Collision-induced Dissociation Research Articles

Enhancing Metabolome Annotation by Electron Impact Excitation of Ions from Organics-Molecular Networking.

Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is widely used in untargeted metabolomics, but large-scale and high-accuracy metabolite annotation remains a challenge due to the complex nature of biological samples. Recently introduced electron impact excitation of ions from organics (EIEIO) fragmentation can generate information-rich fragment ions. However, effective utilization of EIEIO tandem mass spectrometry (MS/MS) is hindered by the lack of reference spectral databases. Molecular networking (MN) shows great promise in large-scale metabolome annotation, but enhancing the correlation between spectral and structural similarity is essential to fully exploring the benefits of MN annotation. In this study, a novel approach was proposed to enhance metabolite annotation in untargeted metabolomics using EIEIO and MN. MS/MS spectra were acquired in EIEIO and collision-induced dissociation (CID) modes for over 400 reference metabolites. The study revealed a stronger correlation between the EIEIO spectra and metabolite structure. Moreover, the EIEIO spectral network outperformed the CID spectral network in capturing structural analogues. The annotation performance of the structural similarity network for untargeted LC-MS/MS was evaluated. For the spiked NIST SRM 1950 human plasma, the annotation coverage and accuracy were 72.94 and 74.19%, respectively. A total of 2337 metabolite features were successfully annotated in NIST SRM 1950 human plasma, which was twice that of LC-CID MS/MS. Finally, the developed method was applied to investigate prostate cancer. A total of 87 significantly differential metabolites were annotated. This study combining EIEIO and MN makes a valuable contribution to improving metabolome annotation.

Inclusion of deuterated glycopeptides provides increased sequence coverage in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike glycoprotein.

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein's conformational dynamics across varied states, such as heat-denatured versus native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of peptides post-translationally modified by asparagine-bound glycans (glycopeptides) has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We detected deuterated glycopeptides with a Tribrid Orbitrap Eclipse mass spectrometer performing data-dependent acquisition. An MS scan was used to identify precursor ions; if high-energy collision-induced dissociation MS/MS of the precursor indicated oxonium ions diagnostic for complex glycans, then electron transfer low-energy collision-induced dissociation MS/MS scans of the precursor identified the modified asparagine residue and the glycan's mass. As in traditional HDX-MS, the identified glycopeptides were then analyzed at the MS level in samples labeled with D2 O. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric prefusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their average isotopic mass shifts from deuteration. Inclusion of the deuterated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural rearrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.

UV-A-Induced Photoisomerization and Photodimerization of Curcumin: An Ion Mobility Mass Spectrometry Study.

Curcumin, the bioactive compound present in spice plant turmeric, has been shown to exhibit selective phototoxic activities toward mammalian cancer cells, and it is being used extensively as a photosensitizer (PS) in photodynamic therapies (PDT). However, so far, the fate of curcumin toward photochemical transformations is not well understood. Here we report our findings of a number of novel photochemical reaction channels of curcumin in water-methanol mixture, like photoisomerization, photodimerization, and photooxidation (H2-loss). The reaction was performed by irradiating the curcumin solution with ultraviolet (UV) light of wavelength 350 nm, which is abundant in the earth's troposphere. Product identification and structure elucidation are done by employing an integrated method of drift tube ion mobility mass spectrometry (DTIMS) in combination with high-performance liquid chromatography (HPLC) and collision-induced dissociation (CID) of the mass-selected molecular ions. Two photoisomers of curcumin produced as a result of trans-cis configurational changes about C═C double bonds in the excited state have been identified, and it has been shown that they could serve as the precursors for formation of isomeric dimers via [2 + 2] cycloaddition and H2-loss products. Comparisons of the experimentally measured collision cross-section (CCS) values of the reactant and product ions obtained by the DTIMS method with those predicted by the electronic structure theory are found to be very effective for the discrimination of the produced photoisomers. The observed photochemical reaction channels are potentially significant toward uses of curcumin as a photosensitizer in photodynamic therapy.

Enrichment of nitrogen compounds in heavy oils by complexation with ZrCl4 and detailed characterization using FT-ICR MS and ion mobility spectrometry

Nitrogen compounds in heavy oils have significant deleterious impacts on the petroleum products and processes. It is of great significance to characterize the structures of nitrogen compounds during hydrodenitrogenation (HDN) in heavy oils, but the low content of nitrogen compounds after HDN is not conducive to structural analysis. Zirconium tetrachloride (ZrCl4) was found as an efficient complexing agent to enrich both basic and non-basic nitrogen compounds in heavy oils. The molecular weight ranges of the basic and non-basic nitrogen compounds were similar before and after ZrCl4 enrichment. The distribution of carbon number and double bond equivalent (DBE) of basic N1 species in the enriched feedstock was very close to that of the original feedstock, while the basic N1 species in the enriched product behaved a higher DBE distribution. The non-basic nitrogen compounds with higher DBE in the feedstock and product were also more likely to be enriched. Moreover, multi-heteroatomic non-basic nitrogen compounds were more inclined to be enriched than the non-basic N1 species due to the possible synergism of multi-heteroatoms. The numbers of detected multi-heteroatomic non-basic N2, N1O1, and N1O2 compounds obtained by high resolution mass spectrometry increased by 40 to nearly 70 times. The double bond equivalent (DBE) of these refractory multi-heteroatomic non-basic nitrogen compounds in the deep HDN product was much lower than those in the feedstock, due to the hydrogenation saturation reaction during HDN. The representative core structures of refractory basic nitrogen compounds were deduced by ESI+ FT-ICR MS coupled with collision-induced dissociation (CID), and the side chains were proposed by ion mobility spectrometry (IMS). Two typical kinds of refractory basic N1 compounds were suggested in the HDN product. One was a compact structure with multiple naphthenic rings and short side chains. The other had a large molecular size with aromatic rings and long side chains. ZrCl4 as a complexing agent can effectively enrich nitrogen compounds in heavy oil, especially for the hydrotreated heavy oils. This enrichment method facilitates the structural characterization of refractory nitrogen compounds in heavy oil HDN process by FT-ICR MS and IMS. These results provide valuable information for the improvement of HDN processes and catalysts.

Ultra-high-performance liquid chromatography with tandem mass spectrometry method for cellular toxicity and pharmacokinetic study of PEG1K polymers.

Polyethylene glycol (PEG) is one of the most commonly used polymers in drug delivery systems. The investigation of the pharmacokinetic behavior of PEG is important for revealing the toxicity and efficiency of PEG-related Nano-drug delivery systems. A high through-put and selective ultra-high-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) method coupled with collision-induced dissociation (CID) in source technique was developed and validated to determine PEG1K polymers in cellular samples in this study. The countless precursor ions of PEG1K are dissociated in the source to generate numerous product ions which have different numbers of subunits. The transition of [M+H]+ precursor ions → product ions at m/z 177.1 (four subunits)→89.1 (two subunits) was selected to determine PEG1K due to its high sensitivity. The UHPLC-MS/MS method coupled with CID in the source showed good linearity over the range of 0.1-10μg/mL. Intra-day and inter-day accuracies and precisions of the assay were all within±12.39%. The assay was successfully applied to a cellular pharmacokinetic study of PEG1K in human breast cancer cells. The cytotoxicity of PEG1K polymers was also studied and the results indicated that the cytotoxicity of PEG1K was not significant in the range of 5-1200μg/mL.

Ion mobility mass spectrometry uncovers regioselectivity in the carboxylate-assisted C-H activation of palladium N-heterocyclic carbene complexes.

Carboxylate-assisted Pd-catalyzed C-H bond activation constitutes a mild and versatile synthetic tool to efficiently and selectively cleave inert C-H bonds. Herein, we demonstrate a simple method to experimentally evaluate both reactivity and selectivity in such systems using mass spectrometry (MS) methods. The N-heterocyclic carbene (NHC) cations [(NHC)PdX]+, bearing as X- ligand bases commonly used to promote the C-H activation (carboxylates and bicarbonate), are generated in the gas-phase by ESI-MS. Their C-H bond activation at the N-bound groups of the NHC is then studied using Collision Induced Dissociation (CID) experiments. Ion Mobility Spectrometry (IM)-MS is exploited to identify a number of regioisomers associated with the distinctive site selective C-H activations. It is demonstrated that such C-H activation concomitant with acetic acid release occurs from a mixture of activated [(NHC-H)Pd(CH3CO2H)]+ and non-activated [(NHC)Pd(CH3CO2)]+ complexes. The identity of the X-type ligands (X = Cl-, carboxylates and bicarbonate) has a significant impact on the regioisomer branching ratio upon CID conditions. IM-MS in conjunction with a DFT mechanistic study is presented for the acetate-assisted C-H activation of the [(NHC)Pd(CH3CO2)]+ cation featuring butyl and aryl as N-donor groups.

Generation and reactivity of the fragment ion [B12I8S(CN)]- in the gas phase and on surfaces.

Gaseous fragment ions generated in mass spectrometers may be employed as "building blocks" for the synthesis of novel molecules on surfaces using ion soft-landing. A fundamental understanding of the reactivity of the fragment ions is required to control bond formation of deposited fragments in surface layers. The fragment ion [B12X11]- (X = halogen) is formed by collision-induced dissociation (CID) from the precursor [B12X12]2- dianion. [B12X11]- is highly reactive and ion soft-landing experiments have shown that this ion binds to the alkyl chains of organic molecules on surfaces. In this work we investigate whether specific modifications of the precursor ion affect the chemical properties of the fragment ions to such an extent that attachment to functional groups of organic molecules on surfaces occurs and binding of alkyl chains is prevented. Therefore, a halogen substituent was replaced by a thiocyanate substituent. CID of the precursor [B12I11(SCN)]2- ion preferentially yields the fragment ion [B12I8S(CN)]-, which shows significantly altered reactivity compared to the fragment ions of [B12I12]2-. [B12I8S(CN)]- has a previously unknown structural element, wherein a sulfur atom bridges three boron atoms. Gas-phase reactions with different neutral reactants (cyclohexane, dimethyl sulfide, and dimethyl amine) accompanied by theoretical studies indicate that [B12I8S(CN)]- binds with higher selectivity to functional groups of organic molecules than fragment ions of [B12I12]2- (e.g., [B12I11]- and [B12I9]-). These findings were further confirmed by ion soft-landing experiments, which showed that [B12I8S(CN)]- ions attacked ester groups of adipates and phthalates, whereas [B12I11]- ions only bound to alkyl chains of the same reagents.

Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS.

Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.

Reactions of gas-phase uranyl formate/acetate anions: reduction of carboxylate ligands to aldehydes by intra-complex hydride attack.

In a previous study, electrospray ionization, collision-induced dissociation (CID), and gas-phase ion-molecule reactions were used to create and characterize ions derived from homogeneous precursors composed of a uranyl cation (UVIO22+) coordinated by either formate or acetate ligands [E. Perez, C. Hanley, S. Koehler, J. Pestok, N. Polonsky and M. Van Stipdonk, Gas phase reactions of ions derived from anionic uranyl formate and uranyl acetate complexes, J. Am. Soc. Mass Spectrom., 2016, 27, 1989-1998]. Here, we describe a follow-up study of anionic complexes that contain a mix of formate and acetate ligands, namely [UO2(O2C-CH3)2(O2C-H)]- and [UO2(O2C-CH3)(O2C-H)2]-. Initial CID of either anion causes decarboxylation of a formate ligand to create carboxylate-coordinated U-hydride product ions. Subsequent CID of the hydride species causes elimination of acetaldehyde or formaldehyde, consistent with reactions that include intra-complex hydride attack upon bound acetate or formate ligands, respectively. Density functional theory (DFT) calculations reproduce the experimental observations, including the favored elimination of formaldehyde over acetaldehyde by hydride attack during CID of [UO2(H)(O2C-CH3)(O2C-H)]-. We also discovered that MSn CID of the acetate-formate complexes leads to generation of the oxyl-methide species, [UO2(O)(CH3)]-, which reacts with H2O to generate [UO2(O)(OH)]-. DFT calculations support the observation that formation of [UO2(O)(OH)]- by elimination of CH4 is favored over H2O addition and rearrangement to create [UO2(OH)2(CH3)]-.

Cyclic ion mobility of doped [MAu24L18]2- superatoms and their fragments (M = Ni, Pd and Pt; L = alkynyl).

Collision-induced dissociation and high-resolution cyclic ion mobility mass spectrometry, along with quantum chemical calculations and trajectory simulations, were used to compare the structures of isolated [MAu24(CCR)18]2-, M = Ni, Pd, or Pt, and their associated fragment ions. The three different alkynyl ligand-stabilized (CCR, R = 3,5-(CF3)2C6H3), transition metal-doped, gold cluster dianions showed mutually resolvable collision cross sections (CCS), which were ordered consistently with their molecular structures from X-ray crystallography. All three [MAu24(CCR)18]2- species fragment by sequential diyne loss to form [MAu24(CCR)18-n]2-, with n up to 12. The resultant fragment isomer distributions are significantly n- and M-dependent, and hint at a process involving concerted elimination of adjacent ligands. In particular [NiAu24(CCR)18]2- also fragments to generate alkyne-oligomers, an inference supported by the parallel observation of precursor dianion isomerization as collision energy is increased.

Fatty acid isomerism: analysis and selected biological functions.

The biological functions of fatty acids and the lipids in which they are esterified are determined by their chain length, double bond position and geometry and other structural motifs such as the presence of methyl branches. Unusual isomeric features in fatty acids of human foods such as conjugated double bonds or chain branching found in dairy products, some seeds and nuts, and marine foods potentially have important effects on human health. Recent advancements in identifying fatty acids with unusual double bond positions and pinpointing the position of methyl branches have empowered the study of their biological functions. We present recent advances in fatty acid structural elucidation by mass spectrometry in comparison with the more traditional methods. The double bond position can be determined by purely instrumental methods, specifically solvent-mediated covalent adduct chemical ionization (SM-CACI) and ozone induced dissociation (OzID), with charge inversion methods showing promise. Prior derivatization using the Paternò-Büchi (PB) reaction to yield stable structures that, upon collisional activation, yield the double bond position has emerged. The chemical ionization (CI) based three ion monitoring (MRM) method has been developed to simultaneously identify and quantify low-level branched chain fatty acids (BCFAs), unattainable by electron ionization (EI) based methods. Accurate identification and quantification of unusual fatty acid isomers has led to research progress in the discovery of biomarkers for cancer, diabetes, nonalcoholic fatty liver disease (NAFLD) and atherosclerosis. Modulation of eicosanoids, weight loss and the health significance of BCFAs are also presented. This review clearly shows that the improvement of analytical capacity is critical in the study of fatty acid biological functions, and stronger coupling of the methods discussed here with fatty acid mechanistic research is promising in generating more refined outcomes.

Magic cluster sizes of cationic and anionic sodium chloride clusters explained by statistical modeling of the complete phase space.

As one of the main components of sea salt aerosols, sodium chloride is involved in numerous atmospheric processes. Gas-phase clusters are ideal models to study fundamental physical and chemical properties of sodium chloride, which are significantly affected by the cluster size. Of particular interest are magic cluster sizes, which exhibit high intensities in mass spectra. In order to understand the origin of these magic cluster sizes, quantum chemical calculations at the CCSD(T)//DFT level are performed, yielding structures and binding energies of neutral (NaCl)x, anionic (NaCl)xCl- and cationic (NaCl)xNa+ clusters up to x = 8. Our calculations show that the clusters can easily isomerize, enabling dissociation into the lowest-energy isomers of the fragments. Energetics can explain the special stability of (NaCl)4Cl-, but (NaCl)4Na+ actually offers low-lying dissociation channels, despite being a magic cluster size. Collision-induced dissociation experiments reveal that the loss of neutral clusters (NaCl)x, x = 2, 4, is in most cases more favorable than the loss of NaCl or the atomic ion, i.e. sodium chloride clusters actually fragment via the cleavage of the entire cluster, not by evaporating small cluster building blocks. This is rationalized by the calculated high stability of even-numbered neutral clusters (NaCl)x, especially x = 2, 4. Analysis of the density of states and rate constants calculated with a modified Rice-Ramsperger-Kassel-Marcus (RRKM) equation called AWATAR - considering all energetically accessible isomers of reactants and fragments - shows that entropic effects are responsible for the magic cluster character of (NaCl)4Na+. In particular, low-lying vibrational modes provide a high density of states of the near-planar cluster. Together with the small contribution of an atomic ion to the sum of states in a loose transition state for dissociation, this leads to a very small unimolecular rate constant for dissociation into (NaCl)4 and Na+, which is the lowest energy fragmentation pathway. Thus, entropic effects may override energetics for certain magic cluster sizes.

Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation.

In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.

Stability of [10-12]cycloparaphenylene complexes with pristine fullerenes C76,78,84 and endohedral metallofullerenes M3N@C78,80.

[n]Cycloparaphenylenes ([n]CPPs) are strained macrocycles, comprising only sp2-hybridized carbon atoms. In recent years, [n]CPPs have become of great research interest in the field of supramolecular chemistry since their special structure enables the formation of novel host-guest complexes. In this work, we investigate the gas-phase chemistry of noncovalent complexes of [10-12]CPP with the pristine fullerenes C76/78/84 and the endohedral metallofullerenes (EMFs) Sc3N@D3h-C78, Sc3N@D5h-C80 and M3N@Ih-C80 (M = Sc, Y, Lu, Gd). The [1 : 1] complexes with [10-12]CPP are detected as radical cations. The stability and charge distributions of these complexes are studied using energy-resolved collision-induced dissociation (ER-CID). Our results assess the size complementarity, the influence of fullerene symmetry and size as well as the role of the metal size inside the EMF on the binding affinity and complex stability. Two main trends in complex stability have been found: First, [10-12]CPP form more stable complexes with EMFs than with pristine fullerenes and second, all complexes of EMFs with the C80 skeleton show similar stability despite the different metal clusters encapsulated. Another major finding is the fact that [11]CPP is generally the most suitable host for fullerenes with a C76/78/80/84 skeleton. Considering the charge distributions, we observe the existence of two different fragmentation channels for complexes with EMFs where the radical cation is either located at the CPP or at the EMF: (1) [n]CPP+˙ + EMF and (2) [n]CPP + EMF+˙. This behavior allows a clear distinction of the cage isomers ([11]CPP⊃Sc3N@Ih-C80)+˙ and ([11]CPP⊃Sc3N@D5h-C80)+˙ in the MS2 experiment. The experimental results are accompanied by density functional theory (DFT) calculations of ionization potentials (IPs) and fragmentation energies. The computational results fully confirm the measured order of complex stabilities and explain the prevalence of EMF or CPP signals in the spectra by the trend in ionization potentials.

Differentiation of oligosaccharide isomers by direct infusion multidimensional mass spectrometry.

Oligosaccharides demonstrate many bioactivities with applications in the pharmaceutical, cosmetic, and food industries. They also serve as biomarkers for various diseases including cancer and glycogen storage disorders. These make the structural characterization of oligosaccharides very important. Unfortunately, the structural diversity found in saccharides make their characterization challenging, necessitating the development of sophisticated instrumentation to enable isomer differentiation. Herein, we report the ability of halide (Cl- and Br-) adducts to enable direct differentiation of oligosaccharide isomers using conventional collision-induced dissociation (CID) tandem MS (MS/MS). The halide adducts were generated by direct infusion nano-electrospray ionization (nESI). For the first time, this traditional nESI CID MS/MS platform was used to differentiate stereoisomers of trisaccharides (cellotriose β(1 → 4) and maltotriose α(1 → 4), tetrasaccharides (cellotetraose and maltotetraose), and pentasaccharides (cellopentaose and maltopentaose)). In addition, the MS/MS of halide adducts enabled the differentiation of positional, structural, and linkage isomers from a total of 14 oligosaccharides. The isomer differentiation was realized by the generation of distinct diagnostic fragment ions in CID. We also performed principal component analysis using the entire range of MS/MS fragment ion profiles and found that negative-ion mode halide adduction provided more effective isomer differentiation compared with positive-ion mode sodium adduction. Finally, we demonstrated complex mixture analysis by spiking all 14 oligosaccharides into raw urine, of which we successfully distinguished species based on molecular weight (first dimension) and CID MS/MS fragmentation patterns as the second dimension separation. This work effectively showcases the potential to use direct infusion nESI-MS/MS to characterize synthetic oligosaccharide isomers in unpurified reaction mixture as well as from biofluids for diagnostic purposes.

Structural analysis of C8H6˙+ fragment ion from quinoline using ion-mobility spectrometry/mass spectrometry.

This study investigated the structures of fragment ions derived from the quinoline (C9H7N) radical cation using ion-mobility spectrometry and mass spectrometry. Ion mobility and mass analysis revealed that C8H6˙+ is the primary dissociation product resulting from the loss of HCN during collision-induced dissociation of the quinoline radical cation. The reduced mobility (K0) of the C8H6˙+ fragment product in helium gas was measured over a range of reduced electric fields (E/N = 20.8-27.4 Td) at room temperature. The experimental K0 values indicated that C8H6˙+ is a mixture of phenylacetylene and pentalene radical cations. Furthermore, quantum chemical calculations revealed two potential energy surfaces delineating the loss of HCN from the quinoline radical cation to form phenylacetylene radical cations.

Dynamics and thermochemistry of the negatively charged clusters in a 2-hydroxyethylhydrazinium nitrate ionic liquid system.

The formation and fragmentation of negatively charged 2-hydroxyethylhydrazinium nitrate ([HOCH2CH2NH2NH2]+NO3-, HEHN) ionic liquid clusters were examined using a guided-ion beam tandem mass spectrometer furnished with collision-induced dissociation of selected ions with Xe atoms. Measurements included the compositions of cluster ions formed in the ionization source, and the dissociation products, cross sections, and 0 K threshold energies for individually selected cluster ions. To identify the structures of the main cluster ion series [(HEHN)n(HNO3)0-1NO3]- formed, molecular dynamics simulations were employed to create initial geometry guesses, followed by optimization at the ωB97XD/6-31+G(d,p) level of theory, from which global minimum structures were identified for reaction thermodynamics analyses. A comparison was made between the cluster formation and fragmentation in the negatively charged 2-hydroxyethylhydrazinium nitrate with those in the positive mode (reported by W. Zhou et al., Phys. Chem. Chem. Phys., 2023, 25, 17370). In both modes, the cluster ions were predominantly composed of m/z below 350; loss of a neutral 2-hydroxyethylhydrazinium nitrate ion pair represents the most important cluster fragmentation pathway, followed by intra-ion pair proton transfer-mediated 2-hydroxyethylhydrazine and HNO3 elimination; and all clusters started to dissociate at threshold energies less than 1.5 eV. The overwhelming similarities in the formation and fragmentation chemistry of positively vs. negatively charged 2-hydroxyethylhydrazinium nitrate clusters may be attributed to their inherent ionic nature and high electric conductivities.

Gas-phase Ni(II) affinities of alternative metal binding peptides from competitive threshold collision-induced dissociation

The Ni(II) affinity of the polyhistidine tag is used in the purification of recombinant proteins by immobilized metal affinity chromatography. Here we measured the relative gas-phase Ni(II) affinities of four alternative metal binding (amb) peptides and the 7xHis tag using the competitive threshold collision-induced dissociation (TCID) technique. The general primary structure of the four amb peptides was acetyl-Aa1-Aa2-Gly3-Pro4-Aa5-Gly6-Cys7, designed to test whether the His1-Cys2 or Asp1-His2 would exhibit the higher Ni(II) affinity and whether the Tyr5 with its ability of forming long-range π-nickel interaction and hydrogen bonding would contribute to the Ni(II) affinity. The Cys7 is retained in all the amb sequences because previous research has shown that both the thiolate side group and carboxylate terminus simultaneously coordinate the metal ion. The Ni(II) affinity was measured using the dissociation of the [amb + Ni(II) + NTA]− complex, where NTA = nitrilotriacetic acid, which is a commonly used ligand for Ni(II) inside the IMAC column. The dissociation of [amb + Ni(II) + NTA]− produced two main product channels; [amb + Ni(II)]− + NTA and [NTA + Ni(II)]− + amb, whose competition was modeled by TCID to extract the relative gas-phase Ni(II) affinities. Extensive molecular modeling using PM6 located the low-energy structures whose molecular parameters were used in the TCID analyses if their collision cross sections agreed with those measured by traveling-wave ion mobility mass spectrometry and they were compatible with a concerted reaction. We compare the final results by conducting the TCID analyses using alternative PM6 parameters and by making the ternary complexes in acidic and basic solutions.

Robustness of Threshold Collision-Induced Dissociation Simulations for Bond Dissociation Energies.

The threshold collision-induced dissociation (T-CID) method is the workhorse for gas-phase bond dissociation energy (BDE) measurements. However, T-CID does not measure BDEs directly; instead, BDEs are obtained by fitting simulated data to the experimental data. We previously observed several large discrepancies between the computed and experimental BDEs. To analyze the reliability of the experimental values, we previously reported a study of the dissociation rate models in the simulation. Here, we report a study of the collision simulation part, specifically in the L-CID (ligand CID) program. We show that the BDE values are robust even to intentionally introduced mistakes in the simulations, varying in most cases by less than 3 kcal mol-1. The most significant exception is the collisional energy transfer (CET) simulation, which led to deviations larger than 10 kcal mol-1. However, we found that the BDEs obtained with explicitly simulated CET distributions deviated by only 3 kcal mol-1 from those simulated with the original model. Collectively, our results suggest that the T-CID-derived BDE values are robust and are likely to be accurate.

Characterization of the Oxazolone and Macrocyclic Motifs in the bn (n = 2-5) Product Ions from Collision-Induced Dissociation of Protonated Oligoglycine Peptides with Isomer-Selective, Cryogenic Vibrational Spectroscopy.

Collision-induced dissociation (CID) of small, protonated peptides leads to the formation of b-type fragment ions that can occur with several structural motifs driven by different covalent intramolecular bonding arrangements. Here, we characterize the so-called "oxazolone" and "macrocycle" bn ion structures that occur upon CID of oligoglycine peptides (Gn) ions (n = 2-6). This is determined by acquiring the vibrational band patterns of the cryogenically cooled, D2-tagged bn ions obtained using isomer-selective, two-color IR-IR photobleaching and analyzing them with predicted (DFT) harmonic spectra for the candidate structures. Both oxazolone and macrocyclic isomers are formed by b4, whereas only oxazolone species are created for b2 and b3 and the macrocycle is created for b5. As such, n = 4 corresponds to the minimum size where both Oxa and MC forms are present.