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Lee J, Tantillo DJ, Wang LP, Fiehn O. Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling. J Chem Inf Model 2024; 64:7457-7469. [PMID: 39329341 PMCID: PMC11492807 DOI: 10.1021/acs.jcim.4c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.
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Affiliation(s)
- Jesi Lee
- Department of Chemistry, University of California, Davis, California 95616, United States
- West Coast Metabolomics Center, University of California, Davis, California 95616, United States
| | - Dean Joseph Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, California 95616, United States
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2
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Armentrout PB. Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation. Phys Chem Chem Phys 2024. [PMID: 39042103 DOI: 10.1039/d4cp00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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3
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Hartmann JC, Madlener SJ, van der Linde C, Ončák M, Beyer MK. Magic cluster sizes of cationic and anionic sodium chloride clusters explained by statistical modeling of the complete phase space. Phys Chem Chem Phys 2024; 26:10904-10918. [PMID: 38525830 PMCID: PMC10989714 DOI: 10.1039/d4cp00357h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
As one of the main components of sea salt aerosols, sodium chloride is involved in numerous atmospheric processes. Gas-phase clusters are ideal models to study fundamental physical and chemical properties of sodium chloride, which are significantly affected by the cluster size. Of particular interest are magic cluster sizes, which exhibit high intensities in mass spectra. In order to understand the origin of these magic cluster sizes, quantum chemical calculations at the CCSD(T)//DFT level are performed, yielding structures and binding energies of neutral (NaCl)x, anionic (NaCl)xCl- and cationic (NaCl)xNa+ clusters up to x = 8. Our calculations show that the clusters can easily isomerize, enabling dissociation into the lowest-energy isomers of the fragments. Energetics can explain the special stability of (NaCl)4Cl-, but (NaCl)4Na+ actually offers low-lying dissociation channels, despite being a magic cluster size. Collision-induced dissociation experiments reveal that the loss of neutral clusters (NaCl)x, x = 2, 4, is in most cases more favorable than the loss of NaCl or the atomic ion, i.e. sodium chloride clusters actually fragment via the cleavage of the entire cluster, not by evaporating small cluster building blocks. This is rationalized by the calculated high stability of even-numbered neutral clusters (NaCl)x, especially x = 2, 4. Analysis of the density of states and rate constants calculated with a modified Rice-Ramsperger-Kassel-Marcus (RRKM) equation called AWATAR - considering all energetically accessible isomers of reactants and fragments - shows that entropic effects are responsible for the magic cluster character of (NaCl)4Na+. In particular, low-lying vibrational modes provide a high density of states of the near-planar cluster. Together with the small contribution of an atomic ion to the sum of states in a loose transition state for dissociation, this leads to a very small unimolecular rate constant for dissociation into (NaCl)4 and Na+, which is the lowest energy fragmentation pathway. Thus, entropic effects may override energetics for certain magic cluster sizes.
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Affiliation(s)
- Jessica C Hartmann
- Universität Innsbruck, Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria.
| | - Sarah J Madlener
- Universität Innsbruck, Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria.
| | - Christian van der Linde
- Universität Innsbruck, Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria.
| | - Milan Ončák
- Universität Innsbruck, Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria.
| | - Martin K Beyer
- Universität Innsbruck, Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria.
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4
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Szabó D, Gömöry Á, Ludányi K, Vékey K, Drahos L. Very Low-Pressure CID Experiments: High Energy Transfer and Fragmentation Pattern at the Single Collision Regime. Molecules 2023; 29:211. [PMID: 38202794 PMCID: PMC10780993 DOI: 10.3390/molecules29010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
We have performed CID experiments on a triple quadrupole instrument, lowering the collision gas pressure by 50 times compared to its conventional value. The results show that at very low-collision gas pressure, single collisions dominate the spectra. Indirectly, these results suggest that under conventional conditions, 20-50 collisions may be typical in CID experiments. The results show a marked difference between low- and high-pressure CID spectra, the latter being characterized in terms of 'slow heating' and predominance of consecutive reactions. The results indicate that under single collision conditions, the collisional energy transfer efficiency is very high: nearly 100% of the center of mass kinetic energy is converted to internal energy.
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Affiliation(s)
- Dániel Szabó
- MS Proteomics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary (Á.G.); (K.V.)
| | - Ágnes Gömöry
- MS Proteomics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary (Á.G.); (K.V.)
| | - Krisztina Ludányi
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre 7–9, H-1092 Budapest, Hungary;
| | - Károly Vékey
- MS Proteomics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary (Á.G.); (K.V.)
| | - László Drahos
- MS Proteomics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary (Á.G.); (K.V.)
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5
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Zamith S, Kassem A, L'Hermite JM, Joblin C, Cuny J. Threshold collision induced dissociation of protonated water clusters. J Chem Phys 2023; 159:184302. [PMID: 37955320 DOI: 10.1063/5.0167551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
We report threshold collision induced dissociation experiments on protonated water clusters thermalized at low temperature for sizes n = 19-23. Fragmentation cross sections are recorded as a function of the collision energy and analyzed with a statistical model. This model allows us to account for dissociation cascades and provides values for the dissociation energies of each cluster. These values, averaging around 0.47 eV, are in good agreement with theoretical predictions at various levels of theory. Furthermore, the dissociation energies show a trend for the n = 21 magic and n = 22 anti-magic numbers relative to their neighbours, which is also in agreement with theory. These results provide further evidence to resolve the disagreement between previously published experimental values. A careful quantitative treatment of cascade dissociation in this model introduces interdependence between the dissociation energies of neighboring sizes, which reduces the number of free fitting parameters and improves both reliability and uncertainties on absolute dissociation energies deduced from experiments.
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Affiliation(s)
- Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/FERMI), UMR5589, Université Toulouse III - Paul Sabatier, CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Ali Kassem
- Laboratoire Collisions Agrégats Réactivité (LCAR/FERMI), UMR5589, Université Toulouse III - Paul Sabatier, CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L'Hermite
- Laboratoire Collisions Agrégats Réactivité (LCAR/FERMI), UMR5589, Université Toulouse III - Paul Sabatier, CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Christine Joblin
- Institut de Recherche en Astrophysique et Planétologie (IRAP), UMR5277, Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 avenue du Colonel Roche, F-31028 Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/FERMI, Université Toulouse III - Paul Sabatier, CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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6
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Tiefenthaler L, Scheier P, Erdmann E, Aguirre NF, Díaz-Tendero S, Luxford TFM, Kočišek J. Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations. Phys Chem Chem Phys 2023; 25:5361-5371. [PMID: 36647750 PMCID: PMC9930733 DOI: 10.1039/d2cp04172c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/20/2022] [Indexed: 01/18/2023]
Abstract
Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.
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Affiliation(s)
- Lukas Tiefenthaler
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Paul Scheier
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Néstor F Aguirre
- Software for Chemistry and Materials (SCM), Amsterdam, The Netherlands
| | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in ChemicalSciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Thomas F M Luxford
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia.
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia.
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7
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Hueber A, Green M, Ujma J, Richardson K, Gimbert Y, Cenac N, Bertrand-Michel J, Tabet JC. Energy-Resolved Ion Mobility Spectrometry: Composite Breakdown Curves for Distinguishing Isomeric Product Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:36-47. [PMID: 36488200 DOI: 10.1021/jasms.2c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Identification of lipopeptides (LpAA) synthesized from bacteria involves the study of structural characterization. Twenty LpAA have been characterized using commercial tandem high-resolution mass spectrometers in negative electrospray, employing nonresonant excitation in "RF only" collision cells and generally behave identically. However, [LpAA-H]- (AA = Asp or Glu) shows surprising fragmentation pathways, yielding a complementary fatty acid carboxylate and dehydrated amino acid fragment anions. In this study, the dissociation mechanisms of [C12Glu-H]- were determinate using energy-resolved mass spectrometry (ERMS). Product ion breakdown profiles are, generally, unimodal with full width at half-maximum (fwhm) increasing as product ion m/z ratios decrease, except for the two product ions of interest (fatty acid carboxylate and dehydrated glutamate) characterized by broad and composite profiles. Such behavior was already shown for other ions using a custom-built guided ion beam mass spectrometer. In this study, we investigate the meaning of these particular profiles from an ERMS breakdown, using fragmentation mechanisms depending on the collision energy. ERMS on line with ion mobility spectrometry (IMS), here called ER-IMS, provides a way to probe such questions. Broad or composite profiles imply that the corresponding product ions may be generated by two (or more) pathways, resulting in common or isomeric product ion structures. ER-IMS analysis indicates that the fatty acid carboxylate product ion is produced with a common structure through different pathways, while dehydrated glutamate has two isomeric forms depending on the mechanism involved. Drift time values correlate with the calculated collision cross section that confirms the product ion structures and fragmentation mechanisms.
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Affiliation(s)
- Amandine Hueber
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- IRSD, Université de Toulouse, INSERM, INRA, INP ENVT, Université de Toulouse 3 Paul Sabatier, ToulouseF-31024, France
- I2MC, INSERM, Université Toulouse 3 Paul Sabatier, ToulouseF-31432, France
| | - Martin Green
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Keith Richardson
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Yves Gimbert
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005Paris, France
- Département de chimie Moléculaire, UMR CNRS, 5250, Université Grenoble Alpes, F-38050Grenoble, France
| | - Nicolas Cenac
- IRSD, Université de Toulouse, INSERM, INRA, INP ENVT, Université de Toulouse 3 Paul Sabatier, ToulouseF-31024, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- I2MC, INSERM, Université Toulouse 3 Paul Sabatier, ToulouseF-31432, France
| | - Jean-Claude Tabet
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005Paris, France
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, F-91191Gif-sur-Yvette, France
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8
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Zamith S, Kassem A, L'Hermite JM, Joblin C. Water Attachment onto Size-Selected Cationic Pyrene Clusters. J Phys Chem A 2022; 126:3696-3707. [PMID: 35670699 DOI: 10.1021/acs.jpca.2c02195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report measurements of the attachment rates of water molecules onto mass-selected cationic pyrene clusters for size from n = 4 to 13 pyrene units and for different collision energies. Comparison of the attachment rates with the collision rates measured in collision-induced dissociation experiments provides access to the values of the sticking coefficient. The strong dependence of the attachment rates on size and collision energy is rationalized through a model in which we use a Langevin-type collision rate and adjust on experimental data the statistical dissociation rate of the water molecule from the cluster after attachment. This allows us to extrapolate our results to the conditions of isolation and long time scales encountered in astrophysical environments.
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Affiliation(s)
- Sébastien Zamith
- Laboratoire Collision Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Ali Kassem
- Laboratoire Collision Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.,Institut de Recherche en Astrophysique et Planétologie (IRAP), UMR5277, Université de Toulouse III - Paul Sabatier, CNRS, CNES, 9 avenue du Colonel Roche, F-31028 Toulouse, France
| | - Jean-Marc L'Hermite
- Laboratoire Collision Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Christine Joblin
- Institut de Recherche en Astrophysique et Planétologie (IRAP), UMR5277, Université de Toulouse III - Paul Sabatier, CNRS, CNES, 9 avenue du Colonel Roche, F-31028 Toulouse, France
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9
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Oeschger RJ, Bissig R, Chen P. Model Compounds for Intermediates and Transition States in Sonogashira and Negishi Coupling: d8- d10 Bonds in Large Heterobimetallic Complexes Are Weaker than Computational Chemistry Predicts. J Am Chem Soc 2022; 144:10330-10343. [PMID: 35639626 DOI: 10.1021/jacs.2c01641] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an experimental study, with accompanying DFT calculations, on a series of heterobimetallic complexes with Pd(II) and Cu(I), Ag(I), or Au(I). The isolable pincer complexes are models for the intermediates and transition state for the transmetalation step in Sonogashira and Negishi coupling reactions, among which, according to the DFT calculations, only the transition state has the two metal centers within bonding distance. Furthermore, we report a substituted version of an analogous heterobimetallic complex in which a competing dissociation sets an upper-bound on the strength of the d8-d10 metal-metal bond. Analysis of the structures in the solid state and in solution, and the competitive dissociation experiment in the gas phase, indicate that the dispersion-corrected DFT method used in the study appears to overestimate the strength of the metal-metal interaction, thus distorting the shape of the computed potential energy surface systematically for transmetalation.
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Affiliation(s)
- Raphael J Oeschger
- Laboratorium für Organische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Raphael Bissig
- Laboratorium für Organische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
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10
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Bubas AR, Iacovino AC, Armentrout PB. Reactions of Atomic Thorium and Uranium Cations with SF 6 Studied by Guided Ion Beam Tandem Mass Spectrometry. J Phys Chem A 2022; 126:3239-3246. [PMID: 35544768 DOI: 10.1021/acs.jpca.2c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fundamental chemistry of the thorium and uranium fluorides continues to be an area of interest because of the use of thorium and uranium fluoride compounds in nuclear fuel systems. Here, we study the reaction of thorium cations with sulfur hexafluoride for the first time and revisit the reaction of uranium cations with sulfur hexafluoride. By using guided ion beam tandem mass spectrometry, we explore the reaction pathways that become accessible well above thermal energies (E ∼ 0.04 eV). Overall, we find that both Th+ and U+ react very efficiently with SF6, approaching the collision limit at both thermal and elevated energies. The primary products observed at low energies include Th1-3+, UF1-4+, and SF1-4+, all of which are formed in barrierless, exothermic processes. SF5+ was also observed, although the pressure dependence of this channel reveals that SF5+ forms exothermically through secondary reactions, which the energy dependences suggest result from reactions between ThF2+ and UF3+ with SF6. At higher energies, both AnF3+ products are observed to decay to AnF+ + F2, and both SF4+ and SF2+ exhibit cross sections with endothermic features. For both systems, the rise in SF4+ can be attributed to a secondary collision between AnF+ with SF6 on the basis of the pressure dependence of the SF4+ channel at higher energies, and the rise in SF2+ appears to result from the decomposition of SF3+ to SF2+ + F.
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Affiliation(s)
- Amanda R Bubas
- Department of Chemistry, University of Utah, 315 S 1400 E Room 2020, Salt Lake City, Utah 84112-0850, United States
| | - Anna C Iacovino
- Department of Chemistry, University of Utah, 315 S 1400 E Room 2020, Salt Lake City, Utah 84112-0850, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S 1400 E Room 2020, Salt Lake City, Utah 84112-0850, United States
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11
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Auth T, Stein CJ, O'Hair RAJ, Koszinowski K. Origin of the different reactivity of the high-valent coinage-metal complexes [RCu iii Me 3 ] - and [RAg iii Me 3 ] - (R=allyl). Chemistry 2022; 28:e202103130. [PMID: 34773654 PMCID: PMC9304237 DOI: 10.1002/chem.202103130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/27/2022]
Abstract
High-valent tetraalkylcuprates(iii) and -argentates(iii) are key intermediates of copper- and silver-mediated C-C coupling reactions. Here, we investigate the previously reported contrasting reactivity of [RMiii Me3 ]- complexes (M=Cu, Ag and R=allyl) with energy-dependent collision-induced dissociation experiments, advanced quantum-chemical calculations and kinetic computations. The gas-phase fragmentation experiments confirmed the preferred formation of the [RCuMe]- anion upon collisional activation of the cuprate(iii) species, consistent with a homo-coupling reaction, whereas the silver analogue primarily yielded [AgMe2 ]- , consistent with a cross-coupling reaction. For both complexes, density functional theory calculations identified one mechanism for homo coupling and four different ones for cross coupling. Of these pathways, an unprecedented concerted outer-sphere cross coupling is of particular interest, because it can explain the formation of [AgMe2 ]- from the argentate(iii) species. Remarkably, the different C-C coupling propensities of the two [RMiii Me3 ]- complexes become only apparent when properly accounting for the multi-configurational character of the wave function for the key transition state of [RAgMe3 ]- . Backed by the obtained detailed mechanistic insight for the gas-phase reactions, we propose that the previously observed cross-coupling reaction of the silver complex in solution proceeds via the outer-sphere mechanism.
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Affiliation(s)
- Thomas Auth
- Institut für Organische und Biomolekulare ChemieUniversität GöttingenTammannstr. 237077GöttingenGermany
| | - Christopher J. Stein
- Theoretical Physics and Center for Nanointegration Duisburg-Essen (CENIDE)University of Duisburg-Essen47048DuisburgGermany
| | - Richard A. J. O'Hair
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne30 Flemington RdParkvilleVictoria3010Australia
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare ChemieUniversität GöttingenTammannstr. 237077GöttingenGermany
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12
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Pham HDM, Boles GC, Armentrout PB. Sodium Binding Interactions with Aliphatic Amino Acids: A Guided Ion Beam and Computational Study. J Phys Chem A 2021; 125:6332-6347. [PMID: 34270256 DOI: 10.1021/acs.jpca.1c04374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal binding affinities play a vital role in medicinal, biological, and industrial applications. In particular, metal cation-amino acid (AA) interactions contribute to protein stability such that analyzing analogous prototypical interactions is important. Here, we present a full description of the interactions of sodium cations (Na+) and six aliphatic amino acids (AA), where AA = glycine (Gly), alanine (Ala), homoalanine (hAla), valine (Val), leucine (Leu), and isoleucine (Ile). Experimentally, these interactions are evaluated using threshold collision-induced dissociation carried out in a guided ion beam tandem mass spectrometer, allowing for the determination of the kinetic-energy-dependent behavior of Na+-AA dissociation. Analysis of these dissociation cross sections, after accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates, allows the determination of absolute Na+-AA bond dissociation energies (BDEs) in kJ/mol of Gly (164.0), Ala (166.9), hAla (167.9), Val (172.7), Leu (173.7), and Ile (174.6). These are favorably compared to quantum chemical calculations conducted at the B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels of theory. Our combination of structural and energetic analyses provides information regarding the specific factors responsible for Na+ interactions with amino acids. Specifically, we find that the BDEs increase linearly with increasing polarizability of the amino acid.
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Affiliation(s)
- Hanh D M Pham
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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13
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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14
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Paenurk E, Chen P. Modeling Gas-Phase Unimolecular Dissociation for Bond Dissociation Energies: Comparison of Statistical Rate Models within RRKM Theory. J Phys Chem A 2021; 125:1927-1940. [PMID: 33635061 DOI: 10.1021/acs.jpca.1c00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Rice-Ramsperger-Kassel-Marcus (RRKM) theory provides a simple yet powerful rate theory for calculating microcanonical rate constants. In particular, it has found widespread use in combination with gas-phase kinetic experiments of unimolecular dissociations to extract experimental bond dissociation energies (BDEs). We have previously found several discrepancies between the computed BDE values and the respective experimental ones, obtained with our empirical rate model, named L-CID. To investigate the reliability of our rate model, we conducted a theoretical analysis and comparison of the performance of conventional rate models and L-CID within the RRKM framework. Using the previously published microcanonical rate data as well as reaction cross-section data, we show that the BDE values obtained with the L-CID model agree with the ones from the other rate models within the expected uncertainty bounds. Based on this agreement, we discuss the possible rationalization of the good performance of the L-CID model.
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Affiliation(s)
- Eno Paenurk
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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15
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Bot M, Gorbachev V, Tsybizova A, Chen P. Bond Dissociation Energies in the Gas Phase for Large Molecular Ions by Threshold Collision-Induced Dissociation Experiments: Stretching the Limits. J Phys Chem A 2020; 124:8692-8707. [PMID: 32955888 DOI: 10.1021/acs.jpca.0c05712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate bond dissociation energies for large molecules are difficult to obtain by either experimental or computational methods. The former methods are hampered by a range of physical and practical limitations in gas-phase measurement techniques, while the latter require incorporation of multiple approximations whose impact on accuracy may not always be clear. When internal benchmarks are not available, one hopes that experiment and theory can mutually support each other. A recent report found, however, a large discrepancy between gas-phase bond dissociation energies, measured mass spectrometrically, and the corresponding quantities computed using density functional theory (DFT)-D3 and DLPNO-CCSD(T) methods. With the widespread application of these computational methods to large molecular systems, the discrepancy needs to be resolved. We report a series of experimental studies that validate the mass spectrometric methods from small to large ions and find that bond dissociation energies extracted from threshold collision-induced dissociation experiments on large ions do indeed behave correctly. The implications for the computational studies are discussed.
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Affiliation(s)
- Marek Bot
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Vladimir Gorbachev
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Alexandra Tsybizova
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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16
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McDonald II DC, Sweeny BC, Viggiano AA, Shuman NS, Ard SG. Role of Spin in the Catalytic Oxidation of CO by N2O Enabled by Co+: New Insights from Temperature-Dependent Kinetics and Statistical Modeling. J Phys Chem A 2020; 124:7966-7972. [DOI: 10.1021/acs.jpca.0c06960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Brendan C. Sweeny
- Institute for Scientific Research, Boston College, Boston, Massachusetts 02467, United States
| | - Albert A. Viggiano
- Space Vehicles Directorate, Air Force Research Laboratory, Kirtland Air Force Base, New Mexico 87117, United States
| | - Nicholas S. Shuman
- Space Vehicles Directorate, Air Force Research Laboratory, Kirtland Air Force Base, New Mexico 87117, United States
| | - Shaun G. Ard
- Space Vehicles Directorate, Air Force Research Laboratory, Kirtland Air Force Base, New Mexico 87117, United States
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17
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Zamith S, L’Hermite JM, Dontot L, Zheng L, Rapacioli M, Spiegelman F, Joblin C. Threshold collision induced dissociation of pyrene cluster cations. J Chem Phys 2020; 153:054311. [PMID: 32770931 PMCID: PMC7116296 DOI: 10.1063/5.0015385] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report threshold collision induced dissociation experiments on cationic pyrene clusters, for sizes n = 2-6. Fragmentation cross sections are recorded as a function of the collision energy and analyzed with a statistical model. This model can account for the dissociation cascades and provides values for the dissociation energies. These values, of the order of 0.7 eV-1 eV, are in excellent agreement with those previously derived from thermal evaporation. They confirm the charge resonance stability enhancement predicted by theoretical calculations. In addition, remarkable agreement is obtained with theoretical predictions for the two smaller sizes n = 2 and 3. For the larger sizes, the agreement remains good, although the theoretical values obtained for the most stable structures are systematically higher by 0.2 eV. This offset could be attributed to approximations in the calculations. Still, there is an indication in the results of an incomplete description of the role of isomerization and/or direct dissociation upon collisions. Finally, by-product clusters containing dehydrogenated species are found to dissociate at energies comparable to the non-dehydrogenated ones, which shows no evidence for covalent bonds within the clusters.
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Affiliation(s)
- Sébastien Zamith
- Laboratoire Collision Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L’Hermite
- Laboratoire Collision Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Léo Dontot
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Linjie Zheng
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Christine Joblin
- Institut de Recherche en Astrophysique et Planétologie (IRAP), UMR5277, Université de Toulouse (UPS) and CNRS, 9 avenue du Colonel Roche, F-31028 Toulouse, France
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18
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Sun Y, Moe MM, Liu J. Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand. Phys Chem Chem Phys 2020; 22:14875-14888. [DOI: 10.1039/d0cp01788d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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19
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Tsybizova A, Fritsche L, Gorbachev V, Miloglyadova L, Chen P. Cryogenic ion vibrational predissociation (CIVP) spectroscopy of a gas-phase molecular torsion balance to probe London dispersion forces in large molecules. J Chem Phys 2019; 151:234304. [DOI: 10.1063/1.5124227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
| | - Lukas Fritsche
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | | | | | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
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20
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Ghale SB, Lanorio JG, Nickel AA, Ervin KM. Conformational Effects on Gas-Phase Acidities of Isomeric C3 and C5 Alkanols. J Phys Chem A 2018; 122:7797-7807. [DOI: 10.1021/acs.jpca.8b06851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Surja B. Ghale
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, MS 216, Reno, Nevada 89557-0216, United States
| | - Jerry G. Lanorio
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, MS 216, Reno, Nevada 89557-0216, United States
| | - Alex A. Nickel
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, MS 216, Reno, Nevada 89557-0216, United States
| | - Kent M. Ervin
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, MS 216, Reno, Nevada 89557-0216, United States
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21
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Brendle K, Kordel M, Schneider E, Wagner D, Bräse S, Weis P, Kappes MM. Collision Induced Dissociation of Benzylpyridinium-Substituted Porphyrins: Towards a Thermometer Scale for Multiply Charged Ions? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:382-392. [PMID: 29086339 DOI: 10.1007/s13361-017-1835-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/08/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
We have determined breakdown curves for a range of multiply charged benzylpyridinium-substituted porphyrin cations by collision induced dissociation measurements (CID) as mediated by resonant pulsed radio-frequency (rf) excitation in a helium-filled linear ion trap. Measurements were compared with the predictions of DFT calculations. We find a linear correlation between experimental fragmentation thresholds (in instrumental units of "normalized collision energy") and theoretical dissociation energies, suggesting that these species can be used as calibrants to gauge the fragmentation energetics of closely related systems. We have confirmed this by also studying the fragmentation thresholds of metalloporphyrin-based ions - including multiply negatively charged metalloporphyrin oligomers. Unfortunately, the slope of the linear correlation obtained for benzylpyridinium-substituted porphyrin multications differs significantly from that obtained by us for a set of smaller, singly charged substituted benzylpyridines put forward as "thermometer" ions in previous work. Multiplying the threshold energies in an ad hoc fashion by the ion charge basically reconciles both calibration curves. We conclude that one should use caution when applying small, singly charged benzylpyridines as calibrants to gauge the CID of large, multiply charged ions in ion-trap mass spectrometers. Graphical Abstract.
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Affiliation(s)
- Katrina Brendle
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Max Kordel
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Erik Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Danny Wagner
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany
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22
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Andris E, Andrikopoulos PC, Schulz J, Turek J, Růžička A, Roithová J, Rulíšek L. Aurophilic Interactions in [(L)AuCl]...[(L′)AuCl] Dimers: Calibration by Experiment and Theory. J Am Chem Soc 2018; 140:2316-2325. [DOI: 10.1021/jacs.7b12509] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Erik Andris
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Prokopis C. Andrikopoulos
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-166 10 Prague 6, Czech Republic
| | - Jiří Schulz
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Jan Turek
- Department
of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic
| | - Aleš Růžička
- Department
of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic
| | - Jana Roithová
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Lubomír Rulíšek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-166 10 Prague 6, Czech Republic
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23
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Ivanova B, Spiteller M. Quantitative collision induced mass spectrometry of substituted piperazines – A correlative analysis between theory and experiment. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.07.107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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24
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Rezaee M, McNary CP, Armentrout PB. Threshold collision-induced dissociation and theoretical study of protonated azobenzene. J Chem Phys 2017; 147:164308. [DOI: 10.1063/1.5000683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Mohammadreza Rezaee
- Department of Physics, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Christopher P. McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112, USA
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112, USA
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25
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Haeffner F, Irikura KK. N-Protonated Isomers and Coulombic Barriers to Dissociation of Doubly Protonated Ala 8Arg. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2170-2180. [PMID: 28699065 DOI: 10.1007/s13361-017-1719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala n (n = 3-11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated Ala8Arg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N9. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Fredrik Haeffner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8320, USA
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467-3860, USA
| | - Karl K Irikura
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8320, USA.
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26
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Irikura KK. Ab Initio Computation of Energy Deposition During Electron Ionization of Molecules. J Phys Chem A 2017; 121:7751-7760. [DOI: 10.1021/acs.jpca.7b07993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl K. Irikura
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, United States
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27
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Coates RA, Armentrout PB. Binding energies of hydrated cobalt hydroxide ion complexes: A guided ion beam and theoretical investigation. J Chem Phys 2017; 147:064305. [DOI: 10.1063/1.4991557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Rebecca A. Coates
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, USA
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, USA
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28
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Armentrout PB, Cox RM. Potential energy surface for the reaction Sm + + CO 2 → SmO + + CO: guided ion beam and theoretical studies. Phys Chem Chem Phys 2017; 19:11075-11088. [PMID: 28435958 DOI: 10.1039/c7cp00914c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The potential energy surface (PES) for the oxidation of samarium cations by carbon dioxide is explored both experimentally and theoretically. Using guided ion beam tandem mass spectrometry, several reactions are examined as a function of kinetic energy. These include the title reaction as well as its reverse along with the collision-induced dissociation of Sm+(CO2) and OSm+(CO) with Xe. Analysis of the kinetic energy dependent cross sections yields barriers for the forward and reverse oxidation reaction of 1.77 ± 0.11 and 2.04 ± 0.13 eV, respectively, and Sm+-OCO and OSm+-CO bond dissociation energies (BDEs) of 0.42 ± 0.03 and 0.97 ± 0.07 eV, respectively. BDEs for Sm+(CO2)x for x = 2 and 3 are also determined as 0.40 ± 0.13 and 0.48 ± 0.12 eV, respectively. The PESs for the title reaction along the sextet and octet spin surfaces are also examined theoretically at the MP2 and CCSD(T) levels using both effective core potential and all-electron basis sets. Reasonable agreement between theory and experiment is obtained for the experimentally characterized intermediates, although all-electron basis sets and spin-orbit effects are needed for quantitative agreement. The observed barrier for oxidation is shown to likely correspond to the energy of the crossing between surfaces corresponding to the ground state electronic configuration of Sm+ (8F,4f66s1) and an excited surface having two electrons in the valence space (excluding 4f), which are needed to form the strong SmO+ bond.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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Martin-Somer A, Spezia R, Yáñez M. Gas-phase reactivity of [Ca(formamide)] 2+ complex: an example of different dynamical behaviours. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0196. [PMID: 28320901 PMCID: PMC5360897 DOI: 10.1098/rsta.2016.0196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)]2+ complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Ana Martin-Somer
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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30
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Homayoon Z, Pratihar S, Dratz E, Snider R, Spezia R, Barnes GL, Macaluso V, Martin Somer A, Hase WL. Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters. J Phys Chem A 2016; 120:8211-8227. [DOI: 10.1021/acs.jpca.6b05884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | | | | | - Riccardo Spezia
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Veronica Macaluso
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - Ana Martin Somer
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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31
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Lightcap J, Hester TH, Patterson D, Butler JT, Goebbert DJ. Formation of a Spin-Forbidden Product, 1[MnO 4] −, from Gas-Phase Decomposition of 6[Mn(NO 3) 3] −. J Phys Chem A 2016; 120:7071-9. [DOI: 10.1021/acs.jpca.6b06978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johnny Lightcap
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487, United States
| | - Thomas H. Hester
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487, United States
| | - Daniel Patterson
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487, United States
| | - Joseph T. Butler
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487, United States
| | - Daniel J. Goebbert
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487, United States
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32
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Hester TH, Albury RM, Pruitt CJM, Goebbert DJ. Fragmentation of [Ni(NO 3) 3] −: A Study of Nickel–Oxygen Bonding and Oxidation States in Nickel Oxide Fragments. Inorg Chem 2016; 55:6634-42. [DOI: 10.1021/acs.inorgchem.6b00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas H. Hester
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Rachael M. Albury
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carrie Jo M. Pruitt
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Daniel J. Goebbert
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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33
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Bauer CA, Grimme S. How to Compute Electron Ionization Mass Spectra from First Principles. J Phys Chem A 2016; 120:3755-66. [DOI: 10.1021/acs.jpca.6b02907] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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34
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Lightcap J, Hester TH, Kamena K, Albury RM, Pruitt CJM, Goebbert DJ. Gas-Phase Fragmentation of Aluminum Oxide Nitrate Anions Driven by Reactive Oxygen Radical Ligands. J Phys Chem A 2016; 120:1501-7. [PMID: 26919711 DOI: 10.1021/acs.jpca.5b12417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase metal nitrate anions are known to yield a variety of interesting metal oxides upon fragmentation. The aluminum nitrate anion complexes, Al(NO3)4(-) and AlO(NO3)3(-) were generated by electrospray ionization and studied with collision-induced dissociation and energy-resolved mass spectrometry. Four different decomposition processes were observed, the loss of NO3(-), NO3(•), NO2(•), and O2. The oxygen radical ligand in AlO(NO3)3(-) is highly reactive and drives the formation of AlO(NO3)2(-) upon loss of NO3(•), AlO2(NO3)2(-) upon NO2(•) loss, or Al(NO2)(NO3)2(-) upon abstraction of an oxygen atom from a neighboring nitrate ligand followed by loss of O2. The AlO2(NO3)2(-) fragment also undergoes elimination of O2. The mechanism for O2 elimination requires oxygen atom abstraction from a nitrate ligand in both AlO(NO3)3(-) and AlO2(NO3)2(-), revealing the hidden complexity in the fragmentation of these clusters.
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Affiliation(s)
- Johnny Lightcap
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
| | - Thomas H Hester
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
| | - Kurt Kamena
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
| | - Rachael M Albury
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
| | - Carrie Jo M Pruitt
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
| | - Daniel J Goebbert
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
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35
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Rodgers MT, Armentrout PB. Cationic Noncovalent Interactions: Energetics and Periodic Trends. Chem Rev 2016; 116:5642-87. [PMID: 26953819 DOI: 10.1021/acs.chemrev.5b00688] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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36
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Carroy G, Lemaur V, De Winter J, Isaacs L, De Pauw E, Cornil J, Gerbaux P. Energy-resolved collision-induced dissociation of non-covalent ions: charge- and guest-dependence of decomplexation reaction efficiencies. Phys Chem Chem Phys 2016; 18:12557-68. [DOI: 10.1039/c6cp01026a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The influence of the charge state on the CID reactions undergone by host–guest complexes is monitored by mass spectrometry and described by computational chemistry.
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Affiliation(s)
- Glenn Carroy
- Organic Synthesis and Mass Spectrometry Laboratory
- Interdisciplinary Center for Mass Spectrometry
- Research Institute for Science and Engineering of Materials
- University of Mons
- UMONS
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers
- Research Institute for Science and Engineering of Materials
- University of Mons
- UMONS
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory
- Interdisciplinary Center for Mass Spectrometry
- Research Institute for Science and Engineering of Materials
- University of Mons
- UMONS
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Edwin De Pauw
- Mass spectrometry Laboratory
- University of Liège
- B-4000 Liège
- Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers
- Research Institute for Science and Engineering of Materials
- University of Mons
- UMONS
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory
- Interdisciplinary Center for Mass Spectrometry
- Research Institute for Science and Engineering of Materials
- University of Mons
- UMONS
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37
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Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies. Met Ions Life Sci 2016; 16:103-31. [DOI: 10.1007/978-3-319-21756-7_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Albury RM, Pruitt CJM, Hester TH, Goebbert DJ. Fragmentation of Cr(NO3)4–: Metal Oxidation upon O•– Abstraction. J Phys Chem A 2015; 119:11471-8. [DOI: 10.1021/acs.jpca.5b08841] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rachael M. Albury
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carrie Jo M. Pruitt
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Thomas H. Hester
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Daniel J. Goebbert
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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39
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Cox RM, Armentrout PB, de Jong WA. Activation of CH4 by Th+ as Studied by Guided Ion Beam Mass Spectrometry and Quantum Chemistry. Inorg Chem 2015; 54:3584-99. [DOI: 10.1021/acs.inorgchem.5b00137] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard M Cox
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Wibe A. de Jong
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, United States
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40
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Wang R, Yang B, Wu RR, Rodgers MT, Schäfer M, Armentrout PB. Guided ion beam and computational studies of the decomposition of a model thiourea protein cross-linker. J Phys Chem B 2015; 119:3727-42. [PMID: 25660315 DOI: 10.1021/jp512997z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The dissociation of protonated methyl-d3 thiourea-4-butyric acid methyl amide (1), a model of thiourea-based protein cross-linking compounds, is examined both experimentally and computationally. Using a guided ion beam tandem mass spectrometer (GIBMS), the threshold collision-induced dissociation (TCID) of [1 + H](+) with Xe is examined as a function of collision energy. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for four primary and four secondary dissociation pathways, after accounting for competition between channels, sequential dissociations, unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Computations are used to explore the pathways for the various processes and elucidation of their rate-limiting transition states. These results indicate that dissociation is initiated by migration of the excess proton from sulfur to one of three nitrogen atoms in 1, similar to the "mobile proton" model of peptide fragmentation. The computational energies for the rate-limiting transition states are generally in good agreement with the experimentally derived threshold energies, with MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) results being particularly favorable. This good comparison validates the mechanisms explored theoretically and allows identification of the structures of the various product ions and neutrals.
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Affiliation(s)
- Ran Wang
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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41
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Qu ZW, Hansen A, Grimme S. Co–C Bond Dissociation Energies in Cobalamin Derivatives and Dispersion Effects: Anomaly or Just Challenging? J Chem Theory Comput 2015; 11:1037-45. [DOI: 10.1021/acs.jctc.5b00007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zheng-wang Qu
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, North Rhine-Westphalia, Germany
| | - Andreas Hansen
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, North Rhine-Westphalia, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, North Rhine-Westphalia, Germany
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42
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Pierson NA, Clemmer DE. An IMS-IMS threshold method for semi-quantitative determination of activation barriers: Interconversion of proline cis↔trans forms in triply protonated bradykinin. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:646-654. [PMID: 25838788 PMCID: PMC4378547 DOI: 10.1016/j.ijms.2014.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Collisional activation of selected conformations by multidimensional ion mobility spectrometry (IMS-IMS), combined with mass spectrometry (MS), is described as a method to determine semi-quantitative activation energies for interconversion of different structures of the nonapeptide bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg). This analysis is based on a calibration involving collision-induced dissociation measurements of ions with known dissociation energies (i.e., "thermometer" ions) such as leucine enkephalin, BK, and amino acid-metal cation systems. The energetic barriers between six conformations of [BK+3H]3+ range from 0.23 ±0.01 to 0.55 ±0.03 eV. Prior results indicate that the major peaks in the IMS distributions correspond to specific combinations of cis and trans configurations of the three proline residues in the peptide sequence. The analysis allows us to directly assess pathways for specific transitions. The combination of structural assignments, experimentally determined barrier heights, onset of the quasi-equilibrium region, and dissociation threshold are used to derive a semi-quantitative potential energy surface for main features of [BK+3H]3+.
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Affiliation(s)
- Nicholas A. Pierson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405 United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405 United States
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43
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Boga Raja UK, Injeti S, Culver T, McCabe JW, Angel LA. Probing the stability of insulin oligomers using electrospray ionization ion mobility mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:759-774. [PMID: 26764306 DOI: 10.1255/ejms.1396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The peptide hormone insulin is central to regulating carbohydrate and fat metabolism in the body by controlling blood sugar levels. Insulin's most active form is the monomer and the extent of insulin oligomerization is related to insulin's activity of controlling blood sugar levels. Electrospray ionization (ESI) of human insulin produced a series of oligomers from the monomer to the undecamer identified using quadrupole ion mobility time-of-flight mass spectrometry. Previous research suggested that only the monomer, dimer and hexamer are native forms of insulin in solution and the range of oligomers observed in the gas-phase are ESI artifacts. Here the properties of three distinct oligomer bands I, II and III, where both the charge state and number of insulin units of the oligomer increase incrementally, were investigated. When Zn(ii) was added to the insulin sample the same oligomers were observed but with 0-6 Zn(ii) ions bound to each of the oligomers. The oligomers of bands I, II and III were characterized by comparing their drift times, collision cross- sections, relative intensities, collision-induced dissociation (CID) patterns and relative breakdown energies. Insulin oligomers of band I dissociated primarily by releasing either the 2+ or 3+ monomer accompanied by an oligomer that conserved the mass, charge and Zn(ii) of the precursor. Insulin oligomers of bands II and III dissociated primarily by releasing the 2+ monomer accompanied by an oligomer which conserved the mass, charge and Zn(ii) of the precursor. Comparison of CID patterns and breakdown energies showed all the oligomers in band II required higher collision energies to dissociate than the oligomers in band I, and the oligomers of band III required higher energies to dissociate than oligomers of band II. These results show that the amount of excess charge on the oligomer in respect to the number of insulin monomers in the oligomer affects their stability.
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Affiliation(s)
- Uday Kumar Boga Raja
- Chemistry Department, Texas A&M University - Commerce, P.O. Box 3011, Commerce, TX 75429, USA.
| | - Srilakshmi Injeti
- Chemistry Department, Texas A&M University - Commerce, P.O. Box 3011, Commerce, TX 75429, USA.
| | - Tiffany Culver
- Chemistry Department, Texas A&M University - Commerce, P.O. Box 3011, Commerce, TX 75429, USA.
| | - Jacob W McCabe
- Chemistry Department, Texas A&M University - Commerce, P.O. Box 3011, Commerce, TX 75429, USA.
| | - Laurence A Angel
- Chemistry Department, Texas A&M University - Commerce, P.O. Box 3011, Commerce, TX 75429, USA.
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Martín-Sómer A, Yáñez M, Gaigeot MP, Spezia R. Unimolecular Fragmentation Induced By Low-Energy Collision: Statistically or Dynamically Driven? J Phys Chem A 2014; 118:10882-93. [DOI: 10.1021/jp5076059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Martín-Sómer
- Departamento
de Química, Facultad de Ciencias, Módulo
13. Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC. Cantoblanco, E-28049 Madrid, Spain
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
| | - Manuel Yáñez
- Departamento
de Química, Facultad de Ciencias, Módulo
13. Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC. Cantoblanco, E-28049 Madrid, Spain
| | - Marie-Pierre Gaigeot
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse
et Modélisation pour la Biologie et
l’Environnement, UMR 8587, Boulevard
F. Mitterrand, 91025 Evry Cedex, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Riccardo Spezia
- Université d’Evry Val d’Essonne, UMR 8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse
et Modélisation pour la Biologie et
l’Environnement, UMR 8587, Boulevard
F. Mitterrand, 91025 Evry Cedex, France
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45
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McNary CP, Armentrout PB. Iron cluster–CO bond energies from the kinetic energy dependence of the Fen+(n = 4–17) + CO association reactions. Phys Chem Chem Phys 2014; 16:26467-77. [DOI: 10.1039/c4cp02040e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Couzijn EPA, Kobylianskii IJ, Moret ME, Chen P. Experimental Gas-Phase Thermochemistry for Alkane Reductive Elimination from Pt(IV). Organometallics 2014. [DOI: 10.1021/om500478y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erik P. A. Couzijn
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Ilia J. Kobylianskii
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marc-Etienne Moret
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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47
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Armentrout PB, Stennett EMS. Thermodynamics and mechanism of protonated cysteine decomposition: a guided ion beam and computational study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:512-523. [PMID: 24496599 DOI: 10.1007/s13361-013-0817-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 06/03/2023]
Abstract
A quantitative molecular description of the decomposition of protonated cysteine, H(+)Cys, is provided by studying the kinetic energy dependence of threshold collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Primary dissociation channels are deamidation (yielding both NH3 loss and NH4(+) formation) and (H2O + CO) loss reactions, followed by an additional six subsequent decompositions. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for six different reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. To identify the mechanisms associated with these reactions, quantum chemical calculations performed at the B3LYP/6-311 + G(d,p) level were used to locate the transition states (TSs) and intermediates for these processes. Single point energies of the reactants, products, and key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311 + G(2d,2p) basis set. The computational characterization of the elementary steps of these reactions, including the structures of the final products, is validated by quantitative agreement with the experimental energetics. In agreement with previous work, deamidation is facilitated by anchimeric assistance of the thio group, which also leads to an interesting rearrangement of the intact amino acid identified computationally.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA,
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Armentrout PB, Austin CA, Rodgers MT. Alkali Metal Cation Interactions with 15-Crown-5 in the Gas Phase: Revisited. J Phys Chem A 2014; 118:8088-97. [DOI: 10.1021/jp4116172] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. B. Armentrout
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - C. A. Austin
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Armentrout PB, Yang B, Rodgers MT. Metal Cation Dependence of Interactions with Amino Acids: Bond Dissociation Energies of Rb+ and Cs+ to the Acidic Amino Acids and Their Amide Derivatives. J Phys Chem B 2014; 118:4300-14. [DOI: 10.1021/jp5001754] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 E, Room 2020, Salt Lake City, Utah 84112, United States
| | - Bo Yang
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Armentrout PB. Gas-phase perspective on the thermodynamics and kinetics of heterogeneous catalysis. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00435c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase studies of small transition metal cluster cations provide thermochemistry of utility to surface science and heterogeneous catalysis.
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