Computing the Nonlinear Vibrational Response of Liquids and Biomolecules

康奈尔大学的Roger Loring得到了理论和计算化学计划的支持，以开发在液体和生物分子中建模非线性红外光谱的方法，并具有原子级的描述。 在两脉冲和三脉冲振动回波测量的实验观测值将使用经典的分子动力学模拟计算。 支撑这项研究的基本理论问题是确定复杂系统的经典力学分子动力学数据的最佳使用，以计算名义上的量子力学可观测量。 两个紧密耦合的研究方向将追求：（1）建立严格的经典机械回波计算的有效性制度，通过执行数值精确的经典和量子计算相同的模型系统，（2）进行经典的回声计算的液体状态和生物分子模型，量子处理是不可行的。 计算将集中在肌红蛋白-CO上，实验现在正在表征蛋白质波动的性质和时间尺度。 计算振动回波肌红蛋白CO将确定特定的蛋白质动力学检测的CO配体，并将指导这些新的激光实验室技术的应用到其他bimolecular systems.Molecular运动在液体溶剂和蛋白质的异质环境中的化学反应和生物过程的动力学的一个组成部分。 新一代的光谱技术可以直接探测这些运动。 这项研究将允许通过解释这些新的测量结果来详细描述这些过程的分子图像。

Roger Loring of Cornell University is supported by the Theoretical and Computational Chemistry Program to develop methods for modeling nonlinear infrared spectroscopy in liquids and biomolecules with an atomistic level of description. Experimental observables in two-pulse and three-pulse vibrational echo measurements will be computed using classical molecular dynamics simulations. The fundamental theoretical issue underpinning this research is determining the optimal use of classical mechanical molecular dynamics data for complex systems to calculate nominally quantum mechanical observables. Two closely coupled research directions will be pursued: (1) to establish rigorously the validity regime of classical mechanical echo calculations, by performing numerically exact classical and quantum calculations for the same model system, and (2) to perform classical echo calculations for liquid-state and biomolecular models, for which quantum treatment is not feasible. Calculations will focus on myoglobin-CO, for which experiments are now characterizing the nature and time scales of protein fluctuations. Computing vibrational echoes in myoglobin-CO will identify the specific protein dynamics sensed by the CO ligand, and will guide the application of these new laser laboratory techniques to other bimolecular systems.Molecular motions in liquid solvents and in the heterogeneous environments of proteins are an integral part of the dynamics of chemical reactions and biological processes. A new generation of spectroscopic techniques can probe these motions directly. This research will allow for a detailed molecular picture of these processes by interpreting these new measurements.