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

Abstract

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.

Undergraduate Independent Study Project: Theoretical vs Computational Approaches to Calculate the Electronic Structure of the D5h symmetric Pentafluoroxenate(IV) Anion

“…Resources detail the projection operator method for point groups containing C 2 , C 3 , and C 4 rotation axes, but few resources detail a procedure for polyatomic molecules with a C 5 rotation axis. ,− The student must build the bridge between the logic of group theory and approximations of computational chemistry to solve the problem of the electronic structure of a C 5 symmetric molecule similar to pedagogical outcomes like Torras’ modeling of thiophene torsion . The C 5 symmetric molecule chosen for the independent study was the D 5 h point group conformation of pentafluoroxenate(IV) anion, [XeF 5 ] − (Figure ).…”

“…2,5−7 The student must build the bridge between the logic of group theory and approximations of computational chemistry to solve the problem of the electronic structure of a C 5 symmetric molecule similar to pedagogical outcomes like Torras' modeling of thiophene torsion. 8 The C 5 symmetric molecule chosen for the independent study was the D 5h point group conformation of pentafluoroxenate(IV) anion, [XeF 5 ] − (Figure 1). 9 The C 5 rotation axis is a challenge as the geometry does not allow for any simplifications of the projector operator method and includes concepts like the "golden ratio" from number theory that may inspire students to explore further into that mathematical space.…”

Enhancing Students’ Understanding of the Structures and Aromaticities of Cyclobutadiene and Cyclooctatetraene through a Computational Chemistry Exercise

“…Thus, introducing computational chemistry to undergraduates is crucial for their education. Numerous computational chemistry laboratory exercises − have significantly improved undergraduate chemistry education. These exercises facilitate conceptual understanding, , provide research opportunities, , complement traditional laboratory experiments, provide problem-solving skills, and foster interdisciplinary collaboration .…”

“…Numerous computational chemistry laboratory exercises − have significantly improved undergraduate chemistry education. These exercises facilitate conceptual understanding, , provide research opportunities, , complement traditional laboratory experiments, provide problem-solving skills, and foster interdisciplinary collaboration . Integrating computational chemistry into the curriculum equips students with essential tools and skills for successful careers in chemistry and related fields.…”