Predicting equilibrium intramolecular isotope distribution within a large organic molecule by the cutoff calculation
© 2019 Elsevier Ltd A predicted equilibrium intramolecular isotope distribution (Intra-ID) serves as a reference for measured position-specific (PS) isotope composition variation in an organic molecule. Equilibrium Intra-ID can be estimated from calculated reduced partition function ratios (RPFR or β factor), which are largely absent to date. For relatively small molecules, the PS β factor can be calculated directly. However, estimating the PS β factor considering an entire, large organic molecule is computationally prohibitive. The isotope effect is local in that the vibrational frequencies of an atom are only affected by its proximal bonding environment. Therefore, the cutoff calculation, which simplifies the calculation of an entire molecule to a local area, was previously proposed for large organic molecules. However, the cutoff size was not validated, which has hindered the application of the cutoff calculation. Here, we calculated a series of small organic molecules with 2–18 carbon atoms to test the influence of cutoff size on the 13β value estimation of a target carbon position in a carbon chain or a carbon ring. We calculated nineteen small molecules that have a methyl carbon and a functional group that is at least three bonds away from the target methyl position. The result showed that the equilibrium 13C enrichment of the methyl group relative to CO2 at 25 °C (ln13α(eq)) for the nineteen molecules varied in a small range, with a standard deviation of 0.2‰. Fourteen aromatic hydrocarbons with a benzene and one adjacent functional group were calculated to test the influence of different adjacent functional groups on similar carbon positions in benzene. The results showed that different adjacent functional groups had significant influence only on the predicted ln13α(eq) value of the carbon position directly connected to them (standard deviation = 1.0‰, n = 14), with a negligible influence on the predicted ln13α(eq) value of the remaining carbons in benzene (standard deviation = 0.2‰, n = 14). The PS 13β value of a specific carbon position in CoA calculated by the cutoff calculation differed from that of the entire-molecule calculation by 0.0–0.3‰. We concluded that the cutoff calculation simplified the calculation of a target position from an entire molecule to a cluster of three proximal bonds in a chain and/ or an adjacent ring, providing PS 13β values of sufficient accuracy for large organic molecules.
Publication Source (Journal or Book title)
Geochimica et Cosmochimica Acta
He, Y., Bao, H., & Liu, Y. (2020). Predicting equilibrium intramolecular isotope distribution within a large organic molecule by the cutoff calculation. Geochimica et Cosmochimica Acta, 269, 292-302. https://doi.org/10.1016/j.gca.2019.10.032