污染物生物与化学转化中的界面电子转移机制
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摘要
界面电子转移在生物反应、化学体系、环境修复中都起着重要作用,与能量的流动和转换密切相关。提高界面的电子传递效率,深入剖析电子转移机制,是促进界面反应的基础。本论文针对污染物生物转化和化学转化中界面电子转移的关键问题,分析微生物电子传递链终端氧化还原酶与电子受体,以及化学催化剂与污染物分子的界面反应,实现了胞外电子传递途径的调控以及催化剂结构和表面特性的优化,提高了系统的能量转换效率,促进了污染物的转化。论文的主要研究内容和结果如下：
1.电化学活性细菌(EAB)与三氧化钨(h-WO3)纳米团簇界面的电子传递机制。EAB在环境、能源、微生物学和生物地球化学领域是一种重要的模式微生物,而六方晶系三氧化钨(h-WO3)纳米团簇可以作为探针对EAB进行高通量筛选。通过分子模拟和电化学实验,在分子水平上分析了WO3纳米团簇筛选EAB胞外电子的机理。结果发现电子传递效率主要受纳米团簇表面细胞色素的分子构型和暴露在溶剂中的亚铁血红素的影响；卟啉分子平面轴向配位的双组氨酸残基能够克服一个较低的热力学能垒而进行界面电子传递,而电子传递速率则主要取决于传递距离。对微生物与纳米团簇界面电子传递的深入分析,有助于设计高效的电子捕获纳米材料。
2.阳极表面微生物胞外电子传递(EET)的过程调控。通过对外膜蛋白细胞色素c (c-Cyt)的血红素结构到石墨电极的EET过程进行分子水平的解析,发现血红素辅基,即卟啉铁分子周围的氨基酸残基的分子构象能显著影响EET过程；c-Cyt表面的赖氨酸残基能形成氢键缩短了电子传递距离从而加快EET；热力学和动力学分析表明石墨电极表面的亲水性的含氧官能团能降低电子传递能垒,利于反应快速达到平衡。有效控制c-Cyts与石墨之间的相互作用,有利于促进EET过程,进而可以设计出高效的生物能量转换系统。
3.吩嗪促进EAB与终端电子受体的电子传递过程的分析。吩嗪是一类含氮杂环化合物,多种细菌能够分泌产生,也可以人工合成,且其性质主要取决于不同取代基的位置和特性。它作为一种电子穿梭体,参与了多种生物过程以帮助微生物进行能量代谢和电子传递。因此,对于特定的电子传递途径,找出最合适的吩嗪取代基和分子结构非常重要。利用量化计算分析了水溶液中取代基对吩嗪类氧化还原媒介电位的影响,计算结果得到了实验结果的有效验证。结果表明反应自由能主要受吩嗪分子取代基的位置和质子化水合团簇的影响；在主要的质子反应过程中,含有供电子基团或吸电子基团的吩嗪与不同的质子化水合团簇相互作用取决于质子转移过程水分子的近程效应。因此,采用合适的含取代基吩嗪分子能够实现电子流动途径的调控,降低生物能量的损耗,实现能量的高效转化。设计高效的氧化还原媒介促进微生物与终端电子受体的电子传递过程,对于废水生物处理和环境修复中的能量回收是十分有益的。
4.纳米Ti02表面光催化硝化和反硝化过程的机理。空气中的N2和O2能够在纳米Ti02表面在紫外光或可见光的条件下形成硝酸盐,这是普遍存在但以前未被发现的硝酸盐形成过程。通过第一性原理密度泛函理论(DFT)计算对该形成机制进行了深入分析,发现该过程中形成了NO中间产物。结果表明,由于NO形成的能垒较低,导带上的形成机制是其主要反应途径,而价带上的形成机制也可能以较低的反应速率同时存在于实际体系中。另一方面,光催化还原硝酸盐转化为N2,是饮用水源中硝酸盐去除的有效方法。我们建立了一种新的生物电-光催化硝酸盐还原方法,其中以TiO2纳米颗粒作为光催化剂,以微生物代谢产生的电子作为空穴清除剂。与传统的反硝化机制相比,生物电-光催化反应途径具有较低的能垒,将硝酸盐完全光催化还原为N2,而无有毒副产物的积累,理论分析结果表明,通过微生物产生的电子来清除空穴,避免了牺牲剂在位点的竞争吸附,从而形成高效的、具有选择性的光催化反硝化过程。
5.TiO2光催化材料的晶面调控和应用。TiO2作为光催化材料被广泛用于污染物的降解,而TiO2表面经过金属团簇的修饰可增强降解效果。利用DFT计算与实验研究相结合的手段,深入探索了模式污染物硝基苯(NB)在Pt团簇负载的锐钛矿TiO2(Pt/TiO2)催化剂表面的降解机制,分析了有机分子的吸附构型以及催化剂表面的活性位点。研究发现,NB的氧化和还原降解分别发生在TiO2(001)和(101)晶面,Pt团簇的负载促进了NB在催化剂表面的吸附,以及空穴-电子对的分离；计算得到的热力学性质和液质色谱分析结果揭示了NB更倾向于在Pt/TiO2的(001)晶面发生氧化降解。因此,在材料合成时进一步增加Pt/TiO2(001)晶面的比例,有利于提高NB的降解效率,这为根据污染物的特点量身定制光催化纳米材料提供了一个新的思路。
Interfacial electron transfer plays an essential role in a broad range of biological reactions, chemical systems and environmental remediation, including energy flow and conversion. The interfacial reaction could be promoted by giving a deep insight into the electron transfer mechanisms and improving the electron transfer efficiency. This study aims to elucidate the interfacial electron transfer mechanism in biological and chemical transformations of pollutants. A high energy conversion efficiency could be achieved by controlling electron flow routes between microbial terminal oxidoreductase and electron acceptors. The effective pollutant transformation could be accomplished by designing contaminant-targeted photocatalytic nanomaterials to reveal the interaction mechanisms and structural evolution of pollutant molecules on catalyst surface. Main contents and results of this dissertation are as follows:
1. Biological transformation of pollutants could be improved by screening and using high efficient electrochemically active bacteria (EAB). Hexagonal tungsten oxide (h-WO3) nanocluster was developed as a high-throughput probe for identification of EAB, the "star" microorganisms in the fields of environment, energy, microbiology, and biogeochemistry. Here, the mechanism for screening EAB by the WO3nanocluster is explored using molecular modeling and electrochemical experiments. The electron transfer efficiency is found to be governed by the special molecular configuration of cytochrome and the solvent exposed heme with respect to the nanocluster surfaces. The axial bishistidine residues bounded to the porphyrin plane enable interfacial electron transfer to occur with a low thermodynamic barrier. The apparent electron transfer rate is dependent primarily on the transfer distance. This work provides deep insights into the interfacial electron transfer at microbe-nanocluster, and is useful for molecular design of highly-efficient electron-capturing nanomaterials.
2. Microbial extracellular electron transfer (EET) could be tuned through modifying anode surface. After a molecular-level investigation, it is revealed that EET from the heme group of c-type cytochrome (c-Cyt), an outer membrane protein, to the graphite nanosheet electrode, a widely used electron acceptor, is significantly influenced by the molecular conformations of the surrounding amino acid residues of c-Cyt and the solvent exposed heme with respect to the EA surface. The lysine residue presented on the surface of c-Cyt provides a weak hydrogen bond to shorten the electron transfer distance and hence accelerate EET. The thermodynamic and kinetic analyses demonstrate that the hydrophilic oxygen-containing groups on graphite surface contribute greatly to the EET through lowering the thermodynamic barrier and allowing rapid reaction equilibrium. Effective control of the c-Cyts/graphite interaction is beneficial to accelerating and engineering EET for designing highly-efficient biological energy-conversion systems.
3. Phenazines, as a type of electron shuttle, are involved in various biological processes to facilitate microbial energy metabolism and electron transfer. They are constituted of a large group of nitrogen-containing heterocyclic compounds, and can be produced either by a diverse range of bacteria or by artificial synthesis. They vary significantly in their properties, depending mainly on the nature and positions of substitutent groups. Thus, it is of great interest to find out the most favorable substituent type and molecular structure of phenazines for electron transfer routes. Here, the impacts of the substituent group on the reduction potentials of phenazine-type redox mediators in aqueous solution were investigated by using quantum chemical calculations, and the calculation results were further validated with experimental data. The results show that the reaction free energy was substantially affected by the location of substituent groups on the phenazine molecule and the protonated water clusters. For the main proton addition process, the phenazines substituted with electron-donating groups and those with electron-withdrawing groups interacted with different protonated water clusters, attributed to the proximity effect of water molecules on proton transfer. Thus, high energy conversion efficiency could be achieved by controlling electron flow route with appropriate substituted phenazines to reduce the biological energy acquisition. This study provides useful information for designing efficient redox mediators to promote electron transfer between microbes and terminal acceptors, which are essential to bioenergy recovery from wastes and environmental bioremediation.
4. Interfacial electron transfer involves in photocatalytic nitrification and denitrification. Nitrate could be formed from abundant atmospheric nitrogen and oxygen on nano-sized titanium dioxide surfaces under ultraviolet or sunlight irradiation. This is an undiscovered nitrate formation process that occurs universally. We suggest that nitric oxide is an intermediate product in this process, and elucidate its formation mechanisms using first-principles density functional theory (DFT) calculations. The results indicate that the conduction band mechanism with a low energy barrier (Ea) can be the dominant pathway for the NO formation, and the valence band mechanism can also possibly occur with h+at a low reaction rate. However, nitrate causes severe ecological and health risks, and nitrate contamination of drinking water sources has become one of the most important water quality concerns all over the world. Photocatalytic reduction of nitrate to molecular nitrogen presents a promising approach to remove nitrate from drinking water sources. We have found an efficient, selective and sustainable bioelectro-photocatalytic nitrate-reducing system by utilizing TiO2nanoparticles as the photocatalyst and bio-electrons from microbial metabolism as the hole scavenger. Compared with the conventional denitrification mechanism, such a bioelectro-photocatalytic reaction pathway has a lower Ea, suggesting that the complete photocatalytic reduction of nitrate to N2without accumulation of toxic intermediates is energetically feasible. The mechanisms of the highly-selective nitrate reduction were elucidated by DFT calculations. The scavenging of holes by the bio-electrons avoids the occupation of extra adsorption competition anions onto the active surface, resulting in the selective and efficient photocatalytic denitrification.
5. Crystal surface of TiO2photocatalyst can be tuned to promote the degradation of pollutants in the practical applications. TiO2-based materials have been widely investigated for the photocatalytic degradation of various persistent pollutants. Especially, modification of TiO2surface with nanosized metallic clusters is found to accelerate the degradation process, but the underlying mechanism and the effective crystal surface for pollutant degradation remain unclear. Photodegradation of nitrobenzene (NB), a model pollutant, on the surface of Pt cluster-loaded anatase TiO2(Pt/TiO2) catalyst is investigated by combining DFT quantum chemistry calculations with experimental studies. The configurations of absorbed organic molecules, the active sites of the composite catalysts as well as the interactions in the NB photodegradation in aqueous phase are elucidated. The mechanism of the oxidative and reductive reactions on the TiO2(001) and (101) surface is proposed, which is found to be appropriate to explain the improved light adsorption and electron-hole separation of anatase TiO2and accelerated NB photodegradation by loading Pt clusters. Furthermore, the thermodynamic analysis and liquid chromatography mass spectrometry results reveal that an oxidative degradation of NB on (001) surface is favored for the Pt/TiO2. Thus, the efficiency of NB degradation in aqueous solution might be enhanced by exposing large ratio of (001) surface in the synthesis of Pt/TiO2. This work provides implications for designing contaminant-targeted photocatalytic nanomaterials.
1.电化学活性细菌(EAB)与三氧化钨(h-WO3)纳米团簇界面的电子传递机制。EAB在环境、能源、微生物学和生物地球化学领域是一种重要的模式微生物,而六方晶系三氧化钨(h-WO3)纳米团簇可以作为探针对EAB进行高通量筛选。通过分子模拟和电化学实验,在分子水平上分析了WO3纳米团簇筛选EAB胞外电子的机理。结果发现电子传递效率主要受纳米团簇表面细胞色素的分子构型和暴露在溶剂中的亚铁血红素的影响；卟啉分子平面轴向配位的双组氨酸残基能够克服一个较低的热力学能垒而进行界面电子传递,而电子传递速率则主要取决于传递距离。对微生物与纳米团簇界面电子传递的深入分析,有助于设计高效的电子捕获纳米材料。
2.阳极表面微生物胞外电子传递(EET)的过程调控。通过对外膜蛋白细胞色素c (c-Cyt)的血红素结构到石墨电极的EET过程进行分子水平的解析,发现血红素辅基,即卟啉铁分子周围的氨基酸残基的分子构象能显著影响EET过程；c-Cyt表面的赖氨酸残基能形成氢键缩短了电子传递距离从而加快EET；热力学和动力学分析表明石墨电极表面的亲水性的含氧官能团能降低电子传递能垒,利于反应快速达到平衡。有效控制c-Cyts与石墨之间的相互作用,有利于促进EET过程,进而可以设计出高效的生物能量转换系统。
3.吩嗪促进EAB与终端电子受体的电子传递过程的分析。吩嗪是一类含氮杂环化合物,多种细菌能够分泌产生,也可以人工合成,且其性质主要取决于不同取代基的位置和特性。它作为一种电子穿梭体,参与了多种生物过程以帮助微生物进行能量代谢和电子传递。因此,对于特定的电子传递途径,找出最合适的吩嗪取代基和分子结构非常重要。利用量化计算分析了水溶液中取代基对吩嗪类氧化还原媒介电位的影响,计算结果得到了实验结果的有效验证。结果表明反应自由能主要受吩嗪分子取代基的位置和质子化水合团簇的影响；在主要的质子反应过程中,含有供电子基团或吸电子基团的吩嗪与不同的质子化水合团簇相互作用取决于质子转移过程水分子的近程效应。因此,采用合适的含取代基吩嗪分子能够实现电子流动途径的调控,降低生物能量的损耗,实现能量的高效转化。设计高效的氧化还原媒介促进微生物与终端电子受体的电子传递过程,对于废水生物处理和环境修复中的能量回收是十分有益的。
4.纳米Ti02表面光催化硝化和反硝化过程的机理。空气中的N2和O2能够在纳米Ti02表面在紫外光或可见光的条件下形成硝酸盐,这是普遍存在但以前未被发现的硝酸盐形成过程。通过第一性原理密度泛函理论(DFT)计算对该形成机制进行了深入分析,发现该过程中形成了NO中间产物。结果表明,由于NO形成的能垒较低,导带上的形成机制是其主要反应途径,而价带上的形成机制也可能以较低的反应速率同时存在于实际体系中。另一方面,光催化还原硝酸盐转化为N2,是饮用水源中硝酸盐去除的有效方法。我们建立了一种新的生物电-光催化硝酸盐还原方法,其中以TiO2纳米颗粒作为光催化剂,以微生物代谢产生的电子作为空穴清除剂。与传统的反硝化机制相比,生物电-光催化反应途径具有较低的能垒,将硝酸盐完全光催化还原为N2,而无有毒副产物的积累,理论分析结果表明,通过微生物产生的电子来清除空穴,避免了牺牲剂在位点的竞争吸附,从而形成高效的、具有选择性的光催化反硝化过程。
5.TiO2光催化材料的晶面调控和应用。TiO2作为光催化材料被广泛用于污染物的降解,而TiO2表面经过金属团簇的修饰可增强降解效果。利用DFT计算与实验研究相结合的手段,深入探索了模式污染物硝基苯(NB)在Pt团簇负载的锐钛矿TiO2(Pt/TiO2)催化剂表面的降解机制,分析了有机分子的吸附构型以及催化剂表面的活性位点。研究发现,NB的氧化和还原降解分别发生在TiO2(001)和(101)晶面,Pt团簇的负载促进了NB在催化剂表面的吸附,以及空穴-电子对的分离；计算得到的热力学性质和液质色谱分析结果揭示了NB更倾向于在Pt/TiO2的(001)晶面发生氧化降解。因此,在材料合成时进一步增加Pt/TiO2(001)晶面的比例,有利于提高NB的降解效率,这为根据污染物的特点量身定制光催化纳米材料提供了一个新的思路。
Interfacial electron transfer plays an essential role in a broad range of biological reactions, chemical systems and environmental remediation, including energy flow and conversion. The interfacial reaction could be promoted by giving a deep insight into the electron transfer mechanisms and improving the electron transfer efficiency. This study aims to elucidate the interfacial electron transfer mechanism in biological and chemical transformations of pollutants. A high energy conversion efficiency could be achieved by controlling electron flow routes between microbial terminal oxidoreductase and electron acceptors. The effective pollutant transformation could be accomplished by designing contaminant-targeted photocatalytic nanomaterials to reveal the interaction mechanisms and structural evolution of pollutant molecules on catalyst surface. Main contents and results of this dissertation are as follows:
1. Biological transformation of pollutants could be improved by screening and using high efficient electrochemically active bacteria (EAB). Hexagonal tungsten oxide (h-WO3) nanocluster was developed as a high-throughput probe for identification of EAB, the "star" microorganisms in the fields of environment, energy, microbiology, and biogeochemistry. Here, the mechanism for screening EAB by the WO3nanocluster is explored using molecular modeling and electrochemical experiments. The electron transfer efficiency is found to be governed by the special molecular configuration of cytochrome and the solvent exposed heme with respect to the nanocluster surfaces. The axial bishistidine residues bounded to the porphyrin plane enable interfacial electron transfer to occur with a low thermodynamic barrier. The apparent electron transfer rate is dependent primarily on the transfer distance. This work provides deep insights into the interfacial electron transfer at microbe-nanocluster, and is useful for molecular design of highly-efficient electron-capturing nanomaterials.
2. Microbial extracellular electron transfer (EET) could be tuned through modifying anode surface. After a molecular-level investigation, it is revealed that EET from the heme group of c-type cytochrome (c-Cyt), an outer membrane protein, to the graphite nanosheet electrode, a widely used electron acceptor, is significantly influenced by the molecular conformations of the surrounding amino acid residues of c-Cyt and the solvent exposed heme with respect to the EA surface. The lysine residue presented on the surface of c-Cyt provides a weak hydrogen bond to shorten the electron transfer distance and hence accelerate EET. The thermodynamic and kinetic analyses demonstrate that the hydrophilic oxygen-containing groups on graphite surface contribute greatly to the EET through lowering the thermodynamic barrier and allowing rapid reaction equilibrium. Effective control of the c-Cyts/graphite interaction is beneficial to accelerating and engineering EET for designing highly-efficient biological energy-conversion systems.
3. Phenazines, as a type of electron shuttle, are involved in various biological processes to facilitate microbial energy metabolism and electron transfer. They are constituted of a large group of nitrogen-containing heterocyclic compounds, and can be produced either by a diverse range of bacteria or by artificial synthesis. They vary significantly in their properties, depending mainly on the nature and positions of substitutent groups. Thus, it is of great interest to find out the most favorable substituent type and molecular structure of phenazines for electron transfer routes. Here, the impacts of the substituent group on the reduction potentials of phenazine-type redox mediators in aqueous solution were investigated by using quantum chemical calculations, and the calculation results were further validated with experimental data. The results show that the reaction free energy was substantially affected by the location of substituent groups on the phenazine molecule and the protonated water clusters. For the main proton addition process, the phenazines substituted with electron-donating groups and those with electron-withdrawing groups interacted with different protonated water clusters, attributed to the proximity effect of water molecules on proton transfer. Thus, high energy conversion efficiency could be achieved by controlling electron flow route with appropriate substituted phenazines to reduce the biological energy acquisition. This study provides useful information for designing efficient redox mediators to promote electron transfer between microbes and terminal acceptors, which are essential to bioenergy recovery from wastes and environmental bioremediation.
4. Interfacial electron transfer involves in photocatalytic nitrification and denitrification. Nitrate could be formed from abundant atmospheric nitrogen and oxygen on nano-sized titanium dioxide surfaces under ultraviolet or sunlight irradiation. This is an undiscovered nitrate formation process that occurs universally. We suggest that nitric oxide is an intermediate product in this process, and elucidate its formation mechanisms using first-principles density functional theory (DFT) calculations. The results indicate that the conduction band mechanism with a low energy barrier (Ea) can be the dominant pathway for the NO formation, and the valence band mechanism can also possibly occur with h+at a low reaction rate. However, nitrate causes severe ecological and health risks, and nitrate contamination of drinking water sources has become one of the most important water quality concerns all over the world. Photocatalytic reduction of nitrate to molecular nitrogen presents a promising approach to remove nitrate from drinking water sources. We have found an efficient, selective and sustainable bioelectro-photocatalytic nitrate-reducing system by utilizing TiO2nanoparticles as the photocatalyst and bio-electrons from microbial metabolism as the hole scavenger. Compared with the conventional denitrification mechanism, such a bioelectro-photocatalytic reaction pathway has a lower Ea, suggesting that the complete photocatalytic reduction of nitrate to N2without accumulation of toxic intermediates is energetically feasible. The mechanisms of the highly-selective nitrate reduction were elucidated by DFT calculations. The scavenging of holes by the bio-electrons avoids the occupation of extra adsorption competition anions onto the active surface, resulting in the selective and efficient photocatalytic denitrification.
5. Crystal surface of TiO2photocatalyst can be tuned to promote the degradation of pollutants in the practical applications. TiO2-based materials have been widely investigated for the photocatalytic degradation of various persistent pollutants. Especially, modification of TiO2surface with nanosized metallic clusters is found to accelerate the degradation process, but the underlying mechanism and the effective crystal surface for pollutant degradation remain unclear. Photodegradation of nitrobenzene (NB), a model pollutant, on the surface of Pt cluster-loaded anatase TiO2(Pt/TiO2) catalyst is investigated by combining DFT quantum chemistry calculations with experimental studies. The configurations of absorbed organic molecules, the active sites of the composite catalysts as well as the interactions in the NB photodegradation in aqueous phase are elucidated. The mechanism of the oxidative and reductive reactions on the TiO2(001) and (101) surface is proposed, which is found to be appropriate to explain the improved light adsorption and electron-hole separation of anatase TiO2and accelerated NB photodegradation by loading Pt clusters. Furthermore, the thermodynamic analysis and liquid chromatography mass spectrometry results reveal that an oxidative degradation of NB on (001) surface is favored for the Pt/TiO2. Thus, the efficiency of NB degradation in aqueous solution might be enhanced by exposing large ratio of (001) surface in the synthesis of Pt/TiO2. This work provides implications for designing contaminant-targeted photocatalytic nanomaterials.
引文
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