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Theoretical Chemistry Accounts

, Volume 107, Issue 6, pp 319–325 | Cite as

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

  • Sandor Kristyan
  • Akos Bencsura
  • Akos Vertes
Regular article

Abstract.

A large succinic acid (HOOC(CH2)2COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation.

Key words: Modeling matrix-assisted laser desorption ionization – Molecular mechanics – Clusters – Succinic acid 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Sandor Kristyan
    • 1
  • Akos Bencsura
    • 1
  • Akos Vertes
    • 2
  1. 1.Chemical Research Center, Institute of Chemistry, Hungarian Academy of Sciences, 1025 Budapest, Pusztaszeri út 59–67, HungaryHU
  2. 2.Department of Chemistry, George Washington University, 725. 21st Street, NW, Washington, DC 20052, USAUS

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