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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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2
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Chudinov AV, Sulimenkov IV, Pikhtelev AR, Kozlovskii VI. Study of H/D-exchange reaction kinetics of polypeptides. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810140121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Fattahi A, Zekavat B, Solouki T. H/D exchange kinetics: experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:358-369. [PMID: 20005740 DOI: 10.1016/j.jasms.2009.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 09/28/2009] [Accepted: 10/22/2009] [Indexed: 05/28/2023]
Abstract
Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b(5)(+) and b(4)(+) fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H](+)) and its b(5)(+) and b(4)(+) fragment ions (with ND(3)) were observed. Isolated (12)C(all) isotopomers of both b(5)(+) and b(4)(+) fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b(5)(+) and b(4)(+) fragment ions exist as combination of slow-exchanging ("s") and fast-exchanging ("f") species. The calculated rate constant for the first labile hydrogen exchange of [M + H](+) (k([M + H](+)) = 3.80 +/- 0.7 x 10(-10) cm(3) mol(-1) s(-1)) was approximately 30 and approximately 5 times greater than those for the "s" and "f" species of b(5)(+), respectively. Data from H/D exchange of isolated "s" species at longer ND(3) reaction times confirmed the existence of different conformers or isomers for b(5)(+) fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that "s" and "f" species of b(5)(+) and b(4)(+) fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed.
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Affiliation(s)
- Alireza Fattahi
- Department of Chemistry, University of Maine, Orono, Maine 04469, USA
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4
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Torvinen M, Neitola R, Sansone F, Baldini L, Ungaro R, Casnati A, Vainiotalo P, Kalenius E. Glucosylthioureidocalix[4]arenes: Synthesis, conformations and gas phase recognition of amino acids. Org Biomol Chem 2010; 8:906-15. [DOI: 10.1039/b916268b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Tian Z, Wang XB, Wang LS, Kass SR. Are Carboxyl Groups the Most Acidic Sites in Amino Acids? Gas-Phase Acidities, Photoelectron Spectra, and Computations on Tyrosine, p-Hydroxybenzoic Acid, and Their Conjugate Bases. J Am Chem Soc 2008; 131:1174-81. [DOI: 10.1021/ja807982k] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhixin Tian
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352
| | - Xue-Bin Wang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352
| | - Lai-Sheng Wang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352
| | - Steven R. Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, and Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352
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6
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Rozman M. Aspartic acid side chain effect-experimental and theoretical insight. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:121-7. [PMID: 17049877 DOI: 10.1016/j.jasms.2006.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 09/13/2006] [Accepted: 09/17/2006] [Indexed: 05/12/2023]
Abstract
Gas-phase H/D exchange and density functional theory study of the Asp and Glu side-chain carboxylic group intrinsic reactivity is reported. H/D exchange site specific treatment and some additional theoretical calculations showed that a side-chain carboxylic group may initiate proton transfer along with bond formation to one of its oxygens, i.e., possibility to initiate selective of cleavage peptide bond ("aspartic acid effect"). That finding is used to select aspartic acid cleavage mechanisms (side-chain proton transfer either to backbone carbonyl or to amide nitrogen) for further computational study. B3LYP/6-31G(d) and G3(MP2)//B3LYP potential energy profiles of both mechanisms on a model system CH3CO-Asp-NHCH3 were constructed. Although energy employed in low-energy collision induced dissociation suffices for both mechanisms thresholds, energy transferred to specific modes suggests a complex one-step mechanism of proton transfer (from the side-chain carboxylic group to the backbone amide group), bond formation (between deprotonated carboxylic group and carbon atom of the backbone carbonyl), and peptide bond cleavage as favorable.
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Affiliation(s)
- Marko Rozman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruder Bosković Institute, Zagreb, Croatia
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7
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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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8
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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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9
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Kovacević B, Rozman M, Klasinc L, Srzić D, Maksić ZB, Yañez M. Gas-Phase Structure of Protonated Histidine and Histidine Methyl Ester: Combined Experimental Mass Spectrometry and Theoretical ab Initio Study. J Phys Chem A 2005; 109:8329-35. [PMID: 16834223 DOI: 10.1021/jp053288t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.
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Affiliation(s)
- Borislav Kovacević
- Quantum Organic Chemistry Group and Laboratory for Chemical Kinetics and Atmospheric Chemistry, Rudjer Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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10
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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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11
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Reuben BG, Ritov Y, Geller O, McFarland MA, Marshall AG, Lifshitz C. Applying a new algorithm for obtaining site specific rate constants for H/D exchange of the gas phase proton-bound arginine dimer. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.08.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Rozman M, Kazazić S, Klasinc L, Srzić D. Kinetics of gas-phase hydrogen/deuterium exchange and gas-phase structure of protonated phenylalanine, proline, tyrosine and tryptophan. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2769-2772. [PMID: 14673825 DOI: 10.1002/rcm.1261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Site-specific rate constants for the gas-phase hydrogen/deuterium (H/D) exchange of four, three, five and five hydrogen atoms in protonated phenylalanine (Phe), proline (Pro), tyrosine (Tyr) and tryptophan (Trp), respectively, were determined from matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) experiments with D(2)O, D(2)S, and CH(3)OD as deuterating agents. No H/D exchange was observed with D(2)S. For exchange with both CD(3)OD and D(2)O, which is about ten times slower in the latter, results indicate for all compounds protonation of the alpha-amino group in agreement with theoretical results. Also, with both reagents, all compounds exchange at the COOH site more than ten times faster than at the protonation site, with OH and NH sites of Tyr and Trp, respectively, exchanging slowest. The observation of H/D exchange despite the high differences in proton affinities between the amino acids and deuterating agent exceeding 200 kJ mol(-1) is in agreement with lowering of the barrier for proton transfer through hydrogen bonding proposed by Lebrilla and coworkers.
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Affiliation(s)
- Marko Rozman
- Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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Solouki T, Fort RC, Alomary A, Fattahi A. Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:1272-1285. [PMID: 11766754 DOI: 10.1016/s1044-0305(01)00315-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-Asp[triple bond]RGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs - H]+ species exhibit the slowest H/D exchange reactivity (reaction rate constant of approximately 6 x 10(-13) cm3molecule(-1)s(-1) for the fastest exchanging labile hydrogen with ND3). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs - H]+. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D0) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D0 disappearance for all [RGD + 2Met - H]+ species (Met[triple bond]Na, K, and Cs) decreases with the alkali metal ion size.
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Affiliation(s)
- T Solouki
- Department of Chemistry, University of Maine, Orono 04469, USA.
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Levy-Seri E, Koster G, Kogan A, Gutman K, Reuben BG, Lifshitz C. An Electrospray Ionization−Flow Tube Study of H/D Exchange in Protonated Bradykinin. J Phys Chem A 2001. [DOI: 10.1021/jp0037145] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elchanan Levy-Seri
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Grielof Koster
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexandra Kogan
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Karnit Gutman
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Bryan G. Reuben
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chava Lifshitz
- Department for Physical Chemistry and The Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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15
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Ustyuzhanin P, Kogan A, Reuben BG, Lifshitz C. An electrospray-ionization?flow-tube study of H/D exchange in protonated leucine-enkephalin. INT J CHEM KINET 2001. [DOI: 10.1002/kin.1067] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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