偶氮、亚胺小分子取代基效应及HNNOH氢键的理论研究
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摘要
本人在攻读博士学位期间主要从事了以下三个方面的研究。第一部分采用B3LYP方法在6-311++G**水平下,利用自然键轨道分析(Natural Bond Orbital, NBO)和分子中的原子理论(Atoms in Molecules)作为分析工具,研究了12种取代基对偶氮分子的两种异构体和亚胺分子三种异构体(至少56个化合物)的几何结构、电子结构、拓扑性质、异构化反应以及异构体的稳定性的影响,并且为了获得更为可靠的能量和反应焓的预测,我们对这些化合物还进行了MP4和G3的计算,此外在这部分工作的初始阶段,我们采用了8种方法(HF、MP2和6种DFT方法)分别在8种基组水平下对10个偶氮分子异构体进行了优化,根据对这些优化结构的比较,我们才确定B3LYP/6-311++G**为这一部分研究的计算水平。而在第二部分,我们采用了MP2/6-311++G**在标准优化和完全均衡校正法(Counterpoise Procedure, CP)两种条件下优化了HNNOH的11种氢键二聚体,并采用了AIM和NBO作为分析工具研究了复合物稳定性与氢键参数间的相关性以及标准优化与CP校正对复合物体系的相互作用能、几何结构的影响。在第三部分,我们采用了HF、B3LYP和MP2方法以及6-311++G**基组对氯代甘氨酸的13种异构体进行了优化,并且对这些优化结构在相同的基组水平下进行了MP4的单点能校正,讨论了电子相关对优化结构的影响,并且主要采用NBO方法对异构体的稳定性进行了分析。
除了以上三方面的研究外,本人在香港浸会大学化学系从事了大约7个月的酶的分子动力学研究,此研究内容没有包括在本论文中。
本文首先使用密度泛函理论的B3LYP方法研究了含N=N双键的偶氮小分子体系HNNR和含C=N双键的亚胺小分子体系(H2C=NR和HN=CHR)的取代基效应,取代基R为H、F、OH、OCH3、OCF3、NH2、NO2、NO、CHO、CN、CH3、CF3。以这些小分子体系作为含-N=N-和 >C=N-官能团的大分子体系的简化模型,我们利用自然键轨道理论(Natural Bond Orbital, NBO)和
分子中的原子理论(Atoms in Molecule, AIM)作为主要的分析工具研究了取代基对这两个体系的几何结构、原子电荷、异构体的相对稳定性、反式/顺式异构化反应的影响,并采用等键反应研究了取代基对偶氮分子和亚胺分子稳定性的影响。为选择足够准确和有效的计算水平,我们对五种偶氮化合物的顺式和反式构型分别在8种基组水平下采用8种方法进行详细的计算和分析,确定出B3LYP/6-311++G**水平为本文研究取代基效应的计算水平。在这一部分的研究中我们尤其关注了Hammett取代基常数、取代基的电负性与分子性质变化的相关性,这种相关性将会为实验家们提供一些直接的信息,有助于他们通过取代基的性质来修饰相关的化合物。我们的研究实践中采用现代量子化学精确计算方法,使取代基效应的研究向着定量化、更有预测性,使理论和实验的更紧密结合的方向发展,做了新的、有益的探索并得到了一些可喜的成绩。
在本文的第二部分,我们以羟基二酰亚胺HNNOH所形成的多种构型的氢键体系(单氢键的链状构型、双氢键的环状构型)为研究对象,使用了MP2方法探讨了二聚体构型以及其中的单体构型对氢键体系结合能和氢键参数间相关性的影响,我们的结果表明单体构型和二聚体的构型都能影响这种相关性的存在,甚至能破坏这种相关性,这种新的思维模式提醒人们在利用氢键参数推测复合物体系的稳定性时应该注意构型的影响。此外,我们主要采用了AIM理论的八个拓扑参数更为可靠地解释了氢键的存在,这种解释有助于进一步理解氢键的本质。另一方面我们在本部分也研究了基组叠加误差(Basis Set Superposition Error, BSSE)校正对复合物体系的几何结构、结合能的影响,其结果表明在研究分子间相互作用时完全均衡校正(Counterpoise-corrected )法是必需的。
第三部分采用了MP2和B3LYP方法在6-311++G**基组水平下研究了13种N-Cl甘氨酸异构体的相对稳定性。为确保B3LYP和MP2计算的能量的可靠性,我们采用了MP4方法在同样的基组水平下对优化结构进行了单点能校正。应用了NBO和AIM方法分析了异构体中轨道间的相互作用、键的本质以及分子内氢键的相互作用,我们的结果表明异构体的相对稳定性是由氢键作用(对于含氢键的异构体)和分子内的其他超共轭作用平衡的结果,本部分的研究为人们了理解电负性基团对甘氨酸构型,进而蛋白质构型的影响提供了有用的线索。
At first, B3LYP method is applied to study substituent effects on diazene derivatives(HNNR) and imine derivatives (H2C=NR and HN=CHR), R=H, F, OH, OCH3, OCF3, NH2, NO2, NO, CHO, CN, CH3, CF3. These simple molecules could be taken as prototype of large diazene and imine compounds. Natural bond orbital and Atoms in Molecules are employed to analyze the substituent effects on geometrical structures, atomic charges, relative stabilities of isomers and trans/cis isomerization reactions. In addition, isodesmic reaction is used to study the substituent effects on stabilities of the diazene and imine molecules. In order to choose reliable computational level, eight methods are applied to optimize trans and cis forms of five diazene molecules, respectively using eight basis sets. With comparison of computation, B3LYP/6-311++G** is selected as computational level in this part. In the study, we pay more attention to the correlation of the molecular properties with the Hammett substituent constants and the electronegativities, while the correlation could provide some direct information for the experimenters.
In the second part, MP2 method is employed to study the effects of conformation of HNNOH monomer and dimmer on correlation of interaction energy with parameters describing hydrogen bond in dimmer systems. Our observations show that the conformation of the complexes and the constituting monomers could affect the correlation, even break down it. The result suggests that we should consider the effect of conformation when applying parameters describing hydrogen
bond to predict stabilities of complex. In addition, the eight topological parameters derived from AIM are applied to determine the hydrogen bond, which is helpful to understand the nature of hydrogen bonding. On the other hand, we discuss effect of basis set superposition error on the geometrical structures and interaction energies of complexes. Our results reveal that it is necessary to use counterpoise-corrected gradient procedure to study intermolecular interactions.
In the third part, MP2 and B3LYP methods are employed to study the relative stabilities of conformers of N-Cl glycine using 6-311++G** basis set. Single-point MP4 calculations using the same basis set are carried out in order to confirm the reliabilities of B3LYP and MP2 on energies and relative stabilities of glycine derivatives. NBO and AIM methods are used to analyze hyperconjugative interaction between the molecular orbitals and the nature of bond as well as intramolecular hydrogen bonds. Our observation indicates that the origin of relative stability comes from the balance of the hydrogen bond and the hyperconjugative effect. These observations provide some useful information to understand the effect of electronegative group on the conformation of glycine, further on conformation of protein.
除了以上三方面的研究外,本人在香港浸会大学化学系从事了大约7个月的酶的分子动力学研究,此研究内容没有包括在本论文中。
本文首先使用密度泛函理论的B3LYP方法研究了含N=N双键的偶氮小分子体系HNNR和含C=N双键的亚胺小分子体系(H2C=NR和HN=CHR)的取代基效应,取代基R为H、F、OH、OCH3、OCF3、NH2、NO2、NO、CHO、CN、CH3、CF3。以这些小分子体系作为含-N=N-和 >C=N-官能团的大分子体系的简化模型,我们利用自然键轨道理论(Natural Bond Orbital, NBO)和
分子中的原子理论(Atoms in Molecule, AIM)作为主要的分析工具研究了取代基对这两个体系的几何结构、原子电荷、异构体的相对稳定性、反式/顺式异构化反应的影响,并采用等键反应研究了取代基对偶氮分子和亚胺分子稳定性的影响。为选择足够准确和有效的计算水平,我们对五种偶氮化合物的顺式和反式构型分别在8种基组水平下采用8种方法进行详细的计算和分析,确定出B3LYP/6-311++G**水平为本文研究取代基效应的计算水平。在这一部分的研究中我们尤其关注了Hammett取代基常数、取代基的电负性与分子性质变化的相关性,这种相关性将会为实验家们提供一些直接的信息,有助于他们通过取代基的性质来修饰相关的化合物。我们的研究实践中采用现代量子化学精确计算方法,使取代基效应的研究向着定量化、更有预测性,使理论和实验的更紧密结合的方向发展,做了新的、有益的探索并得到了一些可喜的成绩。
在本文的第二部分,我们以羟基二酰亚胺HNNOH所形成的多种构型的氢键体系(单氢键的链状构型、双氢键的环状构型)为研究对象,使用了MP2方法探讨了二聚体构型以及其中的单体构型对氢键体系结合能和氢键参数间相关性的影响,我们的结果表明单体构型和二聚体的构型都能影响这种相关性的存在,甚至能破坏这种相关性,这种新的思维模式提醒人们在利用氢键参数推测复合物体系的稳定性时应该注意构型的影响。此外,我们主要采用了AIM理论的八个拓扑参数更为可靠地解释了氢键的存在,这种解释有助于进一步理解氢键的本质。另一方面我们在本部分也研究了基组叠加误差(Basis Set Superposition Error, BSSE)校正对复合物体系的几何结构、结合能的影响,其结果表明在研究分子间相互作用时完全均衡校正(Counterpoise-corrected )法是必需的。
第三部分采用了MP2和B3LYP方法在6-311++G**基组水平下研究了13种N-Cl甘氨酸异构体的相对稳定性。为确保B3LYP和MP2计算的能量的可靠性,我们采用了MP4方法在同样的基组水平下对优化结构进行了单点能校正。应用了NBO和AIM方法分析了异构体中轨道间的相互作用、键的本质以及分子内氢键的相互作用,我们的结果表明异构体的相对稳定性是由氢键作用(对于含氢键的异构体)和分子内的其他超共轭作用平衡的结果,本部分的研究为人们了理解电负性基团对甘氨酸构型,进而蛋白质构型的影响提供了有用的线索。
At first, B3LYP method is applied to study substituent effects on diazene derivatives(HNNR) and imine derivatives (H2C=NR and HN=CHR), R=H, F, OH, OCH3, OCF3, NH2, NO2, NO, CHO, CN, CH3, CF3. These simple molecules could be taken as prototype of large diazene and imine compounds. Natural bond orbital and Atoms in Molecules are employed to analyze the substituent effects on geometrical structures, atomic charges, relative stabilities of isomers and trans/cis isomerization reactions. In addition, isodesmic reaction is used to study the substituent effects on stabilities of the diazene and imine molecules. In order to choose reliable computational level, eight methods are applied to optimize trans and cis forms of five diazene molecules, respectively using eight basis sets. With comparison of computation, B3LYP/6-311++G** is selected as computational level in this part. In the study, we pay more attention to the correlation of the molecular properties with the Hammett substituent constants and the electronegativities, while the correlation could provide some direct information for the experimenters.
In the second part, MP2 method is employed to study the effects of conformation of HNNOH monomer and dimmer on correlation of interaction energy with parameters describing hydrogen bond in dimmer systems. Our observations show that the conformation of the complexes and the constituting monomers could affect the correlation, even break down it. The result suggests that we should consider the effect of conformation when applying parameters describing hydrogen
bond to predict stabilities of complex. In addition, the eight topological parameters derived from AIM are applied to determine the hydrogen bond, which is helpful to understand the nature of hydrogen bonding. On the other hand, we discuss effect of basis set superposition error on the geometrical structures and interaction energies of complexes. Our results reveal that it is necessary to use counterpoise-corrected gradient procedure to study intermolecular interactions.
In the third part, MP2 and B3LYP methods are employed to study the relative stabilities of conformers of N-Cl glycine using 6-311++G** basis set. Single-point MP4 calculations using the same basis set are carried out in order to confirm the reliabilities of B3LYP and MP2 on energies and relative stabilities of glycine derivatives. NBO and AIM methods are used to analyze hyperconjugative interaction between the molecular orbitals and the nature of bond as well as intramolecular hydrogen bonds. Our observation indicates that the origin of relative stability comes from the balance of the hydrogen bond and the hyperconjugative effect. These observations provide some useful information to understand the effect of electronegative group on the conformation of glycine, further on conformation of protein.
引文
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