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Can Semi‐empirical Calculations Help Solve Mass Spectrometry Problems? Protonation Sites and Proton Affinities of Amino Acids
Author(s) -
Amorim Madeira Paulo J.,
Vaz Pedro D.,
Bettencourt da Silva R. J. N.,
Florêncio M. Helena
Publication year - 2013
Publication title -
chempluschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.801
H-Index - 61
ISSN - 2192-6506
DOI - 10.1002/cplu.201300173
Subject(s) - affinities , protonation , proton affinity , proton , chemistry , computational chemistry , stereochemistry , physics , nuclear physics , organic chemistry , ion
Owing to the recent development of the PM6 and PM6‐DH+ semi‐empirical methodologies, which belong to the neglect of diatomic differential overlap (NDDO) family, it was decided to carry out a study to assess whether these inexpensive and fast methodologies could be used with confidence to help solve mass spectrometry problems. As such, a report on the feasibility of using semi‐empirical calculations to identify probable protonation sites in amino acids is presented. The optimised geometries obtained by the semi‐empirical calculations were compared to several structures reported in the literature (obtained through high‐level theoretical calculations) and reasonable agreement was found. The proton affinities derived from semi‐empirical calculations were also compared with experimental data and benchmarked as well with predicted values from the literature (also obtained through high‐level theoretical calculations). Semi‐empirical calculations accurately predicted the most probable protonation site for all amino acids considered; thus leading to results comparable to those obtained by high‐level calculations at an extremely low computational cost. Regarding the proton affinity estimates, deviations from the available experimental values are greater for the semi‐empirical proton affinities than for those observed for high‐level calculations. A statistical analysis of the data, at a confidence level of 99 %, also showed that the semi‐empirical proton affinities were different from experimental values and high‐level proton affinities were equivalent to experimental values. Nevertheless, the overall correlation of the semi‐empirical data with experimental values is, at least, satisfactory. We believe therefore that this paper shows that semi‐empirical methodologies, which are fast and inexpensive, can indeed solve mass spectrometry problems, or at least, facilitate a quicker path to the solution.