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Modesto-Costa L, Martinez ST, Pinto AC, Vessecchi R, Borges I. Elucidating the mass spectrum of the retronecine alkaloid using DFT calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:934-941. [PMID: 29935494 DOI: 10.1002/jms.4253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/18/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Pyrrolizidine alkaloids are natural molecules playing important roles in different biochemical processes in nature and in humans. In this work, the electron ionization mass spectrum of retronecine, an alkaloid molecule found in plants, was investigated computationally. Its mass spectrum can be characterized by three main fragment ions having the following m/z ratios: 111, 94, and 80. In order to rationalize the mass spectrum, minima and transition state geometries were computed using density functional theory. It was showed that the dissociation process includes an aromatization of the originally five-membered ring of retronecine converted into a six-membered ring compound. A fragmentation pathway mechanism involving dissociation activation barriers that are easily overcome by the initial ionization energy was found. From the computed quantum chemical geometric, atomic charges, and energetic parameters, the abundance of each ion in the mass spectrum of retronecine was discussed.
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Affiliation(s)
- Lucas Modesto-Costa
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, 22290-270, Rio de Janeiro, Brazil
| | - Sabrina T Martinez
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, 22290-270, Rio de Janeiro, Brazil
- Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, Bloco A-7° andar, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Angelo C Pinto
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, 22290-270, Rio de Janeiro, Brazil
- Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, Bloco A-7° andar, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Ricardo Vessecchi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14040-901, Brazil
| | - Itamar Borges
- Departamento de Química, Instituto Militar de Engenharia, Praça General Tibúrcio, 80, 22290-270, Rio de Janeiro, Brazil
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Perraud V, Bruns EA, Ezell MJ, Johnson SN, Greaves J, Finlayson-Pitts BJ. Identification of organic nitrates in the NO3 radical initiated oxidation of alpha-pinene by atmospheric pressure chemical ionization mass spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:5887-5893. [PMID: 20608721 DOI: 10.1021/es1005658] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The gas-phase reactions of nitrate radicals (NO3) with biogenic organic compounds are a major sink for these organics during night-time. These reactions form secondary organic aerosols, including organic nitrates that can undergo long-range transport, releasing NOx downwind. We report here studies of the reaction of NO3 with alpha-pinene at 1 atm in dry synthetic air (relative humidity approximately 3%) and at 298 K using atmospheric pressure chemical ionization triple quadrupole mass spectrometry (APCI-MS) to identify gaseous and particulate products. The emphasis is on the identification of individual organic nitrates in the particle phase that were obtained by passing the product mixture through a denuder to remove gas-phase reactants and products prior to entering the source region of the mass spectrometer. Filter extracts were also analyzed by GC-MS and by APCI time-of-flight mass spectrometry (APCI-ToF-MS) with methanol as the proton source. In addition to pinonaldehyde and pinonic acid, five organic nitrates were identified in the particles as well as in the gas phase: 3-oxopinane-2-nitrate, 2-hydroxypinane-3-nitrate, pinonaldehyde-PAN, norpinonaldehyde-PAN, and (3-acetyl-2,2-dimethyl-3-nitrooxycyclobutyl)acetaldehyde. Furthermore, there was an additional first-generation organic nitrate product tentatively identified as a carbonyl hydroxynitrate with a molecular mass of 229. These studies suggest that a variety of organic nitrates would partition between the gas phase and particles in the atmosphere, and serve as a reservoir for NOx.
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Affiliation(s)
- Véronique Perraud
- Department of Chemistry, University of California Irvine, California 92697-2025, USA
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Hastie DR, Gray J, Langford VS, Maclagan RGAR, Milligan DB, McEwan MJ. Real-time measurement of peroxyacetyl nitrate using selected ion flow tube mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:343-348. [PMID: 20049885 DOI: 10.1002/rcm.4400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The on-line detection of gaseous peroxyacetyl nitrate (PAN) using selected ion flow tube mass spectrometry (SIFT-MS) has been investigated using a synthetic sample of PAN in air at a humidity of approximately 30%. Using the H(3)O(+) reagent ion, signals due to PAN at m/z 122, 77 and 95 have been identified. These correspond to protonated PAN, protonated peractetic acid and its water cluster, respectively. These products and their energetics have been probed through quantum mechanical calculations. The rate coefficient of H(3)O(+) has been estimated to be 4.5 x 10(-9) cm(3) s(-1), leading to a PAN sensitivity of 138 cps/ppbv. This gives a limit of detection of 20 pptv in 10 s using the [M+H](+) ion of PAN at m/z 122.
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Affiliation(s)
- Donald R Hastie
- University of Canterbury, Department of Chemistry, PB 4800, Christchurch 8140, New Zealand.
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Sun M, Moon JH, Kim MS. Improved Whitten−Rabinovitch Approximation for the Rice−Ramsperger−Kassel−Marcus Calculation of Unimolecular Reaction Rate Constants for Proteins. J Phys Chem B 2007; 111:2747-51. [PMID: 17300190 DOI: 10.1021/jp066453t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Whitten-Rabinovitch (WR) approximation used in the semi-classical calculation of the Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular reaction rate constant was improved for reliable application to protein reactions. The state sum data for the 10-mer of each amino acid calculated by the accurate Beyer-Swinehart (BS) algorithm were used to obtain the residue-specific correction functions (w). The correction functions were obtained down to a much lower internal energy range than reported in the original work, and the cubic, rather than quadratic, polynomial was used for data fitting. For a specified sequence of amino acid residues in a protein, an average was made over these functions to obtain the sequence-specific correction function to be used in the rate constant calculation. Reliability of the improved method was tested for dissociation of various peptides and proteins. Even at low internal energies corresponding to the RRKM rate constant as small as 0.1 s-1, the rate constant calculated by the present method differed from the accurate BS result by 60% only. In contrast, the result from the original WR calculation differed from the accurate result by a factor of 3000. Compared to the BS method, which is difficult to use for proteins, the main advantage of the present method is that the RRKM rate constant can be calculated instantly regardless of the protein mass.
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Affiliation(s)
- Meiling Sun
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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Turecek F. N[bond]C(alpha) bond dissociation energies and kinetics in amide and peptide radicals. Is the dissociation a non-ergodic process? J Am Chem Soc 2003; 125:5954-63. [PMID: 12733936 DOI: 10.1021/ja021323t] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dissociations of aminoketyl radicals and cation radicals derived from beta-alanine N-methylamide, N-acetyl-1,2-diaminoethane, N(alpha)-acetyl lysine amide, and N(alpha)-glycyl glycine amide are investigated by combined density functional theory and Møller-Plesset perturbational calculations with the goal of elucidating the mechanism of electron capture dissociation (ECD) of larger peptide and protein ions. The activation energies for dissociations of N[bond]C bonds in aminoketyl radicals decrease in the series N[bond]CH(3) > N-CH(2)CH(2)NH(2) >> N[bond]CH(2)CONH(2) approximately N[bond]CH(CONH(2))(CH(2))(4)NH(2). Transition state theory rate constants for dissociations of N[bond]C(alpha) bonds in aminoketyl radicals and cation-radicals indicate an extremely facile reaction that occurs with unimolecular rate constants >10(5) s(-1) in species thermalized at 298 K in the gas phase. In neutral aminoketyl radicals the N[bond]C(alpha) bond cleavage results in fast dissociation. In contrast, N[bond]C(alpha) bond cleavage in aminoketyl cation-radicals results in isomerization to ion-molecule complexes that are held together by strong hydrogen bonds. The facile N[bond]C(alpha) bond dissociation in thermalized ions indicates that it is unnecessary to invoke the hypothesis of non-ergodic behavior for ECD intermediates.
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Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, USA.
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Turecek F, Syrstad EA. Mechanism and energetics of intramolecular hydrogen transfer in amide and peptide radicals and cation-radicals. J Am Chem Soc 2003; 125:3353-69. [PMID: 12630891 DOI: 10.1021/ja021162t] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations. Hypervalent ammonium radicals produced by electron capture in protonated peptides undergo competitive elimination of ammonia, H-atom loss, and H-atom migration to neighboring amide carbonyls. The calculated transition state energies for H-atom migration are slightly but uniformly lower than those for H-atom loss. Transition state theory calculations with inclusion of quantum tunneling effects predict k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration. Intramolecular hydrogen-atom migration in amide and peptide radicals can be described by the proton-coupled electron transfer mechanism. The migrating hydrogen atom shows a negligible spin density and substantial positive charge that are typical of a proton migration. Electron transfer occurs through a pi-orbital system and proceeds in the same (clockwise) or opposite (counterclockwise) direction as the proton motion, depending on the electronic properties of the chain connecting the ammonium group and the amide bond.
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Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
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Kuntz AF, Boynton AW, David GA, Colyer KE, Poutsma JC. The proton affinity of proline analogs using the kinetic method with full entropy analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:72-81. [PMID: 11777201 DOI: 10.1016/s1044-0305(01)00329-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The proton affinity of proline analogs, L-azetidine-2-carboxylic acid (Aze), L-proline (Pro), and L-pipecolic acid (Pip), have been measured using the Armentrout modification of the extended kinetic method in a quadrupole ion trap instrument. Experimental values of 223.0 +/- 1.5, 224.9 +/- 1.6, and 225.6 +/- 1.6 kcal/mol have been determined for the 298K proton affinities of Aze, Pro, and Pip respectively. High level theoretical calculations using both MP2 and B3LYP methods at a variety of basis sets were carried out in order to give theoretical predictions for the 298 K proton affinity and gas phase basicity of all three analogs. Recommended values for the gas phase basicity and proton affinity for proline based on our work and other recent determinations are 216 +/- 2 and 224 +/- 2 kcal/mol.
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Affiliation(s)
- Andrew F Kuntz
- Department of Chemistry, The College of William and Mary, Williamsburg, Virginia 23187-8795, USA
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:107-118. [PMID: 11180652 DOI: 10.1002/1096-9888(200101)36:1<107::aid-jms88>3.0.co;2-q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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