Theoretical Study Of Foldaxanes Shuttling And Cyclohexanol Dehydration Based On Molecular Dynamics Simulatio

Molecular dynamics simulation refers to the simulation method of atomic trajectory obtained by using the classical Newton equation of motion.At present,it has been applied in the fields of materials,chemical industry,biology and so on.However,in molecular dynamics simulation,its time scale and force field accuracy are limited.In order to accurately simulate the dynamic change process of the system,the method of molecular dynamics simulation combined with free energy calculation has become a research hotspot in recent years.In this paper,the shuttle motion of foldaxanes and the dehydration process of cyclohexanol in H-MFI molecular sieve are studied theoretically by using the methods of molecular dynamics simulation and free energy calculation.The specific research contents are as follows:1.Using molecular dynamics simulation combined with enhanced sampling method,the motion of a molecular machine foldaxanes is studied at the molecular level,and the free energy surface diagram characterizing foldaxanes shuttle is drawn.The calculated free energy barrier of foldaxanes shuttle process is 20.7 kcal/mol,which is in good agreement with the experimental results.The results show that the main reason for the formation of the free energy barrier in the foldaxanes shuttle process is the hydrogen bond breaking between the folded body and the chain molecule.By studying the interaction between different components,the mechanism of folding shrinkage and expansion is further analyzed.Therefore,using molecular dynamics simulation combined with free energy calculation to study the complex mechanism of how foldaxanes shuttles can greatly increase the calculation accuracy,deepen the understanding of the internal motion of molecular machines,and then help to build molecular machines with specific functions.2.The dehydration mechanism of cyclohexanol in dry and wet H-MFI molecular sieves was studied by ab initio molecular dynamics simulation and enhanced sampling method.Based on the calculated high-dimensional free energy surface,the dominant conformation of cyclohexanol in the molecular sieve was quantitatively characterized,that is,the conformation in the presence of hydrated hydrogen ion clusters.The analysis shows that for the aqueous phase reaction in the pore gap of molecular sieve,the aggregation of water molecules around Br(?)nsted acid site plays an important role in the dehydration process.As a weak Lewis base,hydrated hydrogen ion clusters change the dehydration of cyclohexanol from syn-E2 mechanism under dry conditions to E1 mechanism under wet conditions.Therefore,molecular dynamics simulation combined with free energy calculation is used to identify and control the structure of heterogeneous catalyst and its complex relationship with solution active center,which provides a new understanding of the effect of water molecules on cyclohexanol dehydration at the Br(?)nsted acid center of molecular sieve,and is a necessary element for the rational design of catalyst.