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Yang Z, Doddipatla S, He C, Goettl SJ, Kaiser RI, Jasper AW, Gomes ACR, Galvão BRL. Can third-body stabilisation of bimolecular collision complexes in cold molecular clouds happen? Mol Phys 2022. [DOI: 10.1080/00268976.2022.2134832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zhenghai Yang
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, HI, USA
| | | | - Chao He
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, HI, USA
| | - Shane J. Goettl
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, HI, USA
| | - Ralf I. Kaiser
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, HI, USA
| | - Ahren W. Jasper
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Alexandre C. R. Gomes
- Centro Federal de Educação Tecnológica de Minas Gerais, CEFET-MG, Minas Gerais, Brazil
| | - Breno R. L. Galvão
- Centro Federal de Educação Tecnológica de Minas Gerais, CEFET-MG, Minas Gerais, Brazil
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2
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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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3
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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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4
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Pollice R, Fleckenstein F, Shenderovich I, Chen P. Compensation of London Dispersion in the Gas Phase and in Aprotic Solvents. Angew Chem Int Ed Engl 2019; 58:14281-14288. [DOI: 10.1002/anie.201905436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/17/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Robert Pollice
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
| | - Felix Fleckenstein
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
| | - Ilya Shenderovich
- Universität Regensburg Fakultät für Chemie und Pharmazie Universitätsstraße 31 Regensburg 93040 Germany
| | - Peter Chen
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
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5
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Pollice R, Fleckenstein F, Shenderovich I, Chen P. Compensation of London Dispersion in the Gas Phase and in Aprotic Solvents. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Robert Pollice
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
| | - Felix Fleckenstein
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
| | - Ilya Shenderovich
- Universität Regensburg Fakultät für Chemie und Pharmazie Universitätsstraße 31 Regensburg 93040 Germany
| | - Peter Chen
- ETH Zürich Laboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich Zürich 8093 Switzerland
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6
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Lamsabhi AM, Mó O, Yáñez M, Salpin JY. Combined Experimental and Theoretical Survey of the Gas-Phase Reactions of Serine-Ca 2+ Adducts. J Phys Chem A 2019; 123:6241-6250. [PMID: 31268328 DOI: 10.1021/acs.jpca.9b03977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The association of Ca2+ to serine and the subsequent gas-phase unimolecular reactivity of the [Ca(Ser)]2+ (Ser = Serine) adduct was investigated throughout the use of tandem mass spectrometry techniques and B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) density functional theory calculations. In a first step, the structure and relative stability of all possible conformers of serine were obtained and analyzed, as well as the most stable [serine-Ca]2+ adducts. For the analysis of the different potential energy surfaces associated with the gas-phase unimolecular reactivity of these adducts, only those that differ by less than 100 kJ·mol-1 from the global minimum were taken into account. In agreement with previous studies, the serine-Ca2+ global minimum corresponds to a charge-solvated structure in which Ca is tricoordinated to neutral serine. The major peaks observed in the nanoelectrospray-MS/MS spectrum of [Ca(Ser)]2+ adduct correspond to both Coulomb explosions, yielding either CaOH+ + [C3,H6,N,O2]+ or [C2,H4,O,N]+ + [Ca(C,H3,O2)]+, and to the loss of neutrals, namely, CH2O and H2O. Our theoretical survey of the energy profile allow us to conclude that, although all the aforementioned fragmentation processes can have their origin at the global minimum, similar fragmentations involving low-lying conformers, both zwitterionic and nonzwitterionic, compete and should be considered to account for the observed reactivity. We have also found that in some specific cases post-transition state dynamics similar to the ones described before in the literature for formamide-Ca2+ reactions, may also play a role.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute of Advanced Chemical Sciences (IadChem) , Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid , Spain
| | - Jean-Yves Salpin
- LAMBE, Univ Evry, CNRS, CEA , Université Paris-Saclay , F-91025 Evry-Courcouronnes , France.,LAMBE, UCP , Université Paris-Seine , F-91025 Evry-Courcouronnes , France
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7
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Bayat P, Gatineau D, Lesage D, Robert V, Martinez A, Cole RB. Investigation of Hemicryptophane Host-Guest Binding Energies Using High-Pressure Collision-Induced Dissociation in Combination with RRKM Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:509-518. [PMID: 30478817 DOI: 10.1007/s13361-018-2109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/20/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
In advancing host-guest (H-G) chemistry, considerable effort has been spent to synthesize host molecules with specific and well-defined molecular recognition characteristics including selectivity and adjustable affinity. An important step in the process is the characterization of binding strengths of the H-G complexes that is typically performed in solution using NMR or fluorescence. Here, we present a mass spectrometry-based multimodal approach to obtain critical energies of dissociation for two hemicryptophane cages with three biologically relevant guest molecules. A combination of blackbody infrared radiative dissociation (BIRD) and high-pressure collision-induced dissociation (high-pressure CID), along with RRKM modeling, was employed for this purpose. For the two tested hemicryptophane hosts, the cage containing naphthyl linkages exhibited stronger interactions than the cage bearing phenyl linkages. For both cages, the order of guest stability is choline > acetylcholine > betaine. The information obtained by these types of mass spectrometric studies can provide new insight into the structural features that most influence the stability of H-G pairs, thereby providing guidance for future syntheses. Graphical Abstract.
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Affiliation(s)
- Parisa Bayat
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
| | - David Gatineau
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
- CNRS, UMR 5250, DCM, University of Grenoble Alpes, Grenoble, France
| | - Denis Lesage
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France
| | - Vincent Robert
- Laboratoire de Chimie Quantique, Université de Strasbourg, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Alexandre Martinez
- UMR CNRS 7313-iSm2, Equipe Chirosciences, Aix Marseille Université, Av. Escadrille Normandie-Niemen, 13397, Marseille, France
| | - Richard B Cole
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75252 Cedex 05, Paris, France.
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8
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Gutierrez MG, Theis Z, Lewis TWR, Bellert DJ. A molecular beam apparatus for performing single photon initiated dissociative rearrangement reactions (SPIDRR) with transition metal cation bound organic clusters. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:074101. [PMID: 30068115 DOI: 10.1063/1.5024939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The study of gas-phase ion-molecule reactions has been influential in the investigation of transition metal mediated bond activation and catalysis. We have furthered this field by developing a new technique capable of measuring the microcanonical kinetics for reactions between transition metal cations and neutral organic molecules. This novel method has been designated as single photon initiated dissociative rearrangement reaction (SPIDRR) technique and provides a nearly direct measurement of microcanonical reaction rate constants. For this reason, SPIDRR offers unique insight into reaction mechanisms and dynamics by assessing the energy dependence of the microcanonical rate constant, as well as measuring product branching fractions and kinetic isotope effects. The following paper provides a detailed overview of SPIDRR and its advantages in the field of gas-phase catalysis research.
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Affiliation(s)
- M G Gutierrez
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798-7348, USA
| | - Z Theis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798-7348, USA
| | - T W R Lewis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798-7348, USA
| | - D J Bellert
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798-7348, USA
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9
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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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10
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Pollice R, Bot M, Kobylianskii IJ, Shenderovich I, Chen P. Attenuation of London Dispersion in Dichloromethane Solutions. J Am Chem Soc 2017; 139:13126-13140. [DOI: 10.1021/jacs.7b06997] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Robert Pollice
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Marek Bot
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ilia J. Kobylianskii
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ilya Shenderovich
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Peter Chen
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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11
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Cooperative Effects in Clusters and Oligonuclear Complexes of Transition Metals in Isolation. STRUCTURE AND BONDING 2016. [DOI: 10.1007/430_2016_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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12
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Zhao YX, Liu QY, Zhang MQ, He SG. Reactions of metal cluster anions with inorganic and organic molecules in the gas phase. Dalton Trans 2016; 45:11471-95. [DOI: 10.1039/c6dt01246a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Progress on the activation and transformation of important inorganic and organic molecules by negatively charged bare metal clusters as well as ligated systems with oxygen, carbon, and nitrogen, among others.
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Affiliation(s)
- Yan-Xia Zhao
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Qing-Yu Liu
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Mei-Qi Zhang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Sheng-Gui He
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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13
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Zhang JW, Miao K, Wang SG, Wang ZB. Note: A novel design of a microwave feed for a microwave frequency standard with a linear ion trap. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:076106. [PMID: 25085191 DOI: 10.1063/1.4891075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Linear ion traps are important tools in many applications, particularly in mass spectrum analyzers and frequency standards. Here a novel design of a microwave feed integrated into one electrode of a linear quadrupole ion trap is demonstrated for the application of a microwave frequency standard based on cadmium ions. The mechanical structure of the microwave feed is compact and easy to build. The ion trap integrated with this microwave feed is successfully applied to measure the hyperfine splitting of the ground state of (113)Cd(+), thus demonstrating the practicality and reliability of the microwave feed.
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Affiliation(s)
- J W Zhang
- NIM-THU Joint Institute for Measurement Science (JMI), Tsinghua University, Beijing 100084, People's Republic of China
| | - K Miao
- NIM-THU Joint Institute for Measurement Science (JMI), Tsinghua University, Beijing 100084, People's Republic of China
| | - S G Wang
- NIM-THU Joint Institute for Measurement Science (JMI), Tsinghua University, Beijing 100084, People's Republic of China
| | - Z B Wang
- NIM-THU Joint Institute for Measurement Science (JMI), Tsinghua University, Beijing 100084, People's Republic of China
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14
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Benassi M, Garcia-Reyes JF, Spengler B. Ambient ion/molecule reactions in low-temperature plasmas (LTP): reactive LTP mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:795-804. [PMID: 23495026 DOI: 10.1002/rcm.6500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 12/24/2012] [Accepted: 12/29/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Ion/molecule reactions are commonly used to characterize structures due to their high specificity. Herein, we present ambient ion/molecule reactions performed in the course of low-temperature plasma (LTP) ionization of condensed-phase analytes in order to increase the specificity of LTP-based ambient analysis. METHODS The ion population of the cold plasma is modified by addition of a reagent to the plasma before it is directed at a surface bearing the analyte. Desorbed ions were analyzed using linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). RESULTS Acylium ions generated from tetramethylurea react with 1,3-dioxane analyte to afford distinctive Eberlin product ions. Reactions of alkylamines, such as n-hexylamine and n-octylamine, with benzaldehyde produce the corresponding imines. Reaction of ruthenocene with trifluoroacetic anhydride forms the unusual trifluoroacetate ruthenocene. CONCLUSIONS A LTP source can be used to generate reagent ions that can undergo ion/molecule reactions in the ambient environment with an analyte at condensed phase on a surface. The experiment is a 'reactive' version of the standard low-temperature plasma (LTP) ambient ionization experiment. This approach provides additional information by combining ion/molecule chemistry with conventional MS and MS/MS data to characterize particular analytes.
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Affiliation(s)
- Mario Benassi
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, 35392, Giessen, Germany
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15
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Jockusch RA, Williams ER. Binding Energies of Proton-Bound Dimers of Imidazole and n-Acetylalanine Methyl Ester Obtained by Blackbody Infrared Radiative Dissociation. J Phys Chem A 2012; 102:4543-50. [PMID: 16604163 PMCID: PMC1434664 DOI: 10.1021/jp980264w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dissociation kinetics of protonated n-acetyl-L-alanine methyl ester dimer (AcAlaME(d)), imidazole dimer, and their cross dimer were measured using blackbody infrared radiative dissociation (BIRD). Master equation modeling of these data was used to extract threshold dissociation energies (E(o)) for the dimers. Values of 1.18 +/- 0.06, 1.11 +/- 0.04, and 1.12 +/- 0.08 eV were obtained for AcAlaME(d), imidazole dimer, and the cross dimer, respectively. Assuming that the reverse activation barrier for dissociation of the ion-molecule complex is negligible, the value of E(o) can be compared to the dissociation enthalpy (DeltaH(d) degrees ) from HPMS data. The E(o) values obtained for the imidazole dimer and the cross dimer are in agreement with HPMS values; the value for AcAlaME(d) is somewhat lower. Radiative rate constants used in the master equation modeling were determined using transition dipole moments calculated at the semiempirical (AM1) level for all dimers and compared to ab initio (RHF/3-21G*) calculations where possible. To reproduce the experimentally measured dissociation rates using master equation modeling, it was necessary to multiply semiempirical transition dipole moments by a factor between 2 and 3. Values for transition dipole moments from the ab initio calculations could be used for two of the dimers but appear to be too low for AcAlaME(d). These results demonstrate that BIRD, in combination with master equation modeling, can be used to determine threshold dissociation energies for intermediate size ions that are in neither the truncated Boltzmann nor the rapid energy exchange limit.
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Affiliation(s)
- R A Jockusch
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
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16
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Jockusch RA, Paech K, Williams ER. Energetics from slow infrared multiphoton dissociation of biomolecules. J Phys Chem A 2012; 104:3188-96. [PMID: 16467893 PMCID: PMC1343445 DOI: 10.1021/jp993147p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photodissociation kinetics of the protonated pentapeptide leucine enkephalin measured using a cw CO(2) laser and a Fourier-transform mass spectrometer are reported. A short induction period, corresponding to the time required to raise the internal energy of the ion population to a (dissociating) steady state, is observed. After this induction period, the dissociation data are accurately fit by first-order kinetics. A plot of the log of the unimolecular dissociation rate constant, k(uni), as a function of the log of laser power is linear at low laser powers (<9 W, k(uni) <0.05 s(-1)), but tapers off at high laser power (9-33 W, k(uni) = 0.05-7 s(-1)). The entire measured dissociation curve can be accurately fit by an exponential function plus a constant. The experiment is simulated using a master equation formalism. In the model, the laser radiation is described as an energetically flat-topped distribution which is spatially uniform. This description is consistent with experimental results which indicate that ion motion within the cell averages out spatial inhomogeneities in the laser light. The model has several adjustable parameters. The effect of varying these parameters on the calculated kinetics and power dependence curves is discussed. A procedure for determining a limited range of threshold dissociation energy, E(o), which fits both the measured induction period and power dependence curves, is presented. Using this procedure, E(o) of leucine enkephalin is determined to be 1.12-1.46 eV. This result is consistent with, although less precise than, values measured previously using blackbody infrared radiative dissociation. Although the blackbody dissociation results were used as a starting point to search for fits of the master equation model to experiment, these results demonstrate that it is, in principle, possible to determine a limited range of E(o) from slow infrared multiphoton dissociation data alone.
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Affiliation(s)
- R A Jockusch
- Department of Chemistry, University of California, Berkeley, California 94720
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17
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Liu S, Geng Z, Wang Y, Yan Y. Methane activation by MH+ (M = Os, Ir, and Pt) and comparisons to the congeners of MH+ (M = Fe, Co, Ni and Ru, Rh, Pd). J Phys Chem A 2012; 116:4560-8. [PMID: 22524674 DOI: 10.1021/jp210924a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of ligated-transition-metal- [MH(+) (M = Os, Ir, and Pt)] catalyzed methane activation has been computed at the B3LYP level of density functional theory. The B3LYP energies of important species on the potential energy surfaces were compared to CCSD(T) single-point energy calculations. Newer kinetic and dispersion-corrected methods such as M05-2X provide significantly better descriptions of the bonding interactions. The reactions take place more easily along the low-spin potential energy surface. The minimum-energy pathway proceeds as MH(+) + CH(4) → M(H)(2)(CH(3))(+) → TS → MH(CH(2))(H(2))(+) → MH(CH(2))(+) + H(2). The ground states are (5)Π, (4)Σ(-), and (1)Σ(+) for OsH(+), IrH(+), and PtH(+), respectively. The energy level differences of the reactants between the high- and low-spin states gradually become smaller from OsH(+) to PtH(+), being 30.66, 9.17, and 0.09 kcal/mol, respectively. The C-H bond can be readily activated by MH(+) (M = Os, Ir, and Pt) with a negligible barrier in the low-spin state; thus, OsH(+), IrH(+), and PtH(+) are likely to be excellent mediators for the activition of the C-H bond of methane. H(2) elimination is quite facile without barriers in the presence of excess reactants. The products of the reactions of MH(+) (M = Os, Ir, and Pt) + methane are all carbene complexes MH(CH(2))(+). The exothermicities of the reactions are 3.99, 15.66, and 12.14 kcal/mol, respectively. The results for MH(+) (M = Os, Ir, and Pt) are compared with those for the first- and second-row congeners, and the differences in behavior and mechanism are discussed.
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Affiliation(s)
- Shaoli Liu
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu 730070, P.R. China
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Boguslavskiy AE, Mikosch J, Gijsbertsen A, Spanner M, Patchkovskii S, Gador N, Vrakking MJJ, Stolow A. The Multielectron Ionization Dynamics Underlying Attosecond Strong-Field Spectroscopies. Science 2012; 335:1336-40. [DOI: 10.1126/science.1212896] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Andrey E. Boguslavskiy
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jochen Mikosch
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Arjan Gijsbertsen
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
- FOM Instituut voor Atoom-en Molecuulfysica (AMOLF), Science Park 102, 1098 XG Amsterdam, Netherlands
| | - Michael Spanner
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Serguei Patchkovskii
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Niklas Gador
- Department of Chemical Physics, Lund University, Box 124, SE-22100 Lund, Sweden
| | - Marc J. J. Vrakking
- FOM Instituut voor Atoom-en Molecuulfysica (AMOLF), Science Park 102, 1098 XG Amsterdam, Netherlands
- Max-Born-Institute, Max Born Strasse 2A, D12489, Berlin, Germany
| | - Albert Stolow
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
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Fischer KH, Schneider M, Fischer I, Pfaffinger B, Braunschweig H, Sztáray B, Bodi A. Bonding in a Borylene Complex Investigated by Photoionization and Dissociative Photoionization. Chemistry 2012; 18:4533-40. [DOI: 10.1002/chem.201103993] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Indexed: 11/11/2022]
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Sztáray J, Memboeuf A, Drahos L, Vékey K. Leucine enkephalin--a mass spectrometry standard. MASS SPECTROMETRY REVIEWS 2011; 30:298-320. [PMID: 20669325 DOI: 10.1002/mas.20279] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/31/2009] [Accepted: 10/31/2009] [Indexed: 05/29/2023]
Abstract
The present article reviews the mass spectrometric fragmentation processes and fragmentation energetics of leucine enkephalin, a commonly used peptide, which has been studied in detail and has often been used as a standard or reference compound to test novel instrumentation, new methodologies, or to tune instruments. The main purpose of the article is to facilitate its use as a reference material; therefore, all available mass spectrometry-related information on leucine enkephalin has been critically reviewed and summarized. The fragmentation mechanism of leucine enkephalin is typical for a small peptide; but is understood far better than that of most other compounds. Because ion ratios in the MS/MS spectra indicate the degree of excitation, leucine enkephalin is often used as a thermometer molecule in electrospray or matrix-assisted laser desorption ionization (ESI or MALDI). Other parameters described for leucine enkephalin include collisional cross-section and energy transfer; proton affinity and gas-phase basicity; radiative cooling rate; and vibrational frequencies. The lowest-energy fragmentation channel of leucine enkephalin is the MH(+) → b(4) process. All available data for this process have been re-evaluated. It was found that, although the published E(a) values were significantly different, the corresponding Gibbs free energy change showed good agreement (1.32 ± 0.07 eV) in various studies. Temperature- and energy-dependent rate constants were re-evaluated with an Arrhenius plot. The plot showed good linear correlation among all data (R(2) = 0.97), spanned over a 9 orders of magnitude range in the rate constants and yielded 1.14 eV activation energy and 10(11.0) sec(-1) pre-exponential factor. Accuracy (including random and systematic errors, with a 95% confidence interval) is ±0.05 eV and 10(±0.5) sec(-1), respectively. The activation entropy at 470 K that corresponds to this reaction is -38.1 ± 9.6 J mol(-1) K(-1). We believe that these re-evaluated values are by far the most accurate activation parameters available at present for a protonated peptide and can be considered as "consensus" values; results on other processes might be compared to this reference value.
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Affiliation(s)
- Judit Sztáray
- Institute of Structural Chemistry, Chemical Research Center Hungarian Academy of Sciences, 1025 Budapest, Pusztaszeri ut 59-67, Hungary
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21
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Flosadóttir HD, Jónsson H, Sigurdsson ST, Ingólfsson O. Experimental and theoretical study of the metastable decay of negatively charged nucleosides in the gas phase. Phys Chem Chem Phys 2011; 13:15283-90. [DOI: 10.1039/c1cp21298b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Duncan MA. Infrared spectroscopy to probe structure and dynamics in metal ion-molecule complexes. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235031000095201] [Citation(s) in RCA: 280] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Michael A. Duncan
- a Department of Chemistry , University of Georgia , Athens , GA , 30602-2556 , USA
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Höckendorf RF, Balaj OP, Linde CVD, Beyer MK. Thermochemistry from ion–molecule reactions of hydrated ions in the gas phase: a new variant of nanocalorimetry reveals product energy partitioning. Phys Chem Chem Phys 2010; 12:3772-9. [DOI: 10.1039/b921395c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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24
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Haupert LJ, Poutsma JC, Wenthold PG. The Curtin-Hammett principle in mass spectrometry. Acc Chem Res 2009; 42:1480-8. [PMID: 19572743 DOI: 10.1021/ar800248n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Curtin-Hammett principle (CHP) is an important concept in physical organic chemistry and is often utilized in the investigation of reaction mechanisms. Two reactants, A and B, in rapid equilibrium, react to form products P(A) and P(B) with rates k(A) and k(B), respectively. If the reaction is under kinetic control and the rate of equilibration between the two reactants is much faster than the reactions to form products, then the branching ratio of products P(A) and P(B) depends solely on the difference in barrier heights for the two product channels. The CHP is based on the fact that the ratio of products formed is not determined by the reactant population ratio. However, the CHP also applies to studies in other areas of chemistry, including mass spectrometry. This Account describes work from our groups in which the results must be interpreted in light of the CHP. These studies illustrate two important implications of the CHP. First, they demonstrate how product distributions cannot be used to assess reactant structure in mechanistic studies in Curtin-Hammett systems. A recent investigation of the structure of hydroxysiliconate anions demonstrated that it was not possible to distinguish between the possible reactant ion structures. A second important implication of the CHP is that the structure of the reactant does not affect the product branching ratio and therefore does not need to be a consideration if the CHP applies. We address this aspect of the discussion through kinetic method studies of the acidities of amino acids and proton affinities of bifunctional compounds. Recently reported mass spectrometric studies illustrate how the CHP puts limitations on what conclusions can be drawn from product distribution studies but also allows experimental methods, such as the kinetic method, to be carried out for complicated systems without having to know all the details of the reactant ion structures. These studies show that although the CHP is most commonly applied in mechanistic studies in physical organic chemistry, it also applies to other areas of chemistry, including mass spectrometry. Although the CHP in some cases limits the conclusions that can be drawn from an experimental study, its proper application can often be used to greatly simplify very complicated chemical systems. Therefore, it is important in mass spectrometry, and indeed, in all areas of chemistry, to recognize those systems in which the CHP should and should not apply.
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Affiliation(s)
- Laura J. Haupert
- The Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, and
| | - John C. Poutsma
- The Department of Chemistry, The College of William and Mary, Williamsburg, Virginia 23185
| | - Paul G. Wenthold
- The Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, and
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25
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26
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Jutier L, Léonard C, Gatti F. Renner–Teller effect in linear tetra-atomic molecules. I. Variational method including couplings between all degrees of freedom on six-dimensional potential energy surfaces. J Chem Phys 2009; 130:134301. [DOI: 10.1063/1.3089354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Li W, Geng Z, Wang Y, Yan P, Zhang X, Wang Z, Liu F. Density Functional Theory Studies of Thermal Activation of Methane by MH+ (M = Ru, Rh, and Pd). J Phys Chem A 2009; 113:1807-12. [DOI: 10.1021/jp808830c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wenqiang Li
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - Zhiyuan Geng
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - Yongcheng Wang
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - PenJi Yan
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - Xu Zhang
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - Zheng Wang
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
| | - Fengxia Liu
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering Northwest Normal University, Lanzhou 730070, People's Republic of China
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28
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Schröder D. Gaseous Rust: Thermochemistry of Neutral and Ionic Iron Oxides and Hydroxides in the Gas Phase. J Phys Chem A 2008; 112:13215-24. [DOI: 10.1021/jp8030804] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Detlef Schröder
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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29
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Zhao X, Hopkinson AC, Bohme DK. Competitive Activation of CH and CX Bonds in Reactions of Pt+ with CH3X (X=F,Cl): Experiment and Theory. Chemphyschem 2008; 9:873-81. [DOI: 10.1002/cphc.200700576] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Guo Z, Ke Z, Phillips DL, Zhao C. Intrinsic Reaction Coordinate Analysis of the Activation of CH4 by Molybdenum Atoms: A Density Functional Theory Study of the Crossing Seams of the Potential Energy Surfaces. Organometallics 2007. [DOI: 10.1021/om7007452] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhen Guo
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China, and School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Zhuofeng Ke
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China, and School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China, and School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Cunyuan Zhao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China, and School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
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31
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Solano Espinoza EA, Stashenko E, Martínez J, Mora U, Kouznetsov V. Linear free energy relationships in C-N bond dissociations in molecular ions of 4-substituted N-(2-furylmethyl)anilines in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:1496-503. [PMID: 17687763 DOI: 10.1002/jms.1258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The substituent effect on the reactivity of the C-N bond of molecular ions of 4-substituted N-(2-furylmethyl)anilines toward two dissociation pathways was studied. With this aim, six of these compounds were analyzed by mass spectrometry using electron ionization with energies between 7.8 and 69.9 eV. Also, the UB3LYP/6-31G (d,p) and UHF/6-31G (d, p) levels of theory were used to calculate the critical energies (reaction enthalpies at 0 K) of the processes that lead to the complementary ions [C(5)H(5)O](+) and [M - C(5)H(5)O](+), assuming structures that result from the heterolytic and homolytic C-N bond cleavages of the molecular ions, respectively. A kinetic approach proposed in the 1960s was applied to the mass spectral data to obtain the relative rate coefficients for both dissociation channels from ratios of the peak intensities of these ions. Linear relationships were obtained between the logarithms of the relative rate coefficients and the calculated critical energies and other thermochemical properties, whose slopes showed to be conditioned by the energy provided to the compounds within the ion source. Moreover, it was found that the dissociation that leads to [C(5)H(5)O](+) is a process strongly dependent upon the electron withdrawing or donating properties of the substituent, favored by those factors that destabilize the molecular ion. On the contrary, the dissociation that leads to [M - C(5)H(5)O](+) is indifferent to the polar electronic effects of the substituent. The abundance of both products was governed by the rule of Stevenson-Audier, according to which the major ion is the one of less negative electronic affinity.
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Affiliation(s)
- Eduardo A Solano Espinoza
- Centro de Investigación en Biomoléculas, Cibimol, Escuela de Química, Universidad Industrial de Santander, A. A. 678, Bucaramanga, Colombia.
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32
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Sunahori FX, Zhang X, Clouthier DJ. Electronic spectroscopy of jet-cooled HCP+: Molecular structure, phosphorus hyperfine structure, and Renner-Teller analysis. J Chem Phys 2007; 127:104312. [PMID: 17867752 DOI: 10.1063/1.2767264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Laser-induced fluorescence spectra of jet-cooled HCP(+) and DCP(+) have been obtained with the pulsed discharge technique using HCPDCP and argon precursor mixtures. Transitions involving all of the excited state vibrations have been observed and a set of vibrational constants has been obtained. High-resolution spectra of the (2)Pi(32) components of the 0(0) (0) bands of both isotopomers have been recorded, and these spectra show resolved phosphorus hyperfine structure which allowed the determination of the excited state Fermi contact parameter. The B values were used to obtain the ground and excited state effective geometric parameters as r(0) (")(CH)=1.077(2) A, r(0) (")(CP)=1.6013(3) A, r(0) (')(CH)=1.082(2) A, and r(0) (')(CP)=1.5331(3) A. A Renner-Teller analysis of the ground state vibrational energy levels obtained from the literature was attempted. All of the observed levels of DCP(+) and the majority of those of HCP(+) were satisfactorily fitted with a standard Renner-Teller model, but three HCP(+) levels showed large systematic deviations which could not be accommodated by reassignments or improvements in the Fermi resonance Hamiltonian. Further improvements in the theory or in the experimental data will be needed to resolve this discrepancy.
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Affiliation(s)
- Fumie X Sunahori
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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Abstract
Studying metal ion solvation, especially hydration, in the gas phase has developed into a field that is dominated by a tight interaction between experiment and theory. Since the studied species carry charge, mass spectrometry is an indispensable tool in all experiments. Whereas gas-phase coordination chemistry and reactions of bare metal ions are reasonably well understood, systems containing a larger number of solvent molecules are still difficult to understand. This review focuses on the rich chemistry of hydrated metal ions in the gas phase, covering coordination chemistry, charge separation in multiply charged systems, as well as intracluster and ion-molecule reactions. Key ideas of metal ion solvation in the gas phase are illustrated with rare-gas solvated metal ions.
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Affiliation(s)
- Martin K Beyer
- Institut für Chemie, Sekr. C4, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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Walker NR, Walters RS, Tsai MK, Jordan KD, Duncan MA. Infrared photodissociation spectroscopy of Mg(+)(H2O)Ar(n) complexes: isomers in progressive microsolvation. J Phys Chem A 2007; 109:7057-67. [PMID: 16834068 DOI: 10.1021/jp051877t] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion-molecule complexes of the form Mg(H2O)Ar(n)+ (n = 1-8) are produced by laser vaporization in a pulsed-nozzle cluster source. These complexes are mass-selected and studied with infrared photodissociation spectroscopy in the O-H stretch region. The spectra are interpreted with the aid of ab initio calculations on the n = 1-5 complexes, including examination of various isomeric structures. The combined spectroscopic and theoretical studies reveal the presence of multiple isomeric structures at each cluster size, as the argon atoms assemble around the Mg(+)(H2O) unit. Distinct infrared resonances are measured for argon-on-metal, argon-on-OH and argon-on-two-OH isomers.
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Affiliation(s)
- N R Walker
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556, USA
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Abstract
With the development of electrospray and matrix-assisted laser desorption ionization, mass spectrometry (MS) evolved into a powerful tool in the field of biochemistry. Whereas MS is primarily analytical in nature, an increasing number of MS research groups employ the method to address fundamental biochemical questions. Probing the interaction of noncovalently bound molecules in the mass spectrometer is one of the most interesting MS-based experiments possible today, with the potential of making a significant contribution to the basic understanding of the structure and function of biochemical complexes. Here we review a number of current research efforts employing primarily MS techniques to investigate intermolecular interactions in biochemical systems. Examples chosen include the interaction of biomolecules with solvent molecules; interactions between nucleic-acid molecules, in particular, interactions in duplex and quadruplex structures; and interactions between proteins involved in neurodegenerative diseases. Finally we conclude by presenting a few examples of very large biomolecular assemblies in the mega-Dalton range analyzed by MS.
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Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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Safi Z, Lamsabhi AM. Gas-phase reactivity of 2,7-dimethyl-[1,2,4]-triazepine thio derivatives toward Cu+ cation: a DFT study. J Phys Chem A 2007; 111:2213-9. [PMID: 17388292 DOI: 10.1021/jp068642h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase interactions of 2,7-dimethyl-[1,2,4]-triazepine and its thio derivatives with Cu+ were studied through the use of high-level density functional theory (DFT) calculations. The structure of all possible tautomers and their conformers was optimized at the B3LYP/6-31G(d) level of theory. Final energies were obtained at the B3LYP/6-311+G(2df,2p) level. It has been found that the direct association of Cu+ occurs at the oxygen atom attached to position 3 in the case of the dioxo derivative and at the sulfur atom in all other cases. For the dithio derivatives, the global minimum of the PES corresponds to the structure in which the metal ion bridges between the heteroatom at position 3 and the nitrogen atom at position 4 of the corresponding enolic tautomer, forming a four-membered ring structure; for the dioxo derivative, this conformer competes with the ketone tautomer. Moreover, the isomerization processes leading from the most stable adduct to the other stable conformers were investigated. Among all the considered compounds, the 3,5-dithiotriazepines-Cu+ is found to be the one that associates Cu+ more tightly in the gas phase. The calculated Cu+ binding energies show a good correlation with the experimental proton affinities.
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Affiliation(s)
- Zaki Safi
- Department of Chemistry, Faculty of Science, Al-Azhar University of Gaza, Gaza, Palestine
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Tang SJ, Chou YC, Lin JJM, Hsu YC. The bending vibrational levels of the acetylene cation: A case study of the Renner-Teller effect in a molecule with two degenerate bending vibrations. J Chem Phys 2006; 125:133201. [PMID: 17029448 DOI: 10.1063/1.2199827] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Forty three vibronic levels of C2H2+, X 2Pi u, with upsilon4 = 0-6, upsilon5 = 0-3, and K = 0-4, lying at energies of 0-3520 cm(-1) above the zero-point level, have been recorded at rotational resolution. These levels were observed by double resonance, using 1+1' two-color pulsed-field ionization zero-kinetic-energy photoelectron spectroscopy. The intermediate states were single rovibrational levels chosen from the A1Au, 4nu3 (K = 1-2), 5nu3 (K = 1), nu2+4nu3 (K = 0), and 47,206 cm(-1) (K = 1) levels of C2H2. Seven of the trans-bending levels of C2H2+ (upsilon4 = 0-3, K = 0-2) had been reported previously by Pratt et al. [J. Chem. Phys. 99, 6233 (1993)]; our results for these levels agree well with theirs. A full analysis has been carried out, including the Renner-Teller effect and the vibrational anharmonicity for both the trans- and cis-bending vibrations. The rotational structure of the lowest 16 vibronic levels (consisting of the complete set of levels with upsilon4 + upsilon5 < or = 2, except for the unobserved upper (2Pi u component of the 2nu4 overtone) could be fitted by least squares using 16 parameters to give an rms deviation of 0.21 cm(-1). The vibronic coupling parameter epsilon5 (about whose magnitude there has been controversy) was determined to be -0.0273(7). For the higher vibronic levels, an additional parameter, r45, was needed to allow for the Darling-Dennison resonance between the two bending manifolds. Almost all the observed levels of the upsilon4 + upsilon5 = 3 and 4 polyads (about half of the predicted number) could then be assigned. In a final fit to 39 vibronic levels with upsilon4 + upsilon5 < or = 5, an rms deviation of 0.34 cm(-1) was obtained using 20 parameters. An interesting finding is that Hund's spin-coupling cases (a) and (b) both occur in the Sigmau components of the nu4 + 2nu5 combination level. The ionization potential of C2H2 (from the lowest rotational level of the ground state to the lowest rotational level of the cation) is found to be 91,953.77 +/- 0.09 cm(-1) (3sigma).
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Affiliation(s)
- Sheunn-Jiun Tang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Republic of China
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Cooks RG, Chen H, Eberlin MN, Zheng X, Tao WA. Polar Acetalization and Transacetalization in the Gas Phase: The Eberlin Reaction. Chem Rev 2006; 106:188-211. [PMID: 16402776 DOI: 10.1021/cr0400921] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R G Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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Boese AD, Schneider H, Glöss AN, Weber JM. The infrared spectrum of Au−∙CO2. J Chem Phys 2005; 122:154301. [PMID: 15945629 DOI: 10.1063/1.1875114] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Au-.CO2 ion-molecule complex has been studied by gas phase infrared photodissociation spectroscopy. Several sharp transitions can be identified as combination bands involving the asymmetric stretch vibrational mode of the CO2 ligand. Their frequencies are redshifted by several hundred cm(-1) from the frequencies of free CO2. We discuss our findings in the framework of ab initio and density-functional theory calculations, using anharmonic corrections to predict vibrational transition energies. The infrared spectrum is consistent with the formation of an aurylcarboxylate anion with a strongly bent CO2 subunit.
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Affiliation(s)
- A Daniel Boese
- Institute of Nanotechnology, Forschungszentrum Karlsruhe, P.O. Box 3640, D-76021 Karlsruhe, Germany
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40
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Viswanathan B, Barden CJ, Ban F, Boyd * RJ. Calibration of a computational scheme for solvation: Group I and II metal ions bound to water, formaldehyde and ammonia. Mol Phys 2005. [DOI: 10.1080/00268970512331317273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Zhang Q, Bowers MT. Activation of Methane by MH+ (M = Fe, Co, and Ni): A Combined Mass Spectrometric and DFT Study. J Phys Chem A 2004. [DOI: 10.1021/jp047943t] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qiang Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510
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Michel M, Korolkov MV, Weitzel KM. State-Selective Predissociation Spectroscopy of HCl+ and DCl+ Ions. J Phys Chem A 2004. [DOI: 10.1021/jp048042n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Michel
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Academy of Science, Stephanov Institute of Physics, Minsk, Belarus, and Fachbereich Chemie, Institut für Physikalische Chemie, Philipps Universität Marburg, Hans Meerwein Strasse, 35032 Marburg, Germany
| | - Mikhail V. Korolkov
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Academy of Science, Stephanov Institute of Physics, Minsk, Belarus, and Fachbereich Chemie, Institut für Physikalische Chemie, Philipps Universität Marburg, Hans Meerwein Strasse, 35032 Marburg, Germany
| | - Karl-Michael Weitzel
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany, Academy of Science, Stephanov Institute of Physics, Minsk, Belarus, and Fachbereich Chemie, Institut für Physikalische Chemie, Philipps Universität Marburg, Hans Meerwein Strasse, 35032 Marburg, Germany
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43
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Liu HC, Yang S, Zhang XH, Wu YD. Unusual Chemistry of the Complex Mg•+(2-Fluoropyridine) Activated by the Photoexcitation of Mg•+. J Am Chem Soc 2003; 125:12351-7. [PMID: 14519021 DOI: 10.1021/ja036476a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photochemistry of a gas-phase complex, Mg*(+)(2-fluoropyridine), has been studied in the spectral range of approximately 230-440 nm with a molecular beam coupled with a time-of-flight mass spectrometer. Surprisingly rich chemistry has been observed. Aside from the evaporative photofragment, Mg*(+), an abundant photoproduct, C(4)H(4)*(+), is observed after the electronic excitation of Mg(+). The formation of this photoproduct is associated with the loss of a stable species, CN[bond]Mg[bond]F. Also identified in this work are reactive pathways that occur with the elimination of HCN, HF, or MgF from the complex. The observed photoreactions have been examined in detail using quantum mechanics methods. A distinct structural feature of the complex is the direct attachment of Mg*(+) to the N atom of fluoropyridine due to the strong electrostatic interaction. The key to the rich photochemistry is the formation of the FMg(+)(C(5)H(4)N) intermediate, through facile fluorine migration. Plausible photoreaction mechanisms have been proposed. These mechanisms account for the evolution of the energized complex with the pre-defined structure en route to the target photoproducts that we have detected.
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Affiliation(s)
- Hai-Chuan Liu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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Gabelica V, Karas M, De Pauw E. Calibration of Ion Effective Temperatures Achieved by Resonant Activation in a Quadrupole Ion Trap. Anal Chem 2003; 75:5152-9. [PMID: 14708790 DOI: 10.1021/ac034473a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present paper describes a calibration of the ion effective temperatures as a function of the resonant activation amplitude in a quadrupole ion trap mass spectrometer. MS/MS experiments are performed on leucine enkephalin (M + H)+, bradykinin (M + H)+, (M + 2H)2+, and (M + 3H)3+, and ubiquitin (M + 11H)11+. For each amplitude, the effective temperature is calculated as the temperature that would give the same dissociation rate constant as the one observed and is calculated using published Arrhenius parameters. The effective temperature is found to be linearly dependent on the activation amplitude on the range investigated. The dependence of the slope and of the intercept of the T(eff) = f (amplitude) functions on the parent ion m/z is examined and an equation is derived to calibrate the ion effective temperature between 365 and 600 K. Below 365 K, a deviation from linearity is expected. Above 600 K, the validity of the equation will depend on whether the rapid energy exchange limit is still reached. Calculating backward, the Arrhenius parameters from the measured dissociation rates using this calibration show excellent agreement with the published values. The calibration can therefore be used to determine Arrhenius activation parameters from dissociation kinetics under resonant activation in quadrupole ion trap mass spectrometers.
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Affiliation(s)
- Valérie Gabelica
- Institüt für Pharmazeutische Chemie, Johann-Wolfgang Goethe Universität Frankfurt, Marie-Curie Strasse 9-11, D-60439 Frankfurt am Main, Germany.
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Walters RS, Brinkmann NR, Schaefer HF, Duncan MA. Infrared Photodissociation Spectroscopy of Mass-Selected Al+(CO2)n and Al+(CO2)nAr Clusters. J Phys Chem A 2003. [DOI: 10.1021/jp030491k] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- R. S. Walters
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - N. R. Brinkmann
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - H. F. Schaefer
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - M. A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
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46
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Zhang G, Li S, Jiang Y. Dehydrogenation of Methane by Gas-Phase Os+: A Density Functional Study. Organometallics 2003. [DOI: 10.1021/om030291v] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ganbing Zhang
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing, 210093, People's Republic of China
| | - Shuhua Li
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing, 210093, People's Republic of China
| | - Yuansheng Jiang
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing, 210093, People's Republic of China
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Galiano L, Alcamí M, Mó O, Yáñez M. Gas-phase chemistry of ethynylamine, -phosphine and -arsine. Structure and stability of their Cu+ and Ni+ complexes. Chemphyschem 2003; 4:72-8. [PMID: 12596468 DOI: 10.1002/cphc.200390011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Cu+ and Ni+ binding energies of ethynylamine, ethynylphosphine and ethynylarsine have been calculated at the B3LYP/6-311 + G(2df,2p)//B3LYP/6-311G(d,p) level of theory. Significant differences between nitrogen-containing and phosphorus- or arsenic-containing compounds have been found regarding structural effects upon metal cation association. While for ethynylamine the global minimum of the potential energy surface corresponds to the complex in which the metal cation binds to the beta-carbon, for ethynylphosphine the most favourable process corresponds to phosphorus attachment. For ethynylarsine, the conventional pi-complex is the most stable one. This behavior resembles that found for the corresponding vinyl analogues, with the only exception being the arsenic derivative. The calculated Cu+ and Ni+ binding energies for attachment to the heteroatom follow a different trend, P > As > N, to that predicted for the corresponding proton affinities, P > N > As. Cu+ and Ni+ binding energies are almost identical when the metal cation binds to the heteroatom. However, Ni+ binding energies are slightly larger than Cu+ binding energies when the metal cation interacts with the C identical to C bond.
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Affiliation(s)
- Luis Galiano
- Departamento de Química C-9, Universidad Autónoma de Madrid Cantoblanco 28049 Madrid, Spain
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Rothschopf GK, Li S, Yang DS. Zero-electron-kinetic-energy photoelectron spectroscopy of transition-metal—ether complexes: Y-O(CH3)2, Y-O(CD3)2, Y-[O(CH3)2]2, and Y-[O(CD3)2]2. J Chem Phys 2002. [DOI: 10.1063/1.1504704] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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49
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Reichert EL, Thurau G, Weisshaar JC. Velocity map imaging of ion-molecule reaction products: Co+(3F4)+isobutane. J Chem Phys 2002. [DOI: 10.1063/1.1482369] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Combariza MY, Vachet RW. Gas-phase ion-molecule reactions of transition metal complexes: the effect of different coordination spheres on complex reactivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:813-825. [PMID: 12148806 DOI: 10.1016/s1044-0305(02)00378-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Using a modified quadrupole ion trap mass spectrometer, a series of metal complex ions have been reacted with acetonitrile in the gas phase. Careful control of the coordination number and the type of coordinating functionality in diethylenetriamine-substituted ligands enable the effects of the coordination sphere on metal complex reactivity to be examined. The association reaction kinetics of acetonitrile with these pentacoordinate complexes are followed in order to obtain information about the starting complexes and the reaction dynamics. The kinetics and thermodynamics of acetonitrile addition to the metal complex ions are strongly affected by the chemical environment around the metal center such that significant differences in reactivity are observed for Co(II) and Cu(II) complexes with various coordination spheres. When thiophene, furan, or benzene moieties are present in the coordination sphere of the complex, addition of two acetonitrile molecules is readily observed. In contrast, ligands with better sigma donors react mainly to add one acetonitrile molecule. Among the ligands with good sigma donors, a clear trend in reactivity is observed in which complexes with nitrogen-containing ligands are the least reactive, sulfur-containing complexes are more reactive, and oxygen-containing complexes are the most reactive. In general, equilibrium and reaction rate constants seem to be consistent with the hard and soft acid and base (HSAB) principle. Interestingly, the presence of certain groups (e.g., pyridine and imidazole) in the coordination sphere clearly can change the acid character of the metal as seen by their effect on the binding properties of other functional groups in the same ligand. Finally, we conclude that because complexes with different coordination spheres react to noticeably different extents, ion-molecule (I-M) reactions may be potentially useful for obtaining coordination structure information for transition metal complexes.
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