In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions

Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSⁿ fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS⁵ level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at –COOH group, the eliminating hydrogen always comes from –NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the –NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.     

Using non-covalent complexes to direct the fragmentation of glycosidic bonds in the gas phase

An investigation of the gas phase chemistry of proton bound oligosaccharide (S)-ligand (L) non-covalent complexes, [S + H + L](+) has been carried out using electrospray ionization (ESI) and tandem mass spectrometry in a quadrupole ion trap. When subjected to collision-induced dissociation (CID), these [S + H + L](+) complexes undergo a range of reactions that can be broadly classified into three main types: (1) Simple dissociation into the individual monomers; (2) cleavage of the oligosaccharide to form B-type sequence ions; (3) cleavage of the ligand species. The second type of reaction is particularly interesting as it can produce a "ladder series" of [B(x) + L](+) ions via ligand induced oligosaccharide bond cleavage. This novel gas phase reaction greatly simplifies the sequencing of oligosaccharides. Both the oligosaccharide and ligand were found to influence the type of reaction pathway observed, with the "ladder series" of [B(x) + L](+) ions being favored for permethylated oligosaccharides and for bifunctional ligands. Cytosine is a particularly good ligand at facilitating the formation of [B(x) + L](+) ions. Analogies with condensed phase chemistry of sugars is made and a potential mechanism for ligand induced oligosaccharide bond cleavage is proposed.     

From oligomers to polymer: convergence in the HOMO-LUMO gaps of conjugated oligomers

[Structure: see text] Extrapolation of HOMO-LUMO gaps for pi-conjugated oligomers at the B3LYP/6-31G(d) level of theory predict accurately (within 0.1-0.2 eV) the band gaps of conjugated polymers only when long (at least 20-mer) pi-conjugated oligomers are used for the extrapolation.     

Observation of Na(+)-bound oligomers of quercetin in the gas phase

While developing a liquid chromatography/tandem mass spectrometry method for the analysis of the flavonoid quercitin, it was observed that quercetin (3,3',4',5,7-pentahydroxyflavone) exhibited clustering in both the positive and negative ion mode. Two series of positive ion clusters were observed; the first series corresponds to singly charged [2M + Na](+) at m/z 627.2 to [13M + Na](+) at m/z 3947.5, while the second series corresponds to doubly charged [7M + 2Na](2+) at m/z 1080.4 to [25M + 2Na](2+) at m/z 3798.5. In the negative ion mode, the behavior of quercetin parallels that of apigenin (4',5,7-trihydroxyflavone) in that [M + NO(3)](-), [2M + NO(3)](-), and [3M + NO(3)](-) were observed at m/z 364.1, 666.0, and 968.9, respectively; in addition, quercitin clusters with chloride ions ([2M + Cl](-) at m/z 638.9 and [3M + Cl](-) at m/z 940. 9) were observed. The results of tandem mass spectrometric examination of several cluster ions are reported.     

Molecular modeling and simulation of conjugated polymer oligomers: ground and excited state chain dynamics of PPV in the gas phase

The ground and excited state dynamics of poly(p-phenylenevinylene) (PPV) chains is studied through an implementation of mixed quantum/classical molecular dynamics simulation. The model used in the simulations combines the semiempirical Pariser-Parr-Pople (PPP) Hamiltonian to treat the pi molecular electronic structure with a mechanical force field capturing all other aspects. Nuclear degrees of freedom are treated classically. We first validate the model by simulating PPV chains of various length, and evaluate the absorption spectra. The thermal disorder contribution to the breadth of the first absorption band is estimated to be 0.2 eV at T = 300 K. To investigate the relationship between the emission and chain conformation, we simulate an isolated ten unit chain of PPV in the ground and the lowest excited state. The emission spectrum, red-shifted with respect to absorption of about 0.2 eV as found in experiments, shows a structured line shape that we relate to the photoinduced CC bond distortions. In accord with earlier studies, the exciton self-traps in the middle of the chain. We introduce two collective variables that reflect geometrical distortion, and find these to be effective in describing the contribution of chain conformation to the emission spectrum. The collective variables are also shown to be effective in describing the bond relaxation dynamics after photoexcitation. Such a relaxation is found to occur in approximately 100 fs and is guided by a compensatory release of energy between the double and single bonds in the vinylene junctions and p-phenyl rings. Finally, we find that the chain has a very slight preference for a more planar conformation in the excited state, compared to the ground state. However, the thermal motions induce the chain to explore out-of-plane conformations in both the ground and the excited states with an amplitude significantly greater than this difference.     

Ionic fragmentation processes of core-excited α-alanine in gas phase

Ionic fragmentation of core-excited α-alanine in gas phase was observed. The most dominant ionic species is COOH⁺ for all core-ionizations at C 1s, N 1s, and O 1s. An increase in COO⁺ and a decrease in COOH⁺, which were observed as core-hole atom selectivity for the O 1s ionization, are explained by the enhancement of O–H bond scission. Further state-selective O–H bond scission, observed at the O 1s second peak, is attributed to the O_OH1s → 3s/σ* transition.     

On the fragmentation pathway of the ionized enol of glycine in the gas phase

Density functional and second-order many body perturbation approaches were used to compute the potential energy surface for the fragmentation of the ionized enol of glycine [H2NCH = C(OH)2]+* into water and aminoketene radical cation [H2N-HC = CO]+*. Two possible pathways were considered. The potential energy surfaces obtained are very similar and both predict the existence of a molecular complex in which the water is coordinated to the aminoketene moiety in two different fashions with a noticeable binding energy. The fragmentation is kinetically controlled by the step in which the molecular complex is formed from the most stable cation enol of glycine. Our quantum-mechanical data confirm the hypothesis that the ylide ion [H3NCHCOOH]+* is an intermediate in the water loss.     

Isomerization and fragmentation of methylfuran ions and pyran ions in the gas phase

The mutual interconversion of the molecular ions [C₅H₆O]⁺ of 2-methylfuran (1), 3-methylfuran (2) and 4H-pyran (3) before fragmentation to [C₅H₅O]⁺ ions has been studied by collisional activation spectrometry, by deuterium labelling, by the kinetic energy release during the fragmentation, by appearance energles and by a MNDO calculation of the minimum energy reaction path. The electron impact and collisional activation mass spectra show clearly that the molecular ions of 1–3 do not equilibrate prior to fragmentation, but that mostly pyrylium ions [C₅H₅O]⁺ arise by the loss of a H atom. This implies an irreversible isomerization of methylfuran ions 1 and 2 into pyran ions before fragmentation, in contrast to the isomerization of the related systems toluene ions/cycloheptatriene ions. Complete H/D scrambling is observed in deuterated methylfuran ions prior to the H/D loss that is associated with an iostope effect k_H/k_D = 1.67–2.16 for metastable ions. In contrast, no H/D scrambling has been observed in deuterated 4H-pyran ions. However, the loss of a H atom from all metastable [C₅H₅O]⁺ ions gives rise to a flat-topped peak in the mass-analysed ion kinetic energy spectrum and a kinetic energy release (T₅₀) of 26 ± 1.5 kJ mol^?1. The MNDO calculation of the minimum energy reaction path reveals that methylfuran ions 1 and 2 favour a rearrangement into pyran ions before fragmentation into furfuryl ions, but that the energy barrier of the first rearrangement step is at least of the same height as the barrier for the dissociation of pyran ions into pyrylium ions. This agrees with the experimental results.     

Glutathione radical cation in the gas phase; generation, structure and fragmentation

Two different chemical methods have been used to form glutathione radical cations: (1) collision-induced dissociations (CIDs) of the ternary complex [Cu(II)(tpy)(M)]˙(2+) (M = GSH, tpy = 2,2':6',2'-terpyridine) and (2) homolysis of the S-NO bond in protonated S-nitrosoglutathione. The radical cations, M˙(+), were trapped and additional CIDs were performed. They gave virtually identical CID spectra, suggesting a facile interconversion between initial structures prior to fragmentation. DFT calculations at the B3LYP/6-31++G(d,p) level of theory have been used to study interconversion between different isomers of the glutathione radical cation and to examine mechanisms by which these ions fragment. The N-terminal α-carbon-centred radical cation, strongly stabilized by the captodative effect, is at the global minimum, which is 8.5 kcal mol(-1) lower in enthalpy than the lowest energy conformer of the S-centred radical cation. The barrier against interconversion is 18.1 kcal mol(-1) above the S-centred radical.     

Polyethylene glycol grafted cotton as phase change polymer

Thermal storage cotton possessing solid–solid phase change properties was prepared by direct grafting of polyethylene glycol (PEG) on cotton fiber/cloth. Attempt has been made to characterize intermediates so that desired grafting could be obtained. The grafting was done by using urethane linkage and the grafted cotton was found to undergo solid–solid phase transition. The modified cotton was characterized by using Fourier transform infrared spectroscopy (FT-IR), ¹³C CPMAS, polarizing optical microscopy, differential scanning calorimetry (DSC) and thermogravimetry respectively. The DSC study revealed quite good storage effect of grafted cotton and the enthalpy of melting was found to be 55–59 J/g with a peak appearing at around 60 °C. During cooling scan, the crystallization peak appeared at around 38 °C. Further, thermogravimetric analysis confirmed good thermal stability up to 300 °C. Appreciable improvement of mechanical properties of cotton has been observed after grafting. The polarizing optical micrograph clearly showed change of morphology after grafting, i.e., the grafted PEG adhering to fiber surface.     

Isomerization and fragmentation of methyl benzofuran ions and chromene ions in the gas phase

The rearrangement of the molecular ions of the isomeric 2- and 3-methyl benzofurans (1 and 2), 2H-chromene (3) and 4H-chromene (4) has been studied as a further example of the isomerization of oxygen-heteroaromatic radical cations via a ring expansion/ring contraction mechanism well documented for molecular ions of alkyl benzenes. The ions 1⁺˙?4⁺˙ fragment mainly by H loss into identical chromylium ions a. The process exhibits consistently a large kinetic energy release and an isotope effect k_H/k_D, which arise from a rate-determining energy barrier of the last dissociation step. Differences of the kinetic energy releases, the isotope effects and the appearance energies of the methyl benzofuran ions and the chromene ions indicate a large energy barrier also for the initial hydrogen migration during the rearrangement of the methyl benzofuran ions. This is substantiated by an MNDO calculation of the minimum energy reaction path. In contrast to the behaviour of alkyl benzene ions, a unidirectional isomerization of the methyl benzofuran ions by ring expansion takes place but no mutual interconversion of the molecular ions of methyl benzofurans and chromenes.     

Reactive processing with difunctional oligomers to compatibilize polymer blends

The addition of telechelic reactive oligomers to a polymer blend as a compatibilization process is investigated. The results presented in this paper suggest that this process provides a mechanism by which blocky copolymeric compatibilizers can be formed during processing, as demonstrated by the changes in the mechanical and optical properties of the phase separated polymer blends. The results also show, however, that the presence of unreacted smaller oligomers can act as a plasticizer in the blend and can thus detrimentally affect the mechanical properties of the blend if any remains after processing. Careful control of the mixing conditions or post processing thermal annealing may be required to minimize this potentially deleterious effect. However, the data suggest that this optimization is possible.     

Negative-ion fragmentation pathways in 2,4,6-trinitrotoluene

The mass spectrum of 2,4,6-trinitrotoluene vapour in air was recorded and the negative-ion fragmentation pathways of the molecular anion were investigated down to the fourth generation. The dissociation of the parent anion led to the production of three fragment anions with masses 46, 197 and 210 u where the last two daughter ions initiated two entirely separate fragmentation pathways. These pathways were studied and the fragmentation mechanisms identified. The background negative-ion mass spectrum, generated by the glow discharge ion source in the airstream which carries the sample vapour into the source, was examined in detail and an assignment of this mass spectrum is included.     

Inverse gas chromatography for the study of one phase and two phase polymer mixtures

Experiment finds that, for a chlorinated polyethylene (chlorine content 62.1% by weight)/poly(ethyl methacrylate) blend, a negative value of χ′_{2 3} is obtained, which indicates compatibility. With increasing temperature, χ′_{2 3} increases towards zero as required by the lower critical solution temperature behaviour of polymer blends. For chlorinated polyethylene/poly(butyl acrylate) blends however the specific retention volume is a linear function of composition and a positive χ′_{2 3} results if calculated by the conventional theory. The magnitude of χ′_{2 3} is determined by the difference between the retention volumes of the pure polymers and decreases with temperature. This effect is assumed to be a result of phase separation during coating the blend onto the support. A theoretical treatment is developed to explain this behaviour.     

The fragmentation pathways of protonated Amiton in the gas phase: towards the structural characterisation of organophosphorus chemical warfare agents by electrospray ionisation tandem mass spectrometry

Amiton (O,O-diethyl-S-[2-(diethylamino)ethyl] phosphorothiolate), otherwise known as VG, is listed in schedule 2 of the Chemical Weapons Convention (CWC) and has a structure closely related to VX (O-ethyl-S-(2-diisopropylamino)ethylmethylphosphonothiolate). Fragmentation of protonated VG in the gas phase was performed using electrospray ionisation ion trap mass spectrometry (ESI-ITMS) and revealed several characteristic product ions. Quantum chemical calculations provide the most probable structures for these ions as well as the likely unimolecular mechanisms by which they are formed. The decomposition pathways predicted by computation are consistent with deuterium-labeling studies. The combination of experimental and theoretical data suggests that the fragmentation pathways of VG and analogous organophosphorus nerve agents, such as VX and Russian VX, are predictable and thus ESI tandem mass spectrometry is a powerful tool for the verification of unknown compounds listed in the CWC.     

Structures and fragmentation of [Cu(uracil-H)(uracil)]+ in the gas phase

Complexes of copper (II) ions and uracil were studied using tandem mass spectrometry (Fourier transform ion cyclotron resonance, FTICR, mass spectrometry) including extensive isotopic labeling as well as theoretical calculations. Positive ion electrospray mass spectra of aqueous solutions of CuCl(2) and uracil show that the [Cu(Ura-H)(Ura)](+) ion is the most abundant ion even at low concentrations of uracil. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments show that the lowest energy decomposition pathway for [Cu(Ura-H)(Ura)](+) , surprisingly, is not the loss of uracil, but the loss of HNCO followed by HCN as the most abundant secondary fragmentation product. MS(n) studies identified primary, secondary and tertiary fragmentation products. Extensive isotopic labeling studies, as well as computational studies allowed for a detailed fragmentation scheme for the [Cu(Ura-H)(Ura)](+) ion, beginning with the lowest energy structure.     

Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase

Protein dynamics are the key to understanding their behavior. The static protein structure alone in most cases is insufficient to describe the vast array of complex functions they perform in vivo. Until recently there were relatively few techniques available to investigate the dynamic nature of these proteins. Mass spectrometry has recently emerged as a powerful biophysical method, capable of providing both structural and dynamic information. By utilizing the labile nature of amide hydrogens as a marker of the backbone dynamics in solution, combined with gas-phase dissociation techniques, we now have a high-resolution tool to locate these exchanging hydrogens within the sequence of the protein and to probe the functional importance of its structural elements. In this paper we describe several applications of these methodologies to illustrate the importance of dynamics to the biological functions of proteins.     

Peroxyl radical acceptors released by polymer materials into the gas phase

Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 973–974, April, 1991.     

Nanoclusters in polymer matrices prepared by co-deposition from a gas phase

This paper reviews the fabrication of organic and metal nanoclusters in polymer matrices by three co-deposition techniques. In particular, the structure and properties of polytetrafluoroethylene (PTFE), polychlortrifluoroethylene (PCTFE), polyparaphenylene sulphide (PPS), polystyrene (PS) and polyparaxylylene (PPX) films, containing gold (Au) and dye clusters are discussed. For the first time, dye-filled polymers and multi-component films, consisting of both Au nanoparticles and dye molecules, dispersed in the PTFE matrix were studied. A low temperature plasma was used for film structure modification. Cluster formation process was studied using optical spectroscopy in situ. Transmission electron microscopy (TEM), atomic force microscopy (AFM) and ellipsometry were used for characterisation of the grown films. During Au-PTFE film growth plasmon band shifted from 460-480 nm to 560 nm. Au cluster diameter was in the 3-7 nm range. Plasma treatment of the vapours led to formation of smaller, but more aggregated clusters. During Au-PPS film deposition a two-step growth mechanism was discovered. At the beginning of film growth the plasmon band at 540 nm appeared, but as thickness increased, the band at 430 nm dominated. Without plasma treatment a disordered mixture was deposited, while with plasma treatment large Au aggregates confined with PPS matrix having plasmon band at 620 nm were formed. Dye cluster formation depends on the dye ability to aggregate, its concentration and the properties of the polymer matrix. But cluster formation can also be tuned by varying the deposition conditions. Laser beam evaporation promoted cluster formation, while plasma treatment and dilution in a polymer matrix prevented cluster formation. In all cases both equilibrium and non-equilibrium film structure can be formed using kinetic factor. Asymmetric molecules with bulky substituents were oriented in polymer matrices by applying an electric field in situ or by corona poling. These molecules did not aggregate even at high dye load. The films exhibited second harmonic generation, which demonstrated chromophore orientation in the polymer matrices.     

Determination of the energetic properties of the ionization and fragmentation of substituted iodobenzenes in the gas phase

Photoionization was used to measure the ionization energy and appearance energy of the ions [M-I]⁺ from substituted iodobenzenes and 1-iodonaphthalene. It is shown that at the threshold of formation the phenyl cation structure (except p-NH₂C₆H₄ ⁺) is not maintained. The enthalpies of formation of XPh⁺ and 1-C₁₀H₇ ⁺ are evaluated.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 548–549, March, 1990.