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Salzburger M, Hütter M, van der Linde C, Ončák M, Beyer MK. Master equation modeling of blackbody infrared radiative dissociation (BIRD) of hydrated peroxycarbonate radical anions. J Chem Phys 2024; 160:134304. [PMID: 38557850 DOI: 10.1063/5.0200253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Molecular cluster ions, which are stored in an electromagnetic trap under ultra-high vacuum conditions, undergo blackbody infrared radiative dissociation (BIRD). This process can be simulated with master equation modeling (MEM), predicting temperature-dependent dissociation rate constants, which are very sensitive to the dissociation energy. We have recently introduced a multiple-well approach for master equation modeling, where several low-lying isomers are taken into account. Here, we experimentally measure the BIRD of CO4●-(H2O)1,2 and model the results with a slightly modified multiple-well MEM. In the experiment, we exclusively observe loss of water from CO4●-(H2O), while the BIRD of CO4●-(H2O)2 leads predominantly to loss of carbon dioxide, with water loss occurring to a lesser extent. The MEM of two competing reactions requires empirical scaling factors for infrared intensities and the sum of states of the loose transition states employed in the calculation of unimolecular rate constants so that the simulated branching ratio matches the experiment. The experimentally derived binding energies are ΔH0(CO4●--H2O) = 45 ± 3 kJ/mol, ΔH0(CO4●-(H2O)-H2O) = 41 ± 3 kJ/mol, and ΔH0(CO2-O2●-(H2O)2) = 37 ± 3 kJ/mol. Quantum chemical calculations on the CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVDZ level, corrected for the basis set superposition error, yield binding energies that are 2-5 kJ/mol higher than experiment, within error limits of both experiment and theory. The relative activation energies for the two competing loss channels are as well fully consistent with theory.
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Affiliation(s)
- Magdalena Salzburger
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Michael Hütter
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Christian van der Linde
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martin K Beyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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2
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Sinenka H, Bruyakin Y, Zaitsevskii A, Isaev T, Bochenkova AV. Zwitterions Functionalized by Optical Cycling Centers: Toward Laser-Coolable Polyatomic Molecular Cations. J Phys Chem Lett 2023:5784-5790. [PMID: 37327400 DOI: 10.1021/acs.jpclett.3c00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Functionalization of large aromatic compounds and biomolecules with optical cycling centers (OCC) is of considerable interest for the design and engineering of molecules with a highly selective optical photoresponse. Both internal and external dynamics in such molecules can be precisely controlled by lasers, enabling their efficient cooling and opening up broad prospects for high-precision spectroscopy, ultracold chemistry, enantiomer separation, and various other fields. The way the OCC is bonded to a molecular ligand is crucial to the optical properties of the OCC, first of all, for the degree of closure of the optical cycling loop. Here we introduce a novel type of functionalized molecular cation where a positively charged OCC is bonded to various organic zwitterions with a particularly high permanent dipole moment. We consider strontium(I) complexes with betaine and other zwitterionic ligands and show the possibility of creating efficient and highly closed population cycling for dipole-allowed optical transitions in such complexes.
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Affiliation(s)
- Hryhory Sinenka
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yurii Bruyakin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrei Zaitsevskii
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- NRC "Kurchatov Institute" - PNPI, Orlova Roscha, 1, 188300 Gatchina, Russia
| | - Timur Isaev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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3
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Lê Anh M, Potapov P, Wolf D, Lubk A, Glatz B, Fery A, Doert T, Ruck M. Freestanding Nanolayers of a Wide-Gap Topological Insulator through Liquid-Phase Exfoliation. Chemistry 2021; 27:794-801. [PMID: 33125781 PMCID: PMC7839554 DOI: 10.1002/chem.202004320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Indexed: 11/11/2022]
Abstract
The layered salt Bi14 Rh3 I9 is a weak three-dimensional (3D) topological insulator (TI), that is, a stack of two-dimensional (2D) TIs. It has a wide non-trivial band gap of 210 meV, which is generated by strong spin-orbit coupling, and possesses protected electronic edge-states. In the structure, charged layers of∞ 2 [ (Bi4 Rh)3 I]2+ honeycombs and∞ 1 [ Bi2 I8 ]2- chains alternate. The non-trivial topology of Bi14 Rh3 I9 is an inherent property of the 2D intermetallic fragment. Here, the exfoliation of Bi14 Rh3 I9 was performed using two different chemical approaches: (a) through a reaction with n-butyllithium and poly(vinylpyrrolidone), (b) through a reaction with betaine in dimethylformamide at 55 °C. The former yielded few-layer sheets of the new compound Bi12 Rh3 I, while the latter led to crystalline sheets of Bi14 Rh3 I9 with a thickness down to 5 nm and edge-lengths up to several ten microns. X-ray diffraction and electron microscopy proved that the structure of Bi14 Rh3 I9 remained intact. Thus, it was assumed that the particles are still TIs. Dispersions of these flakes now allow for next steps towards the envisioned applications in nanoelectronics, such as the study of quantum coherence in deposited films, the combination with superconducting particles or films for the generation of Majorana fermions, or studies on their behavior under the influence of magnetic or electric fields or in contact with various materials occurring in devices. The method presented generally allows to exfoliate layers with high specific charges and thus the use of layered starting materials beyond van der Waals crystals.
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Affiliation(s)
- Mai Lê Anh
- Faculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
| | | | | | - Axel Lubk
- Leibniz IFW Dresden01069DresdenGermany
- Würzburg-Dresden Cluster of Excellence ct.qmatTechnische Universität Dresden01062DresdenGermany
| | - Bernhard Glatz
- Leibniz Institute of Polymer Research Dresden01069DresdenGermany
| | - Andreas Fery
- Leibniz Institute of Polymer Research Dresden01069DresdenGermany
| | - Thomas Doert
- Faculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
| | - Michael Ruck
- Faculty of Chemistry and Food ChemistryTechnische Universität Dresden01062DresdenGermany
- Würzburg-Dresden Cluster of Excellence ct.qmatTechnische Universität Dresden01062DresdenGermany
- Max Planck Institute for Chemical Physics of Solids01187DresdenGermany
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4
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Donor MT, Shepherd SO, Prell JS. Rapid Determination of Activation Energies for Gas-Phase Protein Unfolding and Dissociation in a Q-IM-ToF Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:602-610. [PMID: 32126776 PMCID: PMC8063716 DOI: 10.1021/jasms.9b00055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ion mobility-mass spectrometry has emerged as a powerful tool for interrogating a wide variety of chemical systems. Collision-induced unfolding (CIU), typically performed in time-of-flight instruments, has been utilized to obtain valuable qualitative insight into protein structure and illuminate subtle differences between related species. CIU experiments can be performed relatively quickly, but unfolding energy information obtained from them has not yet been interpreted quantitatively. While several methods can determine quantitative dissociation energetics for small molecules, clusters, and peptides, these methods have rarely been applied to proteins, and never to study unfolding. Here, we present a method to rapidly determine activation energies for protein unfolding and dissociation, built on a model for energy deposition during collisional activation. The method is validated by comparing activation energies for dissociation of three complexes with those obtained using blackbody infrared radiative dissociation (BIRD); values from the two methods are in agreement. Several protein monomers were unfolded using CIU, including multiple charge states of both cations and anions, and activation energies determined. ΔH⧧ and ΔS⧧ values are found to be correlated, leading to ΔG⧧ values that lie within a narrow range (∼70-80 kJ/mol) and vary more with charge state than with protein identity. ΔG⧧ is anticorrelated with charge density, highlighting the key role of Coulombic repulsion in gas-phase unfolding. Measured ΔG⧧ values are similar to those computed for proton transfer within small peptides, suggesting that proton transfer is the rate-limiting step in gas-phase unfolding and providing evidence of a link between the Mobile Proton model and CIU.
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Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
- Address reprint requests to James S. Prell, 1253 University of Oregon, Eugene, OR 97405, Tel: +1 (541) 346-2597,
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5
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Debiossac M, Schätti J, Kriegleder M, Geyer P, Shayeghi A, Mayor M, Arndt M, Köhler V. Tailored photocleavable peptides: fragmentation and neutralization pathways in high vacuum. Phys Chem Chem Phys 2018; 20:11412-11417. [PMID: 29645042 PMCID: PMC5932999 DOI: 10.1039/c8cp01058g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/23/2018] [Indexed: 01/31/2023]
Abstract
Photocleavable tags (PCTs) have the potential for excellent spatio-temporal control over the release of subunits of complex molecules. Here, we show that electrosprayed oligopeptides, functionalized by a tailored ortho-nitroarylether can undergo site-specific photo-activated cleavage under UV irradiation (266 nm) in high vacuum. The comparison of UV photodissociation (UVPD) and collision-induced dissociation (CID) points to the thermal nature of the cleavage mechanism, a picture corroborated by the temperature dependence of the process. Two competing photodissociation pathways can be identified. In one case a phenolate anion is separated from a neutral zwitterion. In the other case a neutral phenol derivative leaves a negatively charged peptide behind. To understand the factors favoring one channel over the other, we investigate the influence of the peptide length, the nature of the phenolic group and the position of the nitro-group (ortho vs. para). The observed gas phase cleavage of a para-nitro benzylic ether markedly differs from the established behavior in solution.
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Affiliation(s)
- M. Debiossac
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - J. Schätti
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
| | - M. Kriegleder
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - P. Geyer
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - A. Shayeghi
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - M. Mayor
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , D-76344 Eggenstein-Leopoldshafen , Germany
- Lehn Institute of Functional Materials (LIFM), Sun Yat-Sen University (SYSU) , Xingang Rd. W. , Guangzhou , China
| | - M. Arndt
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - V. Köhler
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
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6
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Amyes TL, Richard JP. Substituent Effects on Carbon Acidity in Aqueous Solution and at Enzyme Active Sites. Synlett 2017; 28:2407-2421. [PMID: 28993718 DOI: 10.1055/s-0036-1588778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Methods are described for the determination of pKas for weak carbon acids in water. The application of these methods to the determination of the pKas for a variety of carbon acids including nitriles, imidazolium cations, amino acids, peptides and their derivatives and, α-iminium cations is presented. The substituent effects on the acidity of these different classes of carbon acids are discussed; and, the relevance of these results to catalysis of the deprotonation of amino acids by enzymes and by pyridoxal 5'-phosphate is reviewed. The procedure for estimating the pKa of uridine 5'-phosphate for C-6 deprotonation at the active site of orotidine 5'-phosphate decarboxylase is described, and the effect of a 5-F substituent on carbon acidity of the enzyme-bound substrate is discussed.
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Affiliation(s)
- Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000
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7
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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8
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Svane S, Jørgensen TJD, McKenzie CJ, Kjeldsen F. Effect of Metals in Biomimetic Dimetal Complexes on Affinity and Gas-Phase Protection of Phosphate Esters. Anal Chem 2015; 87:7060-8. [DOI: 10.1021/acs.analchem.5b00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Svane
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Thomas J. D. Jørgensen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Christine J. McKenzie
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
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9
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Parry IS, Kartouzian A, Hamilton SM, Balaj OP, Beyer MK, Mackenzie SR. Chemical Reactivity on Gas-Phase Metal Clusters Driven by Blackbody Infrared Radiation. Angew Chem Int Ed Engl 2014; 54:1357-60. [DOI: 10.1002/anie.201409483] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/05/2014] [Indexed: 12/27/2022]
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10
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Parry IS, Kartouzian A, Hamilton SM, Balaj OP, Beyer MK, Mackenzie SR. Durch Schwarzkörperstrahlung angetriebene chemische Reaktivität auf Metallclustern in der Gasphase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Podjava A, Kistkin S, Ausekle E, Priede E, Mekss P, Zicmanis A. Electrospray ionization mass spectrometry of non-covalent complexes formed between N-alkylimidazolium-containing zwitterionic sulfonates and protonated bases. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:467-475. [PMID: 25905871 DOI: 10.1255/ejms.1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This paper describes non-covalent complexes between zwitterionic 3-(1-alkyl-3N-imidazolio)- propane-1-sulfonates and different amines. Electrospray ionization (ESI) mass spectrometry and collision- induced dissociation were used to measure the stability of such complexes in solution and in the gas phase. Generally, zwitterionic sulfonates formed more abundant complexes with protonated 5-methylcytosine (5-MCH) than with aliphatic amines. The results show that the association constants and half-dissociation threshold energies of these complexes nonlinearly depend on the alkyl chain length of the zwitterion. It is shown that the complexes with the lowest stability exist in acetonitrile solution or in the gas phase. The factors responsible for this complicated behavior are discussed. The structure of the complexes was investigated by quantum chemical calculations using molecular mechanics and density functional theory. Hydrogen bonding is proposed as the main type of interaction responsible for the stability of ion-zwitterion complexes. In summary, the information obtained in this study could be used for the development of the new derivatization reagents for some compounds containing amidinium groups, like 5-MCH, to increase selectivity of ESI-based methods.
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Affiliation(s)
- Anton Podjava
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | | | - Elina Ausekle
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | - Elina Priede
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | - Peteris Mekss
- Department of Chemistry, University of Latvia, Riga, Latvia.
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13
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Strittmatter EF, Wong RL, Williams ER. Effects of Gas-Phase Basicity on the Proton Transfer between Organic Bases and Trifluoroacetic Acid in the Gas Phase: Energetics of Charge Solvation and Salt Bridges. J Phys Chem A 2012; 104:10271-9. [PMID: 16554909 PMCID: PMC1409764 DOI: 10.1021/jp0012505] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The unimolecular dissociation pathways and kinetics of a series of protonated trimer ions consisting of two organic bases and trifluoroacetic acid were investigated using blackbody infrared radiative dissociation. Five bases with gas-phase basicities (GB) ranging from 238.4 to 246.2 kcal/mol were used. Both the dissociation pathways and the threshold dissociation energies depend on the GB of the base. Trimers consisting of the two most basic molecules dissociate to form protonated base monomers with an E(0) ~ 1.4 eV. Trimers consisting of the two least basic molecules dissociate to form protonated base dimers with an E(0) ~ 1.1-1.2 eV. These results indicate that the structures of the trimers change as a function of the GB of the basic molecule. The predominant structure of the protonated trimers consisting of the two most basic molecules is consistent with a salt bridge in which both of the basic molecules are protonated, and the trifluoroacetic acid molecule is deprotonated, whereas the predominant structure of the protonated trimers consisting of the two least basic molecules are consistent with charge-solvated complexes in which the proton is shared. The structure of the trimer consisting of the base of intermediate basicity is less clear; it dissociates to form primarily protonated base dimer, but has an E(0) ~ 1.2 eV. These results are consistent with the structure of this trimer as a salt bridge, but the resulting dissociation A(-). BH(+) product does not appear to be stable as an ion pair in the dissociative transition state.
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Affiliation(s)
- E F Strittmatter
- Department of Chemistry, University of California, Berkeley, California 94720-1460
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Yoo EJH, Feketeová L, Khairallah GN, O'Hair RAJ. Intercluster reactions show that (CH3)2S(+)CH2CO2H is a better methyl cation donor than (CH3)3N(+)CH2CO2H. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2011; 17:159-166. [PMID: 21719924 DOI: 10.1255/ejms.1115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The intrinsic methylating abilities of the known biological methylating zwitterionic agents, dimethylsulfonioacetate (DMSA), (CH(3))(2)S⁺CH(2)CO(2)(-) (1) and glycine betaine (GB), (CH(3))(3)N⁺CH(2)CO(2)(-) (2), have been examined via a range of gas phase experiments involving collision-induced dissociation (CID) of their proton-bound homo- and heterodimers, including those containing the amino acid arginine. The relative yields of the products of methyl cation transfer are consistent in all cases and show that protonated DMSA is a more potent methylating agent than protonated GB. Since methylation can occur at more than one site in arginine, the [M+CH(3)](+) ion of arginine, formed from the heterocluster [DMSA+Arg+H](+), was subject to an additional stage of CID. The resultant CID spectrum is virtually identical to that of an authentic sample of protonated arginine-O-methyl ester but is significantly different to that of an authentic sample of protonated N(G)-methyl arginine. This suggests that methylation has occurred within a salt bridge complex of [DMSA+Arg+H](+), in which the arginine exists in the zwitterionic form. Finally, density functional theory calculations on the model salts, (CH(3)CO(2)(-))[(CH(3))(3)S(+)] and (CH(3)CO(2)(-))[(CH(3))(4)N(+)], show that methylation of CH(3)CO(2)(-) by (CH(3))(3)S(+) is both kinetically and thermodynamically preferred over methylation by (CH(3))(4)N(+).
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15
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Yoo EJH, Feketeová L, Khairallah GN, White JM, O'Hair RAJ. Structure and unimolecular chemistry of protonated sulfur betaines, (CH3)2S+(CH2)nCO2H (n = 1 and 2). Org Biomol Chem 2011; 9:2751-9. [DOI: 10.1039/c0ob00770f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Go MK, Koudelka A, Amyes TL, Richard JP. Role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach. Biochemistry 2010; 49:5377-89. [PMID: 20481463 DOI: 10.1021/bi100538b] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report that the K12G mutation in triosephosphate isomerase (TIM) from Saccharomyces cerevisiae results in (1) a approximately 50-fold increase in K(m) for the substrate glyceraldehyde 3-phosphate (GAP) and a 60-fold increase in K(i) for competitive inhibition by the intermediate analogue 2-phosphoglycolate, resulting from the loss of stabilizing ground state interactions between the alkylammonium side chain of Lys-12 and the ligand phosphodianion group; (2) a 12000-fold decrease in k(cat) for isomerization of GAP, suggesting a tightening of interactions between the side chain of Lys-12 and the substrate on proceeding from the Michaelis complex to the transition state; and (3) a 6 x 10(5)-fold decrease in k(cat)/K(m), corresponding to a total 7.8 kcal/mol stabilization of the transition state by the cationic side chain of Lys-12. The yields of the four products of the K12G TIM-catalyzed isomerization of GAP in D(2)O were quantified as dihydroxyacetone phosphate (DHAP) (27%), [1(R)-(2)H]DHAP (23%), [2(R)-(2)H]GAP (31%), and methylglyoxal (18%) from an enzyme-catalyzed elimination reaction. The K12G mutation has only a small effect on the relative yields of the three products of the transfer of a proton to the TIM-bound enediol(ate) intermediate in D(2)O, but it strongly favors catalysis of the elimination reaction to give methylglyoxal. The K12G mutation also results in a >or=14-fold decrease in k(cat)/K(m) for isomerization of bound glycolaldehyde (GA), although the dominant observed product of the mutant enzyme-catalyzed reaction of [1-(13)C]GA in D(2)O is [1-(13)C,2,2-di-(2)H]GA from a nonspecific protein-catalyzed reaction. The observation that the K12G mutation results in a large decrease in k(cat)/K(m) for the reactions of both GAP and the neutral truncated substrate [1-(13)C]GA provides evidence for a stabilizing interaction between the cationic side chain of Lys-12 and the negative charge that develops at the enolate-like oxygen in the transition state for deprotonation of the sugar substrate "piece".
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Affiliation(s)
- Maybelle K Go
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, USA
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Beyer M, Williams ER, Bondybey VE. Unimolecular reactions of dihydrated alkaline earth metal dications M2+(H2O)2, M = Be, Mg, Ca, Sr, and Ba: salt-bridge mechanism in the proton-transfer reaction M2+(H2O)2 --> MOH+ + H3O. J Am Chem Soc 2009; 121:1565-73. [PMID: 16554906 PMCID: PMC1409760 DOI: 10.1021/ja982653+] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unimolecular reactivity of M(2+)(H(2)O)(2), M = Be, Mg, Ca, Sr, and Ba, is investigated by density functional theory. Dissociation of the complex occurs either by proton transfer to form singly charged metal hydroxide, MOH(+), and protonated water, H(3)O(+), or by loss of water to form M(2+)(H(2)O) and H(2)O. Charge transfer from water to the metal forming H(2)O(+) and M(+)(H(2)O) is not favorable for any of the metal complexes. The relative energetics of these processes are dominated by the metal dication size. Formation of MOH(+) proceeds first by one water ligand moving to the second solvation shell followed by proton transfer to this second-shell water molecule and subsequent Coulomb explosion. These hydroxide formation reactions are exothermic with activation energies that are comparable to the water binding energy for the larger metals. This results in a competition between proton transfer and loss of a water molecule. The arrangement with one water ligand in the second solvation shell is a local minimum on the potential energy surface for all metals except Be. The two transition states separating this intermediate from the reactant and the products are identified. The second transition state determines the height of the activation barrier and corresponds to a M(2+)-OH(-)-H(3)O(+) "salt-bridge" structure. The computed B3LYP energy of this structure can be quantitatively reproduced by a simple ionic model in which Lewis charges are localized on individual atoms. This salt-bridge arrangement lowers the activation energy of the proton-transfer reaction by providing a loophole on the potential energy surface for the escape of H(3)O(+). Similar salt-bridge mechanisms may be involved in a number of proton-transfer reactions in small solvated metal ion complexes, as well as in other ionic reactions.
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Affiliation(s)
- M Beyer
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85748 Garching, Germany
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18
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Wyer JA, Feketeová L, Brøndsted Nielsen S, O’Hair RAJ. Gas phase fragmentation of protonated betaine and its clusters. Phys Chem Chem Phys 2009; 11:8752-8. [DOI: 10.1039/b909653a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Wu R, McMahon TB. IRMPD spectra of Gly.NH4 + and proton-bound betaine dimer: evidence for the smallest gas phase zwitterionic structures. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1641-1648. [PMID: 18613000 DOI: 10.1002/jms.1449] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Zwitterionic structures exist extensively in biological systems and the electric field resulting from zwitterion formation is the driving force for determination of the properties, function and activity of biological molecules, such as amino acids, peptides and proteins. It is of considerable interest and import to investigate the stabilization of zwitterionic structures in the gas phase. Infrared multiple photon dissociation (IRMPD) spectroscopy is a very powerful and sensitive technique, which may elucidate clearly the structures of both ions and ionic clusters in the gas phase, since it provides IR vibrational fingerprint information. The structures of the clusters of glycine and ammonium ion and of the betaine proton-bound homodimer have been investigated using IRMPD spectroscopy, in combination with electronic structure calculations. The experimental and calculated results indicate that zwitterionic structure of glycine may be effectively stabilized by an ammonium ion. This is the smallest zwitterionic structure of an amino acid to be demonstrated in the gas phase. On the basis of the experimental IRMPD and calculated results, it is very clear that a zwitterionic structure exists in the proton-bound betaine dimer. The proton is bound to one of the carboxylate oxygens of betaine, rather than being equally shared. Investigations of zwitterionic structures in the isolated state are essential for an understanding of the intrinsic characteristics of zwitterions and salt bridge interactions in biological systems.
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Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1, Canada
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Wong FM, Capule CC, Chen DX, Gronert S, Wu W. Surprisingly Low Aqueous Acidity at the α-Positions of Pyridiniums and Pyrimidinium: The Role of Solvation. Org Lett 2008; 10:2757-60. [DOI: 10.1021/ol800892d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Freeman M. Wong
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Christina C. Capule
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - David X. Chen
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Scott Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Weiming Wu
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
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21
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Dega-Szafran Z, Katrusiak A, Szafran M. The O–H···O, O–H···N and C–H···O hydrogen bonds in 1,4-dimethylpiperazine mono-betaine monohydrate. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.10.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Strambini GB, Gonnelli M. Singular Efficacy of Trimethylamine N-Oxide to Counter Protein Destabilization in Ice. Biochemistry 2008; 47:3322-31. [DOI: 10.1021/bi702473g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Margherita Gonnelli
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 56124 Pisa, Italy
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23
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Crugeiras J, Rios A, Riveiros E, Amyes TL, Richard JP. Glycine enolates: the effect of formation of iminium ions to simple ketones on alpha-amino carbon acidity and a comparison with pyridoxal iminium ions. J Am Chem Soc 2008; 130:2041-50. [PMID: 18198876 DOI: 10.1021/ja078006c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Equilibrium constants in D2O were determined by 1H NMR analyses for formation of imines/iminium ions from addition of glycine methyl ester to acetone and from addition of glycine to phenylglyoxylate. First-order rate constants, also determined by 1H NMR, are reported for deuterium exchange between solvent D2O and the alpha-amino carbon of glycine methyl ester and glycine in the presence of increasing concentrations of ketone and Brønsted bases. These rate and equilibrium data were used to calculate second-order rate constants for deprotonation by DO- and by Brønsted bases of the alpha-imino carbon of the ketone adducts. Formation of the iminium ion between acetone and glycine methyl ester and between phenylglyoxylate and glycine is estimated to cause 7 unit and 15 unit decreases, respectively, in the pKa's of 21 and 29 for deprotonation of the parent carbon acids. The effect of formation of iminium ions to phenylglyoxylate and to 5'-deoxypyridoxal (DPL) [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] on the carbon acidity of glycine is similar. However, DPL is a much better catalyst than phenylglyoxylate of deprotonation of glycine, because of the exceptionally large thermodynamic driving force for conversion of the amino acid and DPL to the reactive iminium ion.
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Affiliation(s)
- Juan Crugeiras
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782 Santiago de Compostela, Spain
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24
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Feketeová L, Khairallah GN, O'Hair RAJ. Letter: intercluster chemistry of protonated and sodiated betaine dimers upon collision induced dissociation and electron induced dissociation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2008; 14:107-110. [PMID: 18493100 DOI: 10.1255/ejms.911] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The collision induced dissociation and electron induced dissociation spectra of the [2M + H](+) and [2M + Na](+) clusters of the zwitterionic amino acid, betaine (M), have been examined in a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer. Intercluster reactions are observed in the collision induced dissociation spectra of [2M + H](+) and [2M + Na](+) and in the electron induced dissociation spectrum of [2M + H](+).
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25
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Raczyńska ED, Gal JF, Maria PC, Zientara K, Szelag M. Application of FT-ICR-MS for the study of proton-transfer reactions involving biomolecules. Anal Bioanal Chem 2007; 389:1365-80. [PMID: 17786415 DOI: 10.1007/s00216-007-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/06/2007] [Accepted: 07/12/2007] [Indexed: 10/22/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry, combined with modern ionization (fast atom bombardment , electrospray ionization, matrix-assisted laser desorption-ionization), fragmentation (collision-induced dissociation, surface-induced dissociation, one-photon ultraviolet photodissociation, infrared multiphoton dissociation, blackbody infrared radiative dissociation, electron-capture dissociation), and separation (high-performance liquid chromatography, liquid chromatography, capillary electrophoresis) techniques is now becoming one of the most attractive and frequently used instrumental platforms for gas-phase studies of biomolecules such as amino acids, bioamines, peptides, polypeptides, proteins, nucleobases, nucleosides, nucleotides, polynucleotides, nucleic acids, saccharides, polysaccharides, etc. Since it gives the possibilities to trap the ions from a few seconds up to thousands of seconds, it is often applied to study ion/molecule reactions in the gas phase, particularly proton-transfer reactions which provide important information on acid-base properties. These properties determine in part the three-dimensional structure of biomolecules, most of their intramolecular and intermolecular interactions, and consequently their biological activity. They also indicate the form (unionized, zwitterionic, protonated, or deprotonated) which the biomolecule may take in a nonpolar environment.
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Affiliation(s)
- E D Raczyńska
- Department of Chemistry, Warsaw University of Agriculture (SGGW), 02-726 Warsaw, Poland.
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26
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Kjeldsen F, Silivra OA, Zubarev RA. Zwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet Photodissociation. Chemistry 2006; 12:7920-8. [PMID: 16871505 DOI: 10.1002/chem.200600248] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new method of detecting the presence of deprotonation and determining its position in gas-phase polypeptide cations is described. The method involves 157-nm ultra-violet photodissociation (UVPD) and is based on monitoring the losses of CO2 (44 Da) from electronically excited deprotonated carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+)...(-)...(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding within polypeptide clusters. Collision-activated dissociation (CAD) of decarboxylated cations localizes the position of deprotonation. Fragment abundances can be used for the semiquantitative assessment of the branching ratio of deprotonation among different acidic sites, however, the mechanism of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm UVPD produces abundant radical cations M*+ from protonated molecules through the loss of a hydrogen atom. This method of producing M*+ ions is general and can be applied to any gas-phase peptide cation. The abundance of the molecular radical cations M*+ produced is sufficient for further tandem mass spectrometry (MS/MS), which, in the cases studied, yielded side-chain loss of a basic amino acid as the most abundant fragmentation channel together with some backbone cleavages.
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Affiliation(s)
- Frank Kjeldsen
- Biomedical Center Laboratory for Biological and Medical Mass Spectrometry Box 583, Uppsala University, 75123 Uppsala, Sweden.
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27
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Herrmann KA, Kuppannan K, Wysocki VH. Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD(3)OD. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2006; 249-250:93-105. [PMID: 18802500 PMCID: PMC2542902 DOI: 10.1016/j.ijms.2005.12.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Doubly-protonated bradykinin (RPPGFSPFR) and an angiotensin III analogue (RVYIFPF) were subjected to hydrogen/deuterium (H/D) exchange with CD(3)OD in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. A bimodal distribution of deuterium incorporation was present for bradykinin after H/D exchange for 90 s at a CD(3)OD pressure of 4 x 10(-7) Torr, indicating the existence of at least two distinct populations. Bradykinin ion populations corresponding to 0-2 and 5-11 deuteriums (i.e., D(0), D(1), D(2), D(5), D(6), D(7), D(8), D(9), D(10), and D(11)) were each monoisotopically selected and fragmented via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID). The D(0)-D(2) ion populations, which correspond to the slower exchanging population, consistently require lower SORI amplitude to achieve a similar precursor ion survival yield as the faster-reacting (D(5)-D(11)) populations. These results demonstrate that conformation/protonation motif has an effect on fragmentation efficiency for bradykinin. Also, the partitioning of the deuterium atoms into fragment ions suggests that the C-terminal arginine residue exchanges more rapidly than the N-terminal arginine. Total deuterium incorporation in the b(1)/y(8) and b(2)/y(7) ion pairs matches very closely the theoretical values for all ion populations studied, indicating that the ions of a complementary pair are likely formed during the same fragmentation event, or that no scrambling occurs upon SORI. Deuterium incorporation into the y(1)/a(8) pseudo-ion pair does not closely match the expected theoretical values. The other peptide, doubly-protonated RVYIFPF, has a trimodal distribution of deuterium incorporation upon H/D exchange with CD(3)OD at a pressure of 1 x 10(-7) Torr for 600 s, indicating at least three distinct ion populations. After 90 s of H/D exchange where at least two distinct populations are detected, the D(0)-D(7) ion populations were monoisotopically selected and fragmented via SORI-CID over a range of SORI amplitudes. The precursor ion survival yield as a function of SORI amplitude falls into two distinct behaviors corresponding to slower- and faster-reacting ion populations. The slower-reacting population requires larger SORI amplitudes to achieve the same precursor ion survival yield as the faster exchanging population. Total deuterium incorporation into the y(2)/b(5) ion pairs matches closely the theoretical values over all ion populations and SORI amplitudes studied. This result indicates the y(2) and b(5) ions are likely formed by the same mechanism over the SORI amplitudes studied.
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Affiliation(s)
| | | | - Vicki H. Wysocki
- University of Arizona, Department of Chemistry, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
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28
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Wong RL, Williams ER, Counterman AE, Clemmer DE. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1009-19. [PMID: 15914022 DOI: 10.1016/j.jasms.2005.03.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 03/21/2005] [Accepted: 03/24/2005] [Indexed: 05/02/2023]
Abstract
The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.
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Affiliation(s)
- Richard L Wong
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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29
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Richard JP, Amyes TL. On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon. Bioorg Chem 2005; 32:354-66. [PMID: 15381401 DOI: 10.1016/j.bioorg.2004.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Indexed: 11/19/2022]
Abstract
Carbanion ylides are strongly stabilized by electrostatic interactions between opposing charges at neighboring atoms and this stabilizing electrostatic interaction increases with decreasing dielectric constant of the medium through which the charges interact. Consequently, there is a large increase in the thermodynamic driving force, with decreasing dielectric constant of the reaction medium, for deprotonation of cationic carbon acids and decarboxylation to form related ylides. This favors catalysis of the formation of unstable ylides at enzyme active sites of low dielectric constant. A brief survey of enzymes that catalyze deprotonation of cationic carbon acids and related decarboxylation reactions shows catalysis generally occurs for substrates that are bound in a deep pocket on the protein, with an apparent dielectric constant that is much lower than for the solvent water. In several cases, proton transfer is to a catalytic residue that is relatively weakly solvated in water. We suggest that there is a strong advantage for evolution of protein catalysts that utilize weakly solvated basic side chains which are relatively easily buried in nonpolar active sites that are favorable for zwitterion formation.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
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30
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Affiliation(s)
- Michael Meot-Ner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA.
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31
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Dunbar RC. BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications. MASS SPECTROMETRY REVIEWS 2004; 23:127-158. [PMID: 14732935 DOI: 10.1002/mas.10074] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Blackbody infrared radiative dissociation (BIRD) describes the observation of ion-dissociation reactions at essentially zero pressure by the ambient blackbody radiation field, which is usually studied in the ion-trapping ion cyclotron resonance (ICR) mass spectrometer. A brief summary of the historical context and evolution is provided. Focussing on the quantitative observation of the temperature dependence of BIRD rates, methods are developed for connecting BIRD observations with activation parameters and dissociation thermochemistry. Three regimes are differentiated and described, comprising large molecules, small molecules, and intermediate-sized molecules. The different approaches to interpreting BIRD kinetics in those three regimes are discussed. In less than a decade since its inception, this approach to studying gas-phase ions has spread over a wide variety of applications, which are surveyed. Some major areas of activity are: the characterization of solvent-molecule detachment from solvated ions; dissociation reactions of biomolecules (polypeptides, oligonucleotides, complexes involving polysaccharides) and the structural information to be deduced from them; and dissociations of proton-bound and metal-ion-containing complexes. Studies of blackbody-radiation-driven evaporation of water molecules from large water-cluster ions are surveyed briefly. Several techniques related to BIRD are noted, including collisional dissociation in the FT-ICR ion trap; high-pressure thermal dissociation in quadrupole ion traps and in heated inlet capillary regions; hot-filament-assisted dissociation; and infrared multiphoton dissociation (IRMPD).
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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32
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Schäfer M, Schmuck C, Heil M, Cooper HJ, Hendrickson CL, Chalmers MJ, Marshall AG. Determination of the activation energy for unimolecular dissociation of a non-covalent gas-phase peptide: substrate complex by infrared multiphoton dissociation fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1282-1289. [PMID: 14597118 DOI: 10.1016/s1044-0305(03)00576-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The activation energy for the unimolecular dissociation of a non-covalent supramolecular complex between an Artificial Cationic Receptor A ([Gua-Val-Val-Val-Amide]+, in which Gua is guanidiniocarbonyl pyrrole) and an Anionic Tetrapeptide B ([N-Acetyl-Val-Val-Ile-Ala]-) has been determined by measurement of the dissociation rate constant as a function of infrared CO2 laser power density. Singly-charged quasimolecular [A + B + H]+ ions are isolated, stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and irradiated by IR photons. The rate constant for dissociation of the non-covalent complex is determined at five different laser power densities. A plot of the natural logarithm of the first-order rate constant versus the natural logarithm of the laser power density yields a straight line, the slope of which provides an approximate measure of the activation energy (Ea(laser)) for dissociation. Ea(laser) is calculated by a relationship derived earlier by Dunbar and with a newly proposed equation by Paech et al. The results of the two approaches deliver significantly different activation energy values for the unimolecular dissociation of the non-covalent complex. We obtain EaI(laser) = 0.67 eV (Dunbar approximation) and EaII(laser) = 1.12 eV (Paech et al. approximation). Differences between the two approaches are discussed with respect to non-covalent complexes.
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Affiliation(s)
- Mathias Schäfer
- Institute for Organic Chemistry, University Cologne, Köln, Germany.
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33
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Armentrout PB. Threshold Collision-Induced Dissociations for the Determination of Accurate Gas-Phase Binding Energies and Reaction Barriers. Top Curr Chem (Cham) 2003. [DOI: 10.1007/3-540-36113-8_7] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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34
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Dega-Szafran Z, Katrusiak A, Szafran M. The influence of charges and hydrogen bond on the conformation of zwitterionic 3-(2-hydroxyalkyl-pyridinium)-propionates and their hydrobromides. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(02)00044-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Abstract
The viability of living systems requires that C--H bonds of biological molecules be stable in water, but that there also be a mechanism for shortening the timescale for their heterolytic cleavage through enzymatic catalysis of a variety of catabolic and metabolic reactions. An understanding of the mechanism of enzymatic catalysis of proton transfer at carbon requires the integration of results of studies to determine the structure of the enzyme-substrate complex with model studies on the mechanism for the non-enzymatic reaction in water, and the effect of the local protein environment on the stability of the transition state for this reaction. A common theme is the importance of electrostatic interactions in providing stabilization of bound carbanion intermediates of enzyme-catalyzed proton-transfer reactions.
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Affiliation(s)
- J P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
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36
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Gronert S, Huang R. A strong preference for a salt-bridge structure in the gas phase: reactions of deprotonated amino acids with borane. J Am Chem Soc 2001; 123:8606-7. [PMID: 11525673 DOI: 10.1021/ja010966q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- S Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
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37
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Gal JF, Maria PC, Raczyńska ED. Thermochemical aspects of proton transfer in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:699-716. [PMID: 11473393 DOI: 10.1002/jms.202] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The beginning of the twentieth century saw the development of new theories of acidity and basicity, which are currently well accepted. The thermochemistry of proton transfer in the absence of solvent attracted much interest during this period, because of the fundamental importance of the process. Nevertheless, before the 1950s, few data were available, either from lattice energy evaluations or from calculations using the emerging molecular orbital theory. Advances in mass spectrometry during the last 40 years allowed studies of numerous systems with better accuracy. Thousands of accurate gas-phase acidities or basicities are now available, for simple atomic and molecular systems and for large biomolecules. The intrinsic effect of structure on the Brønsted basic or acidic properties of molecules and the influence of solvents have been unravelled. In this tutorial, the basics of the thermodynamic principles involved are given, and the mass spectrometric techniques are briefly reviewed. Advances in the design and measurements of gas-phase superacids and superbases are described. Recent studies concerning biomolecules are also evoked.
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Affiliation(s)
- J F Gal
- Chimie des Matériaux Organiques et Métalliques, Université de Nice--Sophia Antipolis, 06108 Nice Cedex 2, France.
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38
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Rak J, Skurski P, Gutowski M. Anab initiostudy of the betaine anion–dipole-bound anionic state of a model zwitterion system. J Chem Phys 2001. [DOI: 10.1063/1.1373689] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Desfrançois C, Carles S, Schermann JP. Weakly bound clusters of biological interest. Chem Rev 2000; 100:3943-62. [PMID: 11749335 DOI: 10.1021/cr990061j] [Citation(s) in RCA: 202] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C Desfrançois
- Laboratoire de Physique des Lasers, Université Paris Nord, Villetaneuse, 93430, France
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Rodgers MT, Armentrout PB. Noncovalent metal-ligand bond energies as studied by threshold collision-induced dissociation. MASS SPECTROMETRY REVIEWS 2000; 19:215-247. [PMID: 10986693 DOI: 10.1002/1098-2787(200007)19:4<215::aid-mas2>3.0.co;2-x] [Citation(s) in RCA: 245] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This review focuses on noncovalent metal ion-ligand complexes and measurements of the bond energies of such species. The method utilized in this work is threshold collision-induced dissociation (CID), as achieved using a guided ion beam tandem mass spectrometer. Accurate determination of bond energies requires attention to many details of the experiments and data analysis. These details are discussed thoroughly and compared to other methods. A comprehensive listing of metal-ligand bond dissociation energies determined by threshold CID is provided. This list includes a variety of metals (alkalis, magnesium, aluminum, and first and second row transition metals), many different types of ligands, and variations in the number of ligands. The trends in these values are discussed, and we elucidate the importance of ion-dipole and ion-induced dipole interactions, chelation, different conformers and tautomers, steric interactions, solvation phenomena, and electronic effects such as hybridization and promotion.
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Affiliation(s)
- MT Rodgers
- Chemistry Department, Wayne State University, Detroit, MI, USA
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Zhu C, Lifshitz C. The protonated betaine/ammonia complex: how stable is the gas-phase zwitterion structure? Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00285-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Strittmatter EF, Wong RL, Williams ER. Gas-phase basicity of (CH3)3N+-C6H4-COO- zwitterions: a new class of organic super bases. J Am Chem Soc 2000; 122:1247-8. [PMID: 16554907 PMCID: PMC1409761 DOI: 10.1021/ja9934495] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E F Strittmatter
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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Schaaff TG, Stephenson JL, McLuckey SA. Gas phase H/D exchange kinetics: DI versus D2O. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:167-171. [PMID: 10689670 DOI: 10.1016/s1044-0305(99)00137-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The gas phase H/D exchange reactions of bradykinin (M + 3H)3+ ions with D2O and DI were monitored in a quadrupole ion trap mass spectrometer. The H/D exchange kinetics of both chemical probes (D2O and DI) indicate the presence of two noninterconverting reactive gas phase ion populations of bradykinin (M + 3H)3+ at room temperature. The H/D exchange involving DI, however, generally proceeds faster than that involving D2O. The rate observations described here can be rationalized on the basis of the "relay mechanism" (see Campbell et al. J. Am. Chem. Soc. 1995, 117, 12840-12854) recently proposed to account for H/D exchange between D2O and gaseous protonated polypeptides. The higher exchange rate with DI is believed to arise primarily as a result of its lower gas-phase acidity relative to that of D2O and, secondarily, as a result of the longer bond length of DI relative to that of OD in D2O.
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Affiliation(s)
- T G Schaaff
- Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Tennessee 37831-6365, USA
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Schaaff TG, Stephenson JL, McLuckey SA. The Reactivity of Gaseous Ions of Bradykinin and Its Analogues with Hydro- and Deuteroiodic Acid. J Am Chem Soc 1999. [DOI: 10.1021/ja991553g] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Gregory Schaaff
- Contribution from the Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6365
| | - James L. Stephenson
- Contribution from the Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6365
| | - Scott A. McLuckey
- Contribution from the Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6365
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Abstract
Approaches for analyzing kinetic and thermochemical data from the reactions of multiply charged ions are presented. A method for estimating the electrostatic repulsion in a multiply charged ion is described followed by examples of the potential energy surfaces for two representative reactions of multiply charged ions, proton transfer and nucleophilic substitution (S(N)2). The effect of electrostatic repulsion on reaction barriers is discussed and approaches for extracting thermochemical data from kinetic results are described. For reactions with small intrinsic barriers (i.e. proton transfer), considerable internal electrostatic repulsion is released at the transition state and multiply charged ions exhibit much greater reactivity than singly charged analogs. In contrast, relatively little electrostatic repulsion is released at the transition states of reactions with large intrinsic barriers (i.e. S(N)2) and multiply charged ions with moderate charge separations (>10 A) can exhibit reactivity that is very similar to that of singly charged analogs.
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Affiliation(s)
- S Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA.
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Conformational analysis of N-methylpiperidine betaine studied by X-ray diffraction, FTIR spectroscopy and ab initio calculations. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00662-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Freitas MA, Hendrickson CL, Marshall AG. Gas phase activation energy for unimolecular dissociation of biomolecular ions determined by focused RAdiation for gaseous multiphoton ENergy transfer (FRAGMENT). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:1639-1642. [PMID: 10421907 DOI: 10.1002/(sici)1097-0231(19990815)13:15<1639::aid-rcm691>3.0.co;2-s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a novel approach for the determination of activation energy for the unimolecular dissociation of a large (>50 atoms) ion, based on measurement of the unimolecular dissociation rate constant as a function of continuous-wave CO(2) laser intensity. Following a short ( approximately 1 s) induction period, CO(2) laser irradiation produces an essentially blackbody internal energy distribution, whose 'temperature' varies inversely with laser intensity. The only currently available method for measuring such activation energies is blackbody infrared radiative dissociation (BIRD). Compared with BIRD, FRAGMENT: (a) eliminates the need to heat the surrounding ion trap and vacuum chamber to each of several temperatures (each requiring hours for temperature equilibration); (b) offers a three-fold wider range of effective blackbody temperature; and (c) extends the range of applications to include initially cold ions (e.g., gas-phase H/D exchange). Our FRAGMENT-determined activation energy for dissociation of protonated bradykinin, 1.2 +/- 0.1 eV, agrees within experimental error to the value, 1.3 +/- 0.1 eV, previously reported by Williams et al. from BIRD experiments. Copyright 1999 John Wiley & Sons, Ltd.
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Affiliation(s)
- MA Freitas
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310, USA
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Olumee Z, Vertes A. Protonation of Glyn Homologues in Matrix-Assisted Laser Desorption Ionization. J Phys Chem B 1998. [DOI: 10.1021/jp981123x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zohra Olumee
- Department of Chemistry, The George Washington University, Washington, D.C. 20052
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, D.C. 20052
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