The kinetic isotope effect (KIE) of a molecule is the difference in reaction rate between isotopologues. Certain atoms having a greater contribution to the overall KIE indicates that these atoms are more prominent in a reaction mechanism, such as a conformational change. Understanding the KIE elucidates key information about molecular reactivity, mechanisms, and selectivity of pathways. Although enthalpic and entropic origins of KIE can be examined theoretically, atomic origins are difficult to isolate if they cannot be determined experimentally or intuitively . Kurt Mislow’s doubly bridged diketone is an optically active molecule with such indeterminable KIE origin .<br/><br/>LUCKIE is a Python software programmed to calculate the atomic contributions to the KIE of any unimolecular system and produce a PyMOL display. LUCKIE implements the NumPy library and PyMOL API. Vibrational frequency and atomic displacement data are produced through quantum mechanical calculations with the Gaussian 09 package using the B3LYP/6-31G(d,p) basis set, particularly freqchk, scan, and natural bond orbital (NBO) functionalities. LUCKIE has been debugged and reviewed for accuracy and robustness with test case molecules with known KIE origins. KIE calculations for each molecule are done via the Bigeleisen-Meyer equation as well as the enthalpy-entropy method. Molecular structures are extracted from literature.<br/><br/>LUCKIE concludes that the KIE origin of Mislow’s diketone lies on the exomethylene bridging protons. A study of priopionaldehyde as a model molecule of the diketone poses the hypothesis that hyperconjugation interactions may be largely responsible. The overarching goal of the project is to not only unravel the KIE origin of this molecule through computational methods, but to illustrate the utility and robustness of LUCKIE, a new tool designed for physical-organic chemists.

Visualizing the origin of kinetic isotope effects with Python

255th National Meeting (2018)

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