Building a Torsional Potential between Thiophene Rings to Illustrate the Basics of Molecular Modeling

Modeling an inter-ring torsional profile of a simple 2,2 '- bithiophene molecule has been used to illustrate the main concepts associated with basic molecular modeling within an introductory course in a master's degree on computational modeling. The methodology proposed in the activity has been used to guide and train the student along the classical and quantum model concepts visited along the main subject. The common thread that links the different concepts being learned is based on the deficiencies that usual force fields present in the right description of the torsional profiles. The students have learned how to obtain and implement the torsional profile of 2,2 '- bithiophene to obtain the correct conformer population distribution and compare it to the distribution obtained using a predetermined classical force field. On the basis of the results obtained along the implementation of this activity and the student surveys, we conclude that this lab activity was successful as a complement to help students to understand the basic concepts of molecular modeling.

Automated summary

This article introduces the basic concepts of molecular modeling in a master's degree course on computational modeling through modeling a 2,2'-bithiophene molecule. The students learn how to obtain and implement the torsional profile of the molecule and compare it with a classical force field to obtain the correct conformer population distribution. Based on the results and student feedback, this lab activity is successful in complementing the understanding of molecular modeling basics.