Computer Simulation of Chemical Dynamics

理论与计算化学项目将在未来三年资助韦恩州立大学的William Hase教授。在本研究项目中，经典分子动力学模拟将用于研究单个分子和化学反应系统的微观原子运动，目的是与实验进行比较，并确定分子内动力学、能量传递、化学反应动力学和动力学的基本信息。由于统计理论被广泛用于解释实验，因此将进行统计计算以与分子动力学模拟进行比较。研究的具体问题有：(1)CH3和H原子与金刚石表面的结合动力学；(2)碰撞诱导离解（CID）和表面诱导离解（SID）的能量传递动力学；(3)气相亲核取代动力学；(4)直接从头计算和半经验动力学。经典分子动力学有望为这些研究问题提供准确的结果，而考虑到它们的复杂性，量子动力学计算将是困难的。在直接动力学中，通过将电子结构理论直接与分子动力学模拟相结合，将轨迹“动态地”集成在一起。这是执行模拟的前沿方法，与现代计算机的计算能力直接相关。直接半经验动力学可用于长时间研究大系统（如CID和SID），而从头算直接动力学可用于短时间研究小系统。后者的一个例子是当它们从势能势垒移动到产品时，轨迹的出口通道和能量分配动力学。将采用最先进的矢量和并行处理计算机体系结构来增强直接动力学模拟。在这个研究项目中，分子建模和模拟被用来研究单个分子的运动和分子碰撞导致的化学反应和能量传递。分子模拟方法已经变得足够复杂，它们通常是预测性的，给出接近定量的结果。在接下来的三年里，将进行的研究包括应用成熟的模拟方法来解释新的实验结果和测试理论模型，以及开发更直接的模拟方法来研究大分子系统。要进行的具体模拟有：(1)导致金刚石膜生长的反应；(2)离子与表面碰撞时团簇破碎和离子破碎的质谱实验。后者已被提议作为测序肽的程序；(3)离子与分子之间的反应；(4)高能量分子的碎片化。

The Theoretical and Computational Chemistry Program is supporting Professor William Hase of Wayne State University for the next three years. In this research project classical molecular dynamics simulations will be used to study the microscopic atomistic motion of individual molecules and of chemical reactive systems, with the goals of comparing with experiment and determining fundamental information about intramolecular dynamics, energy transfer, and chemical reaction dynamics and kinetics. Since statistical theories are widely used to interpret experiment, statistical calculations will be performed to compare with the molecular dynamics simulations. The specific problems chosen for study are: (1) the kinetics of CH3 and H atom association with diamond surfaces; (2) energy transfer dynamics in collision-induced dissociation (CID) and surface-induced dissociation (SID); (3) the dynamics of gas-phase nucleophilic substitution; and (4) direct ab initio and semiempirical dynamics. Classical molecular dynamics is expected to give accurate results for these research problems and, given their complexity, quantum dynamical calculations would be difficult. In direct dynamics, trajectories are integrated `on the fly` by interfacing electronic structure theory directly with the molecular dynamics simulations. This is a frontier approach for performing simulations, which is directly linked to the computational power of modern computers. Direct semiempirical dynamics may be used to study large systems for long times (e.g. CID and SID), while ab initio direct dynamics may be applied to small systems for short times. An example of the latter is the exit-channel and energy partitioning dynamics of trajectories as they move from a potential energy barrier to products. State-of-the art vector and parallel processing computer architecture will be used to enhance the direct dynamics simulations. In this research project molecular modeling and simulation is used to study the motion of individual molecules and of molecular collisions leading to chemical reaction and energy transfer. Molecular simulation methodologies have become sufficiently sophisticated that they are often predictive, giving near-quantitative results. The research to be performed during the upcoming three year period includes applications of well-developed simulation methods to interpret new experimental results and test theoretical models, as well as the development of more direct simulation approaches for studying large molecular systems. The specific simulations to be performed are of: (1) reactions leading to diamond film growth; (2) mass-spectroscopy experiments of cluster fragmentation and fragmentation of ions when they collide with the surfaces. The latter has been proposed as a procedure for sequencing peptides; (3) reactions between ions and molecules; and (4) the fragmentation of highly energized molecules.