Carbon cluster cations with up to 84 atoms: structures, formation mechanism, and reactivity

Helden, Gert von; Hsu, Ming‐Teh; Gotts, Nigel G.; Bowers, Michael T.

doi:10.1021/j100133a011

Cited by 587 publications

(564 citation statements)

References 7 publications

(10 reference statements)

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“…The theoretical cross section of an each structure was calculated using the SIGMA 'project approximation' algorithm with atomic radii determined from the ion-helium Lennard-Jones parameters. [23,24] Average cross section was obtained from the candidate group. The conformational stability of the lowest energy structure (representative structure) was then tested with a 1ns MD simulation at 300 K.…”

Section: Molecular Modelling and Theoretical Cross Sectionsmentioning

confidence: 99%

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Rožman

Gaskell

2010

J. Mass Spectrom.

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The complexes formed by alkali metal cations (Cat + = Li + ,Na + ,K + ,Rb + ) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M+H +Cat] 2+ tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li + or Na + ) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb + ) is cation expulsion and formation of [M + H] + . The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M+H+Cat] 2+ ion. Finally, the fact that [M+H+Cat] 2+ peptides dissociate similarly as [M + H] + (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.

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Section: Molecular Modelling and Theoretical Cross Sectionsmentioning

confidence: 99%

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Rožman

Gaskell

2010

J. Mass Spectrom.

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“…The ␣ and ␤ domain structures were obtained from Protein Data Bank [26]. Two collision cross-section prediction models, projection [27] and trajectory [28], were employed. Software for calculations based on these models was obtained under MOBCAL courtesy of M. F. Jarrold [29].…”

Section: Cross-section Predictions From Available Structuresmentioning

confidence: 99%

Combined ion-mobility and mass-spectrometry investigations of metallothionein complexes using a tandem mass spectrometer with a segmented second quadrupole

Guo

Ling

Thomson

et al. 2005

J. Am. Soc. Mass Spectrom.

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Rabbit metallothionein (MT) 2A complexes with Cd(II), Zn(II), Ag(I), Cu(I), Hg(II), arsenite, monomethylarsonous acid (MMA), and dimethylarsinous acid (DMA) have been examined using ion-mobility measurements and mass spectrometry in a triple-quadrupole mass spectrometer equipped with a segmented second quadrupole that doubled as an ion-mobility cell [Guo, Y.; Wang, J.; Javahery, G.; Thomson, B. A.; Siu, K. W. M. An Ion-Mobility Spectrometer with Radial Collisional Focusing. Anal. Chem. 2005, 77, 266 -275]. The metal ions confer conformational rigidity on the MT complexes, which counteracts Coulombic repulsion among protons added as a result of electrospray. Triply and quadruply protonated Cd 7 MT2A have smaller cross-sections than the Cd 7 MT2A structure deduced from published NMR data. For the 6ϩ ions, the As 6 MT2A complex has a cross-section of 790 Å 2 ; the MMA 10 MT2A complex, 920 Å 2 ; and the DMA 20 MT2A complex, 1220 Å 2 . This increase in cross-section of the As(III) species, from As 3ϩ to MMA to DMA, is interpreted as a consequence of decreasing multiple coordination and increasing number of methyl groups. I on mobility, K, is a measure of the ion's effective size by virtue of its collision cross-section, ⍀ T , at temperature T, with a given buffer gas, typically helium, under the influence of a weak electric field. Provided that the number density of the buffer gas, N, is sufficiently high and the imposed electric field, E, is sufficiently low, the drift velocity, v d , is proportional to E with K being the proportionality constant.⍀ T can be determined from K using the Mason-Schamp equation [1, 2]:where z is the numerical charge, e is the elementary charge, is the reduced mass of the ion and helium, and k is the Boltzmann's constant.The collision cross-section of an ion is one of the most readily measurable, albeit somewhat crude, structure-related parameter that has come under close scrutiny in the last decade or so. Coupled to comparisons with theoretical cross-sections calculated from probable structures found by optimizations using molecular dynamics and first-principle methods, measurements of ⍀ T have allowed insights into three-dimensional structures of peptides and proteins in the gas-phase [3][4][5].Ion-mobility measurements are typically made in drift tubes at atmospheric or subatmospheric pressure containing a stack of ring electrodes which maintain a constant electric field in the axial direction [6]. Highresolution operation requires the use of high (nearatmospheric) pressure and high voltages; the need for high pressure in the drift tube necessitates the use of small apertures in interfacing with the mass-analyzer region of the spectrometer (which requires lowpressure operation) and leads to radial diffusion because of increased ion residence time. This combination typically results in modest sensitivity. Recently, we reported construction and testing of an ion-mobility spectrometer that has its mobility cell as a 20-segment rf-only quadrupole and functionally the second quadrupole (q2)...

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“…ically, candidate low-energy structures are identified by using molecular mechanics or a combination of mechanics with ab initio methods, and cross sections are determined for each of these structures by either projection approximation [26], exact hard sphere scattering [23], or trajectory calculations [24,27]. The method used to obtain cross sections from ion mobility measurements has been described in detail elsewhere [68,69].…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

“…Higher level calculations are often done on low-energy structures identified at the mechanics level. Ion mobility has been used to characterize a wide range of ion structures including carbon clusters [25][26][27], amino acids [28,29], peptides [30][31][32][33][34][35][36][37], proteins [39][40][41][42][43], DNA [44][45][46][47], and synthetic polymers [48][49][50]. Bowers and coworkers showed that the cross sections of gas-phase valinomycin-alkali ion complexes are the same for lithiated and sodiated species, but steadily increase for potassiated, rubidiated, and cesiated complexes [51].…”

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confidence: 99%

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Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

Wong

Williams

Counterman

et al. 2005

J. Am. Soc. Mass Spectrom.

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The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs. T he structure of a molecule in solution depends both on intramolecular interactions and on intermolecular interactions between the molecule and solvent. Gas-phase studies can provide information about the intrinsic properties of a molecule. From such measurements, information about solvent effects can be inferred. A number of different methods can provide information about molecular structure in the gas phase, even complex systems, such as large synthetic or biological polymers. These methods include spectroscopy [1][2][3][4][5], hydrogen/deuterium exchange [6-12], dissociation [13][14][15][16][17][18], proton transfer reactivity [19][20][21][22], and ion mobility mass spectrometry . These methods have been used to obtain information about protein conformation and folding, DNA duplex structure, and in a wide variety of other interesting applications.Of these methods, ion mobility mass spectrometry, a method pioneered by Bowers and Jarrold for ion structure characterization, has several advantages, including rapid measurement time, minimal perturbation of ground state structure, exquisite temperature control, and the ability to investigate kinetics of structural change over a limited time. With ion mobility, ions are injected into a drift tube where they thermalize through collisions with an introduced background gas, typically helium. In the presence of an applied electric field, ions are made to drift through an elevated pressure region. Based on the drift time through this tube...

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Carbon cluster cations with up to 84 atoms: structures, formation mechanism, and reactivity

Cited by 587 publications

References 7 publications

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Non‐covalent interactions of alkali metal cations with singly charged tryptic peptides

Combined ion-mobility and mass-spectrometry investigations of metallothionein complexes using a tandem mass spectrometer with a segmented second quadrupole

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

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