Conformation Changes, Complexation, and Phase Transition in Matrix-Assisted Laser Desorption

Abstract

Using molecular dynamics simulations we have demonstrated that the guest species in matrix-assisted laserdesorption exhibits significantly different conformations in the gas phase, on the crystal surface, and embeddedinto the matrix. Our model fully accounted for the internal structure of matrix and guest molecules; thus, wewere able to follow the details of conformational changes in the guest molecule within the crystal and throughoutthe desorption. During the embedding process, simulated by sinapinic acid crystal growth around the substanceP guest species, changes in the guest species conformation were investigated. While the guest species placedon the surface of the host crystal exhibited two hydrogen bonds on the backbone and one turn, the conformationof the embedded species contained three hydrogen bonds and two turns. Independent of the burial depth, theconformation of the guest species within the crystal remained the same. After laser heating and during thedesorption process, no preferred gas-phase conformation was observed. Investigation of the radius-of-gyrationof the guest species originating from different layers of the crystal revealed that, upon desorption, the guestspecies did not sustain a stable conformation in the gas phase. Liftoff velocities of the guest species embeddedin various layers of the host crystal and on the surface were similar to the liftoff velocities of the matrixmolecules around them. This is an indication of the entrainment of guest species by the matrix plume.Investigation of the energy histories of the matrix and guest species showed lower internal and kinetictemperatures for the latter, which could explain the absence of fragmentation in MALDI. Results also showedthat maximum energy transfer occurred during the phase transition of the host crystal at which time the guestspecies were released from the crystal. Examining the noncovalent complex of the guest species and sinapinicacid anions showed that the complex remained intact throughout the desorption process. A similar phenomenonis often reflected in MALDI mass spectra, in the form of guest-matrix adduct peaks.