Computational Method for Organic Chemistry Class: Finding an Accurate and Time-Efficient Theoretical Level for Modelling Benzene and Nitrobenzene Nitration Reaction Mechanism
Luthfan Irfana, Muhammad Khaffin Suhaimi, Budi Arifin

Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Tanjung Street, IPB Darmaga Campus, Bogor, West Java, 16680

Abstract

The organic reaction mechanism is challenging for most students of organic chemistry undergraduate courses. However, most students often find it hard to imagine how a reaction^s elementary step may occur in 3D space. Computational chemistry with the Nudged Elastic Band (NEB) method enabled one to build a 3D reaction mechanism model relatively quickly. NEB devises minimum energy paths (MEP) between a pair of given reactant and product geometry. In addition to the calculation^s thermodynamics and kinetics profile prediction, the optimized MEP can also be animated using standard molecular visualization software. To get accurate results, one often needs to employ time-consuming computations, rendering this approach inefficient for a class or assignment framework. This study aims to evaluate the computation time and accuracy of NEB implementation with B3LYP-D3, HF-3c, and PBEh-3c theoretical levels in predicting the rate-limiting step of benzene and nitrobenzene nitration. MEP from PBEh-3c NEB calculation can predict the most recent mechanism version of benzene nitration through three reaction intermediates with good geometries and the most time-efficient calculation. Nevertheless, the thermodynamics and kinetics profiles from PEBh-3c NEB calculation are somewhat higher than the more accurate M06-2x result reported elsewhere. Within the framework of class assignment in an undergraduate organic chemistry course, PBEh-3c is highly potential to be applied. General steps to obtain results reported here will be used as animated tutorial video in the Physical Organic Chemistry course at the Undergraduate Chemistry Program, Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University. Moreover, the obtained 3D animations may also be used to enrich lecture presentation materials.

Keywords: organic chemistry, reaction mechanism, aromatic nitration, computational chemistry, NEB, PBEh-3c, physical organic chemistry class, video

Topic: Chemistry Education