What Factors Govern the Escapability of a Molecule from a Liquid?
Many chemical experiments give us a macroscopic view of a chemical system, but we still have to develop an interpretation of what we observe in terms of the interaction between molecules. Static models of molecules typically give us a view of these systems that does not reflect their dynamical nature at the submicroscopic level. We can use molecular dynamics simulations to gain a better sense of the kinds of motions that molecules typically execute and the timescales on which these motions occur. We can also examine properties that are pretty much inaccessible to experiment, such as the relative importance of Coulomb and van der Waals forces in a simulation. We can also use visualization techniques to develop pictorial models of molecular structure and motion. Such visualizations are often helpful in pointing the way toward other simulations and data analysis that can further explain the nature of the chemical system.
Learning Objectives
Content objectives
Students will
- Describe the relationship between molecular shape, van der Waals energy, and enthalpy of vaporization;
- Differentiate between intermolecular and intramolecular energies (nonbonded and bonded interactions);
- Predict macroscopic properties such as the enthalpies and temperatures of phase transitions using molecular dynamics simulations.
Process objectives
Students will
- Describe the importance of locating equilibrium in a molecular dynamics simulation;
- Perform an energy decomposition and analyze the contributions of different forms of energy to the total energy of a system.
Timing
The complete experiment typically takes two lab periods, each at least three hours long. Instructors can choose to do only Part One, which can be done in one lab period with perhaps some extra out-of-class work. Another option is to have students do calculations for Part Two outside of lab and then discuss the results in a class or partial lab session. (Note that students often want to perform additional calculations for Part Two once they see their initial results.)
Location
https://drive.google.com/file/d/1MnlHyAVikmAnplWKJelAX1yT3H5A_omJ/view?usp=sharing
An instructor’s handbook is available upon request.
A supplemental document provides instructions for using ChemCompute to perform the molecular dynamics calcuations.
License
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Status Reviewed
Reviewed