Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

Abstract

Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd.

Tailored Transition‐Metal Coordination Environments in Imidazole‐Modified DNA G‐Quadruplexes

“…For G 4 L 2 R , the analysis gave the following picture: although the quadruplex was found to be unstable in absence of Cu II cations, hence denatured to single strands in the gas phase, the addition of one equiv of Cu II led to the observation of [G 4 L 2 R K 3 Cu] 4− as main species, besides a series of additional unspecific potassium adducts. Corresponding values for the TIMS‐derived collisional cross‐sections (CCS) (G 4 L 2 R =814 Å 2 , G 4 L 2 S =814 Å 2 ) were comparable to reported values for unmodified G‐quadruplexes . Compared to the reported CCS for G 4 L 1 R (793 Å 2 ), this corresponded to an increase of 21 Å 2 , which was ascribed to the longer linker of L 2 …”

“…Corresponding values for the TIMS-derived collisional cross-sections( CCS) (G 4 L 2R = 814 2 , G 4 L 2S = 814 2 )w ere comparable to reported values for unmodified G-quadruplexes. [16] Compared to the reported CCS for G 4 L 1R (793 2 ), this corresponded to an increase of 21 2 ,w hich was ascribed to the longer linker of L 2 . [13] Considering that we were interested in comparingC CS valueso ff olded G-quadruplexes in the presence and absence of Cu II ,t he more stable sequence G 5 L 2R consisting of one additional G-tetradw as investigated.…”

Drift Tube Ion Mobility: How to Reconstruct Collision Cross Section Distributions from Arrival Time Distributions?

“…The narrow distribution is attributed to the rigidity of the parallel G-quadruplex stem. 13 Other examples of narrow CCS distributions are shown in Figures 4A (tunemix, m = 922 and z = 1) and 4B (the foldamer of Figure 1). The blue distributions are reconstructed using Eq.…”

A Unique (3+2) Annulation Reaction between Meldrum's Acid and Nitrones: Mechanistic Insight by ESI‐IMS‐MS and DFT Studies

“…[3a] Electrosprayi onization mass spectrometry (ESI-MS)a long with directi nfusion of liquid solutions has proven to be a usefult ool that allows the "off-line" monitoring of reactions in almostareal-time mode. [12] In IMS, ions are separated as af unctiono ft heir charge,s hape, and size throught heir collisionc ross-section (CCS, W). [7,8] This is a salient feature to tackle the determination of heat-sensitive speciess uch as the ones putatively encountered from Meldrum's acid (1)( e.g., 4 and 5).…”