Applying Computational Chemistry to the Undergraduate Laboratory: A "Wet" Lab - "Dry" Lab Experience

学生很难理解化学中抽象的原子世界。他们经常通过算法方法学习概念，而不是真正理解潜在的理论。这个问题在一定程度上是由于化学的三维、动态性质，以及用于预测化学行为的数学模型。计算化学有能力克服学生学习的这些障碍。它使学生能够感知分子和电子结构的三维。它显示了对化学行为至关重要的动态信息。学生们可以操纵数学参数并观察原子的后果。为了帮助学生学习，这个项目将计算化学纳入我们的物理、有机和生物化学课程。计算化学越来越多地应用于工作场所的所有化学和生物化学领域。通过体验与实验紧密相关的计算课程，学生学会在最常使用的背景下欣赏计算化学，以预测和解释实验数据。自由能模拟被用来研究蛋白质折叠、配体结合和溶剂化效应以及其他大系统的热力学。这些方法还没有在本科课程中使用，在给出热力学的分子基础的具体例子方面具有很大的教学价值。由于它们依赖于经典牛顿物理学，其基本理论对本科生来说非常容易理解。通过这个项目，使用基于分子动力学的自由能模拟来开发本科生实验室。在这里的图形工作站上开发、测试和改进的实验室可以在下一代PC上轻松执行。*

Students have difficulty understanding the abstract atomic world of chemistry. They often learn concepts by an algorithmic approach rather than by truly understanding the underlying theory. This problem is in part due to the three-dimensional, dynamic nature of chemistry, as well as the mathematical models used to predict chemical behavior. Computational chemistry has the power to overcome these obstacles to student learning. It allows students to perceive molecules and electronic structure in three dimensions. It displays dynamical information critical to chemical behavior. Students can manipulate mathematical parameters and observe the atomic consequences. To aid student learning, this project incorporates computational chemistry into our physical, organic, and biochemistry curricula. Computational chemistry is increasingly applied at the workplace in all fields of chemistry and biochemistry. By experiencing a computational curriculum closely tied to experiments, students learn to appreciate computational chemistry in the context in which it is most often used, to predict and interpret experimental data. Free energy simulations are used to study the thermodynamics of protein folding, ligand binding, and solvation effects and of other large systems. These methods, not yet exploited in the undergraduate curriculum, have great pedagogical value in giving concrete examples of the molecular basis for thermodynamics. Since they depend on classical Newtonian physics, the underlying theory is very accessible to the undergraduate student. Through this project, undergraduate laboratories are developed using molecular-dynamics-based free energy simulations. The laboratories developed, tested, and refined here on graphics workstations are easily performed on the next generation of PCs. *