Influence of the environment on the infrared spectrum of alanine: An effective mode analysis

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 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 Atomic Multipole Optimized Energetics for Biomolecular Simulation 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 us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. 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.

Automated summary

The vibrational spectrum of alanine amino acid was computationally determined in different environments and phases using molecular dynamics trajectories and an optimized polarizable force field. The analysis revealed significant differences between the spectra of neutral and zwitterionic forms of alanine in the gas phase, and provided insights into the molecular origins of vibrational bands in condensed phases.