Square Parametric Excitation: A Digital Resonant Method for the Quadrupole Ion Trap.

Digital ion trap technology is an alternate method for driving quadrupole ion traps and mass filters using variable frequency, fixed amplitude RF square waves in place of variable amplitude, fixed frequency RF sine waves. This technique offers some advantages such as an increase in the high mass analysis range by varying frequency and lower overall voltage requirements. Here, we present a complex square waveform developed for resonant parametric excitation in a quadrupole linear ion trap. Unlike traditional resonance methods, the driving RF square wave and auxiliary square wave are coupled using the same digital circuitry without the need for transformer coupling. In this work, we use this complex waveform to selectively excite the first order parametric resonances of ion motion. The square parametric excitation method presented here employs a simple and repetitive circuit design consisting of a low-voltage waveform generator followed by a series of high-voltage MOSFET switches. This design allows for resonance methods to be easily implemented in the all-digital quadrupole. The complex square waveform can perform the same useful functions as sine wave auxiliary signals, such as selective mass elimination and mass isolation. We also demonstrate that the mass resolution performance and S/N of our digital mass spectrometer is improved by applying the complex square waveform during ion ejection.

Spectroscopic Quantification of the Inverted Singlet-Triplet Gap in Pentaazaphenalene.

We report the direct and accurate spectroscopic quantification of the inverted singlet-triplet gap in 1,3,4,6,9b-pentaazaphenalene. This measurement is achieved by directly probing the lowest singlet and triplet states via high-resolution cryogenic anion photoelectron spectroscopy. The assignment of the first excited singlet state is confirmed by visible absorption spectroscopy in an argon matrix at 20 K. Our measurements yield an inverted singlet-triplet gap with ΔEST= -0.047(7) eV. The accurate quantification of the singlet-triplet gap presented here allows for direct evaluation of various computational electronic structure methods and highlights the critical importance of the proper description of the double excitation character of these electronic states. Overall, this study validates the idea that despite Hund's multiplicity rule, useful organic chromophores can have inherently inverted singlet-triplet gaps.

The impact of solvation on the structure and electric field strength in Li+GlyGly complexes.

To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.

Tandem Mass-Selective Cryogenic Digital Ion Traps for Enhanced Cluster Formation.

We present the implementation of tandem mass-selective cryogenic ion traps, designed to enhance the range of ion processing capabilities that can be performed prior to spectroscopic interrogation. We show that both the formation of ion clusters and mass filtering steps can be combined in a single cryogenic linear quadrupole ion trap driven by RF square waves. Mass filtering and mass isolation can be achieved by manipulation of the RF frequency and duty cycle. Very importantly, this scheme circumvents the need for high-amplitude RF voltages that can be incompatible with typical cryogenic ion processing conditions. In addition, proper adjustment of the stability boundaries during the clustering process allows for the preferential formation of a specific cluster size rather than a broad distribution of sizes. Lastly, we show that a specific cluster size can be formed, mass-selected, and then transferred to another ion trap for a second completely separate ion processing step. The instrumentation and modular design developed here expand the scope of ionic species and clusters that can be accessed by processing electrosprayed ions.

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.

The impact of the electric field of metal ions on the vibrations and internal hydrogen bond strength in alkali metal ion di- and triglycine complexes.

Using infrared predissociation spectroscopy of cryogenic ions, we revisit the vibrational spectra of alkali metal ion (Li+, Na+, K+) di- and triglycine complexes. We assign their most stable conformation, which involves metal ion coordination to all C=O groups and an internal NH⋯NH2 hydrogen bond in the peptide backbone. An analysis of the spectral shifts of the OH and C=O stretching vibrations across the different metal ions and peptide chain lengths shows that these are largely caused by the electric field of the metal ion, which varies in strength as a function of the square of the distance. The metal ion-peptide interaction also remotely modulates the strength of internal hydrogen bonding in the peptide backbone via the weakening of the amide C=O bond, resulting in a decrease in internal hydrogen bond strength from Li+ > Na+ > K+.

Spectroscopy and Theoretical Modeling of Tetracene Anion Resonances.

The positions and widths of the optically allowed electronic states of the tetracene radical anion located above the detachment threshold energy (i.e anion resonances) are mapped out using total photodetachment yield spectroscopy of cryogenically cooled ions. The presence of these states is detected via the sharp increase in the photodetachment yield compared to that of the monotonic nonresonant direct photodetachment background. The resolution of the resulting spectrum is limited by the ∼5 cm-1 line width of the tunable laser and thus provides a stringent benchmark for computations of the energies and autodetachment lifetimes of these resonance states. The experimental results are compared to high-level electronic structure computations and line width modeling using the orbital stabilization method. These theoretical results are found to be in near quantitative agreement with the experimental data, highlighting their capability to accurately describe the energies and lifetimes of anion resonances for relatively large molecules.

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.

Anion Resonances and Photoelectron Spectroscopy of the Tetracenyl Anion.

The photoelectron spectroscopy of the tetracenyl anion using slow electron velocity-map imaging (SEVI) of cryogenically cooled ions is presented. The total photodetachment yield as a function of photon energy is used to reveal a rich manifold of anion excited states above the detachment threshold. The lowest energy anionic resonance has a sufficiently long lifetime to yield a vibrationally resolved absorption spectrum that can be directly compared with theoretical predictions. Excitation of this state mostly results in electron detachment via thermionic emission. The total photodetachment yield spectrum is used to select photon wavelengths that minimize the indirect detachment signal to allow acquisition of vibrationally resolved photoelectron spectra that can inform on the neutral tetracenyl radical. Assignment of spectral features corresponding to the ground and first excited state of the neutral 12-tetracenyl isomer is made with the aid of Franck-Condon simulations. This yields adiabatic electron affinity and term energies that differ significantly from the previously reported values. Weak features corresponding to the ground state of the minor 2-teracenyl and 1-tetracenyl isomers are also identified, which allows for the experimental determination of their electron affinities for the first time.

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+.

Vibrationally resolved photoelectron spectroscopy of oligothiophene radical anions.

Vibrationally resolved photoelectron spectroscopy of terthiophene, quaterthiophene, and quinquethiophene radical anions is presented. The increased spectral resolution afforded by the combination of slow photoelectron velocity-map imaging and ion cooling in a cryogenic ion trap allows the characterization of vibronic structures within the S0 and T1 states. Analysis of the spectra, aided by electronic structure calculations and Franck-Condon simulations, revealed evidence for significant contributions from kinetically trapped higher energy conformers in the anion-to-triplet transitions. Unlike the lowest energy structures, where all the thiophene linkers are in the trans configuration, these higher energy conformers contain at least one cis linker. We also found that the adiabatic Franck-Condon simulations drastically underestimated the intensities of some vibronic features in the singlet ground state spectra due to large geometry changes upon photodetachment and anharmonic couplings in the singlet state.

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.

Probing Solvation-Induced Structural Changes in Conformationally Flexible Peptides: IR Spectroscopy of Gly3H+·(H2O).

IR predissociation spectroscopy of the Gly3H+(H2O) complex formed inside of a cryogenic ion trap reveals how the flexible model peptide structurally responds to solvation by a single water molecule. The resulting one-laser spectrum is quite congested, and the spectral analyses were assisted by both H2O/D2O substitution and IR-IR double resonance spectroscopy, revealing the presence of two contributing isomers and extensive anharmonic features. Comparisons to structures found via a systematic computational search identified the geometries of these two isomers. The major isomer, with all trans amide bonds and protonation on the terminal amine, represents ∼90% of the overall population. It noticeably differs from the unsolvated Gly3H+, which exists in two isomeric forms: one with a cis amide bond and the other with protonation on an amide C═O. These results indicate that interactions with just one water molecule can induce significant structural changes, i.e., cis- trans amide bond rotation and proton migration, even as the clustering occurs within an 80 K cryogenic ion trap. Calculations of the isomerization pathways further reveal that the binding energy of the water molecule provides sufficient internal energy to overcome the barriers for the observed structural changes, and the minor solvation isomer results from a small fraction of the ions being kinetically trapped along one of the pathways.

Ground and low-lying excited states of phenoxy, 1-naphthoxy, and 2-naphthoxy radicals via anion photoelectron spectroscopy.

We present the slow electron velocity map imaging spectroscopy of cryogenically cooled phenoxide, 1-naphthoxide, and 2-naphthoxide anions. The results allow us to examine the ground state and the lowest energy excited state in the corresponding neutral radicals. Care was taken to minimize autodetachment signals in the photoelectron spectra, allowing for more straightforward comparisons with Franck-Condon analyses. The ground states of these three aromatic oxide radicals all have the unpaired electron residing in a π orbital delocalized throughout the molecule. The electron affinity of 1-naphthoxy is measured to be 2.290(2) eV, while that of 2-naphthoxy is measured to be 2.404(2) eV, both of which are higher than that of the smaller phenoxy molecule at 2.253(1) eV. The first excited states have the unpaired electron residing in a more localized σ orbital, yielding measured term energies for the à state of 1.237(2) eV in 1-naphthoxy and 1.068(1) eV in 2-naphthoxy, while that of phenoxy is lower at 0.952(1) eV. The calculated Franck-Condon spectra generally showed good agreement with the experimental spectra, yielding assignments of the more active vibrations in each electronic state. Significant autodetachment signals arising from dipole bound states near the ground states of all three radicals were observed in our efforts to avoid them, and comparably less autodetachment signals were observed near the excited states. Besides this type of non-Franck-Condon intensities in the photoelectron spectra, we also observed minor features arising due to vibronic coupling in the ground states of all three radicals.

Spectroscopy of Reactive Complexes and Solvated Clusters: A Bottom-Up Approach Using Cryogenic Ion Traps.

In this paper, applications of cryogenic ion traps for forming reaction intermediates and solvated clusters from precursor ions generated by electrospray ionization are presented and discussed. These studies are motivated by the aim of spectroscopically probing isolated complexes that exhibit higher levels of complexity in chemical compositions and intermolecular interactions, which make them more closely resemble the systems existing in real-world environments. Illustrative examples are provided to highlight the current capabilities, showcase the detailed information available in the spectroscopic results, and outline general future directions.

Photoelectron spectroscopy of anthracene and fluoranthene radical anions.

We report the slow electron velocity map imaging spectroscopy of cryogenically cooled anthracene and fluoranthene radical anions, two similarly sized polycyclic aromatic hydrocarbon molecules. The results allow us to examine the lowest energy singlet and triplet states in the neutral molecules on equal footing from the anionic ground state. The analysis of the experimental spectra is aided by harmonic calculations and Franck-Condon simulations, which generally show good agreement with experimental values and spectra. The electron affinity of fluoranthene is measured to be 0.757(2) eV, which is larger than that of anthracene at 0.532(3) eV. The lowest energy triplet state in anthracene is observed at 1.872(3) eV above the singlet ground state, while that of fluoranthene is observed at 2.321(2) eV above its singlet ground state. Comparisons of experimental and calculated spectra show that in addition to the Franck-Condon active modes, there is a clear presence of vibrational modes that gain intensity via vibronic coupling in both the singlet and triplet states in both molecules. In addition, the triplet state generally exhibits increased vibronic coupling compared to the singlet state, with the fluoranthene triplet state exhibiting evidence of distortion from C2v symmetry.

Accessing the Vibrational Signatures of Amino Acid Ions Embedded in Water Clusters.

We present an infrared predissociation (IRPD) study of microsolvated GlyH+(H2O) n and GlyH+(D2O) n clusters, formed inside of a cryogenic ion trap via condensation of H2O or D2O onto the protonated glycine ions. The resulting IRPD spectra, showing characteristic O-H and O-D stretches, indicate that H/D exchange reactions are quenched when the ion trap is held at 80 K, minimizing the presence of isotopomers. Comparisons of GlyH+(H2O) n and GlyH+(D2O) n spectra clearly highlight and distinguish the vibrational signatures of the water solvent molecules from those of the core GlyH+ ion, allowing for quick assessment of solvation structures. Without the aid of calculations, we can already infer solvation motifs and the presence of multiple conformations. The use of a cryogenic ion trap to cluster solvent molecules around ions of interest and control H/D exchange reactions is broadly applicable and should be extendable to studies of more complex peptidic ions in large solvated clusters.

IR-IR Conformation Specific Spectroscopy of Na+(Glucose) Adducts.

We report an IR-IR double resonance study of the structural landscape present in the Na+(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na+(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five ß-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination. Graphical Abstract ᅟ.