A potential energy surface experiment for the undergraduate computational chemistry laboratory

Abstract

148. Bits and pieces, 49. Computer visuals to help students understand potential energy surfaces.

Computer-based molecular modeling in the curriculum

“…This exercise illustrates cooperativity of group motion during conformational changes in molecules characteristic "softness" of dynamic molecules which defies illustration with traditional molecular models. A similar exercise recently has been reported by Buss and Fountain (48). The present case involves the MMX calculation of total strain energy for incremental rotations about the two carboncarbon bonds using PCModel.…”

A Computational Experiment Introducing Undergraduates to Geometry Optimizations, Vibrational Frequencies, and Potential Energy Surfaces

“…Furthermore, several studies in this Journal have attempted to illustrate the portions of the PES relevant to chemical reactions in low-dimensional (i.e., visualizable) representations. 7,8,10,21 As an example of a simple cut of a PES along one coordinate, a plot of energy versus torsional rotation angle about the C2−C3 bond in butane is given in Figure 1. The anti conformation, the conformation where the C2−C3 bond is rotated so that the methyl groups on C1 and C4 are the furthest from one another, is the lowest energy conformation.…”

“…Today, commercial computational chemistry and physics software packages can be utilized to find the ground state equilibrium geometry, albeit in a relatively complex and opaque way. Several studies in this Journal have utilized the process of geometry optimization, though mostly as a “black box” procedure in which the user does not see any details of the calculation nor a discussion of how it works. − The goal of this exercise is to illustrate some basic ideas of geometry optimizations while providing a practical introduction to computational chemistry for upper-level undergraduate physical chemistry students. The authors acknowledge that we are not completely unveiling the “black box” nature of quantum chemical software packages, as we neglect to discuss the self-consistent-field (SCF) algorithms used for determining the electronic energy, gradients, etc.…”

“…In practice, geometry optimizations find a local stationary point on the PES and one must conduct a large number of geometry optimizations to gain confidence that the global minimum has been determined. Furthermore, several studies in this Journal have attempted to illustrate the portions of the PES relevant to chemical reactions in low-dimensional (i.e., visualizable) representations. ,,, …”

Understanding Chemical Structure/Physical Property Relationships in Polymers through Molecular Modeling and Thermal Analysis Techniques

“…Molecular modeling, in particular, has experienced a renaissance in this regard, moving from a relatively specialized technique for highly trained theoretical chemists to a tool routinely employed throughout our profession (10,11). In our department and in others, simple modeling exercises in the general and organic chemistry laboratories have been effective interest-building and visualization tools (12)(13)(14).…”