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On the structure elucidation using ion mobility spectrometry and molecular dynamics.

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      A new approach is described for the elucidation of gas-phase peptide ion structures combining ion mobility spectrometry (IMS) data and molecular dynamics (MD)-cluster analysis (CA) prediction. The new approach is based on the determination of the gas-phase ion structure identity vectors (e.g., structure and population vectors) that generate the total conformational space of the gas-phase ion as a function of the IMS experimental conditions (e.g., field strength, pressure, bath gas temperature, and IM cell geometry). Two methods to efficiently sample the gas-phase conformational space of molecular ions as a function of the effective ion temperature characteristic of the IMS experiments are described: (i) a simulated annealing MD-CA-constant temperature MD-CA, and (ii) a generalized non-Boltzmann sampling MD-free energy analysis-CA. The new theoretical method has been successfully applied to two model peptide ions (Bradykinin fragments 1-5 and 1-8, RPPGF and RPPGFSPF, respectively) for which multiple conformations sensitive to the effective ion temperature have been suggested in previous studies.

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      [1 ] Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
      J Phys Chem A
      The journal of physical chemistry. A
      American Chemical Society (ACS)
      Jul 23 2009
      : 113
      : 29
      19569657 10.1021/jp811150q


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