{"title":"小沸石窄孔内分子扩散的过渡态理论模拟","authors":"Yali Feng, Fang Zhao, Xiaofeng Yang","doi":"10.1007/s00894-024-06273-9","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard–Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF<sub>4</sub>, CH<sub>4</sub>, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model. The results show that the three molecules CF<sub>4</sub>, CH<sub>4</sub>, and Ar meet the predictions of the model, while the Ne molecule does not. At the same time, by analyzing the trend of the diffusion coefficient with the load, we further explain the reason for this difference. In short, this study reveals the diffusion mechanism of molecules in the narrow pores of Brewsterite zeolite. This provides new ideas for optimizing the performance of zeolite materials and applying them to catalysis and separation processes.</p><h3>Methods</h3><p>The simulations were carried out with Refson’s MOLDY code in the NVT ensemble. The short-range Lennard–Jones forces were calculated with the link cell method. A Nose–Hoover thermostat was used to realize the thermal equilibrium state of the samples. In the simulation, the time steps were 1 fs and the total simulation time was 51 ns. The initial temperature was set to 300 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Transition state theoretical modelling of molecular diffusion within the narrow pores of brewsterite zeolite\",\"authors\":\"Yali Feng, Fang Zhao, Xiaofeng Yang\",\"doi\":\"10.1007/s00894-024-06273-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Context</h3><p>Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard–Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF<sub>4</sub>, CH<sub>4</sub>, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model. The results show that the three molecules CF<sub>4</sub>, CH<sub>4</sub>, and Ar meet the predictions of the model, while the Ne molecule does not. At the same time, by analyzing the trend of the diffusion coefficient with the load, we further explain the reason for this difference. In short, this study reveals the diffusion mechanism of molecules in the narrow pores of Brewsterite zeolite. This provides new ideas for optimizing the performance of zeolite materials and applying them to catalysis and separation processes.</p><h3>Methods</h3><p>The simulations were carried out with Refson’s MOLDY code in the NVT ensemble. The short-range Lennard–Jones forces were calculated with the link cell method. A Nose–Hoover thermostat was used to realize the thermal equilibrium state of the samples. In the simulation, the time steps were 1 fs and the total simulation time was 51 ns. The initial temperature was set to 300 K.</p></div>\",\"PeriodicalId\":651,\"journal\":{\"name\":\"Journal of Molecular Modeling\",\"volume\":\"31 2\",\"pages\":\"\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2025-01-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Molecular Modeling\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s00894-024-06273-9\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Modeling","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s00894-024-06273-9","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Transition state theoretical modelling of molecular diffusion within the narrow pores of brewsterite zeolite
Context
Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard–Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF4, CH4, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model. The results show that the three molecules CF4, CH4, and Ar meet the predictions of the model, while the Ne molecule does not. At the same time, by analyzing the trend of the diffusion coefficient with the load, we further explain the reason for this difference. In short, this study reveals the diffusion mechanism of molecules in the narrow pores of Brewsterite zeolite. This provides new ideas for optimizing the performance of zeolite materials and applying them to catalysis and separation processes.
Methods
The simulations were carried out with Refson’s MOLDY code in the NVT ensemble. The short-range Lennard–Jones forces were calculated with the link cell method. A Nose–Hoover thermostat was used to realize the thermal equilibrium state of the samples. In the simulation, the time steps were 1 fs and the total simulation time was 51 ns. The initial temperature was set to 300 K.
期刊介绍:
The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling.
Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry.
Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.