Influence of the environment on the infrared spectrum of alanine: an effective modes analysis

06 February 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range of 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories carried out with the AMOEBA polarizable force field. An effective mode analysis was performed in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of the amino acid. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.


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