Untangling Hydrogen Bond Networks with Ion Mobility Spectrometry and Quantum Chemical Calculations: A Case Study on H⁺XPGG

Abstract

Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of singly protonated XaaProGlyGly peptides: H + DPGG, H + NPGG, H + EPGG, and H + QPGG. The IMS distributions are similar, suggesting the peptides adopt closely related structures in the gas phase. Quantum chemical calculations show that all conformers seen in the experimental spectrum correspond to the cis configuration about the Xaa-Pro peptide bond, significantly different from the behavior seen previously for H + GPGG. Density functional theory and quantum theory of atoms in molecules (QTAIM) investigations uncover a silent drama as a minor conformer not observed in the H + DPGG spectrum becomes the preferred conformer in H + QPGG, with both conformers being coincident in collision cross section. Investigation of the highly coupled hydrogen bond network, replete with CH•••O interactions and bifurcated hydrogen bonds, reveals the cause of this effect as well as the absence of trans conformers from the spectra. A series of generalized observations are provided to aid in enzyme and ligand design using these coupled hydrogen bond motifs.

Tautomerization of H+KPGG: Entropic Consequences of Strong Hydrogen-Bond Networks in Peptides

“…To begin analyzing the effect of hydrogen bonding on the entropic differences reported in the previous section, Table details the potential energy density, V ( r ), at the bond critical point (bcp) for each hydrogen bond of both tautomers shown in Figure , ordered from strongest to weakest. The previous study on D, N, E, and QPGG detailed the correlation between hydrogen-bond length and V ( r ), employing this quantity to detail changes in the hydrogen-bonding networks of cis species as the N-terminal residue was changed . Compared to the intricate and bifurcated hydrogen-bonding networks detailed in the previous studies, the hydrogen-bonding patterns seen in Figure are refreshingly simple.…”

“…The conformer making up the minor peak, Figure (A), will be referred to throughout this report as Nt- cis -1, with Nt referring to the placement of the excess proton on the N-terminal amino group, cis referring to the cis orientation of the Pro and Lys α carbons (illustrated by the green line in Figure (A)), and −1 referring to this being the lowest-lying Nt- cis conformer in terms of Gibbs free energy. Of relevance to the previous studies, Nt- cis -1 corresponds to the cis -1r structures reported in the study of H + XPGG, where X = D, N, E, and Q, with −1 r corresponding to a specific arrangement of the hydrogen-bonding network as well as an interaction between the C-terminal hydroxyl group and the N-terminal residue’s side chain . However, here we are more interested in the tautomers rather than individual conformers and number the structures of any given conformer of each tautomer by relative Gibbs free energies.…”

“…Previous work outlined how frequency scaling, the most common method for correcting this deficiency, does not significantly affect the overall conformational energies even in drastic circumstances . However, given the previous work on D, N, E, and QPGG, this is a good opportunity to explore the effects of hydrogen-bonding differences on the entropy . Finding a correlation between hydrogen-bonding strength and entropy would be interesting not only from a purely theoretical point of view but also in validating and motivating the use of uncorrected entropic differences between skeletally similar conformers here and in the future.…”

“…7 Collision cross sections were obtained via the trajectory method as implemented in MOBCAL 31 and were averaged over 100 runs for each conformer, as they were in our previous work. 8 Intensities were derived via a simple Boltzmann analysis and normalized with respect to the lowest-energy conformer. Interestingly, while the previous studies had some emphasis on the "chair" and "boat" configurations of the proline residue (following the nomenclature from the study on H + GPGG), 7 in the majority of cases only one conformer was found ("boat" in most of these cases), and in cases where both forms were obtained, the lowest Gibbs free energy conformer is reported.…”

“…Previously we have reported ion mobility spectrometry coupled with mass spectrometry (IMS-MS) of singly protonated GPGG to calibrate and test quantum chemical methods for the elucidation of peptide conformational distributions. Furthermore, we used our calibrated methodology along with the quantum theory of atoms in molecules (QTAIM) to probe the hydrogen-bond network of structurally similar singly protonated hairpin peptides (XPGG, X = D, E, N, Q) and understand how slight changes to hydrogen-bond networks affect electronic energies. , These previous studies built up a theoretical framework we can take advantage of for the study of lysine. In line with this framework, we report the IMS spectrum of gas-phase H + KPGG, the simplest lysine-containing hairpin allowing intramolecular hydrogen-bonding interactions not taken into account when studying isolated lysine, as has been done with high-level quantum chemical calculations in the past. ,− …”