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Quantum and mixed quantum-classical dynamics studies of chemical reactions and biological system.

机译：化学反应和生物系统的量子和混合量子经典动力学研究。

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In recent years, there is dramatic progress in doing quantum reaction dynamics for small system particularly for three-atom and four-atom systems. For general polyatomic systems with more than four atoms, reduced dimensional methods have been widely used. In most cases, a group of atoms are treated as one pseudo-atom, therefore methods are classified as three-atom or four-atom system. The biggest shortcoming in the above pseudo-atom models, the stereo geometry information of polyatomic molecule is lost. Considering this disadvantage, semi-rigid vibrating rotor target (SVRT) model were proposed by Prof. Zhang. The SVRT model could be applied to general polyatomic systems, and correctly treat the stereodynamics of the polyatomic system.; In this thesis, SVRT model was implemented to study atom-polyatomic reactions H + CH4 → H2+CH3 as well as O( 3P) + CH4 → OH + CH3. In these calculations, the reaction probabilities, cross section and rate constants were computed. The calculated rate constants are in a good agreement with experimental results, much better than those of pseudo-atom models. Stereodynamics is also explored using the SVRT model. We found that the initial orientation of CH4 plays an important role in reaction dynamics, which could not studied in pseudo-atom methods.; As the reduced mass between atom and polyatomic molecule is relatively large for O(3P) + CH4 → OH + CH3 reaction, the pure quantum computation is becoming expensive. Therefore, mixed quantum/classical approach was implemented and applied to O(3P) + CH4 → OH + CH3, where the translation mode is treated by classical mechanics, while the other coordinates are treated quantum mechanically. Calculation indicates that the QC results agree with the quantum results reasonably, particularly for rate constants.; Finally, the mixed quantum/classical approach is developed to study the energy transfer between Na+ and a dipeptide based on widely used force field. We found that the Na+ could be trapped by peptide at some approaching angles, which resulted in the energy transfer to torsional mode of the dipeptide.
机译：近年来，在小型系统，特别是三原子和四原子系统的量子反应动力学中，取得了巨大的进步。对于具有四个以上原子的普通多原子系统，降维方法已被广泛使用。在大多数情况下，一组原子被视为一个伪原子，因此方法被分类为三原子或四原子系统。上述伪原子模型的最大缺点是多原子分子的立体几何信息丢失。考虑到这一缺点，张教授提出了半刚性振动转子靶（SVRT）模型。 SVRT模型可以应用于一般的多原子系统，并正确对待多原子系统的立体动力学。本文采用SVRT模型研究了H + CH 4 →H 2 + CH 3 以及O（ 3 P）+ CH 4 →OH + CH 3 。在这些计算中，计算了反应概率，截面和速率常数。计算出的速率常数与实验结果非常吻合，远优于伪原子模型。还使用SVRT模型探索了立体动力学。我们发现，CH 4 的初始取向在反应动力学中起着重要作用，而伪原子方法尚无法研究。由于对于O（ 3 P）+ CH 4 →OH + CH 3 反应，原子与多原子分子之间的还原质量较大。纯量子计算变得越来越昂贵。因此，实现了混合量子/经典方法并将其应用于O（ 3 P）+ CH 4 →OH + CH 3 ，其中模态由经典力学处理，而其他坐标则由量子力学处理。计算表明，质控结果与量子结果合理吻合，特别是对于速率常数而言。最后，基于广泛使用的力场，发展了混合量子/经典方法来研究 Na +与二肽之间的能量转移。我们发现， Na +可能在某些接近角度处被肽捕获，从而导致能量转移至二肽的扭转模式。

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