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

Chinese Journal of Chemical Engineering 2024年第5期69卷 79-91页

作者： Liwei Cheng Yunfei Li Jinlong Cui Huibo Qin Fulong Ning Bei Liu Guangjin Chen Faculty of Engineering China University of GeosciencesWuhan 430074China State Key Laboratory of Heavy Oil Processing China University of PetroleumBeijing 102249China College of Science Nanchang Institute of TechnologyNanchang 330099China School of Chemical Engineering Guangdong University of Petrochemical TechnologyMaoming 525000China National Center for International Research on Deep Earth Drilling and Resource Development China University of Geosciences(Wuhan)Wuhan 430074China

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 ***,the underlying mechanism of this effect remains *** gain a better understanding of the mechanism,we conducted molecular dynamic simulations to simulate the initial formation and reformation processes of methane *** this work,we showed the evolution process of hydrate residual structures into hydrate *** 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 *** hydrate dissociation,the locally ordered structures still exist after hydrate dissociation and can promote the formation of cluster structures,thus accelerating hydrate ***,the nucleation process of hydrate and the formation process of clusters are *** size of clusters composed of cup-cage structures is critical for hydrate *** residence time at high temperature after hydrate decomposition will affect the strength of the hydrate memory *** 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.

关键词： Memory effect molecular simulation Hydrate reformation Residual structures

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

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Chinese Physics B 2024年第3期33卷 80-87页

作者：唐一鸣杨中元姚逸飞周运谈圆王子超潘瞳熊瑞孙俊力韦广红 Department of Physics State Key Laboratory of Surface Physicsand Key Laboratory for Computational Physical Sciences (Ministry of Education)Shanghai 200438China

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational *** 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 *** review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational *** 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 ***,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein ***,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann ***,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

关键词： machine learning molecular simulation protein conformational space enhanced sampling

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

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Chinese Journal of Chemical Engineering 2024年第6期70卷 118-129页

作者： Hongyan Shen Lingrui Cui Xingguo Wei Yuanqin Zhang Lian Cen Jun Xu Fahai Cao Engineering Research Center of Large Scale Reactor East China University of Science and TechnologyShanghai 200237China

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 *** 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 *** such context,an interesting strategy was proposed in this study for producing B-COPNA resin using crosslinked light fractions of ethylene tar(ETLF,boiling pointmolecular simulation.1,4-Benzenedimethanol(PXG)was first selected as the crosslinking agent according to the findings of molecular *** 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 *** reaction mechanism of resin production was studied by analyzing the molecular structure and transition state of ETLF and crosslinking *** was shown that PXG exhibited a superior capacity of withdrawing electrons and a higher electrophilic reactivity than other crosslinking *** addition to the highest yield and greatest heat properties,PXG-prepared resin contained the most condensed *** 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 ***,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.

关键词： Ethylene tar Crosslinking COPNA resin molecular simulation Transient state

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The interaction mechanism between zein and folic acid in alkaline aqueous solutions:an experimental and molecular simulation study

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Food Quality and Safety 2024年第1期8卷 166-178页

作者： Jun Zhu Yiling Yao Yuying Liao Lala Cai Wenqi Zhang Nuo Hong Wenlin Sun Chunhua Xiong Lanying Yao School of Food Science and Biotechnology Zhejiang Gongshang UniversityHangzhouChina

Objectives:Folic acid is a vitamin that is not highly soluble in water and is sensitive to the ***,it is important to find suitable *** study aimed to exemplify the interaction of folic acid with zein in alkaline aqueous solutions and shed light on how zein can be used as a carrier for folic *** and Methods:Zein and folic acid were separately dissolved in NaOH solutions with a PH of *** solution and folic acid solution were combined in specific *** methods including multi-spectroscopy,dynamic light scattering,and electron microscopy combining with molecular dynamics simulations were used to study the interaction mechanism between zein and folic acid in alkaline aqueous ***:Fluorescence spectroscopy showed that the quenching of zein by folic acid was mainly static,and the main driving force behind this interaction was van der Waals forces and hydrogen *** formation of zein–folic acid complexes was confirmed by ultraviolet–visible spectroscopy,Fourier transform infrared spectroscopy,and circular dichroism *** results also showed that the structure of zein changed when it interacted with folic *** light scattering analysis revealed that the addition of folic acid caused proteins to *** aggregates of the complexes had an irregular shape and were large,as observed by scanning electron microscopy and transmission electron *** simulation was used to further investigate the interaction *** to these findings,the folic acid molecule interacted with zein in a shallow recess near the protein *** dominant forces at play in the zein–folic acid interaction were van der Waals forces and electrostatic forces,including hydrogen ***:The zein alkali-soluble system is very suitable for folic acid delivery.

关键词： Zein folic acid alkaline aqueous solutions molecular simulation interaction mechanism.

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Effects of Different Concentrations of Sulfate Ions on Carbonate Crude Oil Desorption:Experimental Analysis and molecular simulation

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Fluid Dynamics & Materials Processing 2024年第8期20卷 1731-1741页

作者： Nannan Liu Hengchen Qi Hui Xu Yanfeng He School of Petroleum and Natural Gas Engineering Changzhou UniversityChangzhou213164China

Low salinity water containing sulfate ions can significantly alter the surface wettability of carbonate ***,the impact of sulfate concentration on the desorption of oil film on the surface of carbonate rock is still *** study examines the variations in the wettability of the surface of carbonate rocks in solutions containing varying amounts of sodium sulfate and pure *** problem is addressed in the framework of molecular dynamics simulation(Material Studio software)and *** experiment’s findings demonstrate that sodium sulfate can increase the rate at which oil moisture is turned into water *** final contact angle is smaller than that of pure *** 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 *** 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.

关键词： Carbonate rocks wettability sulfate ions concentration molecular simulation desorption

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molecular simulation of Methane Adsorption in Different Micro Porous Activated Carbons at Different Temperatures

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Journal of Wuhan University of Technology(Materials Science) 2023年第1期38卷 1-11页

作者： Rugarabamu John Rwiza 赵东风 SONG Kunli LI Shi College of Chemical Engineering China University of Petroleum(East China)Qingdao 266580China College of Earth Sciences and Engineering The University of DodomaDodomaTanzania

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 *** studying methane adsorption behavior,we used Grand Canonical Monte Carlo and molecular Dynamics methods at different temperatures of 273.15,298.15 and303.15 *** isotherms,isosteric heats of adsorption,adsorption energy distributions and porosity changes of the models during adsorption process were analyzed and ***,radial distribution Functions,relative distribution and diffusion coefficients of methane molecules in activated carbon models at different temperatures were *** 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 ***,the developed model structures showed high capacities to store methane molecule at ambient temperatures and low pressure.

关键词： molecular simulation activated carbon methane adsorption MD GCMC

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molecular simulation study of the stabilization process of NEPE propellant

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Defence Technology（防务技术） 2023年第7期25卷 220-230页

作者： Ling-ze Kong Ke-hai Dong Ai-min Jiang Chuan-lu Yang Yan-hui Tang Yun-dong Xiao Department of Aircraft Engineering Naval Aviation UniversityYantai264001China School of Physics and Optoelectronic Engineering Ludong UniversityYantai264001China

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 ***, 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

关键词： NEPE propellant Stabilizer Stabilization process molecular simulation DFT VTST

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molecular simulation on carbon dioxide capture performance for carbons doped with various elements

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Energy Storage and Saving 2023年第2期2卷 435-441页

作者： Chen Zhang Yiheng Zhang Tingyu Su Bingzhi Yuan Xinqi Zhang Liwei Wang Yongqiang Tian Jiawang Wang Institute of Refrigeration and Cryogenics Key Laboratory of Power Machinery and Engineering of MOEShanghai Jiao Tong UniversityShanghai200240China China-UK Low Carbon College Shanghai Jiao Tong UniversityShanghai201306China College of Smart Energy Shanghai Jiao Tong UniversityShanghai200240China SPIC Xinjiang Energy Chemical CO. LTD.Urumqi830000China SPIC Xinjiang Wucaiwan Power Generation Co. LTD.ChangjiXinjiang Uygur Autonomous Region831100China

Among the different types of CO_(2)capture technologies for post-combustion,sorption CO_(2)capture technology with carbon-based sorbents have been extensively explored with the purpose of enhancing their sorption perfor-mance by doping hetero elements due to the rapid reaction kinetics and low ***,sorption capacity and selectivity for CO_(2)and N 2 on carbon-based sorbents doped with elements such as nitrogen,sulfur,phosphorus,and boron,are evaluated and compared using the grand canonical Monte Carlo(GCMC)method,the universal force field(UFF),and transferable potentials for phase equilibria(TraPPE).The sorption capacities of N-doped porous carbons(PCs)at 50℃were 76.1%,70.7%,50.6%,and 35.7%higher than those of pure PCs,S-doped PCs,P-doped PCs,and B-doped PCs,*** sorption selectivity at 50℃was approximately 14.0,nearly twice that of pure PCs or other hetero-element-doped *** N-doped PCs showed the largest sorption heat at 50℃among all the PCs,approximately 20.6 kJ·mol^(−1),which was 9.7%−25.5%higher than that of the pure PCs under post-combustion ***,with the product purity of 41.7 vol.%−75.9 vol.%for vacuum pressure swing sorption,and 53.4 vol.%−83.6 vol.%for temperature swing sorption,the latter is more suitable for post-combustion conditions than pressure-swing sorption.

关键词： Carbon dioxide capture Post-combustion Active carbon molecular simulation Grand canonical Monte Carlo(GCMC)

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A large-scale screening of metal-organic frameworks for iodine capture combining molecular simulation and machine learning

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Frontiers of Environmental Science & Engineering 2023年第12期17卷 71-84页

作者： Min Cheng Zhiyuan Zhang Shihui Wang Kexin Bi Kong-qiu Hu Zhongde Dai Yiyang Dai Chong Liu Li Zhou Xu Ji Wei-qun Shi School of Chemical Engineering Sichuan UniversityChengdu 610065China Laboratory of Nuclear Energy Chemistry Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China College of Architecture and Environment Sichuan UniversityChengdu 610065China School of Carbon Neutrality Future Technology Sichuan UniversityChengdu 610065China Department of Bioprocess Engineering Institute of BiotechnologyTechnische Universität BerlinBerlin 10623Germany

We performed large-scale molecular simulation to screen and identify metal-organic framework materials for gaseous iodine capture,as part of our ongoing effort in addressing management and handling issues of various radionuclides in the grand scheme of spent nuclear fuel *** from the computation-ready experimental(CoRE)metal-organic frameworks(MOFs)database,grand canonical Monte Carlo simulation was employed to predict the iodine uptake values of the MOFs.A ranking list of MOFs based on their iodine uptake capabilities was generated,with the Top 10 candidates identified and their respective adsorption sites ***,machine learning was used to establish structure-property relationships to correlate MOFs’various structural and chemical features with their corresponding performances in iodine capture,yielding interpretable common features and design rules for viable MOF *** research strategy and framework of the present study could aid the development of high-performing MOF adsorbents for capture and recovery of radioactive iodine,and moreover,other volatile environmentally hazardous species.

关键词： Iodine capture Metal-organic framework Large-scale screening molecular simulation Machine learning

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

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Chinese Journal of Chemical Engineering 2023年第1期53卷 260-269页

作者： Peng Yang Shengzhe Jia Yan Wang Zongqiu Li Songgu Wu Jingkang Wang Junbo Gong School of Chemical Engineering and Technology State Key Laboratory of Chemical EngineeringTianjin UniversityTianjin 300072China School of Pharmaceutical Sciences(Shandong Analysis and Testing Center) Qilu University of Technology(Shandong Academy of Sciences)Jinan 250014China

In this study,the solid structure,dissolution behavior,thermodynamic properties and nucleation kinetics of malonamide were ***,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 ***,the solubility of malonamide in 12 solvents was determined by dynamic method at temperatures from 278.15 K to 318.15 *** thermodynamic models were applied to analyze solubility *** addition,the thermodynamic properties were calculated to further analyze and discuss the dissolution behavior of ***,the physicochemical properties of solvents were explored to express the solvent *** results illustrate“like dissolves like”,“mass transfer”and“solvent–solute interaction”rules play the synergistic effects on the dissolution *** molecular dynamic simulation,including radial distribution function analysis and solvent free energy,was used to further explain the dissolution *** last,the nucleation rate and effective interfacial energy in methanol solvent was measured and calculated to reveal the nucleation behaviour.

关键词： Malonamide Solubility Thermodynamic properties molecular simulation Nucleation rate

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