SummaryDetails of progress are provided in the sections which follow but first, for convenience, a short summary is given:· We have succeeded in developing simulation methods that reliably predict performance of ion trap mass spectrometers including the relationship between geometry, electric fields, ion motion, and mass spectra · These procedures have been used to optimize cylindrical ion traps (CITs) including those used in the commercial Griffin Analytical Technologies instruments · We have generalized the simulation program (ITSIM) to allow calculation of ion motion and of mass spectra in 3D electric fields of any arbitrary shape · We have invented the rectilinear ion traps (RIT), a version of linear ion trap which traps an order of magnitude more ions than previous 3D (Paul) ion traps · We have simulated and built arrays of ion traps suited to multiplexed mass analysis and other purposes · Practical applications of our ion traps in miniature mass spectrometers include air monitoring applications (DHS supported) and explosives monitoring experiments (TSA supported) both based on the fundamental DOE-supported work · Applications and simulations of ion motion in the newly commercialized high resolution mass spectrometer (Orbitrap) employed for the understanding of ion motion and its control developed using the ITSIM program · Large inverse KIEs have been discovered in halogen cluster ions and are interesting for their magnitude and mechanistic implications (threshold angular momentum effects on rotational predissociation) · The kinetic method of thermochemical estimation has been extended to quantitative chiral analysis and the methodology has been transferred to the pharmaceutical industry through lectures, discussions and collaborations · The kinetic method has also been successfully applied to the quantatitave analysis of structural isomers, especially isomeric peptides · The serine octamer has been generated by sublimation; this magic-number cluster exists in two isomeric forms and has a strong preference for homochirality. The implications of these and related observations on sprayed serine for the origin of homochirality on earth confirm our work in this area ITSIM: Ion SimulationsNew Version of ITSIM 6.0 The ion trap simulation program ITSIM has been developed and used in this laboratory since 1990. The main goal in using this program is to improve data for use in enhancing ion trap performance and developing new types of ion trap mass spectrometers. A field computational/trajectory simulation approach is adopted to obtain a detailed understanding of ion motion in ion trap instruments. The key