Effects of Methyl Side Chains on the Microsolvation Structure of Protonated Tripeptides.

The infrared predissociation spectra of the Gly3H+(H2O)1-2 and Ala3H+(H2O)1-2 clusters are presented and analyzed with the goal of revealing the influence of methyl side chains on the microsolvated structures of these flexible tripeptides. We have shown previously that the presence of methyl side chains can modulate the strengths of the intramolecular hydrogen bonds, thereby influencing the structures adopted by the bare tripeptides composed of glycine and alanine residues. This effect was attributed to the electron-donating nature of the methyl group, whose presence alters the proton affinities of the functional groups that are involved in hydrogen bonding. Here, we expand this work to the microsolvated tripeptides to determine how the effects of the presence of the methyl group evolve with the addition of water solvent molecules. For each solvated cluster, we found multiple solvated structures present, and their relative populations were disentangled using isomer-specific spectroscopic techniques and comparisons to calculation. The results showed that while the glycine and alanine tripeptides display similar structures for the dominant solvation population, they do have different structures for their minor solvation constituents stemming from their different bare tripeptide structures. The relative populations of these minor constituents indicate that the influence of the methyl side chain on intramolecular hydrogen bonding persists to some extent with solvation.

Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues.

We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR-IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. These observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.

Comment on "Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy".

This Viewpoint presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev, et al. 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D2-tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Once these spectral effects are taken into account, we show that both clustering approaches yield similar cluster structures for the small GlyH+(H2O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298 K is explored using a series of model polyalanine chains.

Continuous measurements of volatile gases as detection of algae crop health.

Algae cultivation in open raceway ponds is considered the most economical method for photosynthetically producing biomass for biofuels, chemical feedstocks, and other high-value products. One of the primary challenges for open ponds is diminished biomass yields due to attack by grazers, competitors, and infectious organisms. Higher-frequency observations are needed for detection of grazer infections, which can rapidly reduce biomass levels. In this study, real-time measurements were performed using chemical ionization mass spectrometry (CIMS) to monitor the impact of grazer infections on cyanobacterial cultures. Numerous volatile gases were produced during healthy growth periods from freshwater Synechococcus elongatus Pasteur Culture Collection (PCC) 7942, with 6-methyl-5-hepten-2-one serving as a unique metabolic indicator of exponential growth. Following the introduction of a Tetrahymena ciliate grazer, the concentrations of multiple volatile species were observed to change after a latent period as short as 18 h. Nitrogenous gases, including ammonia and pyrroline, were found to be reliable indicators of grazing. Detection of grazing by CIMS showed indicators of infections much sooner than traditional methods, microscopy, and continuous fluorescence, which did not detect changes until 37 to 76 h after CIMS detection. CIMS analysis of gases produced by PCC 7942 further shows a complex temporal array of biomass-dependent volatile gas production, which demonstrates the potential for using volatile gas analysis as a diagnostic for grazer infections. Overall, these results show promise for the use of continuous volatile metabolite monitoring for the detection of grazing in algal monocultures, potentially reducing current grazing-induced biomass losses, which could save hundreds of millions of dollars.

Direct Measurement of the Visible to UV Photodissociation Processes for the PhotoCORM TryptoCORM.

PhotoCORMs are light-triggered compounds that release CO for medical applications. Here, we apply laser spectroscopy in the gas phase to TryptoCORM, a known photoCORM that has been shown to destroy Escherichia coli upon visible-light activation. Our experiments allow us to map TryptoCORM's photochemistry across a wide wavelength range by using novel laser-interfaced mass spectrometry (LIMS). LIMS provides the intrinsic absorption spectrum of the photoCORM along with the production spectra of all of its ionic photoproducts for the first time. Importantly, the photoproduct spectra directly reveal the optimum wavelengths for maximizing CO ejection, and the extent to which CO ejection is compromised at redder wavelengths. A series of comparative studies were performed on TryptoCORM-CH3 CN which exists in dynamic equilibrium with TryptoCORM in solution. Our measurements allow us to conclude that the presence of the labile CH3 CN facilitates CO release over a wider wavelength range. This work demonstrates the potential of LIMS as a new methodology for assessing active agent release (e.g. CO, NO, H2 S) from light-activated prodrugs.

Competition between Solvation and Intramolecular Hydrogen-Bonding in Microsolvated Protonated Glycine and ß-Alanine.

Infrared predissociation (IRPD) spectroscopy is used to reveal and compare the microsolvation motifs of GlyH+(H2O)n and ß-AlaH+(H2O)n. The chemical structure of these amino acids differ only in the length of the carbon chain connecting the amine and carboxyl terminals, which nonetheless leads to a significant difference in the strength of the intramolecular C═H-N hydrogen bond in the unsolvated ions. This difference makes them useful in our studies of the competition between solvation and internal hydrogen bonding interactions. Analysis of the IRPD results reveals that the sequential addition of water molecules leads to similar effects on the intramolecular interaction in both GlyH+(H2O)n and ß-AlaH+(H2O)n. Solvation of the -NH3+ group leads to a weakening of the C═O···H-N hydrogen bond, while solvation of the carboxyl -OH leads to a strengthening of this bond. Additionally, we have found that for ß-AlaH+, the addition of a H2O to the second solvation shell can still influence the strength of the C═O···H-N hydrogen bonding interaction. Finally, because the C═O···H-N interaction in ß-AlaH+ is stronger than that in GlyH+, more solvent molecules are needed to sufficiently weaken the intramolecular hydrogen bond such that isomers without this bond begin to be energetically competitive; this occurs at n = 5 for ß-AlaH+ and n = 1 for GlyH+.

Microsolvation Structures of Protonated Glycine and l-Alanine.

The IR predissociation spectra of microsolvated glycine and l-alanine, GlyH+(H2O) n and AlaH+(H2O) n, n = 1-6, are presented. The assignments of the solvation structures are aided by H2O/D2O substitution, IR-IR double resonance spectroscopy, and computational efforts. The analysis reveals the water-amino acid as well as the water-water interactions, and the subtle effects of the methyl side chain in l-alanine on the solvation motif are also highlighted. The bare amino acids exhibit an intramolecular hydrogen bond between the protonated amine and carboxyl terminals. In the n = 1-2 clusters, the water molecules preferentially solvate the protonated amine group, and we observed differences in the relative isomer stabilities in the two amino acids due to electron donation from the methyl weakening the intramolecular hydrogen bond. The structures in the n = 3 clusters show a further preference for solvation of the carboxyl group in l-alanine. For n = 4-6 clusters, the solvation structure of the two amino acids is remarkably similar, with one dominant isomer present in each cluster size. The first solvation shell is completed at n = 4, evidenced by a lack of free NH and OH stretches on the amino acid, as well as the first observation of H2O-H2O interactions in the spectra of n = 5. Finally, we note that calculations at the density functional theory (DFT) level show excellent agreement with the experiment for the smaller clusters. However, when water-water interactions compete with water-amino acid interactions in the larger clusters, DFT results show greater disagreement with experiment when compared to MP2 results.