Collision energy effects in tanden mass spectrometry as revealed by a proton-bound dimer ion

Mass spectra resulting from collision-induced decomposition of the proton-bound dimer of iso-propylamine and sec-butylamine have been obtained as a function of laboratory collision energy over the range 10-6000 eV. The ratio of the two principal fragment ions from the dimer ion measured as a function of collision energy is compared with the ratio expected as a function of internal energy as calcualted based on the statistical theory of mass spectra. This comparison indicates that the average energy deposited into the dimer ion upon collision reaches a maximum at a collision energy of ～70 eV. The average internal energy of the ions at this collision energy is ～4.3 eV. Other fragment ions which arise from higher energy decompositions are also observed in the spectra at much lower intensities. The relative intensities of these fragments indicate that the probability for large energy transfers are highest at ke V collision energies. These observations are interpreted on the basis of differences in the postcollision internal energy distributions resulting from keV and eV collisions.     

Reactive landing of peptide ions on self-assembled monolayer surfaces: an alternative approach for covalent immobilization of peptides on surfaces

Soft landing of mass-selected peptide ions onto reactive self-assembled monolayer surfaces (SAMs) was performed using a newly constructed ion deposition apparatus. SAM surfaces before and after soft landing were characterized ex situ using time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and infrared reflection-absorption spectroscopy (IRRAS). We demonstrate that reactive landing (RL) results in efficient covalent linking of lysine-containing peptides onto the SAM of N-hydroxysuccinimidyl ester-terminated alkylthiol on gold (NHS-SAM). Systematic studies of the factors that affect the efficiency of RL revealed that the reaction takes place upon collision and is promoted by the kinetic energy of the ion. The efficiency of RL is maximized at ca. 40 eV collision energy. At high collision energies the RL efficiency decreases because of the competition with scattering of ions off the surface. The reaction yield is independent of the charge state of the projectile ions, suggesting that peptide ions undergo efficient neutralization upon collision. Chemical and physical properties of the SAM surface are also important factors that affect the outcome of RL. The presence of chemically reactive functional groups on the SAM surface significantly improves the reaction efficiency. RL of mass- and energy-selected peptide ions on surfaces provides a highly specific approach for covalent immobilization of biological molecules onto SAM surfaces.     

Total cross sections for K + Br2 at relative energies between 0 and 8000 eV

Trajectory Surface Hopping (TSH) calculations have been applied to the non-elastic scattering in the K + Br₂ collision system over a wide range of relative kinetic energies from 0 to 8000 eV. Absolute total cross sections have been computed for the formation of various collision products with an accuracy of 5% with respect to statistical errors. The following non-elastic processes have been studied: chemical reaction, inelastic neutral scattering, neutral dissociation and ion pair formation, yielding atomic as well as molecular negative bromine ions together with PC ions. The absolute values of the respective total cross sections, obtained from the TSH calculations, are in close agreement with the available experimental data, both for chemical reaction and for ion pair formation, over the whole energy range considered. The three particle character of the collision system is important in describing the experimental results quantitatively at relative kinetic energies below 100 eV.     

Stability of the homopentameric b subunits of shiga toxins 1 and 2 in solution and the gas phase as revealed by nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry

The assembly of the B subunits of Shiga toxins (Stx) 1 and 2 and the influence of solution conditions (protein concentration, temperature, pH, and ionic strength) on it are investigated using temperature-controlled nanoflow electrospray (nano-ES) ionization and Fourier-transform ion cyclotron resonance mass spectrometry. Despite the similar higher order structure predicted by X-ray crystallography analysis, the B(5) homopentamers of Stx1 and Stx2 exhibit differences in stability under the solution conditions investigated. At solution temperatures ranging from 0 to 60 degrees C and subunit concentrations ranging from 5 to 85 microM, the Stx1 B subunit exists almost entirely as the homopentamer in aqueous solutions, independent of the ionic strength. In contrast, the degree of assembly of Stx2 B subunit is strongly dependent on temperature, subunit concentration, and ionic strength. At subunit concentrations of more than 50 microM, the Stx2 B subunit exists predominantly as a pentamer, although smaller multimers (dimer, trimer, and tetramer) are also evident. At lower concentrations, the Stx2 B subunit exists predominantly as monomer and dimer. The relative abundance of multimeric species of the Stx2 B subunit was insensitive to the ion source conditions, suggesting that gas-phase dissociation of the pentamer ions in the source does not influence the mass spectrum. Blackbody infrared radiative dissociation of the protonated B(5) ions of Stx2 at the +12 and +13 charge states proceeds, at reaction temperatures of 120 to 180 degrees C, predominantly by the ejection of a single subunit from the complex. Dissociation into dimer and trimer ions constitutes a minor pathway. It follows that the dimer and trimer ions and, likely, the monomer ions observed in the nano-ES mass spectra of Stx2 B subunit originated in solution and not from gas-phase reactions. It is concluded that, under the solution conditions investigated, the homopentamer of Stx2 B subunit is thermodynamically less stable than that of Stx1 B subunit. Arrhenius activation parameters determined for the protonated Stx2 B(5) ions at the +12 and +13 charge states were compared with values reported for the corresponding B(5) ions of Stx1 B subunit. In contrast to the differential stability of the Stx1 and Stx2 B pentamers in solution, the dissociation activation energies (E(a)) determined for the gaseous complexes are indistinguishable at a given charge state. The similarity in the E(a) values suggests that the protonated pentamer ions of both toxins are stabilized by similar intersubunit interactions in the gas phase, a result that is in agreement with the X-ray crystal structures of the holotoxins.     

Investigating ion-surface collisions with a niobium superconducting tunnel junction detector in a time-of-flight mass spectrometer

The performance of an energy sensitive, niobium superconducting tunnel junction (STJ) detector is investigated by measuring the pulse height produced by impacting molecular and atomic ions at different kinetic energies. Ions are produced by laser desorption and matrix-assisted laser desorption in a time-of-flight mass spectrometer. Our results show that the STJ detector pulse height decreases for increasing molecular ion mass, passes through a minimum at around 2000 Da, and then increases with increasing mass of molecular ions above 2000 Da. The detector does not show a decline in sensitivity for high mass ions as is observed with microchannel plate ion detectors. These detector plus height measurements are discussed in terms of several physical mechanisms involved in an ion-surface collision.     

Collision energy transfer in collision of NH(4) (+)(NH(3))(n-1) (n=3-9) with ND(3)

An incorporation of ND(3) into protonated ammonia cluster ions NH(4)(+)(NH(3))(n-1) (n=3-9), together with a dissociation of the cluster ions, was observed in the collision of the cluster with ND(3) at collision energies ranging from 0.04 to 1.4 eV in the center-of-mass frame. The branching fractions of the cluster ion species produced in the reactions were obtained as a function of the collision energy. The branching fractions of the incorporation products were successfully explained in terms of the Rice-Ramsperger-Kassel (RRK) theory at collision energies lower than the binding energy of the cluster ion. In addition, the internal energy distributions of the parent cluster ions were determined, and found to be in good agreement with those predicted using the evaporative ensemble model. In incorporations at collision energies lower than the binding energy of the cluster ion, all of the collision energy was transferred to the internal energy of the cluster ions; subsequently, an evaporation of ammonia molecules occurred in an equilibrium process after a complete energy redistribution in the clusters. In contrast, at collision energies higher than the binding energy of the cluster ion, a release of an ammonia molecule from the incorporation products occurred in a nonequilibrium process. The transition from the complex mode to the direct mode in the incorporation was observed at collision energies approximately equal to the binding energy. On the other hand, the collision energy dependence of the cross sections for the dissociation and for a nonreactive collision were estimated by a RRK simulation in which the collision energy transfer was interpreted by using the classical hard-sphere collision model. A relationship between reactivity and reaction modes in the collision of NH(4)(+)(NH(3))(4) with ND(3) is discussed via a comparison of the experimental results with the RRK simulation.     

Phenoxyaluminium compounds : VI. Mass spectral investigation of the association of dimethylaluminium phenoxide

The mass spectra of Me₂AlOPh dimer and trimer were recorded. A skeleton fragmentation was mainly observed at low temperature. Higher temperature spectra (of the trimer) have many more peaks were only partly assigned. The spectrum of the trimer indicates the presence of ions with at least 5 aluminium atoms. Based on these ions the existence of higher associated intermediates in the reassociation reaction trimer » dimer is proposed.     

Size-dependent barriers for reaction of aluminum cluster ions with oxygen

Reactions of cooled, size-selected aluminum cluster ions (Al_n⁺, n = 1–8) with oxygen have been studied at collision energies from 0.15 to 10.0 eV (center-of-mass) under single-collision conditions. With the exception of the atomic ion, all size clusters undergo exoergic reactions which result in extensive fragmentation of the metal cluster framework. Significant energy barriers are found for reaction of all clusters except the dimer. The barrier height increases with cluster size from Al₃⁺ to Al₇⁺, then drops for Al₈⁺.     

Energy deposition in [Fe(CO)5]+˙ upon collision with a metal surface

Collision of the title ion upon a stainless steel surface at near-normal incidence leads to deposition of internal energy in a well-defined narrow distribution. The energy deposited increases with laboratory collision energy and exceeds 7 eV (average) for 100 eV collisions. The translational-to-vibrational energy transfer efficiency is 15% (assuming an infinitely massive target) at 25 eV collision energy. Comparison is made with the internal energy distributions associated with gas-phase collisional activation using both low and high ion kinetic energies. The narrowness of the distribution of internal energies, the easy access to ions excited to different extents, and the high internal energies accessible, make the ion/surface collision process superior to gas-phase collisional activation for this system.     

Direct Observation of Atomic Dynamics and Silicon Doping at a Topological Defect in Graphene

Chemical decoration of defects is an effective way to functionalize graphene and to study mechanisms of their interaction with environment. We monitored dynamic atomic processes during the formation of a rotary Si trimer in monolayer graphene using an aberration‐corrected scanning‐transmission electron microscope. An incoming Si atom competed with and replaced a metastable C dimer next to a pair of Si substitutional atoms at a topological defect in graphene, producing a Si trimer. Other atomic events including removal of single C atoms, incorporation and relocation of a C dimer, reversible C? C bond rotation, and vibration of Si atoms occurred before the final formation of the Si trimer. Theoretical calculations indicate that it requires 2.0 eV to rotate the Si trimer. Our real‐time results provide insight with atomic precision for reaction dynamics during chemical doping at defects in graphene, which have implications for defect nanoengineering of graphene.     

Fragmentation dynamics of size-selected pyrrole clusters prepared by electron impact ionization: forming a solvated dimer ion core

Structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiments and ab initio calculations. Small neutral Pyn clusters were produced in Py/He mixture expansions, and the scattering experiment with a secondary beam of He-atoms was exploited to select the neutral clusters of different sizes. The complete size-selected fragmentation patterns for the neutral dimer to the tetramer after an electron impact ionization at 70 eV were obtained from the measurements of the angular and velocity distributions at different fragment masses. All the investigated cluster sizes decay mainly to the monomer ions Py+1 (from 60 to 80% of the corresponding neutral size) and to the dimer ion Py+2 (20-30%). The trimer ions Py+3 are generated to less than 10% from the neutral trimer and tetramer. To explain the observed results, we have calculated the structures and energetics of pyrrole clusters up to the trimer for the neutral and the ionic state using DFT and PMP2 methods. The ab initio calculations show that ionized pyrrole clusters are formed with a dimeric core that is solvated by neutral pyrrole molecules. In addition, the ground and ionic state of Py-Ar complexes were calculated at CCSD(T) level with extended basis in relevance to the mixed clusters produced in supersonic expansions of Py seeded in Ar. The calculated dissociation energies of the Py-Ar and (Py-Ar)+ complexes indicate that Ar atoms are able to rapidly evaporate after ionization. The combined analysis of the fragmentation probabilities, and calculations allowed us to estimate the distribution of energy deposited in the clusters after the electron impact, which peaks above 1 eV and has a tail up to 5 eV.     

Gas phase hydration of organic ions

In this work, we study the hydration phenomenon on a molecular level in the gas phase where a selected number of water molecules can interact with the organic ion of interest. The stepwise binding energies (DeltaH degrees (n-1,n)) of 1-7 water molecules to the phenyl acetylene cation are determined by equilibrium measurements using an ion mobility drift cell. The stepwise hydration energies DeltaH degrees (n-1,n) are nearly constant at 39.7 +/- 6.3 kJ mol(-1) from n = 1 to 7. The entropy change is larger in the n = 7 step, suggesting cyclic or cage-like water structures. No water addition is observed on the ionized phenyl acetylene trimer consistent with cyclization of the trimer ion to form triphenyl benzene cations C(24)H(18) (+) which are expected to interact weakly with the water molecules due to steric interactions and the delocalization of the charge on the large organic ion. The work demonstrates that hydration studies of organic ions can provide structural information on the organic ions.     

The metastable formation of di-ethylchloronium ions from ethylchloride dimer ions in a seeded molecular beam

Cluster ions of ethylchloride and their dissociation products have been produced in a supersonic expansion of ethylchloride seeded in Ar and energy selected by the threshold photoelectron photoion coincidence (TPEPICO) method. The peak widths of the ion time of flight distribution indicate that all of the clusters are produced by dissociative photoionization of higher order clusters. Thus, trimer ions dissociate to form dimer ions and an ethylchloride monomer. This dimer ion was found to be metastable with respect to the formation of the di-ethylchloronium ion and a chlorine atom. The measured dissociation rate as a function of the dimer ion internal energy was compared to the calculated rates based on the statistical RRKM/QET theory. Good agreement was found when the dimer adiabatic IP was assumed to be 10.2 eV. The Cl loss from the ethylchloride dimer ion is associated with a reverse activation energy of about 0.32 eV.     

Velocity map imaging of ion-molecule reactive scattering: the Ar(+)+ N(2) charge transfer reaction

We present a velocity map imaging spectrometer for the study of crossed-beam reactive collisions between ions and neutrals at (sub-)electronvolt collision energies. The charge transfer reaction of Ar(+) with N(2) is studied at 0.6, 0.8 and 2.5 eV relative collision energies. Energy and angular distributions are measured for the reaction product N. The differential cross section, as analyzed with a Monte Carlo reconstruction algorithm, shows significant large angle scattering for lower collision energies in qualitative agreement with previous experiments. Significant vibrational excitation of N(+)(2) is also observed. This theoretically still unexplained feature indicates the presence of a low energy scattering resonance.     

Positive-ion mass spectra and collision-induced dissociation of some 2,3-didehydro amino acids

The positive-ion mass spectra of a number of didehydro amino acids, ionized by electron impact and/or thermospray, and collision-induced dissociation spectra taken at collision energies of a few electron volts and keV have been performed on multiple quadrupole and reversed geometry sector instruments. Observed differences in the mass spectra and in the fragmentation patterns are explained in terms of different isomeric structures, different internal excitation energies and different ion transit times between the ion source and the collision cell. Molecular ions of unhydrated amino acids are efficiently formed both by electron impact and thermospray, whilst molecular ions of the hydrated compounds are formed more efficiently by the latter technique. The present investigation demonstrates that the use of different ionization techniques combined with mass spectrometry/mass spectrometry measurements at different collision energies yields a wealth of information relevant to structural characterization of this important class of molecules.     

Ligand displacement reactions of dimer and trimer pyridyl ligand/transition metal complexes

Ligand exchange reactions of pyridyl ligand/transition metal complexes are examined in a quadrupole ion trap mass spectrometer to evaluate the ability of multidentate ligands to displace other pyridyl ligands in complexes where the charge is highly delocalized and there is a great degree of ligand repulsions. Partially or fully coordinated transition metal ions in dimer or trimer species involving small mono- or bidentate pyridyl ligands undergo ligand displacement reactions with larger bi- and tridentate pyridyl ligands. Larger ligands with greater chelation abilities, such as 1,10-phenanthroline and 2,2′:6,2″-terpyridine, are often able to simultaneously displace two nonchelating ligands from a partially coordinated metal ion. However, the analogous reactions involving displacement of bidentate chelating ligands from more fully coordinated transition metal ion complexes are nearly quenched. In other cases, mixed-ligand dimer and trimer complexes are observed, indicating step-wise displacement of the initially complexed ligands.     

Applications of collision dynamics in quadrupole mass spectrometry

Some applications of collision dynamics in the field of quadrupole mass spectrometry are presented. Previous data on the collision induced dissociation of ions in triple quadrupole mass spectrometers is reviewed. A new method to calculate the internal energy distribution of activated ions directly from the increase in the cross section for dissociation with center of mass energy is presented. This method, although approximate, demonstrates explicitly the high efficiency of transfer of translational to internal energy of organic ions. It is argued that at eV center of mass energies, collisions between protein ions and neutrals such as Ar are expected to be highly inelastic. The discovery and application of collisional cooling in radio frequency quadrupoles is reviewed. Some previously unpresented data on fragment ion energies in triple quadrupole tandem mass spectrometry are shown that demonstrate directly the loss of kinetic energy of fragment ions in the cooling process. The development of the energy loss method to measure collision cross sections of protein ions in triple quadrupole instruments is reviewed along with a new discussion of the effects of inelastic collisions in these experiments and related ion mobility experiments.     

Characterization of a high-pressure quadrupole collision cell for low-energy collision-indneed dissociation

A RF-only quadrupole collision cell of new design has been evaluated for use in tandem mass spectrometry experiments as a component of a triple quadrupole mass spectrometer. The new design permits operation at values of collision gas thickness higher by 1 order of magnitude than those used in most cells of this type. When operated at sufficiently high collision gas pressures, the transmission efficiency for precursor ions increases with increasing pressure, often to values greater than those observed in the absence of collision gas. Simultaneously, the attainable resolving power for fragment ions across the entire mass-to-charge ratio range, even for multiply charged precursors, also increases to the point where isomers of a quadruply charged fragment are resolved. The performance of the cell, judged in terms of yields and resolution of fragment ions, has been investigated as a function of the nature and pressure of collision gas, the kinetic energy of the precursor ions that enter the cell, and of the size and charge state of the precursors. The enhanced performance is explicable in terms of a marked deceleration of all ions that emerge from the cell to very low energies, probably a few tens of millielectronvolts, so that the cell effectively acts as an ion source for the second mass filter (fragment ion analyzer) to provide a spectrum of ions of fixed axial energy. The high transmission efficiency appears to arise from a collisional focusing effect analogous to that exploited in three-dimensional RF ion traps. The low axial energies imply that ion transit times through the cell are sufficiently long (several milliseconds) that, in precursor ion experiments where the first mass filter is scanned, a hysteresis effect is observed. This implies that in this operating mode compromises must be sought between scan speed and quality of peak shape. Examples are given of spectra obtained under realistic operating conditions that employ flow injection of samples.     

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.     

Tuning Charge Transfer in Ion–Surface Collisions at Hyperthermal Energies

Charge exchange in ion–surface collisions may be influenced by surface adsorbates to alter the charge state of the scattered projectiles. We show here that the positive‐ion yield, observed during ion scattering on metal surfaces at low incident energies, is greatly enhanced by adsorbing electronegative species onto the surface. Specifically, when beams of N⁺ and O⁺ ions are scattered off of clean Au surfaces at hyperthermal energies, no positive ions are observed exiting. Partial adsorption of F atoms on the Au surface, however, leads to the appearance of positively charged primary ions scattering off of Au, a direct result of the increase in the Au work function. The inelastic energy losses for positive‐ion exits are slightly larger than the corresponding ionization energies of the respective N and O atoms, which suggest that the detected positive ions are formed by surface reionization during the hard collision event.