Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

Shivangi Nangia, Barbara J. Garrison

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

Original languageEnglish (US)
Pages (from-to)1744-1747
Number of pages4
JournalNuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms
Issue number14
StatePublished - Jul 15 2011

All Science Journal Classification (ASJC) codes

  • Nuclear and High Energy Physics
  • Instrumentation


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