Molecular Simulation Of The Inclusion Complexes Of Cyclodextrins With Persistent Organic Pollutants

The main difficulty for the remediation of persistent organic pollutions (POPs) contaminated soil is that POPs exist in soil are in an adsorbed form and difficult to be biodegradated, which result in a low efficiency of bioremediation. It has been proved recently that supermolecular hydroxypropy-β-cyclodextrin (HPCD) has the ability to enhance the transport of polycyclic aromatic hydrocarbons (PAHs) in soils and improve the efficiency of bioremediation. However, most of the researches focused mainly on PAHs that can be biodegrated easily, and for the PAHs with low water solubility and highly toxic there are little public rearch until now. The purpose of this paper is to build different kinds of cyclodextrins (CDs) and find the best one that can be used to enhance the transmission speed of POPs to microorganism in order to speed up the repair efficiency of POPs polluted soil.First of all, different kinds of optimize method from MOPAC and Gaussian was used to build cyclodextrin molecular structure in order to find the proper method that can be used. Through the compare of RMSD value and energy analysis of optimized structures with the strand structure the Gaussian software was choosed. For the optimize method the pm3 semiempirical method and the ab initio hf/6-31 g theory was choosed.Using molecular docking method, the inclusion ability of 30 kinds of CDs to 240 kids of POPs are calculated. In triacetyl-β-cyclodextrins and cyclodextrin sulfobutyl-β-cyclodextrin its binding energy with indeno [1,2,3-cd] pyrene were-10.60 kcal / mol,-8.87 kcal / mol, while for the unmodified β-cyclodextrin the binding energy was only -7.10 kcal / mol. Analysis of the docking results prove that the replacement of 2-hydroxy is more helpful to improve the stability of its inclusion with POPs than that of the 6-hydroxy. At the same time, sulfobutyl ether-βcyclodextrin and (2,6-O-methyl)-β-cyclodextrin all meet the actual requirements whether it’s the inclusion ability or the water-solubility.The force field used in the molecular dynamic (MD) calculation were based on CHARMM and CSFF and the missing parameters were add according to the scanning results of Gaussian. MD calculation of cyclodextrin sulfobutyl-β-cyclodextrin and β-cyclodextrin with pyrene in periodic water sphere show that the stability of complex between sulfobutylether-β-cyclodextrin and pyrene which has the value of 94.6% is better than that between β-cyclodextrin and pyrene which has the value of 79.9%.Finally, the 2-sulfobutylether-β-cyclodextrin,6-sulfobutylether-β-cyclodextrin and 2 and 6-tetradeca-O-methyl-β-cyclodextrin which can form stable inclusion complex were choosed out of 30 kinds of CDs. Results of other CDs also show that different position of a certain side chain on CDs have different effects, and the total numbers of side chains also have great effects on the final result. Therefore the type of CDs should be chosen carefully when the CDs is used in the actual bioremediation process for promoting bioremediation efficiency of POPs for different applications.This research provide one of the ways to build cyclodextrins,write the Bash file that can be used to analysis the docking results from PyRx and find the proper way to prepare the missing force field for the molecular dynamitic calculation. The results provide theoretical basis for evaluating the feasibility of CDs with POPs and also provide reference for further molecular docking and molecular dynamic calculation without any published force field that can be used directly.