环糊精与持久性有机污染物相互作用的分子模拟
发布时间：2018-09-09 14:23
【摘要】：持久性有机污染物(Persistent Organic Pollutants, POPs)污染土壤修复的主要难点在于POPs以吸附态存在于土壤有机质中,生物修复效率极低。已有通过羟丙基环糊精作为增溶剂提高土壤中多环芳烃生物修复效率的报道,但相关研究多局限于部分较易生物降解的污染物,对疏水及生物毒性更强的POPs还缺乏相关研究。论文的研究目的在于构建不同的环糊精衍生物(Cyclodextrins, CDs)并从中寻找能够提高土壤中多种POPs分子向微生物的传递效率的CDs,最终加快土壤污染物修复效率。本研究首先考察了MOPA、Gaussian两种软件的不同优化条件、优化方法对环糊精的优化情况。经过与标准结构的RMSD及能量比较,并结合相关文献报道,最终确定采用Gaussian软件依次进行pm3、hf/6-31g的优化方法。并以此为基础构建出所需的CDs及POPs结构。分子对接部分,考察了30种不同结构的CDs与240种POPs的包合效果。以三乙酰基-p-环糊精和磺丁基-β-环糊精为代表,其对茚并[1,2,3-cd]芘的结合能分别为-10.60kcal/mol、-8.87 kcal/mol,而未经修饰的p-环糊精对其结合能仅为.-7.10 kcal/mol。对接分析表明,在环糊精的2位与6位羟基修饰物中,2位修饰更有利于提高其包合稳定性。其中磺丁基环糊精与全(2,6-O-甲基)-p-环糊精在包合效果和水溶性上,均满足实际要求。动力学计算部分,以CHARMM、CSFF力场为基础,补充并完成了磺丁基-β-环糊精的力场制作。在周期性水环境中考察了p-环糊精、磺丁基-p-环糊精对芘的相互作用。相对位置分析发现,磺丁基-β-环糊精在94.6%的情况下可以稳定包合客体分子,而β-环糊精仅在79.9%的情况下稳定包合。最终,从30种CDs中挑选出2-O-磺丁基-β-环糊精、6-O-磺丁基-p-环糊精、(2,6-0-甲基)-p-环糊精三种CDs,其均能与POPs形成稳定包合物。同时通过侧链对环糊精包合效果分析显示,CDs的包合效果不仅与侧链结构和其取代位置、取代度有关,还与POPs分子结构存在相关性。因此,采用POPs的在实际生物修复中,应针对污染物组成,制定个性化的环糊精使用方案。该研究工作,尝试建立了CDs衍生物结构构建方法、编写了对接结果批处理脚本,并完成了CDs缺失力场参数的补充。可以为评价CDs在促进土壤中POPs污染物生物利用率、批量对接数据处理、力场缺失状态下的动力学计算等工作提供参考。
[Abstract]:The main difficulty of soil remediation caused by persistent organic pollutant (Persistent Organic Pollutants, POPs) is that POPs is adsorbed in soil organic matter, and the bioremediation efficiency is very low. It has been reported that hydroxypropyl cyclodextrin can improve the bioremediation efficiency of polycyclic aromatic hydrocarbons (PAHs) in soil, but most of the related studies are limited to some easily biodegradable pollutants, but there are few studies on hydrophobic and biotoxic POPs. The purpose of this paper is to construct different cyclodextrin derivatives (Cyclodextrins, CDs) and find out CDs, which can improve the transfer efficiency of many POPs molecules to microorganism in soil and finally accelerate the remediation efficiency of soil pollutants. In this study, the different optimization conditions of MOPA,Gaussian software and the optimization of cyclodextrin were investigated. After comparing with the RMSD and energy of the standard structure, and combining with the related literature reports, the optimization method of pm3,hf/6-31g using Gaussian software is finally determined. On this basis, the required CDs and POPs structures are constructed. In the molecular docking part, the inclusion effects of CDs with 30 different structures and 240 POPs were investigated. As represented by triacetyl-p-cyclodextrin and sulfur-Ding Ji-尾 -cyclodextrin, the binding energy of pyrene to indeno [1O2O3-cd] pyrene is -10.60 kcal / mol -8.87 kcal/mol, respectively, and the binding energy of unmodified pcyclodextrin to pyrene is only .-7.10 kcal/mol.. The results of docking analysis showed that the stability of cyclodextrin inclusion was improved by the modification of 2 and 6 hydroxyl groups of cyclodextrin. The inclusion effect and water solubility of cyclodextrin and total (2o-o-methyl)-p-cyclodextrin met the practical requirements. In the part of dynamics calculation, based on CHARMM,CSFF force field, the force field fabrication of sulfonDing Ji-尾-cyclodextrin is completed. The interaction of p-cyclodextrin and sulfur-Ding Ji -p-cyclodextrin on pyrene was investigated in periodic water environment. The relative position analysis showed that the inclusion guest molecules could be stabilized in 94.6% of sulfo-Ding Ji 尾 -cyclodextrin, but only 79.9% of 尾 -cyclodextrin. Finally, three kinds of CDs, 2-O- sulfur-Ding Ji-尾 -cyclodextrin, (2-O- 6-methyl-methyl) -p-cyclodextrin, were selected from 30 CDs to form stable inclusion complexes with POPs. At the same time, the inclusion effect of CDs on cyclodextrin was analyzed by side chain analysis. The inclusion effect of CDs was not only related to the side chain structure, its substitution position and degree of substitution, but also related to the molecular structure of POPs. Therefore, the application of POPs in bioremediation should aim at the composition of contaminants and develop a personalized scheme of cyclodextrin use. In this work, the structure construction method of CDs derivatives was established, the batch script of docking results was compiled, and the missing force field parameters of CDs were supplemented. It can be used as a reference for evaluating the bioavailability of POPs pollutants in soil, batch docking data processing, dynamics calculation in the absence of force field, and so on.
【学位授予单位】：大连理工大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：X53
本文编号：2232644
[Abstract]:The main difficulty of soil remediation caused by persistent organic pollutant (Persistent Organic Pollutants, POPs) is that POPs is adsorbed in soil organic matter, and the bioremediation efficiency is very low. It has been reported that hydroxypropyl cyclodextrin can improve the bioremediation efficiency of polycyclic aromatic hydrocarbons (PAHs) in soil, but most of the related studies are limited to some easily biodegradable pollutants, but there are few studies on hydrophobic and biotoxic POPs. The purpose of this paper is to construct different cyclodextrin derivatives (Cyclodextrins, CDs) and find out CDs, which can improve the transfer efficiency of many POPs molecules to microorganism in soil and finally accelerate the remediation efficiency of soil pollutants. In this study, the different optimization conditions of MOPA,Gaussian software and the optimization of cyclodextrin were investigated. After comparing with the RMSD and energy of the standard structure, and combining with the related literature reports, the optimization method of pm3,hf/6-31g using Gaussian software is finally determined. On this basis, the required CDs and POPs structures are constructed. In the molecular docking part, the inclusion effects of CDs with 30 different structures and 240 POPs were investigated. As represented by triacetyl-p-cyclodextrin and sulfur-Ding Ji-尾 -cyclodextrin, the binding energy of pyrene to indeno [1O2O3-cd] pyrene is -10.60 kcal / mol -8.87 kcal/mol, respectively, and the binding energy of unmodified pcyclodextrin to pyrene is only .-7.10 kcal/mol.. The results of docking analysis showed that the stability of cyclodextrin inclusion was improved by the modification of 2 and 6 hydroxyl groups of cyclodextrin. The inclusion effect and water solubility of cyclodextrin and total (2o-o-methyl)-p-cyclodextrin met the practical requirements. In the part of dynamics calculation, based on CHARMM,CSFF force field, the force field fabrication of sulfonDing Ji-尾-cyclodextrin is completed. The interaction of p-cyclodextrin and sulfur-Ding Ji -p-cyclodextrin on pyrene was investigated in periodic water environment. The relative position analysis showed that the inclusion guest molecules could be stabilized in 94.6% of sulfo-Ding Ji 尾 -cyclodextrin, but only 79.9% of 尾 -cyclodextrin. Finally, three kinds of CDs, 2-O- sulfur-Ding Ji-尾 -cyclodextrin, (2-O- 6-methyl-methyl) -p-cyclodextrin, were selected from 30 CDs to form stable inclusion complexes with POPs. At the same time, the inclusion effect of CDs on cyclodextrin was analyzed by side chain analysis. The inclusion effect of CDs was not only related to the side chain structure, its substitution position and degree of substitution, but also related to the molecular structure of POPs. Therefore, the application of POPs in bioremediation should aim at the composition of contaminants and develop a personalized scheme of cyclodextrin use. In this work, the structure construction method of CDs derivatives was established, the batch script of docking results was compiled, and the missing force field parameters of CDs were supplemented. It can be used as a reference for evaluating the bioavailability of POPs pollutants in soil, batch docking data processing, dynamics calculation in the absence of force field, and so on.
【学位授予单位】：大连理工大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：X53
【参考文献】
相关期刊论文 前1条
1 程国玲;李培军;;石油污染土壤的植物与微生物修复技术[J];环境工程学报;2007年06期
，本文编号：2232644
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