CE50: quantifying collision induced dissociation energy for small molecule characterization and identification

Structural and Energetic Effects of the 2-Amino and 2'- and 3'-Hydroxy Substituents of Protonated Guanosine Nucleosides: IRMPD, ER-CID, and Theoretical Studies of Protonated Guanosine and Inosine Nucleosides

Inosine is a naturally occurring modified RNA nucleoside. Guanosine differs from inosine only by the 2-amino substituent of its nucleobase. The effects of the 2-amino and 2'- and 3'-hydroxy substituents on structure and glycosidic bond stability are examined via comparative studies of protonated guanosine vs inosine nucleoside analogues. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments are performed to probe structural effects, whereas energy-resolved collision-induced dissociation (ER-CID) experiments combined with survival yield analyses are performed to probe their effects on glycosidic bond stability. Density functional theory (DFT) calculations are performed to determine the stable low-energy conformations available to these systems, their relative stabilities, and infrared (IR) spectra. The structures experimentally populated are determined via comparisons of the measured IRMPD and predicted IR spectra. DFT calculations are also employed to map detailed mechanistic pathways for N-glycosidic bond cleavage of the protonated guanosine and inosine nucleosides. The influences of the 2-amino and 2'- and 3'-hydroxy substituents on glycosidic bond stability are determined from the trends in the energy-dependence of their ER-CID behavior and the activation energies predicted for glycosidic bond cleavage. The 2-amino substituent of the guanosine nucleosides has little effect on structure and is found to strengthen the glycosidic bond. The 2'- and 3'-hydroxy substituents exert a greater influence on structure via stabilizing hydrogen-bonding interactions enabled by their presence. The influences of the 2'- and 3'-hydroxy substituents on glycosidic bond stability differ. The 2'-hydroxy substituent significantly enhances glycosidic bond stability, whereas the 3'-hydroxy substituent slightly weakens glycosidic bond stability.

Cooperative Anion-π and C-H-Cl Interactions in Multifunctional Naphthalene-Based Receptors for Chloride Recognition: Cage-Size Modulation Through Substitution Patterns

This study introduces a novel approach for chloride recognition utilizing multifunctional naphthalene-based receptors. By strategically modifying the substitution patterns on tetrafluoropyridines, a series of new receptors with customized cavities and enhanced binding capabilities were developed. Density functional theory (DFT) calculations and experimental studies combining NMR spectroscopy and mass spectrometry confirmed the efficacy of these receptors in capturing chloride ions. The relative chloride affinity order determined experimentally is in agreement with DFT predictions. The synergistic effect of anion-π and C-H…Cl interactions, mediated by the TFP groups, played a crucial role in achieving high binding affinity. This work provides valuable insights for designing future anion receptors with improved performance.

Triple three-dimensional MS/MS spectrum facilitates quantitative ginsenosides-targeted sub-metabolome characterization in notoginseng

Although serving as the workhorse, MS/MS cannot fully satisfy the analytical requirements of quantitative sub-metabolome characterization. Because more information intrinsically correlates to more structural and concentration clues, here, efforts were devoted to comprehensively tracing and deciphering MS/MS behaviors through constructing triple three-dimensional (3×3D)-MS/MS spectrum. Ginsenosides-targeted metabolomics of notoginseng, one of the most famous edible medicinal plants, was employed as a proof-of-concept. Serial authentic ginsenosides were deployed to build the correlations between 3×3D-MS/MS spectra and structure/concentration features. Through assaying ginsenosides with progressive concentrations using QTOF-MS to configure 1st 3D spectrum, the generations of MS1 spectral signals, particularly multi-charged multimer anions, e.g., [2M-2H]2- and [2M+2HCOO]2- ions, relied on both concentration and the amount of sugar chains. By programming progressive collision energies to the front collision cell of Qtrap-MS device to gain 2nd 3D spectrum, optimal collision energy (OCE) corresponding to the glycosidic bond fission was primarily correlated with the masses of precursor and fragment ions and partially governed by the glycosidation site. The quantitative relationships between OCEs and masses of precursor and fragment ions were utilized to build large-scale quantitative program for ginsenosides. After applying progressive exciting energies to the back collision chamber to build 3rd 3D spectrum, the fragment ion and the decomposition product anion exhibited identical dissociation trajectories when they shared the same molecular geometry. After ginsenosides-focused quantitative metabolomics, significant differences occurred for sub-metabolome amongst different parts of notoginseng. The differential ginsenosides were confirmatively identified by applying the correlations between 3×3D-MS/MS spectra and structures. Together, 3×3D-MS/MS spectrum covers all MS/MS behaviors and dramatically facilitates sub-metabolome characterization from both quantitative program development and structural identification.

Conformational Landscapes and Energetics of Carbon Nanohoops and their Ring-in-Ring Complexes

Carbon nanohoops are promising precursors for the synthesis of nanotubes, whose structural dynamics are not well understood. Here, we investigate the conformational landscape and energetics of cycloparaphenylenes (CPPs), a methylene-bridged CPP and a carbon nanobelt. These nanohoops can form host-guest complexes with other rings, and understanding their structure is crucial for predicting their properties and identifying potential applications. We used a combination of ion mobility, tandem mass spectrometry, and density functional theory to characterize the nanohoops and their ring-in-ring complexes, following the energetics and conformations of their disassembly from intact complexes to fragment ions. Our results show structural integrity of the nanohoops and host-guest complexes. They also reveal interesting trends in size, packing density, stability, and structure between [6]CPP, the methylene-bridged CPP, and the carbon nanobelt as guests in ring-in-ring complexes. Taken together, our work illustrates how mass spectrometry data can help to unravel the rules that govern the formation of carbon nanohoop assemblies.

Studying Cation Exchange in {Cr7Co} Pseudorotaxanes: Preparatory Studies for Making Hybrid Molecular Machines

In the design of dynamic supramolecular systems used in molecular machines, it is important to understand the binding preferences between the macrocycle and stations along the thread. Here, we apply 1H NMR spectroscopy to investigate the relative stabilities of a series of linear alkylammonium templated pseudorotaxanes with the general formula [H2NRR'][Cr7CoF8(O2CCH2 tBu)16] by exchanging the cation in solution. Our results show that the pseudorotaxanes are able to exchange threads via a dissociative mechanism. The position of equilibrium is dependent upon the ammonium cation and solvent used. Short chain primary ammonium cations are shown to be far less favourable macrocycle stations than secondary ammonium cations. Collision-induced dissociation mass spectrometry (CID-MS) has been used to look at disassembly of the pseudorotaxanes in a solvent-free environment and stability trends compared to those in acetone-d6. The energy needed to induce 50 % of the precursor ion loss (E50) is used and shows a similar trend to the equilibria measured by NMR. The relative stabilities of these hybrid inorganic-organic pseudo-rotaxanes are different to those of host-guest compounds involving crown ethers and this may be valuable for the design of molecular machines.

Characterization of the fragmentation mechanisms in electrospray ionization tandem mass spectrometry of chloroquinoline derivatives with larvicidal activity against Aedes aegypti

RATIONALE

4,7-Dichloroquinoline (DCQ) represents a group of synthetic molecules inspired by natural products with important roles in biological and biomedical areas. This work aimed to characterize DCQ and its derivatives by high-resolution electrospray ionization (ESI) mass spectrometry and tandem mass spectrometry (ESI-MS/MS), supported by theoretical calculations. Biological assays were carried out with DCQ and its derivatives to determine LC50 values against Aedes aegypti larvae.

METHODS

Five DCQ derivatives were synthesized by using previously described protocols. ESI-MS/MS analyses were carried out with a quadrupole/time-of-flight and ion-trap instrument. The proposed gas-phase protonation sites and fragmentation were supported by density functional theory calculations. The larvicidal tests were performed with the Ae. aegypti Rockefeller strain, and the LC50 values were determined by employing five test concentrations. Larval mortality was determined after treatment for 48 h.

RESULTS

DCQ bromides or aldehydes (C-3 or C-8 positions), as well as the trimethylsilyl derivative (C-3 position), were prepared. Detailed ESI-MS/MS data revealed heteroatom elimination through an exception to the even-electron rule, to originate open-shell species. Computational studies were used to define the protonation sites and fragmentation pathways. High activity of DCQ and its derivatives against Ae. aegypti larvae was demonstrated.

CONCLUSION

Our results provided a well-founded characterization of the fragmentation reactions of DCQ and its derivatives, which can be useful for complementary studies of the development of a larvicidal product against Ae. aegypti.

Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox

Understanding the composition, structure and stability of larger synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not always provide this information. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, complementary techniques and computational methods, can be used to structurally characterize synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, nanoclusters, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes.

Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry

Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.

Determination and gas-phase stability evaluation of metal complexes by nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry

RATIONALE

The structures of metal complexes determine their stable functioning in product performance. Electrospray ionization mass spectrometry (ESI-MS) is used in studying metal complexes despite exhibiting limitations in analyzing labile complexes. Therefore, identifying a method for detecting unstable complexes and evaluating their stabilities is necessary, providing a theoretical basis for material selection and performance evaluation.

METHODS

The standard complexes Zn(BTZ)2 , Fe(acac)3 , and Sn(Oct)2 were analyzed using nanoESI quadrupole orbitrap MS (nanoESI-MS) and compared with ESI-MS for two temperature modes. The three complexes and alkylamine-Ag+ complexes were analyzed using nanoESI and collision-induced dissociation MS/MS (CID-MS/MS). Breakdown plots of the survival yield against collision energies expressed in terms of the center-of-mass were constructed according to the obtained product ion spectra. Quantum chemical calculations based on density functional theory were performed to calculate the binding energies between the alkylamines and Ag+ .

RESULTS

The three standard complexes were detected in the native structures using nanoESI-MS, confirming the advantage of nanoESI over ESI for detecting unstable complexes. The gas-phase stabilities of the amine-Ag+ complexes, estimated using the breakdown plots constructed by plotting the data obtained via nanoESI and CID-MS/MS, were consistent with the established theories, previous studies, and binding energies calculated using computational methods.

CONCLUSIONS

NanoESI-MS is suitable for detecting labile complexes and enables the structural analyses of unknown complex additives. A novel approach based on nanoESI and CID-MS/MS was developed to determine the gas-phase stabilities of complexes, enabling their quantification and comparison and providing a technical basis for product improvement, which is essential in developing industrial materials.

Encapsulation in Charged Droplets Generates Distorted Host-Guest Complexes

The ability of various hydrogen-bonded resorcinarene-based capsules to bind α,ω-alkylbisDABCOnium (DnD) guests of different lengths was investigated in solution and in the gas-phase. While no host-guest interactions were detected in solution, encapsulation could be achieved in the charged droplets formed during electrospray ionisation (ESI). This included guests, which are far too long in their most stable conformation to fit inside the cavity of the capsules. A combination of three mass spectrometric techniques, namely, collision-induced dissociation, hydrogen/deuterium exchange, and ion-mobility mass spectrometry, together with computational modelling allow us to determine the binding mode of the DnD guests inside the cavity of the capsules. Significant distortions of the guest into horseshoe-like arrangements are required to optimise cation-π interactions with the host, which also adopt distorted geometries with partially open hydrogen-bonding seams when binding longer guests. Such quasi "spring-loaded" capsules can form in the charged droplets during the ESI process as there is no competition between guest encapsulation and ion pair formation with the counterions that preclude encapsulation in solution. The encapsulation complexes are sufficiently stable in the gas-phase - even when strained - because non-covalent interactions significantly strengthen in the absence of solvent.

Experimental and Theoretical Structure Elucidation of the [2 : 1] Complex Ion of Carbo[n]helicene with n=6, 7 and 8 and Ag. Chemphyschem 2023;24:e202300496. [PMID: 37578805 DOI: 10.1002/cphc.202300496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Gas-phase complexes of [n]helicenes with n=6, 7 and 8 and the silver(I) cation are generated utilizing electrospray ionization mass spectrometry (ESI-MS). Besides the well-established [1 : 1] helicene/Ag+ -complex in which the helicene provides a tweezer-like surrounding for the Ag+ , there is also a [2 : 1] complex formed. Density functional theory (DFT) calculations in conjunction with energy-resolved collision-induced dissociation (ER-CID) experiments reveal that the second helicene attaches via π-π stacking to the first helicene, which is part of the pre-formed [1 : 1] tweezer complex with Ag+ . For polycyclic aromatic hydrocarbons (PAHs) of planar structure, the [2 : 1] complex with silver(I) is typically structured as an Ag+ -bound dimer in which the Ag+ would bind to both PAHs as the central metal ion (PAH-Ag+ -PAH). For helicenes, the Ag+ -bound dimer is of similar thermochemical stability as the π-π stacked dimer, however, it is kinetically inaccessible. Coronene (Cor) is investigated in comparison to the helicenes as an essentially planar PAH. In analogy to the π-π stacked dimer of the helicenes, the Cor-Ag+ -Cor-Cor complex is also observed. Competition experiments using [n]helicene mixtures reveal that the tweezer complexes of Ag+ are preferably formed with the larger helicenes, with n=6 being entirely ignored as the host for Ag+ in the presence of n=7 or 8.

Study of Mono and Di-O-caffeoylquinic Acid Isomers in Acmella oleracea Extracts by HPLC-MS/MS and Application of Linear Equation of Deconvolution Analysis Algorithm for Their Characterization

Chlorogenic acids, the esters of caffeic and quinic acids, are the main phenolic acids detected in Acmella oleracea extracts and have gained increasing interest in recent years due to their important biological activities. Given their structural similarity and instability, the correct analysis and identification of these compounds in plants is challenging. This study aimed to propose a simple and rapid determination of the A. oleracea caffeoylquinic isomers, applying an HPLC-MS/MS method supported by a mathematical algorithm (Linear Equation of Deconvolution Analysis (LEDA)). The three mono- and the three di-caffeoylquinic acids in roots of Acmella plants were studied by an ion trap MS analyzer. A separation by a conventional chromatographic method was firstly performed and an MS/MS characterization by energetic dimension of collision-induced dissociation mechanism was carried out. The analyses were then replicated using a short HPLC column and a fast elution gradient (ten minutes). Each acquired MS/MS data were processed by LEDA algorithm which allowed to assign a relative abundance in the reference ion signal to each isomer present. Quantitative results showed no significant differences between the two chromatographic systems proposed, proving that the use of LEDA algorithm allowed the distinction of the six isomers in a quarter of the time.

Isomers Recognition in HPLC-MS/MS Analysis of Human Plasma Samples by Using an Ion Trap Supported by a Linear Equations-Based Algorithm

The tandem mass spectrometry (MS/MS) approach employing an ion trap mass analyzer (IT) was evaluated in isomers recognition. The proposed approach consists of sole, simple, and rapid liquid chromatographic separation (HPLC) without requiring resolution between the analytes. Then, the MS/MS properties were optimized to solve the signal assignment using post-processing data elaboration (LEDA). The IT-MS/MS experiment uses the same site, helium as collision gas, and different time steps to modify the applied conditions on the studied ions. Nevertheless, helium cannot ensure the quick energization of the precursor ion due to its small cross-section. Then, different combinations between excitation amplitude (ExA) and excitation time (ExT) were tested to achieve the activation of the fragmentation channels and the formation of the MS/MS spectrum. Usually, the IT-MS/MS acquisition cycle is longer for other multistage instruments, decreasing the frequency of sample data collection and influencing the chromatographic profile. To solve these problems, two time segments were set up, and the elution conditions were optimized with a compromise between peaks distinction and run time reduction. The developed HPLC-MS/MS method was checked and applied to analyze a series of human plasma samples spiked with an equimolar mixture of pair of isomers.

Tandem mass spectrometry approaches for recognition of isomeric compounds mixtures

The present review aims to collect the published literature pertaining the recognition of isobaric compounds (isomers or stereoisomers) using the features of tandem mass spectrometry (MS) experiments without any chromatographic separation or chemical modification (derivatization or isotopic enrichment) of the analytes. MS/MS methods possess high selectivity, wide dynamic range and high throughput capabilities. Generally, tandem MS has limited capability for distinguishing isomers that fragment similarly. However, some MS/MS methods have been developed and positively applied to isomers discrimination. Among the literature on this topic, the applications that fit on the review subject can be summarized as follow: (1) chiral discrimination by the kinetic method, (2) the use energy-resolved tandem mass spectra and the survival yield (SY) representation, (3) the kinetics evaluation of the ion-molecule interaction and (4) the postprocessing mathematical algorithm to resolve the isomers in MS/MS signal.

Noncovalent Host-Guest Complexes of Artemisinin with α-, β-, and γ- Cyclodextrin Examined by Structural Mass Spectrometry Strategies

Cyclodextrins (CDs) are a family of macrocyclic oligosaccharides with amphiphilic properties, which can improve the stability, solubility, and bioavailability of therapeutic compounds. There has been growing interest in the advancement of efficient and reliable analytical methods that assist with elucidating CD host-guest drug complexation. In this study, we investigate the noncovalent ion complexes formed between naturally occurring dextrins (αCD, βCD, γCD, and maltohexaose) with the poorly water-soluble antimalarial drug, artemisinin, using a combination of ion mobility-mass spectrometry (IM-MS), tandem MS/MS, and theoretical modeling approaches. This study aims to determine if the drug can complex within the core dextrin cavity forming an inclusion complex or nonspecifically bind to the periphery of the dextrins. We explore the use of group I alkali earth metal additives to promote the formation of various noncovalent gas-phase ion complexes with different drug/dextrin stoichiometries (1:1, 1:2, 1:3, 1:4, and 2:1). Broad IM-MS collision cross section (CCS) mapping (n > 300) and power-law regression analysis were used to confirm the stoichiometric assignments. The 1:1 drug:αCD and drug:βCD complexes exhibited strong preferences for Li+ and Na+ charge carriers, whereas drug:γCD complexes preferred forming adducts with the larger alkali metals, K⁺, Rb⁺, and Cs⁺. Although the ion-measured CCS increased with cation size for the unbound artemisinin and CDs, the 1:1 drug:dextrin complexes exhibit near-identical CCS values regardless of the cation, suggesting these are inclusion complexes. Tandem MS/MS survival yield curves of the [artemisinin:βCD + X]⁺ ion (X = H, Li, Na, K) showed a decreased stability of the ion complex with increasing cation size. Empirical CCS measurements of the [artemisinin:βCD + Li]⁺ ion correlated with predicted CCS values from the low-energy theoretical structures of the drug incorporated within the βCD cavity, providing further evidence that gas-phase inclusion complexes are formed in these experiments. Taken together, this work demonstrates the utility of combining analytical information from IM-MS, MS/MS, and computational approaches in interpreting the presence of gas-phase inclusion phenomena.

Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method

Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]⁺ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]⁺ interaction in the gas phase was determined from E_com50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]⁺ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.

Adduct Ions as Diagnostic Probes of Metallosupramolecular Complexes Using Ion Mobility Mass Spectrometry

Following electrospray ionization, it is common for analytes to enter the gas phase accompanied by a charge-carrying ion, and in most cases, this addition is required to enable detection in the mass spectrometer. These small charge carriers may not be influential in solution but can markedly tune the analyte properties in the gas phase. Therefore, measuring their relative influence on the target molecule can assist our understanding of the structure and stability of the analyte. As the formed adducts are usually distinguishable by their mass, differences in the behavior of the analyte resulting from these added species (e.g., structure, stability, and conformational dynamics) can be easily extracted. Here, we use ion mobility mass spectrometry, supported by density functional theory, to investigate how charge carriers (H⁺, Na⁺, K⁺, and Cs⁺) as well as water influence the disassembly, stability, and conformational landscape of the homometallic ring [Cr₈F₈(O₂C^tBu)₁₆] and the heterometallic rotaxanes [NH₂RR'][Cr₇MF₈(O₂C^tBu)₁₆], where M = Mn^II, Fe^II, Co^II, Ni^II, Cu^II, Zn^II, and Cd^II. The results yield new insights on their disassembly mechanisms and support previously reported trends in cavity size and transition metal properties, demonstrating the potential of adduct ion studies for characterizing metallosupramolecular complexes in general.

5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations

Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.

Benchmarking higher energy collision dissociation (HCD) by investigation of binding energies of gas-phase host-guest complexes of hemicryptophane cages

Synthesis of host molecules that feature well-defined characteristics for molecular recognition of guest molecules is often a major aim of synthetic host-guest (H-G) chemistry. A key consideration in evaluating the selectivity of hosts and the affinities of guests is the measurement of binding energies of obtained H-G complexes. In contrast to nuclear magnetic resonance (NMR) or fluorescence measurements that are capable of measuring binding strengths in solution, mass spectrometry offers the opportunity to measure gas-phase binding energies. Presented in this article is a higher energy collision dissociation (HCD) approach for determining critical energies of dissociation of H-G complexes. Experiments were performed on electrospray ionization (ESI)-generated H-G pairs in an LTQ-XL/Orbitrap hybrid instrument. The presented HCD approach requires preliminary calibration of the internal energy distribution of generated ions that was achieved by the use of activation parameters that were known from previous low-energy collision-induced dissociation (low-energy CID) experiments. Internal energy deposition was modeled based on a truncated Maxwell-Boltzmann distribution and characteristic temperature (T_char ). Using this method, critical energies of dissociation were determined for 10 H-G biologically relevant complexes of the heteroditopic hemicryptophane cage host (Host). Obtained results are compared with those found previously by low-energy CID. The use of this HCD technique is relatively straightforward, although its implementation does require knowledge (or a presumption) about the Arrhenius pre-exponential factor of the complexes to obtain their critical energies of dissociation.

Application of LEDA algorithm for the recognition of P-glycoprotein and Carbonic Anhydrase hybrid inhibitors and evaluation of their plasma stability by HPLC-MS/MS analysis

Design and synthesis of new candidate drugs produces a large number of compounds that must be qualified and tested to evaluate their characteristics and potential applications. Therefore, many studies will be scheduled and, consequently, it will be necessary to arrange specific, reliable, fast and relatively cheap analytic methods to support this research. The manuscript proposes a new approach in the HPLC-MS/MS analysis by using a sole chromatographic set up, tuned to minimize the run time, without requiring high efficiency or resolution between the analytes. The chromatographic column was used only to avoid or limit the interference of sample matrix towards the analyte ionization process (matrix-effects). Then, the MS/MS properties were explored to solve the signal assignment, by performing a series of energy resolved experiments to optimize the parameters and applying an interesting post-processing data elaboration tool (LEDA). The reliability of the new approach was evaluated in a chemical stability study in PBS and human plasma samples of a series of isomeric compounds P-glycoprotein/Carbonic Anhydrase (P-gp/CA) hybrid inhibitors. The obtained results demonstrated the effectiveness (reliability 97%-100%) of the LEDA algorithm to recognize and to separate the possible isomers present in the samples. The obtained matrix-effects values (ME 96%-106%) established that the chromatographic set up (short column and fast elution gradient) was proper to avoid the matrix interferences, while recovery values (RE 88%-108%) indicate a suitable sample preparation, despite only a protein precipitation was carried out. The quantitative performances of proposed HPLC-MS/MS methods showed an accuracy ranging between 92% and 108% and a precision lower than 13% that allows to be confident on the determination of new P-gp/CA hybrid inhibitors in the degradation study. Therefore, the general procedure proposed was found adequate to study a series of isomeric compounds without their chromatographic separation but only by applying and developing the MS/MS features.

Energy-resolved mass spectrometry to investigate nucleobase triplexes – a study applied to triplex-forming artificial nucleobases

This paper discloses the use of an energy-resolved mass spectrometric-based approach to assess the stabilities of base triplexes encompassing artificial nucleobases by using variable energy collision-induced dissociation.

Ion mobility spectrometry-tandem mass spectrometry strategies for the on-line monitoring of a continuous microflow reaction

Continuous flow chemistry is an efficient, sustainable and green approach for chemical synthesis that surpasses some of the limitations of the traditional batch chemistry. Along with the multiple advantages of a flow reactor, it could be directly connected to the analytical techniques for on-line monitoring of a chemical reaction and ensure the quality by design. Here, we aim to use ion mobility, mass and tandem mass spectrometry (IMS-MS and MS/MS) for the on-line analysis of a pharmaceutically relevant chemical reaction. We carried out a model hetero-Diels Alder reaction in a microflow reactor directly connected to the IMS-MS and MS/MS using either electrospray or atmospheric pressure photo ionization methods. We were able to monitor the reaction mechanism of the Diels Alder reaction and structurally characterize the reaction product and synthesis side-products. The chosen approach enabled identification of two isomers of the main reaction product. A new strategy to annotate the ion mobility spectrum in the absence of standard molecules was introduced and tested for its validity. This was achieved by determining the survival yield of each isomer upon ion mobility separation and density functional theory calculations. This approach was verified by comparing the theoretically driven collision cross section values to the experimental data. In this paper, we demonstrated the potential of combined IMS-MS and MS/MS on-line analysis platform to investigate, monitor and characterize structural isomers in the millisecond time scale.

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.

Ambivalent role of ascorbic acid in the metal-catalyzed oxidation of oligopeptides

The effect of ascorbic acid on the metal-catalyzed oxidation of a human prion protein model peptide has been studied. The complex formation of the peptide was clarified first. The studied model peptide contains a methionine and a histidine amino acids which are important both as binding sites for metal ions and sensitive parts of the protein for oxidation. pH-potentiometric, UV-Vis and circular dichroism spectroscopic techniques were applied to study the stoichiometry, stability and structure of the copper(II) complexes, while HPLC-MS and MS/MS were used for identifying the products of metal-catalyzed oxidation. 3N and 4N complexes with (N_im,N^-,N^-,S) and (N_im,N^-,N^-,N^-) coordination modes are formed at pH 7.4, where the oxidation was studied. Singly, doubly and triply oxidized products are formed in which the methionine and/or the histidine side chain is oxidized. The oxidation was carried out with hydrogen peroxide solution by the addition of metal ions, namely copper(II) and iron(III) and/or ascorbic acid.

Structural analysis of a compound despite the presence of an isobaric interference by using in-source Collision Induced Dissociation and tandem mass spectrometry

The presence of an isobaric contaminant can drastically affect MS and MS/MS patterns leading to erroneous structural and quantitative analysis, which is a real challenge in mass spectrometry. Herein, we demonstrate that MS and MS/MS structural analysis of a compound can be successfully performed despite the presence of an isobaric interference with as low as few millidaltons mass difference by using pseudo-MS³ . To this end, in-source collisional excitation (in-source CID) and the Survival Yield (SY) technique (energy-resolved collision induced dissociation MS/MS) were performed on two different source geometries: a Z-spray and an orthogonal spray (with a transfer capillary) ionization sources on two different mass spectrometers. By using soft ionization conditions, the SY curve for the mixture is a linear combination of the SY curves from the pure compounds demonstrating the presence of two components in the mixture. In the case of harsher ionization conditions, the SY curve of the mixture perfectly overlaps the SY curve from the pure analyte. This observation demonstrates the isobaric interference has been completely removed by in-source CID fragmentation, independently of the source design, leaving then the analyte precursor ions only. Therefore, by measuring the MS spectrum in harsh ionization conditions and according to SY criterium, the compound of interest can be made free from isobaric interference paving the way for, for example, unequivocal HPLC-MS as well as HPLC-MS/MS structural and quantitative analysis despite the presence of a co-eluting isobaric interference.

First Steps to Rationalize Host-Guest Interaction between α-, β-, and γ-Cyclodextrin and Divalent First-Row Transition and Post-transition Metals (Subgroups VIIB, VIIIB, and IIB)

Cyclodextrins (CDs) are cyclic oligosaccharides mainly composed of six, seven, and eight glucose units, so-called α-, β-, and γ-CDs, respectively. They own a very particular molecular structure exhibiting hydrophilic features thanks to primary and secondary rims and delimiting a hydrophobic internal cavity. The latter can encapsulate organic compounds, but the former can form supramolecular complexes by hydrogen-bonding or electrostatic interactions. CDs have been used in catalytic processes to increase mass transfer in aqueous-organic two-phase systems or to prepare catalysts. In the last case, interaction between CDs and metal salts was considered to be a key point in obtaining highly active catalysts. Up to now, no work was reported on the investigation of factors affecting the binding of metal to CD. In the study herein, we present the favorable combination of electrospray ionization coupled to mass spectrometry [ESI-MS(/MS)] and density functional theory molecular modeling [B3LYP/Def2-SV(P)] to delineate some determinants governing the coordination of first-row divalent transition metals (Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Fe²⁺) and one post-transition metal (Zn²⁺) with α-, β-, and γ-CDs. A large set of features concerning the metal itself (ionic radius, electron configuration, and spin state) as well as the complexes formed (the most stable conformer, relative abundance in MS, CE₅₀ value in MS/MS, binding energy, effective coordination number, average bond lengths, binding site localization, bond dissociation energies, and natural bond orbital distribution) were screened. Taking into account all of these properties, various selectivity rankings have been delineated, portraying differential association/dissociation behaviors. Nonetheless, unique 3D topologies for each CD-metal complex were emphasized. The combination of these approaches brings a stone for building a compendium of molecular features to serve as a suitable descriptor or predictor for a better first round rationalization of catalytic activities.

Confirmative Structural Annotation for Metabolites of (R)-7,3'-Dihydroxy-4'-methoxy-8-methylflavane, A Natural Sweet Taste Modulator, by Liquid Chromatography-Three-Dimensional Mass Spectrometry

Flavonoids occupy the largest family of natural products and possess a broad spectrum of health benefits. Their metabolites are sometimes the truly effective molecules in vivo. It is still challenging, however, to unambiguously identify flavonoid metabolites using conventional LC-MS/MS. Herein, we aimed to pursue auxiliary structural clues to m/z values in both MS¹ and MS² spectra through LC coupled to three-dimensional MS (LC-3D MS). MS¹, as the first dimension, was in charge of suggesting theoretical molecular formulas, MS², the as second dimension, was responsible for offering substructures, and exactly, online energy-resolved MS (ER-MS), as the third dimension, provided optimal collision energies (OCEs) that reflected the linkage manners among the substructures. Metabolic characterization of a natural sweet taste modulator, namely, (R)-7,3'-dihydroxy-4'-methoxy-8-methylflavane (DHMMF), was conducted as a proof-of-concept. Extensive efforts, such as full MS¹ and MS² scans on IT-TOF-MS and predictive selected-reaction monitoring mode on Qtrap-MS, were made for in-depth metabolite mining. Seventeen metabolites (M1-M17) were captured from DHMMF-treated biological samples, including 17 (M1-M17), 10 (M4-M9, M11, M13, M14, and M16), and 2 (M5 and M10) metabolites from urine, plasma, and feces, respectively. Their structures were configured by integrating MS¹, MS², and OCE information. Except M10, all metabolites were new compounds. LC-MS/MS-guided chromatographic purification yielded three glucuronyl-conjugated metabolites (M5, M8, and M11), and NMR spectroscopic assays consolidated the structures transmitted from LC-3D MS. Demethylation, glucuronidation, and sulfation occurred as the primary metabolic pathways of DHMMF. Above all, LC-3D MS bridged LC-MS/MS from putatively structural annotation toward confidence-enhanced identification, beyond the metabolite characterization of flavonoids.

Determination of coeluted isomers in wine samples by application of MS/MS deconvolution analysis

Two organic acids isomers, 3-isopropylmalic acid (3-IPMA) and 2-isopropylmalic acid (2-IPMA), were identified and quantified in wine samples by using an LC-MS/MS method without any chromatographic separation, but processing the MS/MS data with a recently developed deconvolution algorithm (LEDA: linear equations deconvolution analysis), thus decreasing the time necessary for the process. In particular, the LEDA tool processes the MS/MS signals and assigns the relative concentrations (abundances) of the isomers in the sample, at the mg L^-1 level. The efficiency of MS/MS signal assignment was improved by introducing five linear equations to define the LEDA matrix. Then, as a novel approach, an overdetermined system of linear equations was applied for the deconvolution of isomers. The use of LEDA to identify and quantify the isomers in wine samples, together with the choice of a short LC column and a fast elution gradient, simplifies the process and shortens the time needed. Furthermore, it was evaluated the quantitative determination of the IPMA isomers by using the calibration curve provided by the precursor ion MRM transition data. The calculated values of accuracy (recovery between 82.6% and 99.8%) and precision (RSD between 0.4% and 4.0%) confirm the validity of this quantitative approach and the ability of LEDA to establish the correct percentage of the MS/MS signal for each isomer. Finally, to compare the conventional LC-MS/MS method and our proposed method of LC-MS/MS coupled with LEDA post-processing elaboration, a series of real wine samples were analysed by both methods, and the results were compared.

Ion trap MS using high trapping gas pressure enables unequivocal structural analysis of three isobaric compounds in a mixture by using energy-resolved mass spectrometry and the survival yield technique

Recently, it has been shown that energy-resolved mass spectrometry (MS) can provide quantitative information from two isomeric or isobaric compounds in mixtures by using the survival yield (SY) technique together with "gas-phase collisional purification" (GPCP) strategy (Anal. Chem., 2016, 88, p.10821). Herein, we present an improvement and an extension of this concept to the structural analysis of a model mixture of three isobaric compounds (two peptides and a polyether). By using default collision-induced dissociation (CID) tandem MS parameters on an ion trap instrument, the previous approach did not show any signs of isobaric contamination. However, by modifying CID conditions and using a threefold increase of the He trapping gas pressure (to reach 3.00·10^-5 mbar), the SY curve was unexpectedly and strongly shifted to higher excitation voltages with two plateaus appearing. Those plateaus, indicating clearly the presence of three isobaric compounds, were taken as reliable indicators to perform GPCP at carefully selected excitation voltages in order to selectively fragment one compound after the other. In this way, CID mass spectra of each compound were correctly recovered, both in terms of fragment ion peaks and in terms of relative intensities, from energy-resolved MSⁿ spectra of the three compounds mixture. This feature enables their unequivocal structural analysis as if samples were free from isobaric interferences. In this paper, we also discuss the possibility for recovering SY curves for pure compounds directly from the mixture. Clearly, in this case, the higher He trapping gas pressure made it possible to use the SY technique, for the first time, for the structural analysis in the case of mixtures of three isobaric compounds. This observation, quite unexpected, demonstrates that the trapping gas pressure is of paramount importance although it is usually not considered in energy-resolved MS for structural and/or quantitative analysis.

Hydrogen bonding influences collision-induced dissociation of Na+ -bound guanine tetrads

Na+ -bound guanine (G)-tetrads possess square planar structures formed solely by noncovalent interactions including multiple hydrogen bonds. Unlike G-tetrads facilitated by other alkali metal ions, an intriguing behavior in collision-induced dissociation (CID) has been observed in Na+ -bound G-tetrads, which features a preferential, simultaneous loss of two G ligands in the low energy regime. To understand this unique behavior, we investigated the CID of Na+ -bound G-tetrads with mixed ligands of G and 9-methylguanine (9mG), [Na·Gm ·9mGn ]+ (m + n = 4), and [Li·9mG4 ]+ for comparison. In the CID experiments, the simultaneous losses of two ligands were by far more pronounced than the loss of a single ligand for all five Na+ -bound G-tetrads. However, it appeared that the CID of [Li·9mG4 ]+ prefers to lose single ligands sequentially. An analysis of the fragment abundances suggested that the generation of Na+ -bound dimeric fragments might have occurred with two adjacent ligands. This theoretical study predicted for [Li·9mG4 ]+ that the loss of a single ligand is more energetically favorable than the production of neutral hydrogen-bonded fragments by 35.5 kJ/mol (ΔG). This contradicts our previous calculations for [Na·9mG4 ]+ that a neutral loss of hydrogen-bonded dimers provides the lowest energy product state of Na+ -bound dimeric fragments, which is lower than that of Na+ -bound trimeric fragments by 15.6 kJ/mol. From the results, this comparative study suggests that the pronounced generation of Na+ -bound dimeric fragments in CID of the G-tetrads is likely promoted by the dissociation pathway associated with neutral loss of hydrogen-bonded dimers. It thus demonstrates that multiple hydrogen bonding participating in formation of Na+ -bound G-tetrads may also strongly influence the fate of dissociating complexes of G-tetrads.

Identification of bifucosylated glycoforms using low-energy CID spectra

We have used tandem mass spectrometry (MS/MS)-based analysis of glycopeptides in order to identify the composition and structure of rare glycoforms. The results illustrate utility of low-energy MS/MS for structure identification. We have shown the presence of bifucosylated and trifucosylated glycoforms in human α-1-acid glycoprotein (AGP), a major plasma glycoprotein. Fucosylation in the case of AGP always occurs on the antennae; core fucosylation was not observed.

Structures and Relative Glycosidic Bond Stabilities of Protonated 2'-Fluoro-Substituted Purine Nucleosides

The 2'-substituent is the primary distinguishing feature between DNA and RNA nucleosides. Modifications to this critical position, both naturally occurring and synthetic, can produce biologically valuable nucleoside analogues. The unique properties of fluorine make it particularly interesting and medically useful as a synthetic nucleoside modification. In this work, the effects of 2'-fluoro modification on the protonated gas-phase purine nucleosides are examined using complementary tandem mass spectrometry and computational methods. Direct comparisons are made with previous studies on related nucleosides. Infrared multiple photon dissociation action spectroscopy performed in both the fingerprint and hydrogen-stretching regions allows for the determination of the experimentally populated conformations. The populated conformers of protonated 2'-fluoro-2'-deoxyadenosine, [Adofl+H]⁺, and 2'-fluoro-2'-deoxyguanosine, [Guofl+H]⁺, are highly parallel to their respective canonical DNA and RNA counterparts. Both N3 and N1 protonation sites are accessed by [Adofl+H]⁺, stabilizing syn and anti nucleobase orientations, respectively. N7 protonation and anti nucleobase orientation dominates in [Guofl+H]⁺. Spectroscopically observable intramolecular hydrogen-bonding interactions with fluorine allow more definitive sugar puckering determinations than possible for the canonical systems. [Adofl+H]⁺ adopts C2'-endo sugar puckering, whereas [Guofl+H]⁺ adopts both C2'-endo and C3'-endo sugar puckering. Energy-resolved collision-induced dissociation experiments with survival yield analyses provide relative glycosidic bond stabilities. The N-glycosidic bond stabilities of the protonated 2'-fluoro-substituted purine nucleosides are found to exceed those of their canonical analogues. Further, the N-glycosidic bond stability is found to increase with increasing electronegativity of the 2'-substituent, i.e., H < OH < F. The N-glycosidic bond stability is also greater for the adenine nucleoside analogues than the guanine nucleoside analogues.

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

Abstract

Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that are formed alter the DNA structure, contributing to inhibition of function and ultimately cancer cell death. Despite its success as an anticancer drug, cisPt has a number of drawbacks that reduce its efficacy, including repair of adducts and drug resistance. Some approaches to overcome this problem involve development of compounds that coordinate to other purine nucleobases, including those found in RNA. In this work, amino acid-linked platinum(II) (AAPt) compounds of alanine and ornithine (AlaPt and OrnPt, respectively) were studied. Their reactivity preferences for DNA and RNA purine nucleosides (i.e., 2′-deoxyadenosine (dAdo), adenosine (Ado), dGuo, and guanosine (Guo)) were determined. The chosen compounds form predominantly monofunctional adducts by reacting at the N1, N3, or N7 positions of purine nucleobases. In addition, features of AAPt compounds that impact the glycosidic bond stability of Ado residues were explored. The glycosidic bond cleavage is activated differentially for AlaPt-Ado and OrnPt-Ado isomers. Formation of unique adducts at non-canonical residues and subsequent destabilization of the glycosidic bonds are important features that could circumvent platinum-based drug resistance.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-019-01693-y) contains supplementary material, which is available to authorized users.

Interrogating Proton Affinities of Organophosphonate Species Via Atmospheric Flow Tube Mass Spectrometry and Computational Methods

Within trace vapor analysis in environmental monitoring, defense, and industry, atmospheric flow tube mass spectrometry (AFT-MS) can fill a role that incorporates non-contact vapor analysis with the selectivity and low detection limits of mass spectrometry. AFT-MS has been applied to quantitating certain explosives by selective clustering with nitrate and more recently applied to detecting tributyl phosphate and dimethyl methylphosphonate as protonated species. Developing AFT-MS methods for organophosphorus species is appealing, given that this class of compounds includes a range of pollutants, chemical warfare agent (CWA) simulants, and CWA degradation products. A key aspect of targeting organophosphorus analytes has included the use of dopant ion chemistry to form adducts that impart additional analytical selectivity. The assessment of potential dopant molecules suited to enhance detection of these compounds is hindered by few published ion thermochemical properties for organophosphorus species, such as proton affinity, which can be used for approximating proton-bound dimer bond strength. As a preliminary investigation for the progression of sensing methods involving AFT-MS, we have applied both the extended kinetic method and computational approaches to eight organophosphorus CWA simulants to determine their respective gas-phase proton affinities. Notable observed trends, supported by computational efforts, include an increase in proton affinity as the alkyl chain lengths on the phosphonates increased. Graphical Abstract .

Alternated Branching Ratios by Anomaly in Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pairs of 1-Methylcytosine with 1-Methylguanine and 9-Methylguanine

A comparative study on the proton-bound complexes of 1-methylcytosine (1-mC) with 1-methylguanine (1-mG) and 9-methylguanine (9-mG), [1-mC:1-mG:H]⁺ and [1-mC:9-mG:H]⁺, respectively, was carried out using energy-resolved collision-induced dissociation (ER-CID) experiments in combination with quantum chemical calculations. In ER-CID experiments, the measured survival yields indicated an essentially identical stability for the two proton-bound complexes. In comparison with the lowest-energy structures and base-pairing energetics predicted at the B3LYP/6-311+G(2d,2p) theory level, both complexes produced in this study were suggested to be proton-bound Hoogsteen base pairs. Curiously, despite the similarity in structures, binding energetics, and potential energy surfaces predicted by the B3LYP theory, the fragment branching ratios exhibited an intriguing alternation between the two proton-bound Hoogsteen base pairs. The CID of [1-mC:1-mG:H]⁺ produced protonated cytosines, [1-mC:H]⁺, more abundantly than [1-mG:H]⁺, whereas that of [1-mC:9-mG:H]⁺ gave rise to a more pronounced production of protonated guanines, [9-mG:H]⁺. However, using the proton affinities of moieties predicted by the high-accuracy methods, including CBS-QB3 and the Guassian-4 theory, the anomaly known for [Cytosine:Guanine:H]⁺ (J. Am. Soc. Mass Spectrom. 29, 2368-2379 (2018)) successfully accounted for the alternated branching ratios. Thereby, the anomaly, more specifically, the production of proton-transferred fragments of O-protonated cytosines in the CID of proton-bound Hoogsteen base pairs, is indeed real, which is disclosed as the alternated branching ratios in the CID spectra of [1-mC:1-mG:H]⁺ and [1-mC:9-mG:H]⁺ in this study. Graphical Abstract .

Analysis of unstable degradation impurities of a benzodiazepine and their quantification without isolation using multiple linear regression

This manuscript presents a novel methodology for calculating the relative response factors (RRFs) of unstable degradation impurities of molibresib (1). The degradation impurities were observed by HPLC during stress testing and were accompanied by large mass balance deficits. However, the impurities could not be isolated for traditional RRF determination due to their instability. The RRFs of two degradation impurities were determined without isolation by multiple linear regression analysis of HPLC-UV data. The results permitted accurate quantification of the degradants. The benefits and drawbacks of the approach are discussed, including suggested validation acceptance criteria.

Ambient vapor sampling and selective cluster formation for the trace detection of tributyl phosphate via atmospheric flow tube mass spectrometry

In addition to serving as an f-element ligand and rare-earth method complexing agent, tributyl phosphate is a compound containing core functional groups that mimic those routinely found in degradation products from industrial processes. Because detection of trace quantities of tributyl phosphate can provide insight into the routes of contamination and degradation in the environment, there is a need to develop methods capable of detecting trace quantities of tributyl phosphate. Vapor detection at atmospheric pressure is one approach that is both sensitive and rapid. We present here the use of atmospheric flow tube mass spectrometry for the ambient vapor sampling of tributyl phosphate from headspace of ppb-level solutions in methanol. Gas phase clustering reactions were to enhance detection levels via the addition of small quantities of the dopants diethylamine, triethylamine, and pinacolyl methylphosphonate in the vapor stream. Detection of the tributyl phosphate vapor emanating from these solutions demonstrated a linear range for the protonated tributyl phosphate species of 1-1000 ppb from solution. The clusters of tributyl phosphate with diethylamine, triethylamine, and pinacolyl phosphonate each yielded linear ranges of 1-250 ppb for tributyl phosphate in solution. Despite smaller linear ranges, the addition of these dopant species added a layer of analytical selectivity and reduced variability in signals from quality control samples. These data were obtained using an atmospheric flow tube source coupled to a linear ion trap mass spectrometer, which demonstrates the applicability of trapping systems to the atmospheric flow tube ionization technique while monitoring positive ions.

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.

Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine

To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H⁺∙∙∙G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H⁺∙∙∙G exhibited more abundant productions of C:H⁺, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H⁺. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H⁺ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H⁺ fragments, effectively doubles the apparent reaction rate for production of C:H⁺. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H⁺ in the CID of the proton-bound Hoogsteen base pair, C:H⁺∙∙∙G. Graphical Abstract ᅟ.

Influence of Linkage Stereochemistry and Protecting Groups on Glycosidic Bond Stability of Sodium Cationized Glycosyl Phosphates

Energy-resolved collision-induced dissociation (ER-CID) experiments of sodium cationized glycosyl phosphate complexes, [GP _x +Na]⁺, are performed to elucidate the effects of linkage stereochemistry (α versus β), the geometry of the leaving groups (1,2-cis versus 1,2-trans), and protecting groups (cyclic versus non-cyclic) on the stability of the glycosyl phosphate linkage via survival yield analyses. A four parameter logistic dynamic fitting model is used to determine CID_50% values, which correspond to the level of rf excitation required to produce 50% dissociation of the precursor ion complexes. Present results suggest that dissociation of 1,2-trans [GP _x +Na]⁺ occurs via a McLafferty-type rearrangement that is facilitated by a syn orientation of the leaving groups, whereas dissociation of 1,2-cis [GP_x+Na]⁺ is more energetic as it involves the formation of an oxocarbenium ion intermediate. Thus, the C1-C2 configuration plays a major role in determining the stability/reactivity of glycosyl phosphate stereoisomers. For 1,2-cis anomers, the cyclic protecting groups at the C4 and C6 positions stabilize the glycosidic bond, whereas for 1,2-trans anomers, the cyclic protecting groups at the C4 and C6 positions tend to activate the glycosidic bond. The C3 O-benzyl (3 BnO) substituent is key to determining whether the sugar or phosphate moiety retains the sodium cation upon CID. For 1,2-cis anomers, the 3 BnO substituent weakens the glycosidic bond, whereas for 1,2-trans anomers, the 3 BnO substituent stabilizes the glycosidic bond. The C2 O-benzyl substituent does not significantly impact the glycosidic bond stability regardless of its orientation. Graphical abstract ᅟ.

Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu]+ and [Ura+Ag]<sup/>

The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]⁺ and [Ura+Ag]⁺, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]⁺ and [Ura+Ag]⁺ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]⁺ and [Ura+Ag]⁺. B3LYP suggests that Cu⁺ exhibits a slight preference for O4 binding, whereas Ag⁺ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu⁺ and Ag⁺ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]⁺ than [Ura+Cu]⁺. The dissociation behavior and relative stabilities of the [Ura+M]⁺ complexes, M⁺ = Cu⁺, Ag⁺, H⁺, and Na⁺) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu⁺ and Ag⁺ are compared with previous and present results for those of H⁺ and Na⁺. Graphical Abstract ᅟ.

IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]<sup/>

Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na]⁺ and [Thd+Na]⁺ produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na⁺ binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na]⁺ prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na]⁺ prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H]⁺ < [Thd+H]⁺ < [dThd+Na]⁺ < [Thd+Na]⁺. Graphical Abstract ᅟ.

An approach to estimate the activation energies of fragmentation occurring in quadrupole collision cell of the mass spectrometer

The classical semi-quantitative Rice-Ramsperger-Kassel (RRK) theory was used for the calculation of the internal energy dependent reaction rate coefficient of the collision-induced dissociation (CID) reaction in tandem mass spectrometry (MS/MS). The survival yield (SY) was determined by the reaction rate equation for the unimolecular dissociation of the precursor ion. The parameters of the rate equation and the RRK model were approximated based on the instrumental conditions. We used the RRK equation for the description of the basic behavior of the fragmentation reactions and for the estimation of the internal energy of the precursor ion. The critical energies for fragmentation (E_o ) of various molecules were estimated and compared with those reported in the literature. The model was extended by taking into account the initial internal energy distribution of the ions created in the ion source. It must be emphasized that our approach provides only a crude estimate for E_o .