环境影响下手性分子的结构及对映体转变过程理论研究
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摘要
手性是自然界生物分子重要的内禀属性，也被认为与生命起源直接相关。手性分子对映体结构的稳定性以及在环境影响下的构象转变与一些基本的生命过程紧密联系，且对药物开发及投递起到至关重要的作用，一直以来都是物理、化学、材料科学及生命科学等领域的研究热点之一。本文综合使用了密度泛函理论方法，及以此为基础发展的紧束缚密度泛函理论方法，乃至半经验从头算方法和经典分子动力学模拟方法，研究了一些典型手性分子的结构及受外界环境影响后展现的特性，包括在环境影响下的对映体转变过程。具体研究工作主要包括以下四个部分：
首先，限域下的分子手性转变过程中，极值点的真实结构信息在反应中是非常重要的，但却很难获得，主要是由于复杂的分子相互作用。在本部分，我们基于大量的经典分子动力学模拟的统计结果，阐述了在单壁氮化硼纳米管中，difluorobenzo[c]phenanthrene分子（C18H12F2，称为D分子）的完整手性转变过程，发现在此过程中至少涉及到五个极值点结构，体现出限域环境下手性转变的独特性。我们因此而提议了一种基于经验分子动力学模拟的确定分子间相互作用势能面的方法，这种势能面的求解通常情况下是通过传统的第一性原理计算才可以给出。
其次，基于组合了密度泛函理论和半经验从头算的ONIOM方法分析了手性的difluorobenzo[c]phenanthrene分子(C18H12F2，D分子)在无极富勒烯C260中的对映体间转变过程，以认识限域对手性分子对映体转变过程的影响。我们发现，在红外和拉曼光谱中，与孤立系统相比，限域环境会使D分子谱线整体发生蓝移，于此同时，在0-60cm-1波段内出现6种体现D分子整体运动的独有模式。非常有趣的，在此限域环境下D分子的手性转变过程能垒相比于孤立情况升高了15.88kcal mol-1，展现了这种限域条件可以促进手性分子对映体稳定。而且，在这个限域系统中， D分子的前线分子轨道远离了整个体系的活性区域，使得D分子受到了外面富勒烯的保护而更为稳定。这一结果凸显了纳米尺度限域环境，会对手性分子对映体转变过程具有影响。我们希望，这些结果对手性药物分子的输运乃至手性对映体的稳定具有一定的借鉴意义。
再次，为了进一步探究影响结构稳定性的因素，基于第一性原理密度泛函理论分析了超共轭效应对叔丁基及它的衍生物C4Hn（n=4-10）异构体的结构稳定性的影响。我们发现，n=7-10这四种异构体具有与叔丁基类似的超共轭效应，且超共轭轨道能随参加超共轭效应的氢原子数目的增加而减小。参加超共轭效应的氢原子的带电分布均一，此现象揭示了电子结构当中的离域特征。此外，对红外谱的分析发现，对C-H拉伸振动的峰的贡献主要来自于参加超共轭效应的氢原子。此结果对超共轭效应也展现出一些规律性的认识。
最后，为了促进基于堆垛效应，石墨烯在分子识别方面的可能应用，尤其是在生命科学中，对芳香性氨基酸、乃至测序碱基等带有环状侧链分子的识别，采用密度泛函紧束缚（DFTB）方法，我们研究了石墨烯片段与不同的环状有机碳氢化合物包括苯（C6H6），环己烷（C6H12）,苯炔（C6H4），环己烯（C6H10），1,3-环己二烯（C6H8(1)）及异构体1,4-环己二烯（C6H8(2)）之间的相互作用。结果展现出，在Raman振动谱及紫外可见吸收谱上，均可发现小分子吸附到石墨烯基底具有的明显差异性。也就是，两种光谱都存在一些明显的归属于不同小分子吸附的不同特征峰，而在相应的离子体系中，相应的特征峰更为明显。进一步的分析表明，在中性的环境下，整体的吸附作用能几乎都归因于色散能的存在，并且石墨烯把电子转移给小分子。与此相反，在离子吸附环境下，主要的结合能贡献来自于静电作用。这些结果对在石墨烯基底上不同种类的芳香碳氢化合物环的识别，表明了比较清晰的特征。希望我们的研究有助于基于石墨烯的相应分子识别检测器件的设计。
Chirality is a very important intrinsic property of the natural biological molecules,which is also considered to be directly related to the origin of life. The structuralstability of the enantiomer of chiral molecules as well as the conformation transitionupon the environment is closely associated with some basic life processes. And it alsoplays an important role in drug development and delivery. It has been currentlyreceived much attention in physics, chemistry, material science and life science fields.In this thesis, we synthetically used the density functional theory, density functionaltight binding method developed on this basis, and down to the semi-empirical abinitio as well as the classical molecular dynamics simulation methods, in order tostudy the structures of typical chiral molecules and the feature under environment,including the transition process between enantiomers upon the confinement. Thespecific research work mainly includes the following four parts:
Firstly, reliable structural information of extremal points in a reaction isimportant but difficult to achieve in molecular chiral transitions under confinementdue to the complex molecular interactions. In this part, based on statistical results of anumber of classical molecular dynamics simulations, we expounded the completechiral transition process of a difluorobenzo[c]phenanthrene molecule (C18H12F2, calledD molecule) within a single-walled boron-nitride nanotube involves at least fiveextremal point structures, showing a unique feature of chiral transition in the confinedenvironment and suggesting an alternative to conventional first-principles calculationsto determine the complex potential energy surface of intermolecular interactions.
Secondly, the transition process between chiral difluorobenzo[c]phenanthrenemolecule (C18H12F2, D molecule) enantiomers within non-polar fullerene C260has been studied based on ONIOM method, which combined the density functional theoryand the semi-empirical ab initio method, in order to explore the impact ofconfinement on the transition process of chiral enantiomers. We found that blue shiftoccurred generally in infrared and Raman spectra of D molecule under confinementenvironment, compared with those of isolated systems. Meanwhile, six types ofparticular patterns representing overall movement of D molecules appeared in0-60cm-1band. Interestingly, energy barrier of D molecule chiral transformation under saidconfinement ambience is elevated by15.88kcal·mol-1compared to those underisolated conditions, which means this confinement conditions can facilitate thestability of chiral molecular enantiomers. Moreover, in the confinement system, frontorbital energy of D molecule is lower than that of C260fullerene, so that D molecule isfurther stabilized due to the protection of fullerene matrix, in terms of reactivity. It isconcluded that confinement environment in nanoscale will have an impact onenantiomer transformation process of chiral molecules. These results may instructchiral medicine molecules transport and even the stability of chiral enantiomers.
Thirdly, to further explore the factors that affect the structural stability, thehyperconjugation effect on molecular structural stability is studied by performing firstprinciples density functional theory calculations on the tert-butyl and its derived C4Hn(n=4-10) isomer structures. Four of the isomer structures with n=7-10were found toshow hyperconjugation similar to that in the tert-butyl, with hyperconjugation orbitalenergies decreasing with the increase of the number of hydrogen atoms participatingin the hyperconjugation (PIH). The distribution of charge carried by the PIH hydrogenatoms is uniform, which reveals a delocalization character in the electronic structures;and the PIH hydrogen atoms are found responsible for the main IR spectrum peakrelating to C-H stretching vibration. These findings may provide some regularknowledge on hyperconjugation.
Finally, to promote possible applications of graphene in molecular identificationbased on stacking efects, in particular in recognizing aromatic amino acids and evensequencing nucleobases in life sciences, we study the interaction between graphenesegments and diferent cyclic organic hydrocarbons including benzene (C6H6),cyclohexane (C6H12), benzyne (C6H4), cyclohexene (C6H10),1,3-cyclohexadiene(C6H8(1)) and1,4-cyclohexadiene (C6H8(2)), using the density-functionaltight-binding (DFTB) method. The results present obviously diferent characteristics in Raman vibrational and ultraviolet visible absorption spectra of the small moleculesadsorbed on the graphene sheet. That are both spectra involve clearly diferentcharacteristic peaks, belonging to the diferent small molecules upon adsorption, withthe ones of ionized molecules being more substantial. Further analysis shows that theadsorptions are almost all due to the presence of dispersion energy in neutral casesand involve charge transfer from the graphene to the small molecules. In contrast, themain binding force in the ionic adsorption systems is the electronic interaction. Theresults present clear signatures that can be used to recognize diferent kinds ofaromatic hydrocarbon rings on graphene sheets. We expect that our findings will behelpful for designing molecular recognition devices using graphene.
首先，限域下的分子手性转变过程中，极值点的真实结构信息在反应中是非常重要的，但却很难获得，主要是由于复杂的分子相互作用。在本部分，我们基于大量的经典分子动力学模拟的统计结果，阐述了在单壁氮化硼纳米管中，difluorobenzo[c]phenanthrene分子（C18H12F2，称为D分子）的完整手性转变过程，发现在此过程中至少涉及到五个极值点结构，体现出限域环境下手性转变的独特性。我们因此而提议了一种基于经验分子动力学模拟的确定分子间相互作用势能面的方法，这种势能面的求解通常情况下是通过传统的第一性原理计算才可以给出。
其次，基于组合了密度泛函理论和半经验从头算的ONIOM方法分析了手性的difluorobenzo[c]phenanthrene分子(C18H12F2，D分子)在无极富勒烯C260中的对映体间转变过程，以认识限域对手性分子对映体转变过程的影响。我们发现，在红外和拉曼光谱中，与孤立系统相比，限域环境会使D分子谱线整体发生蓝移，于此同时，在0-60cm-1波段内出现6种体现D分子整体运动的独有模式。非常有趣的，在此限域环境下D分子的手性转变过程能垒相比于孤立情况升高了15.88kcal mol-1，展现了这种限域条件可以促进手性分子对映体稳定。而且，在这个限域系统中， D分子的前线分子轨道远离了整个体系的活性区域，使得D分子受到了外面富勒烯的保护而更为稳定。这一结果凸显了纳米尺度限域环境，会对手性分子对映体转变过程具有影响。我们希望，这些结果对手性药物分子的输运乃至手性对映体的稳定具有一定的借鉴意义。
再次，为了进一步探究影响结构稳定性的因素，基于第一性原理密度泛函理论分析了超共轭效应对叔丁基及它的衍生物C4Hn（n=4-10）异构体的结构稳定性的影响。我们发现，n=7-10这四种异构体具有与叔丁基类似的超共轭效应，且超共轭轨道能随参加超共轭效应的氢原子数目的增加而减小。参加超共轭效应的氢原子的带电分布均一，此现象揭示了电子结构当中的离域特征。此外，对红外谱的分析发现，对C-H拉伸振动的峰的贡献主要来自于参加超共轭效应的氢原子。此结果对超共轭效应也展现出一些规律性的认识。
最后，为了促进基于堆垛效应，石墨烯在分子识别方面的可能应用，尤其是在生命科学中，对芳香性氨基酸、乃至测序碱基等带有环状侧链分子的识别，采用密度泛函紧束缚（DFTB）方法，我们研究了石墨烯片段与不同的环状有机碳氢化合物包括苯（C6H6），环己烷（C6H12）,苯炔（C6H4），环己烯（C6H10），1,3-环己二烯（C6H8(1)）及异构体1,4-环己二烯（C6H8(2)）之间的相互作用。结果展现出，在Raman振动谱及紫外可见吸收谱上，均可发现小分子吸附到石墨烯基底具有的明显差异性。也就是，两种光谱都存在一些明显的归属于不同小分子吸附的不同特征峰，而在相应的离子体系中，相应的特征峰更为明显。进一步的分析表明，在中性的环境下，整体的吸附作用能几乎都归因于色散能的存在，并且石墨烯把电子转移给小分子。与此相反，在离子吸附环境下，主要的结合能贡献来自于静电作用。这些结果对在石墨烯基底上不同种类的芳香碳氢化合物环的识别，表明了比较清晰的特征。希望我们的研究有助于基于石墨烯的相应分子识别检测器件的设计。
Chirality is a very important intrinsic property of the natural biological molecules,which is also considered to be directly related to the origin of life. The structuralstability of the enantiomer of chiral molecules as well as the conformation transitionupon the environment is closely associated with some basic life processes. And it alsoplays an important role in drug development and delivery. It has been currentlyreceived much attention in physics, chemistry, material science and life science fields.In this thesis, we synthetically used the density functional theory, density functionaltight binding method developed on this basis, and down to the semi-empirical abinitio as well as the classical molecular dynamics simulation methods, in order tostudy the structures of typical chiral molecules and the feature under environment,including the transition process between enantiomers upon the confinement. Thespecific research work mainly includes the following four parts:
Firstly, reliable structural information of extremal points in a reaction isimportant but difficult to achieve in molecular chiral transitions under confinementdue to the complex molecular interactions. In this part, based on statistical results of anumber of classical molecular dynamics simulations, we expounded the completechiral transition process of a difluorobenzo[c]phenanthrene molecule (C18H12F2, calledD molecule) within a single-walled boron-nitride nanotube involves at least fiveextremal point structures, showing a unique feature of chiral transition in the confinedenvironment and suggesting an alternative to conventional first-principles calculationsto determine the complex potential energy surface of intermolecular interactions.
Secondly, the transition process between chiral difluorobenzo[c]phenanthrenemolecule (C18H12F2, D molecule) enantiomers within non-polar fullerene C260has been studied based on ONIOM method, which combined the density functional theoryand the semi-empirical ab initio method, in order to explore the impact ofconfinement on the transition process of chiral enantiomers. We found that blue shiftoccurred generally in infrared and Raman spectra of D molecule under confinementenvironment, compared with those of isolated systems. Meanwhile, six types ofparticular patterns representing overall movement of D molecules appeared in0-60cm-1band. Interestingly, energy barrier of D molecule chiral transformation under saidconfinement ambience is elevated by15.88kcal·mol-1compared to those underisolated conditions, which means this confinement conditions can facilitate thestability of chiral molecular enantiomers. Moreover, in the confinement system, frontorbital energy of D molecule is lower than that of C260fullerene, so that D molecule isfurther stabilized due to the protection of fullerene matrix, in terms of reactivity. It isconcluded that confinement environment in nanoscale will have an impact onenantiomer transformation process of chiral molecules. These results may instructchiral medicine molecules transport and even the stability of chiral enantiomers.
Thirdly, to further explore the factors that affect the structural stability, thehyperconjugation effect on molecular structural stability is studied by performing firstprinciples density functional theory calculations on the tert-butyl and its derived C4Hn(n=4-10) isomer structures. Four of the isomer structures with n=7-10were found toshow hyperconjugation similar to that in the tert-butyl, with hyperconjugation orbitalenergies decreasing with the increase of the number of hydrogen atoms participatingin the hyperconjugation (PIH). The distribution of charge carried by the PIH hydrogenatoms is uniform, which reveals a delocalization character in the electronic structures;and the PIH hydrogen atoms are found responsible for the main IR spectrum peakrelating to C-H stretching vibration. These findings may provide some regularknowledge on hyperconjugation.
Finally, to promote possible applications of graphene in molecular identificationbased on stacking efects, in particular in recognizing aromatic amino acids and evensequencing nucleobases in life sciences, we study the interaction between graphenesegments and diferent cyclic organic hydrocarbons including benzene (C6H6),cyclohexane (C6H12), benzyne (C6H4), cyclohexene (C6H10),1,3-cyclohexadiene(C6H8(1)) and1,4-cyclohexadiene (C6H8(2)), using the density-functionaltight-binding (DFTB) method. The results present obviously diferent characteristics in Raman vibrational and ultraviolet visible absorption spectra of the small moleculesadsorbed on the graphene sheet. That are both spectra involve clearly diferentcharacteristic peaks, belonging to the diferent small molecules upon adsorption, withthe ones of ionized molecules being more substantial. Further analysis shows that theadsorptions are almost all due to the presence of dispersion energy in neutral casesand involve charge transfer from the graphene to the small molecules. In contrast, themain binding force in the ionic adsorption systems is the electronic interaction. Theresults present clear signatures that can be used to recognize diferent kinds ofaromatic hydrocarbon rings on graphene sheets. We expect that our findings will behelpful for designing molecular recognition devices using graphene.
引文
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