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How Good Are Force Fields for Gas-Phase Protonated Peptides?

Published

Author(s)

Christopher Kinsinger, Karl K. Irikura

Abstract

With the increase in mass-spectrometry-based proteomics, many research projects depend on the chemistry of peptide fragmentation. Elucidating fragmentation mechanisms requires a thorough exploration of the potential energy surface. Conformational searching tools have not yet been tested for gas-phase, protonated peptides. Herein we present and validate a method for identifying low-energy conformations and calculating reliable energetic data. This method uses a molecular mechanics force field for conformational searching and then optimizes low-energy structures with a quantum mechanical method. When compared to grid-based conformational searches by the same quantum mechanical method, the method combining molecular and quantum mechanical calculations is more efficient and locates the same global minimum.
Citation
Journal of Computational Chemistry

Keywords

computational chemistry, conformational search method, force field, molecular mechanics, peptide fragmentation, quantum mechanics

Citation

Kinsinger, C. and Irikura, K. (2008), How Good Are Force Fields for Gas-Phase Protonated Peptides?, Journal of Computational Chemistry (Accessed June 25, 2024)

Issues

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Created October 16, 2008