For larger molecules as in biological or pharmaceutical applications, DFT takes too long, and thus other approaches such as force field calculations and/or molecular modeling are used. For smaller molecules, density functional theory (DFT) is an often used example. To calculate the (optimized) geometry, a lot of options exist regarding the mathematical approach. This mobility value is directly available from flight time measurements in an ion mobility spectrometer : Here is the length of the drift tube, is the voltage drop over the whole drift tube length, and is the analyte’s drift time directly obtainable in the measurements. The standard approach is that model structures are optimized (typically with help of quantum-chemical calculations), and then their collision cross section is calculated, from which finally the ion mobility can be calculated : and are the masses of the (neutral) drift gas and the analyte, is the analyte’s charge, and is the number density of the drift gas. The collisions are assumed to be elastic. In this method, the angle between the incoming trajectory and outgoing trajectory of a particle colliding with the analyte is used to determine the collision cross section : The variables, , and are the Euler-Angles for the collision geometry between analyte and drift gas, is the scattering angle, is the relative velocity of the drift gas, is the impact parameter defining how far the drift gas atom is positioned from the -axis, is the reduced mass, is the Boltzmann Constant, and is temperature in Kelvin. The method known for delivering the best results and which is also the mathematically most demanding (and thus leading to the longest calculation times) is the Trajectory Method. They represent different compromises between accuracy and calculation time. īasically, there are three methods available to calculate the collision cross section from model structures and thus the ion mobility. A detailed description of the different mathematical approaches employed in order to calculate the most important parameter for structural information, the collision cross section (which furthermore determines the ions’ mobility), can be found in. An overview over the variety of structure analysis based on IMS can be found in, for example. Applications in gas phase peptide ion structure analysis can be found, for example, in, where IMS measurements combined with molecular modeling allowed for the determination of folding structures and backbone orientations. Already in 2004 a review stated that IMS has matured enough to become a mainstream research methodology for structural analysis, especially in combination with mass spectrometry. Much younger is the scientific application of IMS in order to characterize the structure of analytes. Famous for their small device size in the centimeter range, their fast response times in the ms range, and their very high sensitivity in the lower ppbv range, IMS detectors can be found in a number of quite different locations and applications. Ion mobility spectrometry (IMS) has been a tool for the analysis of gases for a long time. In this paper, it is analyzed how well the ion trajectory method is suitable to reproduce the measured ion mobility of small organic molecules such as the water clusters forming the positively charged reactant ions, simple aromatic substances, and n-alkanes. With help of theoretic principles, it is possible to develop molecular models that can be verified by the comparison of their calculated cross sections with experimental data. In particular, the collision cross section, which is related to the mobility, is of interest here. In the last 15 years, this technique has been further developed as a tool for structural analysis, for example, in pharmaceutical applications. Examples are military applications, but also safety related applications, for example, for protection of employees in industries working with hazardous gases. Ion mobility spectrometry is a well-known technique for analyzing gases.
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