Aggregation of sphigomyelin (SM) in biomembrane, which forms a platform of the “lipid raft”, has been intensively studied due to its relevance in biological functions. Vibrational spectroscopy is a powerful tool to investigate the dynamical behavior of SM (and lipids in general) in a membrane; yet the assignment of the observed spectrum is often non-trivial. Here, we propose a novel approach to simulate the vibrational spectrum of condensed phase systems, which helps assign the vibrational bands and understand their physical origin. The proposed method takes advantage of the locality of molecular vibrational states, divides the system into molecular fragments, and provides the vibrational spectrum by a statistical weight average over spectra of the fragments. We have carried out molecular dynamics simulations for the SM bilayer to obtain the weight of SM clusters in NPT ensemble formed by intermolecular hydrogen bonds of the amide group. Then, vibrational structure calculations have been carried out for each cluster at the level of B3LYP/6-31++G(d,p). The resulting weight averaged spectrum with anharmonic correction, shown in Figure 1, is found to be in excellent agreement with the experimental one. The calculated spectrum unambiguously assigns the observed two bands to CC stretching and amide I (CO stretching) bands. Furthermore, the analysis of the amide I band indicates that the dominant cluster in bilayer is the dimer with the minor being monomer and trace amounts of trimer.

Statistically weight averaged vibrational spectrum over molecular fragments for studying the amide I vibration of sphingomyelin bilayer

249th National Meeting (2015)

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