Benzhydrylpyridinium Ions: A New Class of Thermometer Ions for the Characterization of Electrospray-Ionization Mass Spectrometers

Tuning the Internal Energy of Ions Produced by Atmospheric and High-Pressure Electrospray by Modulating the Gas Throughput into the First Vacuum Stage

In a high-pressure environment, electrospray ionization (ESI) can be achieved without discharge between the emitter and the counter electrode, thus enabling the generation of gas-phase ions from liquid with high surface tension, such as pure water, which requires a high onset voltage for stable ESI. In this study, the ion dissociation during the transferring of ions/charged droplets from a superatmospheric pressure environment to vacuum has been systematically investigated using benzyl ammonium thermometer ions. The ion source pressure did not affect the internal energy distribution of ions, whereas the gas throughput into the first vacuum stage clearly influences the internal energy distribution of the ions. The increase in the gas throughput increased the density of molecules/atoms presented in ion transfer/focusing electrodes located in the first vacuum stage. As a result, the mean free path of ions in the first vacuum stage decreases, and the energy of ions decreases by decreasing the kinetic energy involved in each collision between ions and residue gas. The gas throughput into the first vacuum stage is found to describe the internal energy distribution of ions associated with the local conditions more quantitatively instead of using the measured pressure of the vacuum stage, which is different from the effective local pressure. This study also demonstrated the controlled dissociation of ions using the ion transfer settings of the instrument in combination with ion inlet tubes of different sizes.

Pentafluorobenzylpyridinium: new thermometer ion for characterizing the ions produced by collisional activation during tandem mass spectrometry

In this study, pentafluorobenzylpyridinium (F5-BnPy+), which has the highest dissociation energy among the reported benzylpyridinium thermometer ion, is proposed to characterize the internal energy distributions of ions activated by higher energy collisional dissociation (HCD) and ion-trap collision-induced dissociation (CID) during tandem mass spectrometry. The dissociation threshold energies of F5-BnPy+ was determined using quantum chemistry calculations at the CCSD(T)/6-311++G(d,p)//M06-2X-D3/6-311++G(d,p) level of theory, and the appearance energies for ion dissociation in HCD and ion-trap CID were estimated using Rice-Ramsperger-Kassel-Marcus theory. The main differences between HCD and ion-trap CID are the collision energies used and the timescales of collisional activation. For both HCD and ion-trap CID, the average internal energy of the ions increased with increasing collision energy. In contrast, the average value for the internal energy of the ions activated by ion-trap CID was lower than that of ions activated by HCD, probably because of the smaller collisional energy and longer activation time of the ion-trap CID experiments. The reported method will aid in the determination of the optimum tandem mass spectrometry parameters for the analysis of small molecules such as metabolites.

Differences in the internal energies of ions in electrospray ionization mass spectrometers equipped with capillary-skimmer and capillary-RF lens interfaces

Small metabolites are commonly analyzed using electrospray ionization mass spectrometry (ESI-MS). Although the protonated form of a compound of interest is typically the target ion in ESI-MS, the protonated forms of small metabolites occasionally undergo fragmentation during ion transmission from ambient conditions to vacuum conditions, hindering the unambiguous identification of analyte molecules. To estimate the fragmentation efficiency during ESI processes, the internal energy distribution of the ions (P(E)) must be evaluated. The common approach for the P(E) evaluation is the survival yield method, which uses thermometer ions. In this study, the P(E) of ions produced by an ESI source in a commercial triple quadrupole mass spectrometer equipped with a capillary-skimmer and capillary-RF lens interfaces was evaluated using benzyl ammonium thermometer ions. Furthermore, this study proposes the use of 3-(aminomethyl)indole and related compounds, which have the lowest Eapp values among the reported thermometer ions, to obtain P(E) values of the ions more accurately. Results showed that P(E) strongly depends on whether a capillary-skimmer interface or capillary-RF lens interface was used for ion transport to the vacuum. ESI-MS with a capillary-skimmer interface provided a considerably lower and narrower P(E) of ions than that with a capillary-RF lens interface, thereby producing intact protonated molecules without significant fragmentation of most small metabolites. However, ESI-MS equipped with capillary-RF lens interfaces provided a higher efficiency of ion transmission than ESI-MS equipped with a capillary-skimmer interface, allowing for highly sensitive analysis of metabolites.

From electrospray ionization to cold-spray ionization: How to evaluate the cooling effect on the gaseous ions?

Two methods of survival yields (SY) measurement treatment of thermometer ions whose fragmentation is activated by in-source collision induced dissociation have been investigated for evaluating the mean internal () and thermal () energies of gaseous ions produced by electrospray ionization and cold-spray ionization (CSI). One of the methods is based on the use of the internal energy distributions (P (Eint )) as sigmoid derivatives connecting the experimental survival yields of different substituted benzylpyridinium cations. The values are therefore converted in a thermal-like parameter called vibrational temperature (Tvib ) then obtained at each value of the voltage of the desolvation area. The second method is based on the modelling of ion behavior by the MassKinetics software where the value of the characteristic temperature parameter (Tchar ) is used for fitting theoretical survival yields (SYtheo ) with experimental data (SYexp ) calculated at several activation energy. A linear correlation is evidenced between the values of internal or thermal energy and the voltage of the orifice 1 at the origin of the ion activation in the desolvation area. The extrapolation at zero voltage of the thermal-like parameters (Tvib and Tchar ) indicates that, in agreement with the literature data, the ions are relatively hot in ESI (~650 K). But the use of a CSI source lowers this temperature down to ~300 K. In addition, with cold-spray ionization, this cooling effect is more important when methanol is used instead of acetonitrile although these two solvents have no influence on the gaseous ion temperature in electrospray ionization.

Evaluation for Ion Heating of H2A-H2B Dimer in Ion Mobility Spectrometry-Mass Spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS) provides m/z values and collision cross sections (CCSs) of gas-phase ions. In our previous study, an intrinsically disordered protein, the H2A-H2B dimer, was analyzed using IMS-MS, resulting in two conformational populations of CCS. Based on experimental and theoretical approaches, this resulted from a structural diversity of intrinsically disordered regions. We predicted that this phenomenon is related to ion heating in the IMS-MS instrument. In this study, to reveal the effect of ion heating from parameters in the IMS-MS instrument on the conformational population of the H2A-H2B dimer, we investigated the arrival time distributions of the H2A-H2B dimer by changing values of three instrumental parameters, namely, cone voltage located in the first vacuum chamber, trap collision energy (trap CE) for tandem mass spectrometry, and trap bias voltage for the entrance of IMS. These results revealed that the two populations observed for the H2A-H2B dimer were due to the trap bias voltage. Furthermore, to evaluate the internal energies of the analyte ions with respect to each parameter, benzylpyridinium derivatives were used as temperature-sensitive probes. The results showed that the trap CE voltage imparts greater internal energy to the ions than the trap bias voltage. In addition, this slight change in the internal energy caused by the trap bias voltage resulted in the structural diversity of the H2A-H2B dimer. Therefore, the trap bias voltage should be set with attention to the properties of the analytes, even if the effect of the trap bias voltage on the internal energy is negligible.

Dual Tunability for Uncatalyzed N-Alkylation of Primary Amines Enabled by Plasma-Microdroplet Fusion

The fusion of non-thermal plasma with charged microdroplets facilitates catalyst-free N-alkylation for a variety of primary amines, without halide salt biproduct generation. Significant reaction enhancement (up to >200×) is observed over microdroplet reactions generated from electrospray. This enhancement for the plasma-microdroplet system is attributed to the combined effects of energetic collisions and the presence of reactive oxygen species (ROS). The ROS (e.g., O2 ⋅- ) act as a proton sink to increase abundance of free neutral amines in the charged microdroplet environment. The effect of ROS on N-alkylation is confirmed through three unique experiments: (i) utilization of radical scavenging reagent, (ii) characterization of internal energy distribution, and (iii) controls performed without plasma, which lacked reaction acceleration. Establishing plasma discharge in the wake of charged microdroplets as a green synthetic methodology overcomes two major challenges within conventional gas-phase plasma chemistry, including the lack of selectivity and product scale-up. Both limitations are overcome here, where dual tunability is achieved by controlling reagent concentration and residence time in the microdroplet environment, affording single or double N-alkylated products. Products are readily collected yielding milligram quantities in eight hours. These results showcase a novel synthetic strategy that represents a straightforward and sustainable C-N bond-forming process.

Phenyl Sulfate Derivatives: New Thermometer Ions for Characterization of Internal Energy of Negative Ions Produced by Electrospray Ionization

Although positive thermometer ions are widely used for evaluating the internal energy distribution of gas-phase ions, negative thermometer ions have not yet been proposed. In this study, phenyl sulfate derivatives were tested as thermometer ions to characterize the internal energy distribution of ions produced by electrospray ionization (ESI) in the negative mode because the activation of phenyl sulfate preferentially undergoes SO₃ loss, providing a phenolate anion. The dissociation threshold energies for the phenyl sulfate derivatives were determined using quantum chemistry calculations at the CCSD(T)/6-311++G(2df,p)//M06-2X-D3/6-311++G(d,p) level of theory. The values for the appearance energies of the fragment ions of the phenyl sulfate derivatives depend on the dissociation time scale in the experiment; therefore, the dissociation rate constants of the corresponding ions were estimated using the Rice-Ramsperger-Kassel-Marcus theory. The phenyl sulfate derivatives were used as thermometer ions to determine the internal energy distribution of negative ions activated by the in-source collision-induced dissociation (CID) and higher-energy collisional dissociation. Both mean and full width at half-maximum values increased with increasing ion collision energy. In the in-source CID experiments, the internal energy distributions obtained by phenyl sulfate derivatives are similar to that when all voltages are mirrored, and the traditional benzylpyridinium thermometer ions are used. The reported method will aid in determining the optimum voltage for ESI mass spectrometry and the subsequent tandem mass spectrometry of acidic analyte molecules.

Hydrogen Bonding Effect on the Oxygen Binding and Activation in Cobalt(III)-Peroxo Complexes

Cobalt(III)peroxo complexes serve as model metal complexes mediating oxygen activation. We report a systematic study of the effect of hydrogen bonding on the O₂ binding energy and the O-O bond activation within the cobalt(III)peroxo complexes. To this end, we prepared a series of tris(pyridin-2-ylmethyl)amine-based cobalt(III)peroxo complexes having either none, one, two, or three amino groups in the secondary coordination sphere. The hydrogen bonding between the amino group(s) and the peroxo ligand was investigated within the isolated complexes in the gas phase using helium tagging infrared photodissociation spectroscopy, energy-resolved collision-induced dissociation experiments, and density functional theory. The results show that the hydrogen bonding stabilizes the cobalt(III)peroxo core, but the effect is only 10-20 kJ mol^-1. Introducing the first amino group to the secondary coordination sphere has the largest stabilization effect; more amino groups do not change the results significantly. The amino group can transfer a hydrogen atom to the peroxo ligands, which results in the O-O bond cleavage. This process is thermodynamically favored over the O₂ elimination but entropically disfavored.

Cationic Gold(II) Complexes: Experimental and Theoretical Study

Gold(II) complexes are rare, and their application to the catalysis of chemical transformations is underexplored. The reason is their easy oxidation or reduction to more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of [AuII (L)(X)]+ complexes (L=ligand, X=halogen) from the corresponding gold(III) precursors and investigated their stability and spectral properties in the IR and visible range in the gas phase. The results show that the best ancillary ligands L for stabilizing gaseous [AuII (L)(X)]+ complexes are bidentate and tridentate ligands with nitrogen donor atoms. The electronic structure and spectral properties of the investigated gold(II) complexes were correlated with quantum chemical calculations. The results show that the molecular and electronic structure of the gold(II) complexes as well as their spectroscopic properties are very similar to those of analogous stable copper(II) complexes.

Characterization of the Internal Energy of Ions Produced by Electrospray Ionization Using Substituted Benzyl Ammonium Thermometer Ions

We propose the use of substituted benzyl ammonium species as thermometer ions to characterize the internal energy distribution of the ions produced by electrospray ionization (ESI). Crucially, we found that the activation of the benzyl ammonium species preferentially provided a benzyl cation via N-Cα bond cleavage. In addition, calculations at the CCSD(T)/cc-PVTZ//M06-2X-D3/6-311++G(d,p) level of theory revealed that the threshold energies of fragmentation of the tested model ions ranged from 86 to 192 kJ mol^-1, significantly lower than those of conventional 4-substituted benzylpyridinium thermometer ions. Thus, the substituted benzyl ammoniums are suitable for the characterization of the ESI process under typical experimental conditions. Further, the internal energies of the ions were found to depend on the radiofrequency voltage of the ion funnel, which is used to increase the transport efficiency of the ions from atmospheric to vacuum conditions. Our reported method will aid the determination of the optimum ion-funnel radiofrequency voltage for the analysis of small molecules such as metabolites. Furthermore, benzyl ammoniums are commercially available, which will facilitate the routine and widespread measurement of the internal energy distributions of ions.

From QCEIMS to QCxMS: A Tool to Routinely Calculate CID Mass Spectra Using Molecular Dynamics

Mass spectrometry (MS) is a powerful tool in chemical research and substance identification. For the computational modeling of electron ionization MS, we have developed the quantum-chemical electron ionization mass spectra (QCEIMS) program. Here, we present an extension of QCEIMS to calculate collision-induced dissociation (CID) spectra. The more general applicability is accounted for by the new name QCxMS, where "x" refers to EI or CID. To this end, fragmentation and rearrangement reactions are computed "on-the-fly" in Born-Oppenheimer molecular dynamics (MD) simulations with the semiempirical GFN2-xTB Hamiltonian, which provides an efficient quantum mechanical description of all elements up to Z = 86 (Rn). Through the explicit modeling of multicollision processes between precursor ions and neutral gas atoms as well as temperature-induced decomposition reactions, QCxMS provides detailed insight into the collision kinetics and fragmentation pathways. In combination with the CREST program to determine the preferential protonation sites, QCxMS becomes the first standalone MD-based program that can predict mass spectra based solely on molecular structures as input. We demonstrate this for six organic molecules with masses ranging from 159 to 296 Da, for which QCxMS yields CID spectra in reasonable agreement with experiments.

"Thermometer" Ions Can Fragment Through an Unexpected Intramolecular Elimination: These Are Not the Fragments You Are Looking For

Benzylpyridinium analogs are effective thermometer ions since monitoring the formation of the benzylium fragment produced from heterolytic cleavage of the C-N bond can be linked to the ion's internal energy. In this study, three para-substituted benzylpyridinium ions containing ethoxy (OEt), isopropoxy (OiPr) and tert-butoxy (OtBu) substitutents were synthesized and evaluated as chemical thermometers. Intriguingly, the product ion spectra of the three benzylpyridinium ions were dominated by m/z 107 instead of the anticipated benzylium species. Deuterium labeling suggested that the m/z 107 fragment resulted from an intramolecular elimination (E_i), which formed via a four-membered transition state (TS). The fragmentation pathway appears to be an anomaly within the mass spectrometry literature, as four-membered pericyclic TSs are usually accompanied by the formation of an exceptionally stable neutral molecule (e.g., CO₂). Quantum-chemical calculations confirmed our hypothesis that stabilization of the strained TS is afforded by hyperconjugation (ΔG^‡ tert-butoxy < isopropyoxy < ethoxy).

Direct Detection of Free and Counterion-Bound Carbanions by Electrospray-Ionization Mass Spectrometry

We propose electrospray-ionization (ESI) mass spectrometry as a robust and powerful method for the in situ analysis of carbanions. ESI mass spectrometry selectively probes the charged components of the sampled solution and, thus, is ideally suited for the detection of free carbanions. We demonstrate the potential of this method by analyzing acetonitrile solutions of 15 different carbon acids AH, whose acidities cover a range of 11.1 ≤ pK_a(DMSO) ≤ 29.5. After treatment with KO^tBu as a strong base, all but the two least acidic compounds were successfully detected as free carbanions A^- and/or as potassium-bound aggregates [K_n-1A_n]^-. The association equilibria can be shifted toward smaller aggregates and free carbanions by the addition of the crown ether 18-crown-6, which facilitates the evaluation of the mass spectra. When KO^tBu was replaced by other bases (LiOH, LiNⁱPr₂, NaH, NaOH, KOH, NBu₄OH) or when tetrahydrofuran or methanol was used as a solvent, carbanions were also successfully observed. For further demonstrating the utility of the proposed method, we applied it to the analysis of the Michael addition of deprotonated dimedone to butenone. ESI mass spectrometry allowed us to follow the decrease of the reactant carbanion and the buildup of the product carbanion in time.

Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations

Thermometer ions are widely used to calibrate the internal energy of the ions produced by electrospray ionization in mass spectrometry. Typically, benzylpyridinium ions with different substituents are used. More recently, benzhydrylpyridinium ions were proposed for their lower bond dissociation energies. Direct dynamics simulations using M06-2X/6-31G(d), DFTB, and PM6-D3 are performed to characterize the activation energies of two representative systems: para-methylbenzylpyridinium ion (p-Me-BnPy⁺) and methyl,methylbenzhydrylpyridinium ion (Me,Me-BhPy⁺). Simulation results are used to calculate rate constants for the two systems. These rate constants and their uncertainties are used to find the Arrhenius activation energies and RRK fitted threshold energies which give reasonable agreement with calculated bond dissociation energies at the same level of theory. There is only one fragmentation mechanism observed for both systems, which involves C-N bond dissociation via a loose transition state, to generate either benzylium or benzhydrylium ion and a neutral pyridine molecule. For p-Me-BnPy⁺ using DFTB and PM6-D3 the formation of tropylium ion, from rearrangement of benzylium ion, was observed but only at higher excitation energies and for longer simulation times. These observations suggest that there is no competition between reaction pathways that could affect the reliability of internal energy calibrations. Finally, we suggest using DFTB with a modified-Arrhenius model in future studies.

Fragmentation study of tryptophan-derived metabolites induced by electrospray ionization mass spectrometry for highly sensitive analysis

ESI of tryptophan-derived metabolites produced an intense signal of fragment ion with a spiro[cyclopropane-indolium] backbone. The use of corresponding fragment ions for the precursor of MRM transitions could improve the detection limit.

Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions

A key aspect of reduced pressure ion mobility spectrometry (IMS) experiments is to identify experimental conditions that minimize the role of collisional energy transfer that allows for assessing effective ion-neutral collision cross sections of metabolites, peptides, and proteins in "native-like" or compact states. Across two separate experimental campaigns using a prototype trapped ion mobility spectrometer (TIMS) coupled to a time-of-flight mass spectrometer, we present independent findings that support the results recently published by Morsa et al. using a different set of thermometer ions (Morsa et al. Anal. Chem. 2020, 92 (6), 4573-4582). First, using five para-substituted benzylammonium ions, we conducted survival yield experiments to assess ion internal energy across different experimental settings. Results from the present set of experiments illustrate that greater ion heating occurs at lower pressures and higher voltage settings applied to the TIMS. At the "softest" settings where the benzylammonium thermometer ions have an effective average energy of 1.73 eV, we observe the majority of bradykinin in the compact state. Under more extreme operating conditions where the energy of the benzylammonium ions varies from 1.83 to 1.86 eV, the bradykinin transitions from the compact to the elongated state. In addition to independently confirming the findings of Morsa et al., we also report the mobilities for the benzylammonium parent and fragment ions using the tandem drift-tube-TIMS calibration procedure described by Naylor et al. ( J. Am. Soc. Mass Spectrom. 2019, 30 (10), 2152-2162).

How Hot Are Your Ions in Differential Mobility Spectrometry?

Ions can experience significant field-induced heating in a differential mobility cell. To investigate this phenomenon, the fragmentation of several para-substituted benzylpyridinium "thermometer" ions (R = OMe, Me, F, Cl, H, CN) was monitored in a commercial differential mobility spectrometer (DMS). The internal energy of each benzylpyridinium derivative was characterized by monitoring the degree of fragmentation to obtain an effective temperature, T_eff, which corresponds to a temperature consistent with treating the observed fragmentation ratio using a unimolecular dissociation rate weighted by a Boltzmann distribution at a temperature T. It was found that ions are sufficiently thermalized after initial activation from the ESI process to the temperature of the bath gas, T_bath. Once a critical field strength was surpassed, significant fragmentation of the benzylpyridinium ions was detected. At the maximum bath gas temperature (450 K) and separation voltage (SV; 4400 V) for our instrument, T_eff for the benzylpyridinium derivatives ranged from 664 ± 9 K (p-OMe) to 759 ± 17 K (p-H). The extent of activation at a given SV depends on the ion's mass, degrees of freedom, (N_DoF), and collision frequency as represented by the ion's collision cross section. Plots of T_eff vs the product of ion mass and N_DoF and the inverse of collision cross section produce strong linear relationships. This provides an attractive avenue to estimate ion temperatures at a given SV using only intrinsic properties. Moreover, experimentally determined T_eff correlate with theoretically predicted T_eff using with a self-consistent method based on two-temperature theory. The various instrumental and external parameters that influence T_eff are additionally discussed.

Rapid Determination of Activation Energies for Gas-Phase Protein Unfolding and Dissociation in a Q-IM-ToF Mass Spectrometer

Ion mobility-mass spectrometry has emerged as a powerful tool for interrogating a wide variety of chemical systems. Collision-induced unfolding (CIU), typically performed in time-of-flight instruments, has been utilized to obtain valuable qualitative insight into protein structure and illuminate subtle differences between related species. CIU experiments can be performed relatively quickly, but unfolding energy information obtained from them has not yet been interpreted quantitatively. While several methods can determine quantitative dissociation energetics for small molecules, clusters, and peptides, these methods have rarely been applied to proteins, and never to study unfolding. Here, we present a method to rapidly determine activation energies for protein unfolding and dissociation, built on a model for energy deposition during collisional activation. The method is validated by comparing activation energies for dissociation of three complexes with those obtained using blackbody infrared radiative dissociation (BIRD); values from the two methods are in agreement. Several protein monomers were unfolded using CIU, including multiple charge states of both cations and anions, and activation energies determined. ΔH^⧧ and ΔS^⧧ values are found to be correlated, leading to ΔG^⧧ values that lie within a narrow range (∼70-80 kJ/mol) and vary more with charge state than with protein identity. ΔG^⧧ is anticorrelated with charge density, highlighting the key role of Coulombic repulsion in gas-phase unfolding. Measured ΔG^⧧ values are similar to those computed for proton transfer within small peptides, suggesting that proton transfer is the rate-limiting step in gas-phase unfolding and providing evidence of a link between the Mobile Proton model and CIU.