1
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Meyer KAE, Nickson KA, Garand E. The impact of the electric field of metal ions on the vibrations and internal hydrogen bond strength in alkali metal ion di- and triglycine complexes. J Chem Phys 2022; 157:174301. [DOI: 10.1063/5.0117311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Using infrared predissociation spectroscopy of cryogenic ions, we revisit the vibrational spectra of alkali metal ion (Li+, Na+, K+) di- and triglycine complexes. We assign their most stable conformation, which involves metal ion coordination to all C=O groups and an internal NH⋯NH2 hydrogen bond in the peptide backbone. An analysis of the spectral shifts of the OH and C=O stretching vibrations across the different metal ions and peptide chain lengths shows that these are largely caused by the electric field of the metal ion, which varies in strength as a function of the square of the distance. The metal ion–peptide interaction also remotely modulates the strength of internal hydrogen bonding in the peptide backbone via the weakening of the amide C=O bond, resulting in a decrease in internal hydrogen bond strength from Li+ > Na+ > K+.
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Affiliation(s)
- Katharina A. E. Meyer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Kathleen A. Nickson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
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2
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Sanguantrakun N, Chanthamontri C, Gross ML. Top-Down Analysis of In-Source HDX of Native Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1151-1154. [PMID: 32275420 PMCID: PMC7489294 DOI: 10.1021/jasms.9b00149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hydrogen/deuterium exchange (HDX) is used in protein biophysics to probe folding dynamics, intermolecular interactions, epitope and other mapping. A typical procedure often involves HDX in buffered D2O solution followed by pepsin digestion, and liquid chromatography/electrospray ionization mass spectrometry analysis. In this work, HDX of protein ions was conducted in the ESI source. Both native electrospray droplets of ubiquitin and denatured myoglobin were exposed to D2O vapor in the source region of a Bruker SolariX 12T FTICR-mass spectrometer. Electron capture dissociation was used to assess deuterium incorporation at the residue level. This in-source HDX, on the millisecond-time scale, exchanges side-chain hydrogens and fast-exchanging amides compared to conventional minutes-to-hours HDX of backbone hydrogens in solution with less sample preparation (i.e., no D2O/protein mixing and incubation, no quenching, protein digestion, or LC separation).
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Affiliation(s)
- Nawaporn Sanguantrakun
- Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Chamnongsak Chanthamontri
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
- Millipore Sigma, 2909 Laclede Avenue, St. Louis, MO 63103
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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3
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Straus RN, Jockusch RA. Hydrogen-Deuterium Exchange and Electron Capture Dissociation to Interrogate the Conformation of Gaseous Melittin Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:864-875. [PMID: 30834508 DOI: 10.1007/s13361-019-02150-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
There is a need in the field of biological mass spectrometry for structural tools which can report on regional, rather than solely global, structure of gaseous protein ions. Site-specific hydrogen-deuterium (H/D) exchange has shown promise in fulfilling this need, but requires additional method development to prove its utility. In this study, we use H/D exchange and electron capture dissociation (ECD) to probe the gaseous structure of two peptides which are α-helical in solution and which differ by a single point mutation. Global H/D exchange levels, ECD fragmentation profiles, and region specific H/D exchange profiles are compared between wild type (WT) melittin, which adopts a hinged helix conformation in solution, and a mutant P14A melittin which folds into a single helix in solution. High protection from H/D exchange by both peptides is consistent with retention of secondary structure in the gas phase (or refolding into some other compact structure). The P14A mutant melittin exhibits lower ECD fragmentation efficiency than WT melittin, suggesting that it contains more secondary structure in the gas phase, which may indicate that these peptides retain some memory of their solution-phase structures. Examination of the isotopic distributions of fragment ions derived from H/D exchange with subsequent ECD reveals that the C-terminus of these peptides adopts multiple conformations. The results reported here offer insight into the stability of alpha helices in the gas phase, and also highlight the value of combining gas-phase H/D exchange with electron capture dissociation to interrogate gaseous peptide conformation.
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Affiliation(s)
- Rita N Straus
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Rebecca A Jockusch
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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4
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Puttreddy R, Beyeh NK, Ras RHA, Rissanen K. Host-Guest Complexes of C-Ethyl-2-methylresorcinarene and Aromatic N, N'-Dioxides. ChemistryOpen 2017. [PMID: 28638775 PMCID: PMC5474659 DOI: 10.1002/open.201700026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The C‐ethyl‐2‐methylresorcinarene (1) forms 1:1 in‐cavity complexes with aromatic N,N′‐dioxides, only if each of the aromatic rings has an N−O group. The structurally different C‐shaped 2,2′‐bipyridine N,N′‐dioxide (2,2′‐BiPyNO) and the linear rod‐shaped 4,4′‐bipyridine N,N′‐dioxide (4,4′‐BiPyNO) both form 1:1 in‐cavity complexes with the host resorcinarene in C4v crown and C2v conformations, respectively. In the solid state, the host–guest interactions between the 1,3‐bis(4‐pyridyl)propane N,N′‐dioxide (BiPyPNO) and the host 1 stabilize the unfavorable anti‐gauche conformation. Contrary to the N,N′‐dioxide guests, the mono‐N‐oxide guest, 4‐phenylpyridine N‐oxide (4PhPyNO), does not form an in‐cavity complex in the solid state. The host–guest complexation and the relative guest affinities were studied through 1H NMR competition experiments in methanol. Single‐crystal X‐ray crystallography of the 1:1 complexes supports the proposed solution‐state structures, also revealing strong hydrogen bonds between the host and the guests, not observed in solution owing to hydrogen/deuterium (H/D) exchange processes in methanol.
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Affiliation(s)
- Rakesh Puttreddy
- University of Jyvaskyla Department of Chemistry Nano Science Center PO Box 3540014 Jyvaskyla Finland
| | - Ngong Kodiah Beyeh
- Aalto University School of Science Department of Applied Physics Puumiehenkuja 2FIN-02150 Espoo Finland
| | - Robin H A Ras
- Aalto University School of Science Department of Applied Physics Puumiehenkuja 2FIN-02150 Espoo Finland
| | - Kari Rissanen
- University of Jyvaskyla Department of Chemistry Nano Science Center PO Box 3540014 Jyvaskyla Finland
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5
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Zhu S, Campbell JL, Chernushevich I, Le Blanc JCY, Wilson DJ. Differential Mobility Spectrometry-Hydrogen Deuterium Exchange (DMS-HDX) as a Probe of Protein Conformation in Solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:991-999. [PMID: 26965162 DOI: 10.1007/s13361-016-1364-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Differential mobility spectrometry (DMS) is an ion mobility technique that has been adopted chiefly as a pre-filter for small- to medium-sized analytes (<1 000 Da). With the exception of a handful of studies that employ an analogue of DMS-field asymmetric waveform ion mobility spectroscopy (FAIMS)-the application of DMS to intact biomacromolecules remains largely unexplored. In this work, we employ DMS combined with gas-phase hydrogen deuterium exchange (DMS-HDX) to probe the gas-phase conformations generated from proteins that were initially folded, partially-folded, and unfolded in solution. Our findings indicate that proteins with distinct structural features in solution exhibit unique deuterium uptake profiles as function of their optimal transmission through the DMS. Ultimately we propose that DMS-HDX can, if properly implemented, provide rapid measurements of liquid-phase protein structural stability that could be of use in biopharmaceuticals development. Graphical Abstract ᅟ.
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Affiliation(s)
- Shaolong Zhu
- Chemistry Department, York University, Toronto, ON, M3J 1P3, Canada
| | | | | | | | - Derek J Wilson
- Chemistry Department, York University, Toronto, ON, M3J 1P3, Canada.
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.
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6
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Miladi M, Olaitan AD, Zekavat B, Solouki T. Competing noncovalent host-guest interactions and H/D exchange: reactions of benzyloxycarbonyl-proline glycine dipeptide variants with ND3. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1938-1949. [PMID: 26289383 DOI: 10.1007/s13361-015-1218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/26/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
A combination of density functional theory calculations, hydrogen/deuterium exchange (HDX) reactions, ion mobility-mass spectrometry, and isotope labeling tandem mass spectrometry was used to study gas-phase "host-guest" type interactions of a benzyloxycarbonyl (Z)-capped proline (P) glycine (G) model dipeptide (i.e., Z-PG) and its various structural analogues with ND3. It is shown that in a solvent-free environment, structural differences between protonated and alkali metal ion (Na(+), K(+), or Cs(+))-complexed species of Z-PG affect ND3 adduct formation. Specifically, [Z-PG + H](+) and [Z-PG-OCH3 + H](+) formed gas-phase ND3 adducts ([Z-PG (or Z-PG-OCH3) + H + ND3](+)) but no ND3 adducts were observed for [Z-PG + alkali metal](+) or [Z-PG + H - CO2](+). Experimentally measured and theoretically calculated collision cross sections (CCSs) of protonated and alkali metal ion-complexed Z-PG species showed similar trends that agreed with the observed structural differences from molecular modeling results. Moreover, results from theoretical ND3 affinity calculations were consistent with experimental HDX observations, indicating a more stable ND3 adduct for [Z-PG + H](+) compared to [Z-PG + alkali metal](+) species. Molecular modeling and experimental MS results for [Z-PG + H](+) and [Z-PG + alkali metal](+) suggest that optimized cation-π and hydrogen bonding interactions of carbonyl groups in final products are important for ND3 adduct formation. Graphical Abstract ᅟ.
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Affiliation(s)
- Mahsan Miladi
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Abayomi D Olaitan
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Behrooz Zekavat
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA.
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7
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McMahon TB, Ohanessian G. Probing the mechanisms and dynamics of gas phase hydrogen-deuterium exchange reactions of sodiated polyglycines. Phys Chem Chem Phys 2015; 17:4237-49. [PMID: 25573245 DOI: 10.1039/c4cp03960b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rate constants for H-D exchange reactions of sodiated polyglycines (GnNa(+), n = 2-8) and polyalanines (AnNa(+), n = 2, 3 and 5) with ND3 have been measured in the cell of an FT-ICR mass spectrometer. All peptides except G2Na(+) are found to undergo three exchange reactions, all of which are consecutive with no sign of multiple exchanges within a single collision event. This information has been used to construct full mechanistic scenarios with the help of detailed quantum chemical calculations of the possible reaction paths for H-D exchange. The first exchange is always located at the C terminus however with different mechanisms depending upon whether the peptide termini can (larger peptides) or cannot (smaller peptides) interact directly without strong energy penalty. The most favourable mechanisms for the second and third exchanges of the N terminus protons, are found to be different from those for the first for all peptide sizes. The peptide distortions that are necessary in order for some of these reactions to occur are made possible by the energy reservoir provided by the favorable interaction of the peptide ion with ND3. Their occurrence and variety preclude any general relationship between H-D exchange kinetics and the most stable ion structures. There is however a break at G7Na(+) in the kinetics trend, with a first exchange rate which is much smaller than for all other peptide sizes. This break can be directly related to a different structural type in which the C terminus is neither free nor close to the N terminus.
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Affiliation(s)
- T B McMahon
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
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8
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Rajabi K. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:71-82. [PMID: 25318698 DOI: 10.1007/s13361-014-1004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 06/04/2023]
Abstract
A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.
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Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, University of British Columbia (UBC), 2036 Mail Mall, Vancouver, BC, V6T 1Z1, Canada,
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9
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Cera L, Schalley CA. Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes. Chem Soc Rev 2014; 43:1800-12. [PMID: 24435245 DOI: 10.1039/c3cs60360a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase.
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Affiliation(s)
- Luca Cera
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany.
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10
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Balaj OP, Semrouni D, Steinmetz V, Nicol E, Clavaguéra C, Ohanessian G. Structure of Sodiated Polyglycines. Chemistry 2012; 18:4583-92. [DOI: 10.1002/chem.201102812] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 11/11/2022]
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11
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Kang Y, Terrier P, Ding C, Douglas DJ. Solution and gas-phase H/D exchange of protein-small-molecule complexes: Cex and its inhibitors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:57-67. [PMID: 22006406 DOI: 10.1007/s13361-011-0263-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
The properties of noncovalent complexes of the enzyme exo-1,4-β-D-glycanase ("Cex") with three aza-sugar inhibitors, deoxynojirimycin (X(2)DNJ), isofagomine lactam (X(2)IL), and isofagomine (X(2)IF), have been studied with solution and gas-phase hydrogen deuterium exchange (H/Dx) and measurements of collision cross sections of gas-phase ions. In solution, complexes have lower H/Dx levels than free Cex because binding the inhibitors blocks some sites from H/Dx and reduces fluctuations of the protein. In mass spectra of complexes, abundant Cex ions are seen, which mostly are formed by dissociation of complexes in the ion sampling interface. Both complex ions and Cex ions formed from a solution containing complexes have lower cross sections than Cex ions from a solution of Cex alone. This suggests the Cex ions formed by dissociation "remember" their solution conformations. For a given charge, ions of the complexes have greater gas-phase H/Dx levels than ions of Cex. Unlike cross sections, H/Dx levels of the complexes do not correlate with the relative gas-phase binding strengths measured by MS/MS. Cex ions from solutions with or without inhibitors, which have different cross sections, show the same H/Dx level after 15 s, indicating the ions may fold or unfold on the seconds time scale of the H/Dx experiment. Thus, cross sections show that complexes have more compact conformations than free protein ions on the time scale of ca. 1 ms. The gas-phase H/Dx measurements show that at least some complexes retain different conformations from the Cex ions on a time scale of seconds.
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Affiliation(s)
- Yang Kang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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12
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Pan J, Heath BL, Jockusch RA, Konermann L. Structural Interrogation of Electrosprayed Peptide Ions by Gas-Phase H/D Exchange and Electron Capture Dissociation Mass Spectrometry. Anal Chem 2011; 84:373-8. [DOI: 10.1021/ac202730d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jingxi Pan
- Department of Chemistry, The University of Western Ontario, London,
Ontario, N6A 5B7, Canada
| | - Brittany L. Heath
- Department of Chemistry, University of Toronto, Toronto, Ontario
M5S 3H6, Canada
| | - Rebecca A. Jockusch
- Department of Chemistry, University of Toronto, Toronto, Ontario
M5S 3H6, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London,
Ontario, N6A 5B7, Canada
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13
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Maroto E, Filippone S, Martín-Domenech A, Suárez M, Martín N, Martínez-Alvarez R. Effect of substituents and protonation on the mechanism of 1,3-dipolar retro-cycloaddition reaction of pyrrolidino[60]- and [70]fullerenes. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1016-1029. [PMID: 22012668 DOI: 10.1002/jms.1983] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The mass spectra of new substituted pyrrolidino[60]- and [70]fullerenes have been obtained using electrospray ionization conditions in the positive and negative mode of detection with two different mass spectrometers, a quadrupole ion trap and a Fourier transform ion cyclotron resonance. Radical anions M(●-) and deprotonated molecules [M-H](-) are formed under negative electrospray ionization mass spectrometry conditions, and the collision-induced dissociations of both ionic species have been studied. Either negative odd-electron ions or negative even-electron ions undergo a retro-cycloaddition process forming the corresponding fullerene product ions C(60)(●-) and C(70)(●-). The generation of fullerene radical anions from deprotonated molecules is a new exception of the "even-electron rule." In contrast, the protonated molecules [M + H](+) obtained from the positive mode of detection do not undergo this cycloreversion reaction, and the MS(n) experiment reveals a variety of eliminations of neutral molecules involving different hydrogen shifts and multiple bond cleavages that lead eventually to substituted methanofullerene fragment ions. The observed fragmentations can be correlated with the electronic character of the substituents attached to the heterocyclic moiety. The results obtained from the thermal reactions of these compounds, carried out under different pH conditions, correlate well with those obtained in gas phase. The different behaviors between protonated and unprotonated molecules and ions can be explained assuming that the retro-cycloaddition reaction takes place only when the nitrogen atom of the pyrrolidine ring (the basic center of the molecule) is unprotonated both in gas and condensed phase. The protonation of the NH group inhibits the cycloreversion process, and therefore different fragmentations take place. The detailed mechanisms of the formation and evolution of the intermediate fragments are described.
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Affiliation(s)
- Enrique Maroto
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
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14
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Mertens LA, Marzluff EM. Gas Phase Hydrogen/Deuterium Exchange of Arginine and Arginine Dipeptides Complexed with Alkali Metals. J Phys Chem A 2011; 115:9180-7. [DOI: 10.1021/jp204896z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura A. Mertens
- Department of Chemistry, Grinnell College, Grinnell, Iowa, 50112 United States
| | - Elaine M. Marzluff
- Department of Chemistry, Grinnell College, Grinnell, Iowa, 50112 United States
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15
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Kang Y, Douglas DJ. Gas-phase ions of human hemoglobin A, F, and S. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1187-1196. [PMID: 21953101 DOI: 10.1007/s13361-011-0138-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/16/2011] [Accepted: 03/18/2011] [Indexed: 05/31/2023]
Abstract
Hemoglobin (Hb) (α(2)β(2)) is a tetrameric protein-protein complex. Collision cross sections, hydrogen exchange levels, and tandem mass spectrometry have been used to investigate the properties of gas-phase monomer, dimer, and tetramer ions of adult human hemoglobin (Hb A, α(2)β(2)), and two variant hemoglobins: fetal hemoglobin (Hb F, α(2)γ(2)) and sickle hemoglobin (Hb S, α(2)β(2), E6V[β]). All three proteins give similar mass spectra. Monomers of Hb S and Hb F have similar cross sections, ca. 10% greater than those of Hb A. Cross sections of dimer ions of Hb S are 11% greater than those of Hb A and 6% greater than those of Hb F. Tetramers of Hb S are 13% larger than tetramers of Hb A or Hb F. Monomers and dimers of all three Hb have similar hydrogen-deuterium exchange (HDX) levels. Tetramers of Hb S exchange 16% more hydrogens than Hb A and Hb F. In tandem mass spectrometry, monomers of Hb S and Hb F require ca. 10% greater internal energy for heme loss than Hb A. Dimers (+11) of Hb A and Hb S dissociate to monomers with asymmetrical charge division; dimers of Hb F (+11) dissociate with nearly equal charge division. Tetramer ions dissociate to monomers and trimers, unlike solution Hb, which dissociates to dimers. The most stable dimers are from Hb S; the most stable tetramers from Hb F. The results with Hb S show that a single mutation in the β chain can change the physical properties of this gas-phase protein-protein complex.
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Affiliation(s)
- Yang Kang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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16
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Carlton DD, Schug KA. A review on the interrogation of peptide–metal interactions using electrospray ionization-mass spectrometry. Anal Chim Acta 2011; 686:19-39. [DOI: 10.1016/j.aca.2010.11.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 11/27/2022]
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17
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Winkler HDF, Dzyuba EV, Sklorz JAW, Beyeh NK, Rissanen K, Schalley CA. Gas-phase H/D-exchange reactions on resorcinarene and pyrogallarene capsules: Proton transport through a one-dimensional Grotthuss mechanism. Chem Sci 2011. [DOI: 10.1039/c0sc00539h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Winkler HDF, Dzyuba EV, Schalley CA. Gas-phase H/D-exchange experiments in supramolecular chemistry. NEW J CHEM 2011. [DOI: 10.1039/c0nj00634c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Rožman M, Gaskell SJ. Non-covalent interactions of alkali metal cations with singly charged tryptic peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1409-1415. [PMID: 21031360 DOI: 10.1002/jms.1856] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
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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Affiliation(s)
- Marko Rožman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, HR-10002 Zagreb, Croatia.
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Ziegler BE, McMahon TB. Energetics and Structural Elucidation of Mechanisms for Gas Phase H/D Exchange of Protonated Peptides. J Phys Chem A 2010; 114:11953-63. [DOI: 10.1021/jp105170f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Blake E. Ziegler
- Department of Chemistry University of Waterloo Waterloo, Ontario
| | - Terry B. McMahon
- Department of Chemistry University of Waterloo Waterloo, Ontario
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Semrouni D, Balaj OP, Calvo F, Correia CF, Clavaguéra C, Ohanessian G. Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:728-38. [PMID: 20189824 DOI: 10.1016/j.jasms.2010.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/25/2023]
Abstract
The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.
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Affiliation(s)
- David Semrouni
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique and CNRS, Palaiseau, France
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Semrouni D, Ohanessian G, Clavaguéra C. Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field. Phys Chem Chem Phys 2010; 12:3450-62. [DOI: 10.1039/b924317h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Huang Y, Marini JA, McLean JA, Tichy SE, Russell DH. A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing di- and tripeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2049-2057. [PMID: 19747842 DOI: 10.1016/j.jasms.2009.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 07/17/2009] [Accepted: 07/18/2009] [Indexed: 05/28/2023]
Abstract
The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di- and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M + H]+ ions with deuterated ammonia (ND3) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and arginine-containing tri-peptide [M + H]+ ions, whereas the di-peptide [M + H]+ ions undergo a single H/D exchange. In addition, C-terminal methylation blocks H/D exchange of arginine and the arginine-containing peptide [M + H]+ ions, and a single H/D exchange is observed for N-terminal acetylated arginine [M + H]+ ions. A general mechanism for H/D exchange involving a collision complex that is best described as a "solvated salt-bridge" structure is proposed.
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Affiliation(s)
- Yiqun Huang
- Department of Chemistry, The Laboratory for Biological Mass Spectrometry, Texas A&M University, College Station, Texas 77843, USA
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24
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Highly dynamic motion of crown ethers along oligolysine peptide chains. Nat Chem 2009; 1:573-7. [DOI: 10.1038/nchem.352] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 07/24/2009] [Indexed: 11/08/2022]
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Prell JS, O’Brien JT, Steill JD, Oomens J, Williams ER. Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges. J Am Chem Soc 2009; 131:11442-9. [DOI: 10.1021/ja901870d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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Wright PJ, Douglas DJ. Gas-phase H/D exchange and collision cross sections of hemoglobin monomers, dimers, and tetramers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:484-495. [PMID: 19101164 DOI: 10.1016/j.jasms.2008.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 05/27/2023]
Abstract
The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.
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Affiliation(s)
- P John Wright
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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Prell JS, Demireva M, Oomens J, Williams ER. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J Am Chem Soc 2008; 131:1232-42. [DOI: 10.1021/ja808177z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Maria Demireva
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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Sang-Aroon W, Ruangpornvisuti V. Conformational analysis of alkali metal complexes of anionic species of aspartic acid, their interconversion and deprotonation: A DFT investigation. J Mol Graph Model 2008; 26:982-90. [PMID: 17884644 DOI: 10.1016/j.jmgm.2007.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/10/2007] [Accepted: 08/14/2007] [Indexed: 11/27/2022]
Abstract
Gas-phase geometry-optimized structures of aspartate complexes of anionic species (Hasp(-)) with lithium, sodium and potassium metal cations and transition-state structures for their interconversions were obtained using the density functional theory computations at the B3LYP/6-311++G(d,p) level of theory. The metal ion affinities of Hasp(-) species and deprotonation energies of [Hasp-M] complexes, M=Li+, Na+ and K+, and their conformers were obtained. Relative energies of the [Hasp-M] complex conformers, reaction energies, thermodynamic properties, rate and equilibrium constants of their complexation are reported. Binding energies of the most stable complexes with Li+, Na+ and K+ are -168.53, -133.34 and -117.68kcal/mol, respectively. The most stable complex conformer as a tri-coordinated form for aspartate complex with Li(+) and bi-coordinated form for aspartate complexes with Na+ and K+ were found.
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Affiliation(s)
- Wichien Sang-Aroon
- Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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29
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Ai H, Zhang C, Li Y, Zhang L, Li F. Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter. J Phys Chem B 2007; 111:13786-96. [DOI: 10.1021/jp074198m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Chong Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Yun Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Liang Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Fang Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
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Forbes MW, Bush MF, Polfer NC, Oomens J, Dunbar RC, Williams ER, Jockusch RA. Infrared Spectroscopy of Arginine Cation Complexes: Direct Observation of Gas-Phase Zwitterions. J Phys Chem A 2007; 111:11759-70. [DOI: 10.1021/jp074859f] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Niemeyer ED, Brodbelt JS. Isomeric differentiation of green tea catechins using gas-phase hydrogen/deuterium exchange reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1749-59. [PMID: 17702600 PMCID: PMC2048816 DOI: 10.1016/j.jasms.2007.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 06/29/2007] [Accepted: 07/02/2007] [Indexed: 05/16/2023]
Abstract
Hydrogen/deuterium exchange reactions in a quadrupole ion trap mass spectrometer are used to differentiate galloylated catechin stereoisomers (catechin gallate and epicatechin gallate; gallocatechin gallate and epigallocatechin gallate) and the nongalloylated analogs (catechin and epicatechin, gallocatechin and epigallocatechin). Significant differences in the hydrogen/deuterium exchange behavior of the four pairs of deprotonated catechin stereoisomers are observed upon reaction with D(2)O. Interestingly, the nongalloylated catechins undergo H/D exchange to a much greater extent than the galloylated species, incorporating deuterium at both aromatic/allylic and active phenolic sites. Nongalloylated catechin isomers are virtually indistinguishable by their H/D exchange kinetics over a wide range of reaction times (0.05 to 10 s). Our experimental results are explained using high-level ab initio calculations to elucidate the subtle structural variations in the catechin stereoisomers that lead to their differing H/D exchange kinetics.
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Affiliation(s)
- Emily D Niemeyer
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, Texas 78626, USA.
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32
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Sang-Aroon W, Ruangpornvisuti V. Conformational analysis of alkali metal complexes of aspartate dianion and their interactions in gas phase. J Mol Graph Model 2007; 26:342-51. [PMID: 17276112 DOI: 10.1016/j.jmgm.2007.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 12/23/2006] [Accepted: 01/03/2007] [Indexed: 11/29/2022]
Abstract
The gas-phase geometry optimizations of mono and dinuclear complexes of dianionic species of aspartic acid, asp(2-) with lithium, sodium and potassium cations were carried out using density functional calculation at the B3LYP/6-311++G(d,p) level. The metal ion affinities (MIAs) of asp(2-) species and its complexes [asp-M](-), M=Li(+), Na(+) and K(+) were determined using the vibrational frequency calculations at the same level of theory. The most stable complex conformer for aspartate complexes with Li(+), Na(+) and K(+) alkali cations were found as a tri-coordinated form. All complexations of [asp-M](-) and [asp-M(2)] complexes were found to be exothermic reactions. Relative bond distances between the alkali metal cation M(+) and the binding atoms of aspartate ion in [asp-M](-) and [asp-M(2)] complexes are in decreasing order: K(+)>Na(+)>Li(+).
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Affiliation(s)
- Wichien Sang-Aroon
- Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Chipuk JE, Brodbelt JS. Gas-phase hydrogen/deuterium exchange of 5'- and 3'-mononucleotides in a quadrupole ion trap: exploring the role of conformation and system energy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:724-36. [PMID: 17289398 DOI: 10.1016/j.jasms.2006.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2006] [Revised: 12/18/2006] [Accepted: 12/19/2006] [Indexed: 05/13/2023]
Abstract
Gas-phase hydrogen/deuterium (H/D) exchange reactions for deprotonated 2'-deoxy-5'-monophosphate and 2'-deoxy-3'-monophosphate nucleotides with D(2)O were performed in a quadrupole ion trap mass spectrometer. To augment these experiments, molecular modeling was also conducted to identify likely deprotonation sites and potential gas-phase conformations of the anions. A majority of the 5'-monophosphates exchanged extensively with several of the compounds completely incorporating deuterium in place of their labile hydrogen atoms. In contrast, most of the 3'-monophosphate isomers exchanged relatively few hydrogen atoms, even though the rate of the first two exchanges was greater than observed for the 5'-monophosphates. Mononucleotides that failed to incorporate more than two deuterium atoms under default reaction conditions were often found to exchange more extensively when reactions were performed under higher energy conditions. Integration of the experimental and theoretical results supports the use of a relay exchange mechanism and suggests that the exchange behavior depends highly on the identity and orientation of the nucleobase and the position and flexibility of the deprotonated phosphate moiety. These observations also highlight the importance of the distance between the various participating groups in addition to their gas-phase acidity and basicity.
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Affiliation(s)
- Joseph E Chipuk
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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Ai H, Li Y, Zhang C, Feng J. The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Polfer NC, Dunbar RC, Oomens J. Observation of zwitterion formation in the gas-phase H/D-exchange with CH(3)OD: solution-phase structures in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:512-6. [PMID: 17174103 DOI: 10.1016/j.jasms.2006.10.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/17/2006] [Accepted: 10/18/2006] [Indexed: 05/13/2023]
Abstract
Infrared spectroscopy of gas-phase singly deuterated [Trp + K](+) (formed by H/D exchange with CH(3)OD) shows that some (approximately 20%) kinetically stable zwitterionic (ZW) conformer is formed, based on the diagnostic antisymmetric CO stretch of the deprotonated carboxylate moiety, upsilon(as)(CO(2)(-)), at 1680 cm(-1). A majority of the deuterated [Trp + K](+) is found to be in the charge solvation (CS) conformation, with deuterium exchange occurring on both the acid and amino groups, which is consistent with H/D scrambling. Interestingly, H/D exchange with the more basic ND(3) reagent did not result in the stabilization of a kinetically stable zwitterion, although it is not clear yet what causes this observation. The result for CH(3)OD shows that H/D exchange can in fact alter the structure of the analyte and, hence, care needs to be taken when interpreting gas-phase H/D exchange studies. Moreover, this result shows the possibility of forming solution-phase structures that are thermodynamically disfavored in the gas phase, thus opening a new area of study.
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Affiliation(s)
- Nick C Polfer
- FOM-Institute for Plasma Physics Rijnhuizen, Nieuwegein, The Netherlands.
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36
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Polfer NC, Oomens J. Reaction products in mass spectrometry elucidated with infrared spectroscopy. Phys Chem Chem Phys 2007; 9:3804-17. [PMID: 17637973 DOI: 10.1039/b702993b] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of limited use when sample quantities are low. Mass spectrometry (MS) on the other hand has been very successful in analyzing biological molecules down to atto-mole quantities and has hence begun to challenge XRD and NMR as the key technology in the life sciences. This trend has been further assisted by the development of MS techniques that yield structural information on biomolecules. Of these techniques, collision-induced dissociation (CID) and hydrogen/deuterium exchange (HDX) are among the most popular. Despite advances in applying these techniques, little direct experimental evidence had been available until recently to verify their proposed underlying reaction mechanisms. The possibility to record infrared spectra of mass-selected molecular ions has opened up a novel avenue in the structural characterization of ions and their reaction products. On account of its high pulse energies and wide wavelength tunability, the free electron laser for infrared experiments (FELIX) at FOM Rijnhuizen has been shown to be ideally suited to study trapped molecular ions with infrared photo-dissociation spectroscopy. In this paper, we review recent experiments in our laboratory on the infrared spectroscopic characterization of reaction products from CID and HDX, thereby corroborating some of the reaction mechanisms that have been proposed. In particular, it is shown that CID gives rise to linear fragment ion structures which have been proposed for some time, but also yields fully cyclical ring structures. These latter structures present a possible challenge for using tandem MS in the sequencing of peptides/proteins, as they can lead to a scrambling of the amino acid sequence information. In gas-phase HDX of an amino acid it is shown that the structure can be changed from a charge solvated to a zwitterionic structure, thereby demonstrating that HDX can be an invasive technique, in fact changing the structure of the analyte. These results emphasize that more fundamental work is required in order to understand the underlying mechanisms in two of the most important structural techniques in MS.
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Affiliation(s)
- Nick C Polfer
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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Rožman M, Bertoša B, Klasinc L, Srzić D. Gas phase H/D exchange of sodiated amino acids: why do we see zwitterions? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:29-36. [PMID: 16352438 DOI: 10.1016/j.jasms.2005.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 08/26/2005] [Accepted: 08/26/2005] [Indexed: 05/05/2023]
Abstract
The gas-phase interaction of sodiated amino acids and sodiated amino acid methyl esters with various deuterium donors is investigated by combining results of H/D exchange reactions with those from density functional theory and molecular dynamics calculations. Discrepancy between experimentally and theoretically obtained structures for sodium cationized amino acids is explained by deuterium donor caused perturbation of the most stable amino acid conformation. Detailed study of H/D exchange mechanism on sodiated amino acids shows that the H/D exchange reaction is preceded by a multistep quasi-isoenergetic transition (perturbation) from a charge solvated to zwitterionic structure in the amino acid. Although the computation refers to the system AlaNa(+) and D(2)O, these mechanisms apply to all amino acids, except those where a functional side-chain group takes part in the perturbation process. The suggested perturbation mechanism applies also for other deuterium donors such as CD(3)OD or even ND(3) and indicates that a single water molecule suffices to convert the sodiated amino acid from charge solvated to zwitterionic form.
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Affiliation(s)
- Marko Rožman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia
| | - Branimir Bertoša
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory of Chemical and Biological Crystallography, Croatia
| | - Leo Klasinc
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia
| | - Dunja Srzić
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia.
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia.
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Rozman M. The gas-phase H/D exchange mechanism of protonated amino acids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1846-52. [PMID: 16198597 DOI: 10.1016/j.jasms.2005.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 07/20/2005] [Accepted: 07/28/2005] [Indexed: 05/04/2023]
Abstract
A mass spectrometry and Density Functional Theory study of gas-phase H/D exchange in protonated Ala, Cys, Ile, Leu, Met, and Val is reported. Site-specific rate constants were determined and results identify the alpha-amino group as the protonation site. Lack of exchange on the Cys thiol group is explained by the absence of strong intramolecular hydrogen bonding within the reaction complex. In aliphatic amino acids the presence of a methyl group at the beta-C atom was found to lower the site-specific H/D exchange rate for amino hydrogens. Study of the exchange mechanism showed that isotopic exchange occurs in two independent reactions: in one, only the carboxylic hydrogen is exchanged and in the other, both carboxylic and amino group hydrogens exchange. The proposed reaction mechanisms, calculated structures of various species, and a number of structural findings are consistent with experimental data.
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Affiliation(s)
- Marko Rozman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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Rozman M. Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1357-61. [PMID: 16220525 DOI: 10.1002/jms.926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations.
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Affiliation(s)
- Marko Rozman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruder Bosković Institute, Bijenicka 54, HR-10002, Zagreb, Croatia.
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Robinson EW, Williams ER. Multidimensional separations of ubiquitin conformers in the gas phase: relating ion cross sections to H/D exchange measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1427-1437. [PMID: 16023362 PMCID: PMC2735248 DOI: 10.1016/j.jasms.2005.04.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2005] [Revised: 04/13/2005] [Accepted: 04/13/2005] [Indexed: 05/03/2023]
Abstract
Investigating gas-phase structures of protein ions can lead to an improved understanding of intramolecular forces that play an important role in protein folding. Both hydrogen/deuterium (H/D) exchange and ion mobility spectrometry provide insight into the structures and stabilities of different gas-phase conformers, but how best to relate the results from these two methods has been hotly debated. Here, high-field asymmetric waveform ion mobility spectrometry (FAIMS) is combined with Fourier-transform ion cyclotron resonance mass spectrometry (FT/ICR MS) and is used to directly relate ubiquitin ion cross sections and H/D exchange extents. Multiple conformers can be identified using both methods. For the 9+ charge state of ubiquitin, two conformers (or unresolved populations of conformers) that have cross sections differing by 10% are resolved by FAIMS, but only one conformer is apparent using H/D exchange at short times. For the 12+ charge state, two conformers (or conformer populations) have cross sections differing by <1%, yet H/D exchange of these conformers differ significantly (6 versus 25 exchanges). These and other results show that ubiquitin ion collisional cross sections and H/D exchange distributions are not strongly correlated and that factors other than surface accessibility appear to play a significant role in determining rates and extents of H/D exchange. Conformers that are not resolved by one method could be resolved by the other, indicating that these two methods are highly complementary and that more conformations can be resolved with this combination of methods than by either method alone.
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Affiliation(s)
- Errol W Robinson
- Department of Chemistry, University of California at Berkeley, 94720, Berkeley, CA, USA
| | - Evan R Williams
- Department of Chemistry, University of California at Berkeley, 94720, Berkeley, CA, USA.
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Geller O, Lifshitz C. A Fast Flow Tube Study of Gas Phase H/D Exchange of Multiply Protonated Ubiquitin. J Phys Chem A 2005; 109:2217-22. [PMID: 16838993 DOI: 10.1021/jp044737c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An electrospray ionization (ESI)/fast-flow technique has been applied to the study of gas phase hydrogen/deuterium (H/D) exchange kinetics. Multiply charged ubiquitin ions [ubiquitin + nH](n)(+), in charge states n = 7-13, were reacted with ND(3). The behavior of ND(3) as exchange reagent is different from that of the previously studied reagents, D(2)O and CH(3)OD. Contrary to those, the maximum number of exchanged hydrogen atoms and the overall exchange rate were observed to increase with increasing charge state of the ubiquitin ions. The results are reagent-dependent because the exchange mechanisms are different for the different reagents. This observation is in agreement with a recent conclusion by Beauchamp and co-workers that contrary to the assumption often expressed in earlier studies, H/D exchange kinetics may not directly reflect ion structures. The results for all three reagents are, however, consistent with observations of previous ion mobility experiments that with increasing charge state the conformers change from more compact, partially folded structures to elongated nearly linear ones. H/D exchange of (ubiquitin + 13H)(13+) with ND(3) leads to two separated ion populations reflecting the possible existence of two conformers with different exchange rates. The ions (ubiquitin + 8H)(8+) and (ubiquitin + 11H)(11+) represent a partially folded structure and an unfolded structure, respectively, and were studied in greater detail. The relative abundances of ions were measured in steps of 0.5 m/z (mass-to-charge ratio), as a function of the ND(3) flow rate. The experimental results were simulated by computer fitted curves based on a recently developed algorithm. The algorithm allows the extraction of sets of grouped rate constants. Eight rate constant groups were deduced for each of the two ions. These rate constants correspond to 32 and 44 H/D exchanges for the 8+ and 11+ charged ions, respectively. The results indicate higher individual rates for most of the exchanged atoms in the 11+ ion compared to the 8+ ion.
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Affiliation(s)
- Orit Geller
- Department of Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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