds with tertiary carbon atoms are preferential reaction sites,the reaction activation energy of which is about 190.11 kJ/mol.展开更多
The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an eg...The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an egg-white derived peptide,LAPYK,using the amino acids with different properties to produce the LAPYK-modified peptides.The ACE inhibitory activities of the modified peptides were determined to explore the structural requirements of ACE inhibitory peptides(ACEIPs).Molecular simulation and isothermal titration calorimetry analysis were used to investigate interactions between the peptides and ACE.We found that hydrophobicity and the amino acids with ring structures were benefi cial for the ACE inhibitory activities of the peptides.The results of the molecular mechanics poisson boltzmann surface area(MMPBSA)binding free energy calculations indicated that the polar solvation free energy(ΔG_(polar))of the charged peptides(LAPYK,LAPYE)were unfavorable for binding to ACE.On the other hand,the results of isothermal titration calorimetry analyses suggested that the enthalpy-driven ACE-peptide interactions were more favorable than the entropy-driven ACE-peptide interaction counterparts.展开更多
Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviou...Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviour of different polar fluid molecules(i.e., water, methanol and decane) confined in monolayer Mo S2 nanoslits. The pore width effect(i.e., 1.2, 1.6 and 2.0 nm) was also evaluated. Results revealed that decane molecules exhibited good lubricating performance compared to the other two kinds of molecules. The friction coefficient followed the order of decane b methanol b water, and decreased evidently as the slit width increased, except for decane. Analysis of the spatial distribution and mobility of different confined fluid molecules showed that a solid-like layer was formed near the slit wall. This phenomenon led to the extra low friction coefficient of confined decane molecules.展开更多
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 bul...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展开更多
Graphyne is expected to be a new-class of highly-efficient sieving membranes due to its controllable uniform pore structure and ultrathin single-atom thickness. Herein, we computationally investigate the permeation pe...Graphyne is expected to be a new-class of highly-efficient sieving membranes due to its controllable uniform pore structure and ultrathin single-atom thickness. Herein, we computationally investigate the permeation performance of liquid ethanol–water mixtures across polyporous two-dimensional γ-graphyne sheets. It was found that, in the mixture, ethanol with larger molecular diameter permeates faster through the graphyne pores than water. The simulations demonstrate that pristine graphynes could act as highly-efficient ethanol-permselective membranes for separation of ethanol–water mixtures, with ethanol permeability remarkably higher than conventional membranes. This separation mechanism is distinctly different from the molecular-size dependent sieving process. The stronger hydrophobic interfacial affinity between graphyne and ethanol makes ethanol molecules preferentially adsorb on graphyne surface and selectively penetrate through graphyne pores. This penetration mechanism provides new understanding of molecular transport through atomically thick two-dimensional nanoporous membranes and this work is expected to be valuable in the potential development of highly-efficient membranes for liquid-phase mixture separation.展开更多
Using molecular dynamics simulations based on classical mechanic method, the mechanism of competitive adsorption between gasoline detergent and deposit on Fe(110) surface was investigated. The representative simulatio...Using molecular dynamics simulations based on classical mechanic method, the mechanism of competitive adsorption between gasoline detergent and deposit on Fe(110) surface was investigated. The representative simulation relating to the deposit molecule and the gasoline detergent molecule with high market share were selected as the model compound. It was found that when the detergent and deposit molecules exist at the same time, the detergent molecules would compete with the deposit molecules to reduce the adsorption of the deposit on Fe(110) so as to protect the metal surface. In addition, the ESP distribution is further confirmed that the detergent molecule has higher adsorption ability than the deposit molecule with the DFT theory. The essence of competitive adsorption is further revealed in detail, which is very important for the development of new type high-efficiency detergent additives.展开更多
The exhaust gases, including SO_2,NH_3, H_2S, NO_2, NO, and CO, are principal air pollutants due to their severe harms to the ecological environment.Zeolites have been considered as good absorbent candidates to captur...The exhaust gases, including SO_2,NH_3, H_2S, NO_2, NO, and CO, are principal air pollutants due to their severe harms to the ecological environment.Zeolites have been considered as good absorbent candidates to capture the six exhaust gases.In this work, we performed grand canonical ensemble Monte Carlo(GCMC) simulations to examine the capability of 95 kinds of all-silica zeolites in the removal of the six toxic gases, and to predict the adsorption isotherms of the six gases on all the zeolites.The simulation results showed that, H_2S, NO, NO_2, CO and NH_3 are well-captured by zeolite structures with accessible surface area of 1600–1800 m^2·g^(-1) and pore diameter of 0.6–0.7 nm, such as AFY and PAU, while SO_2 is well-adsorbed by zeolites containing larger accessible surface area(1700–2700 m^2·g^(-1)) and pore diameter(0.7–1.4 nm) at room temperature and an atmospheric pressure.However, at saturated adsorption, zeolites RWY, IRR, JSR, TSC, and ITT are found to exhibit better abilities to capture these gases.Our study provides useful computational insights in choosing and designing zeolite structures with high performance to remove toxic gases for air purification, thereby facilitating the development and application of exhaust gas-processing technology in green industry.展开更多
基金Project supported by the National Key Research and Development Program of China(Grant No.2023YFF1204402)the National Natural Science Foundation of China(Grant Nos.12074079 and 12374208)+1 种基金the Natural Science Foundation of Shanghai(Grant No.22ZR1406800)the China Postdoctoral Science Foundation(Grant No.2022M720815).
文摘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.
基金financially supported by National Natural Science Foundation of China(22008073,22078100,21878091)Shanghai Sailing Program(20YF1410600)。
文摘Silicon-containing aryl acetylene resin(PSA)is a new type of high-temperature resistant resin with excellent oxidation resistance,whereas antioxidant reaction mechanism of PSA resin under ultra-high temperatures still remains unclear.Herein,the oxidation behavior and mechanisms of PSA resin are systematically investigated combining kinetic analysis and Reax FF molecular dynamics(MD)simulations.Thermogravimetric analysis indicates that the oxidation process of PSA resin undergoes two main steps:oxidative mass gain and oxidative degradation.The distributed activation energy model(DAEM)is employed for describing oxidation processes and the best-fit one is obtained using genetic algorithms and differential evolution.DAEM model demonstrates that the oxidative weight gain stage is dominated by two virtual reactants and the oxidative degradation stage consists of three virtual reactants.Correspondingly,the observation of MD reaction pathways indicates that oxygen oxidation of unsaturated structures occurs in the initial stage,which results in the formation of PSA resin oxides.Furthermore,cracked pieces react with O_(2)to generate CO and other chemicals in the second step.The resin matrix's great antioxidation resilience is illustrated by the formation of SiO_(2).The analysis based on MD simulations exhibits an efficient computational proof with the experiments and DAEM methods.Based on the results,a two-stage reaction mechanism is proposed,which provides important theoretical support for the subsequent study of the oxidation behavior of silica-based resins.
基金the support provided by the School of Physics and Optoelectronic Engineering of Ludong University。
文摘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.
基金Funded by Natural Science Foundation of Shandong Province(No.ZR201702150018)China Postdoctoral Science Foundation Funding Scheme(No.2018M632747)+1 种基金the Fundamental Research Funds for the Central Universities(Nos.18CX02143A,17CX05017)New Faculty Start-up Funding from China University of Petroleum(No.YJ20170019).
文摘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.
基金financially supported by the Innovative Group Project of China (21621004)Demonstration Project of Integration of Science, Education and Industry in Qilu University of Technology (2020KJC-ZD09)
文摘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.
基金funded by the National Natural Science Foundation of China (21908165 and 21878234)Regional Innovation System Project (21ZYQCSY00050)。
文摘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.
基金supported by the National Natural Science Foundation of China(21776093,21376089,41976203,21506178,21908066)。
文摘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.
文摘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.
基金supported by the National Natural Science Foundation of China(NSFC 21706163)the Foundation from Liaoning Province Department of Education(LQGD2017020)
文摘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.
基金supported by National Nataral Science Foundation of China-Deutsche Forschungsgemeinschaft(Grant number21761132032)National Key R&D Program of China(2017YFB0304300&2017YFB0304303)National Key R&D Program of China(2017YFB0304000)。
文摘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.
文摘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.
基金supported by the National Natural Science Foundation of China(Grant Nos.11974173 and 11774158)the HPC center of Nanjing University。
文摘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.
基金jointly supported by Pilot National Laboratory for Marine Science and Technology (Qingdao)the IGGCAS (IGGCAS-201903 and SZJJ201901)the Chinese Academy of Sciences (ZDBSLY-DQC003)。
文摘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.
基金The authors are grateful for the calculation support of the Key Laboratory of Molecular Oil Refining of Research Institute of Petroleum Processing in SINOPECthe financial supports from the University of Science and Technology Liaoning Talent Project Grants(No.601010314)+1 种基金the Liaoning Province Doctoral Research Start-up Fund Plan Project(No.2021-BS-243)the University of Science and Technology Liaoning Young Teachers Fund(2019QN08).
文摘Chain initiation reactions in the oxidation process of lubricant base stock molecules were studied by molecular simulations.Two ways to initiate lubricant oxidation were investigated.They included the dissociation of chemical bonds in base stock molecules and the reaction between base stock molecules and oxygen(O_(2)),respectively.Reaction activation energy of above methods was calculated.The results show that C‒C bonds are more likely to break than C‒H bonds to generate free radicals by the pyrolysis of chemical bonds.The C‒C bonds with tertiary carbon atoms are preferential positions to crack.However,their bond dissociation energy is above 360 kJ/mol,which is difficult to occur under lubricant working conditions.The chain initiation is more likely to occur by the way that O_(2) attacks the two atoms in C‒H bonds at the same time,and is then embedded into the C‒H bond to produce hydrocarbon peroxides.And then,the O‒O bond is cracked to form hydroxyl radicals and alkoxy radicals.The C‒H bonds with tertiary carbon atoms are preferential reaction sites,the reaction activation energy of which is about 190.11 kJ/mol.
基金funded by the National Natural Science Foundation of China(31972096)Jilin Province Science and Technology Youth Talent Support Project(QT202021)Interdisciplinary Integration and Innovation Project of JLU(JLUXKJC2021QZ11)。
文摘The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an egg-white derived peptide,LAPYK,using the amino acids with different properties to produce the LAPYK-modified peptides.The ACE inhibitory activities of the modified peptides were determined to explore the structural requirements of ACE inhibitory peptides(ACEIPs).Molecular simulation and isothermal titration calorimetry analysis were used to investigate interactions between the peptides and ACE.We found that hydrophobicity and the amino acids with ring structures were benefi cial for the ACE inhibitory activities of the peptides.The results of the molecular mechanics poisson boltzmann surface area(MMPBSA)binding free energy calculations indicated that the polar solvation free energy(ΔG_(polar))of the charged peptides(LAPYK,LAPYE)were unfavorable for binding to ACE.On the other hand,the results of isothermal titration calorimetry analyses suggested that the enthalpy-driven ACE-peptide interactions were more favorable than the entropy-driven ACE-peptide interaction counterparts.
基金Supported by the National NaturalScience Foundation of China(21576130,21490584)Project of Jiangsu Natural Science Foundation of China(BK20171464)+1 种基金Qing Lan ProjectJiangsu Overseas Visiting Scholar Program for University Prominent Young&Middleaged Teachers and Presidents
文摘Monolayer molybdenum disulfide(MoS2) is a novel two-dimensional material that exhibits potential application in lubrication technology. In this work, molecular dynamics was used to investigate the lubrication behaviour of different polar fluid molecules(i.e., water, methanol and decane) confined in monolayer Mo S2 nanoslits. The pore width effect(i.e., 1.2, 1.6 and 2.0 nm) was also evaluated. Results revealed that decane molecules exhibited good lubricating performance compared to the other two kinds of molecules. The friction coefficient followed the order of decane b methanol b water, and decreased evidently as the slit width increased, except for decane. Analysis of the spatial distribution and mobility of different confined fluid molecules showed that a solid-like layer was formed near the slit wall. This phenomenon led to the extra low friction coefficient of confined decane molecules.
文摘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
基金Supported by the National Natural Science Foundation of China(21676136 and 21376116)A PAPD Project of Jiangsu Higher Education Institution
文摘Graphyne is expected to be a new-class of highly-efficient sieving membranes due to its controllable uniform pore structure and ultrathin single-atom thickness. Herein, we computationally investigate the permeation performance of liquid ethanol–water mixtures across polyporous two-dimensional γ-graphyne sheets. It was found that, in the mixture, ethanol with larger molecular diameter permeates faster through the graphyne pores than water. The simulations demonstrate that pristine graphynes could act as highly-efficient ethanol-permselective membranes for separation of ethanol–water mixtures, with ethanol permeability remarkably higher than conventional membranes. This separation mechanism is distinctly different from the molecular-size dependent sieving process. The stronger hydrophobic interfacial affinity between graphyne and ethanol makes ethanol molecules preferentially adsorb on graphyne surface and selectively penetrate through graphyne pores. This penetration mechanism provides new understanding of molecular transport through atomically thick two-dimensional nanoporous membranes and this work is expected to be valuable in the potential development of highly-efficient membranes for liquid-phase mixture separation.
文摘Using molecular dynamics simulations based on classical mechanic method, the mechanism of competitive adsorption between gasoline detergent and deposit on Fe(110) surface was investigated. The representative simulation relating to the deposit molecule and the gasoline detergent molecule with high market share were selected as the model compound. It was found that when the detergent and deposit molecules exist at the same time, the detergent molecules would compete with the deposit molecules to reduce the adsorption of the deposit on Fe(110) so as to protect the metal surface. In addition, the ESP distribution is further confirmed that the detergent molecule has higher adsorption ability than the deposit molecule with the DFT theory. The essence of competitive adsorption is further revealed in detail, which is very important for the development of new type high-efficiency detergent additives.
基金Supported by the National Natural Science Foundation of China(21406172)the Natural Science Foundation of Hubei Province,China(2016CFB388 and 2013CFA091)
文摘The exhaust gases, including SO_2,NH_3, H_2S, NO_2, NO, and CO, are principal air pollutants due to their severe harms to the ecological environment.Zeolites have been considered as good absorbent candidates to capture the six exhaust gases.In this work, we performed grand canonical ensemble Monte Carlo(GCMC) simulations to examine the capability of 95 kinds of all-silica zeolites in the removal of the six toxic gases, and to predict the adsorption isotherms of the six gases on all the zeolites.The simulation results showed that, H_2S, NO, NO_2, CO and NH_3 are well-captured by zeolite structures with accessible surface area of 1600–1800 m^2·g^(-1) and pore diameter of 0.6–0.7 nm, such as AFY and PAU, while SO_2 is well-adsorbed by zeolites containing larger accessible surface area(1700–2700 m^2·g^(-1)) and pore diameter(0.7–1.4 nm) at room temperature and an atmospheric pressure.However, at saturated adsorption, zeolites RWY, IRR, JSR, TSC, and ITT are found to exhibit better abilities to capture these gases.Our study provides useful computational insights in choosing and designing zeolite structures with high performance to remove toxic gases for air purification, thereby facilitating the development and application of exhaust gas-processing technology in green industry.
