大分子的动力学理论研究
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摘要
用量子力学的方法理解化学反应的动力学规律、研究分子的物理化学特性是原子分子物理研究的重要课题之一。
本文分两大部分,第一部分是用半刚性振转靶(SVRT)模型研究多原子分子反应,第二部分是生物大分子的共轭帽分子分割法(MFCC)的理论计算研究。
在过去的二十年中,量子反应动力学理论得到了极大发展,已经可以对四原子反应体系进行严格的全量子计算。然而,在化学和生物等领域往往涉及更多个原子的反应,目前还不能对超过四原子的反应体系进行全维的量子动力学计算。为了对多原子分子反应进行定量的动力学计算,可以采用约化维数的方法来降低计算难度,如绝热修正法、固定几何性质近似法、以及量子—经典力学方法等。本文采用纽约大学张增辉教授提出的一种约化维数模型—半刚性振转靶模型来研究多原子分子反应。
半刚性振转靶模型将反应分子(靶分子)看作由两部分组成,在反应过程中两部分各自保持刚性,两部分之间的距离可以发生变化,同时两部分可以绕共同分子轴转动。此时靶分子可以看作一个半刚性的振转子,它的空间运动可视为一个非对称转子的运动,包括一维相对运动(振动)和转动。由于它考虑了空间转动,所以SVRT模型能够正确地体现反应体系的立体动力学效应,这一点对研究多原子分子反应非常重要。此模型特别适合用于靶分子中有一个较弱的键,且反应结束后此键断开的反应体系。运用SVRT模型,一般的双多原子—多原子分子反应体系,可将自由度约化为7个,单原子—多原子分子反应体系自由度可约化为4个。
本文研究了单原子—多原子分子反应的4个反应体系,其中:
在Garcia的势能面上对O(~3P)+CH_4→CH_3+OH反应进行了4维的量子动力学研究,计算了其初始基态、振动激发态、转动激发态的态态反应几率和散射截面,发现Garcia势能面上反应阈能在0.6eV附近;反应几率在近能垒高度时有较
Quantum dynamics study of polyatomic reaction and accurate quantum mechanical calculation for biological molecules such as proteins are very important topics in computational chemistry and biology.
This dissertation is organized as follows: Part I: Semirigid vibrating rotor target (SVRT) model is applied to study the reaction of atom-polyatoms using time-dependent wave packet method. Part II: Molecular fractionation with conjugate caps (MFCC) approach is applied to calculate electron density and electrostatic potential of proteins.
Over the past twenty years, with the development of quantum scatting theory and the enhancement of computational capacity, it has been possible to take full quantum calculation on reactions with no more than four atoms. But in chemical and biological fields, reactions always deal with more than four atoms. So, to take accurate full quantum calculations on such reactions, some models and dimension-reduced computational methods have been development to reduce the calculational difficulty such as adiabatic approach, fixed geometry approximations and mixed quantum-classical dynamics methods.
In the SVRT model, the reacting molecule is treated as a semirigid vibrating rotor which can be considered as a three-dimensional generalization of the diatomic molecule. This model provides a realistic framework to treat reaction dynamics of polyatomic systems. Using the SVRT model, it becomes computationally practical to carry out quantitatively accurate quantum dynamics calculation for a variety of dynamics problems in which the reacting molecule is a polyatomic or complex molecule.
Since the SVRT model can deal with the special locomotion, it correctly includes
本文分两大部分,第一部分是用半刚性振转靶(SVRT)模型研究多原子分子反应,第二部分是生物大分子的共轭帽分子分割法(MFCC)的理论计算研究。
在过去的二十年中,量子反应动力学理论得到了极大发展,已经可以对四原子反应体系进行严格的全量子计算。然而,在化学和生物等领域往往涉及更多个原子的反应,目前还不能对超过四原子的反应体系进行全维的量子动力学计算。为了对多原子分子反应进行定量的动力学计算,可以采用约化维数的方法来降低计算难度,如绝热修正法、固定几何性质近似法、以及量子—经典力学方法等。本文采用纽约大学张增辉教授提出的一种约化维数模型—半刚性振转靶模型来研究多原子分子反应。
半刚性振转靶模型将反应分子(靶分子)看作由两部分组成,在反应过程中两部分各自保持刚性,两部分之间的距离可以发生变化,同时两部分可以绕共同分子轴转动。此时靶分子可以看作一个半刚性的振转子,它的空间运动可视为一个非对称转子的运动,包括一维相对运动(振动)和转动。由于它考虑了空间转动,所以SVRT模型能够正确地体现反应体系的立体动力学效应,这一点对研究多原子分子反应非常重要。此模型特别适合用于靶分子中有一个较弱的键,且反应结束后此键断开的反应体系。运用SVRT模型,一般的双多原子—多原子分子反应体系,可将自由度约化为7个,单原子—多原子分子反应体系自由度可约化为4个。
本文研究了单原子—多原子分子反应的4个反应体系,其中:
在Garcia的势能面上对O(~3P)+CH_4→CH_3+OH反应进行了4维的量子动力学研究,计算了其初始基态、振动激发态、转动激发态的态态反应几率和散射截面,发现Garcia势能面上反应阈能在0.6eV附近;反应几率在近能垒高度时有较
Quantum dynamics study of polyatomic reaction and accurate quantum mechanical calculation for biological molecules such as proteins are very important topics in computational chemistry and biology.
This dissertation is organized as follows: Part I: Semirigid vibrating rotor target (SVRT) model is applied to study the reaction of atom-polyatoms using time-dependent wave packet method. Part II: Molecular fractionation with conjugate caps (MFCC) approach is applied to calculate electron density and electrostatic potential of proteins.
Over the past twenty years, with the development of quantum scatting theory and the enhancement of computational capacity, it has been possible to take full quantum calculation on reactions with no more than four atoms. But in chemical and biological fields, reactions always deal with more than four atoms. So, to take accurate full quantum calculations on such reactions, some models and dimension-reduced computational methods have been development to reduce the calculational difficulty such as adiabatic approach, fixed geometry approximations and mixed quantum-classical dynamics methods.
In the SVRT model, the reacting molecule is treated as a semirigid vibrating rotor which can be considered as a three-dimensional generalization of the diatomic molecule. This model provides a realistic framework to treat reaction dynamics of polyatomic systems. Using the SVRT model, it becomes computationally practical to carry out quantitatively accurate quantum dynamics calculation for a variety of dynamics problems in which the reacting molecule is a polyatomic or complex molecule.
Since the SVRT model can deal with the special locomotion, it correctly includes
引文
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