1
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Surendran A, Pereverzev AY, Roithová J. Intricacies of Mass Transport during Electrocatalysis: A Journey through Iron Porphyrin-Catalyzed Oxygen Reduction. J Am Chem Soc 2024; 146:15619-15626. [PMID: 38778765 PMCID: PMC11157527 DOI: 10.1021/jacs.4c04989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Electrochemical steps are increasingly attractive for green chemistry. Understanding reactions at the electrode-solution interface, governed by kinetics and mass transport, is crucial. Traditional insights into these mechanisms are limited, but our study bridges this gap through an integrated approach combining voltammetry, electrochemical impedance spectroscopy, and electrospray ionization mass spectrometry. This technique offers real-time monitoring of the chemical processes at the electrode-solution interface, tracking changes in intermediates and products during reactions. Applied to the electrochemical reduction of oxygen catalyzed by the iron(II) tetraphenyl porphyrin complex, it successfully reveals various reaction intermediates and degradation pathways under different kinetic regimes. Our findings illuminate complex electrocatalytic processes and propose new ways for studying reactions in alternating current and voltage-pulse electrosynthesis. This advancement enhances our capacity to optimize electrochemical reactions for more sustainable chemical processes.
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Affiliation(s)
- Adarsh
Koovakattil Surendran
- Department of Spectroscopy and Catalysis,
Institute for Molecules and Materials, Radboud
University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Aleksandr Y. Pereverzev
- Department of Spectroscopy and Catalysis,
Institute for Molecules and Materials, Radboud
University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jana Roithová
- Department of Spectroscopy and Catalysis,
Institute for Molecules and Materials, Radboud
University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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2
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Tureček F. UV-vis spectroscopy of gas-phase ions. MASS SPECTROMETRY REVIEWS 2023; 42:206-226. [PMID: 34392556 DOI: 10.1002/mas.21726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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3
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Roithová J, Bakker JM. Ion spectroscopy in methane activation. MASS SPECTROMETRY REVIEWS 2022; 41:513-528. [PMID: 34008884 PMCID: PMC9292810 DOI: 10.1002/mas.21698] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 05/25/2023]
Abstract
This review is devoted to ion spectroscopy studies of complexes relevant for the understanding of methane activation with metal ions and clusters. Methane activation starts with the formation of a complex with a metal ion. The degree of the interaction between an intact methane molecule and the ion can be monitored by the perturbations of C-H stretch vibrations in the methane molecule. Binding mediated by the electrostatic interaction results in a η3 type coordination of methane. In contrast, binding governed by orbital interactions results in a η2 type coordination of methane. We further review the spectroscopic characterization of activation products of metal-methane reactions, such as the metal-carbene and carbyne products resulting from the interaction of selected 5d metals with methane. The focus of recent research in the field has shifted towards the investigation of interactions between methane and metal clusters. We show examples highlighting that metal clusters can be more reactive in methane activation reactions.
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Affiliation(s)
- Jana Roithová
- Department of Spectroscopy and CatalysisRadboud University NijmegenNijmegenThe Netherlands
| | - Joost M. Bakker
- Radboud University, Institute for Molecules and MaterialsFELIX LaboratoryNijmegenThe Netherlands
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4
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Braak FT, Elferink H, Houthuijs KJ, Oomens J, Martens J, Boltje TJ. Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations. Acc Chem Res 2022; 55:1669-1679. [PMID: 35616920 PMCID: PMC9219114 DOI: 10.1021/acs.accounts.2c00040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
A detailed
understanding of the reaction mechanism(s) leading to
stereoselective product formation is crucial to understanding and
predicting product formation and driving the development of new synthetic
methodology. One way to improve our understanding of reaction mechanisms
is to characterize the reaction intermediates involved in product
formation. Because these intermediates are reactive, they are often
unstable and therefore difficult to characterize using experimental
techniques. For example, glycosylation reactions are critical steps
in the chemical synthesis of oligosaccharides and need to be stereoselective
to provide the desired α- or β-diastereomer. It remains
challenging to predict and control the stereochemical outcome of glycosylation
reactions, and their reaction mechanisms remain a hotly debated topic.
In most cases, glycosylation reactions take place via reaction mechanisms
in the continuum between SN1- and SN2-like pathways.
SN2-like pathways proceeding via the displacement of a
contact ion pair are relatively well understood because the reaction
intermediates involved can be characterized by low-temperature NMR
spectroscopy. In contrast, the SN1-like pathways proceeding
via the solvent-separated ion pair, also known as the glycosyl cation,
are poorly understood. SN1-like pathways are more challenging
to investigate because the glycosyl cation intermediates involved
are highly reactive. The highly reactive nature of glycosyl cations
complicates their characterization because they have a short lifetime
and rapidly equilibrate with the corresponding contact ion pair. To
overcome this hurdle and enable the study of glycosyl cation stability
and structure, they can be generated in a mass spectrometer in the
absence of a solvent and counterion in the gas phase. The ease of
formation, stability, and fragmentation of glycosyl cations have been
studied using mass spectrometry (MS). However, MS alone provides little
information about the structure of glycosyl cations. By combining
mass spectrometry (MS) with infrared ion spectroscopy (IRIS), the
determination of the gas-phase structures of glycosyl cations has
been achieved. IRIS enables the recording of gas-phase infrared spectra
of glycosyl cations, which can be assigned by matching to reference
spectra predicted from quantum chemically calculated vibrational spectra.
Here, we review the experimental setups that enable IRIS of glycosyl
cations and discuss the various glycosyl cations that have been characterized
to date. The structure of glycosyl cations depends on the relative
configuration and structure of the monosaccharide substituents, which
can influence the structure through both steric and electronic effects.
The scope and relevance of gas-phase glycosyl cation structures in
relation to their corresponding condensed-phase structures are also
discussed. We expect that the workflow reviewed here to study glycosyl
cation structure and reactivity can be extended to many other reaction
types involving difficult-to-characterize ionic intermediates.
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Affiliation(s)
- Floor ter Braak
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hidde Elferink
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kas J. Houthuijs
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, FELIX Laboratory, Institute of Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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5
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Pereverzev A, Roithová J. Experimental techniques and terminology in gas-phase ion spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4826. [PMID: 35434805 PMCID: PMC9285946 DOI: 10.1002/jms.4826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 06/01/2023]
Abstract
This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.
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Affiliation(s)
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityNijmegenThe Netherlands
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6
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Lee YR, Kwon CH. Innovative mass spectrometer for high-resolution ion spectroscopy. J Chem Phys 2021; 155:164203. [PMID: 34717366 DOI: 10.1063/5.0066348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Conventional ion spectroscopy is inapplicable for ions produced in low concentrations or with low spectral resolutions. Hence, we constructed a high-resolution vacuum ultraviolet mass-analyzed threshold ionization (HR VUV-MATI) spectrometer composed of a four-wave frequency mixing cell capable of generating long-lasting and intense VUV laser pulses of ∼1 × 1010 photons/pulse at wavelengths of 123.6-160.0 nm, a space-focused linear time-of-flight photoionization chamber with a new ion-source assembly, and a compact molecular beam chamber with a temperature-controlled pulsed nozzle for ion spectroscopy. The ion-source assembly and pulsing schemes enabled an ∼15-μs-delayed but extremely weak pulsed-field-ionization of the molecules in the zero-kinetic-energy (ZEKE) states and first-order space focusing of the generated MATI ions. These ZEKE states were effectively generated by a minute electric jitter from the high-lying Rydberg states, which were initially prepared via VUV photoexcitation. The spectral and mass resolutions (∼5 cm-1 and 2400, respectively) and the signal strength were simultaneously enhanced using this spectrometer. Moreover, it could be used to measure the fine vibrational spectrum from the zero-point level of the cation and the exact adiabatic ionization energy of the neutral molecule. Additionally, it could be used to measure the appearance energies of the photoproducts and elucidate the vibrational structures of the cationic isotopomers, utilizing other pulsing schemes. Furthermore, this spectrometer could be used to analyze the congested vibrational spectrum of a cation with multiple conformations. Thus, the HR VUV-MATI spectrometer-a potential alternative to photoelectron spectrometers-can be used to analyze the conformational structure-dependent reactivities.
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Affiliation(s)
- Yu Ran Lee
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Chan Ho Kwon
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
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7
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Marceca E, Noble JA, Dedonder-Lardeux C, Jouvet C. Loss of CO 2 from Monodeprotonated Phthalic Acid upon Photodissociation and Dissociative Electron Detachment. J Phys Chem A 2021; 125:7406-7413. [PMID: 34415759 DOI: 10.1021/acs.jpca.1c04854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The decarboxylation (CO2 loss) mechanism of cold monodeprotonated phthalic acid was studied in a photodissociation action spectrometer by quantifying mass-selected product anions and neutral particles as a function of the excitation energy. The analysis proceeded by interpreting the translational energy distribution of the generated uncharged products, and with the help of quantum calculations. In particular, this study reveals different fragmentation pathways in the deprotonated anion and in the radical generated upon electron photodetachment. Unlike the behavior found in other deprotonated aryl carboxylic acids, which do not fragment in the anion excited state, a double loss of CO2 molecules takes place in the phthalic monoanion. Moreover, at higher excitation energies the phthalic monoanion experiences decarboxylative photodetachment with a statistical distribution of product translational energies, which contrasts with the impulsive dissociation reactions characteristic of other aryl carboxylic anions.
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Affiliation(s)
- Ernesto Marceca
- INQUIMAE (CONICET-Universidad de Buenos Aires), DQIAQF (Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria), 3er piso, Pab. II, 1428 Buenos Aires, Argentina
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8
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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9
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Gorbachev VM, Miloglyadova L, Tsybizova A, Chen P. Application of continuous wave quantum cascade laser in combination with CIVP spectroscopy for investigation of large organic and organometallic ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:083002. [PMID: 34470415 DOI: 10.1063/5.0058625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Rapidly developing mid-infrared quantum cascade laser (QCL) technology gives easy access to broadly tunable mid-IR laser radiation at a modest cost. Despite several applications of QCL in the industry, its usage for spectroscopic investigation of synthetically relevant organic compounds has been limited. Here, we report the application of an external cavity, continuous wave, mid-IR QCL to cryogenic ion vibrational predissociation spectroscopy to analyze a set of large organic molecules, organometallic complexes, and isotopically labeled compounds. The obtained spectra of test molecules are characterized by a high signal-to-noise ratio and low full width at half-maximum-values, allowing the assignment of two compounds with just a few wavenumber difference. Data generated by cw-QCL and spectra produced by another standard Nd:YAG difference-frequency generation system are compared and discussed.
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Affiliation(s)
| | | | | | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
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10
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Liu Y, Ma C, Nováková G, Marek A, Tureček F. Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals. J Phys Chem A 2021; 125:6096-6108. [PMID: 34240862 DOI: 10.1021/acs.jpca.1c03477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.
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Affiliation(s)
- Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Congcong Ma
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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11
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Tureček F. Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms. J Phys Chem B 2021; 125:7090-7100. [PMID: 34166596 DOI: 10.1021/acs.jpcb.1c03674] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion-ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV-visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion-electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson-Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.
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Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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12
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Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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13
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Tsybizova A, Paenurk E, Gorbachev V, Chen P. Perturbation of Pyridinium CIVP Spectra by N 2 and H 2 Tags: An Experimental and BOMD Study. J Phys Chem A 2020; 124:8519-8528. [PMID: 32954731 DOI: 10.1021/acs.jpca.0c06752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In cryogenic ion vibrational predissociation (CIVP) spectroscopy, the influence of the tag on the spectrum is an important consideration. Whereas for small ions several studies have shown that the tag effects can be significant, these effects are less understood for large ions or for large numbers of tags. Nevertheless, it is commonly assumed that if the investigated molecular ion is large enough, the perturbations arising from the tag are small and can therefore be neglected in the interpretation. In addition, it is generally assumed that the more weakly bound the tag is, the less it perturbs the CIVP spectrum. Under these assumptions, CIVP spectra are claimed to be effectively IR absorption spectra of the free molecular ion. Having observed unexpected splittings in otherwise unproblematic CIVP spectra of some tagged ions, we report Born-Oppenheimer molecular dynamics (BOMD) simulations that strongly indicate that mobility among the more weakly bound tags leads to the surprising splittings. We compared the behavior of two tags commonly used in CIVP spectroscopy (H2 and N2) with a large pyridinium cation. Our experimental results surprisingly show that under the appropriate circumstances, the more weakly bound tag can perturb the CIVP spectra more than the more strongly bound tag by not just shifting but also splitting the observed bands. The more weakly bound tag had significant residence times at several spectroscopically distinct sites on the molecular ion. This indicates that the weakly bound tag is likely to sample several binding sites in the experiment, some of which involve interaction with the reporter chromophore.
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Affiliation(s)
- Alexandra Tsybizova
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Eno Paenurk
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Vladimir Gorbachev
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter Chen
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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14
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McDonald DC, Rittgers BM, Theis RA, Fortenberry RC, Marks JH, Leicht D, Duncan MA. Infrared spectroscopy and anharmonic theory of H 3 +Ar 2,3 complexes: The role of symmetry in solvation. J Chem Phys 2020; 153:134305. [PMID: 33032436 DOI: 10.1063/5.0023205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectra of H3 +Ar2,3 and D3 +Ar2,3 are investigated in the 2000 cm-1 to 4500 cm-1 region through a combination of mass-selected infrared laser photodissociation spectroscopy and computational work including the effects of anharmonicity. In the reduced symmetry of the di-argon complex, vibrational activity is detected in the regions of both the symmetric and antisymmetric hydrogen stretching modes of H3 +. The tri-argon complex restores the D3h symmetry of the H3 + ion, with a concomitant reduction in the vibrational activity that is limited to the region of the antisymmetric stretch. Throughout these spectra, additional bands are detected beyond those predicted with harmonic vibrational theory. Anharmonic theory is able to reproduce some of the additional bands, with varying degrees of success.
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Affiliation(s)
- D C McDonald
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - B M Rittgers
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - R A Theis
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia 30460, USA
| | - R C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
| | - J H Marks
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - D Leicht
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - M A Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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15
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Brathwaite AD, Ward TB, Marks JH, Duncan MA. Coordination and Solvation in Gas-Phase Ag+(C2H2)n Complexes Studied with Selected-Ion Infrared Spectroscopy. J Phys Chem A 2020; 124:8562-8573. [DOI: 10.1021/acs.jpca.0c08081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Timothy B. Ward
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Joshua H. Marks
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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16
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Leicht D, Rittgers BM, Douberly GE, Wagner JP, McDonald DC, Mauney DT, Tsuge M, Lee YP, Duncan MA. Infrared spectroscopy of H+(CO)2 in the gas phase and in para-hydrogen matrices. J Chem Phys 2020; 153:084305. [DOI: 10.1063/5.0019731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Leicht
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | | | - Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J. Philipp Wagner
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - David C. McDonald
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Daniel T. Mauney
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Masashi Tsuge
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Yuan-Pern Lee
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Atomic and Molecular Sciences Academia Sinica, Taipei 10617, Taiwan
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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17
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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18
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Carnegie PD, Marks JH, Brathwaite AD, Ward TB, Duncan MA. Microsolvation in V +(H 2O) n Clusters Studied with Selected-Ion Infrared Spectroscopy. J Phys Chem A 2020; 124:1093-1103. [PMID: 31961153 DOI: 10.1021/acs.jpca.9b11275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gas-phase ion-molecule clusters of the form V+(H2O)n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit redshifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V+ ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of acceptor-acceptor-donor (AAD)-coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly charged or doubly charged cation-water clusters. This indicates that cation identity and charge-site location in the cluster can produce discernable spectral differences for clusters in this size range.
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Affiliation(s)
- Prosser D Carnegie
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Joshua H Marks
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Antonio D Brathwaite
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Timothy B Ward
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Michael A Duncan
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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19
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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20
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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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21
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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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22
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Simons J. Concluding remarks for advances in ion spectroscopy Faraday Discussion. Faraday Discuss 2019; 217:623-643. [PMID: 31169273 DOI: 10.1039/c9fd00058e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Because the Introductory Lecture of this Faraday Discussion emphasized the recent history and exciting developments in the fields of experimental methods and applications of gaseous ion spectroscopy, these Concluding Remarks are, by design, directed somewhat more toward the roles played by theory. In discussing both the experimental and theoretical studies of gaseous ions, it is important to recognize and appreciate the delicate balance workers in the field are pursuing in terms of methodological/tool development and applications to current-day pressing problems in chemistry, physics, materials science, and biology. Without both components of modern research in this field, progress will not be efficient. Substantial discussion is included about the reductive approach that is commonly used to attempt to connect studies of ions in the gas phase (i.e., as isolated species) with properties of these ions as they exist in nature. Issues of how small a model system can be, to what extent surroundings/solvation can be addressed, and how our experimental or theoretical tools might limit us are all discussed in some detail. The current ability of theory to assist in the interpretation of experimental spectral data on gaseous ions is discussed, as are several of the most pressing limitations of theory on this front. Finally, the author offers his thoughts about what advances/improvements in theory are needed and the outlook for when they might be expected, and urges the experimental community to remain in close contact with theory groups developing new methods so that progress can be optimized.
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Affiliation(s)
- Jack Simons
- Dept. of Chemistry, Henry Eyring Center for Theoretical Chemistry, University of Utah, USA.
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23
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Wagner JP, Giles SM, Duncan MA. Gas phase infrared spectroscopy of the H2C NH2+ methaniminium cation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Rodgers MT. Robert C. Dunbar: CURRICULUM VITAE: June 26, 1943, Boston, Massachusetts-October 31, 2017, Cleveland, Ohio. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:8-15. [PMID: 30773921 DOI: 10.1177/1469066718817618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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25
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Wagner JP, McDonald DC, Duncan MA. Spectroscopy of Proton Coordination with Ethylenediamine. J Phys Chem A 2018; 122:5168-5176. [PMID: 29771517 DOI: 10.1021/acs.jpca.8b03592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protonated ethylenediamine monomer, dimer, and trimer were produced in the gas phase by an electrical discharge/supersonic expansion of argon seeded with ethylenediamine (C2H8N2, en) vapor. Infrared spectra of these ions were measured in the region from 1000 to 4000 cm-1 using laser photodissociation and argon tagging. Computations at the CBS-QB3 level were performed to explore possible isomers and understand the infrared spectra. The protonated monomer exhibits a gauche conformation and an intramolecular hydrogen bond. Its parallel shared proton vibration occurs as a broad band around 2785 cm-1, despite the formally equivalent proton affinities of the two amino groups involved, which usually leads to low frequency bands. The barrier to intramolecular proton transfer is 2.2 kcal mol-1 and does not vanish upon addition of the zero-point energy, unlike the related protonated ammonia dimer. The structure of the dimer is formed by chelation of the monomer's NH3+ group, thereby localizing the excess proton and increasing the frequency of the intramolecular shared proton vibration to 3157 cm-1. Other highly fluxional dimer structures with facile intermolecular proton transfer and concomitant structural reorganization were computed to lie within 2 kcal mol-1 of the experimentally observed structure. The spectrum of the trimer is rather diffuse, and a clear assignment is not possible. However, an isomer with an intramolecular proton transfer like that of the monomer is most consistent with the experimental spectrum.
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Affiliation(s)
- J Philipp Wagner
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
| | - David C McDonald
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
| | - Michael A Duncan
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
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26
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Fritsche L, Bach A, Miloglyadova L, Tsybizova A, Chen P. A 4 K FT-ICR cell for infrared ion spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:063119. [PMID: 29960550 DOI: 10.1063/1.5026973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present the design of the newly constructed cryogenic Fourier-transform ion cyclotron resonance (FT-ICR) ion trap for infrared ion spectroscopy. Trapped ions are collisionally cooled by the pulsed introduction of buffer gas into the cell. Using different buffer gases and cell temperatures, we record action spectra of weakly bound neutral gas-analyte complexes with an IR laser source. We show for the first time that ion-He complexes can be observed in an ICR cell at temperatures around 4 K. We compare the experimental vibrational spectra of Ag(PPh3)2+ obtained by tagging with different neutral gases: He, Ne, Ar, H2, and N2 to computed vibrational spectra. Furthermore, the conditions necessary for the formation of neutral tags within an ICR ion trap are studied.
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Affiliation(s)
- Lukas Fritsche
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Andreas Bach
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Alexandra Tsybizova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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27
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Gerlich D. Infrared spectroscopy of cold trapped molecular ions using He-tagging. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800122] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dieter Gerlich
- Department of Physics; University of Technology; Chemnitz Germany
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28
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Wagner JP, McDonald DC, Duncan MA. Infrared Spectroscopy of the Astrochemically Relevant Protonated Formaldehyde Dimer. J Phys Chem A 2017; 122:192-198. [DOI: 10.1021/acs.jpca.7b10573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Philipp Wagner
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - David C. McDonald
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
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29
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30
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Wagner JP, McDonald DC, Duncan MA. Near-infrared spectroscopy and anharmonic theory of the H2O+Ar1,2 cation complexes. J Chem Phys 2017; 147:104302. [DOI: 10.1063/1.4998419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- J. Philipp Wagner
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, USA
| | - David C. McDonald
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, USA
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, USA
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31
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Furuhashi T, Okuda K. Application of GC/MS Soft Ionization for Isomeric Biological Compound Analysis. Crit Rev Anal Chem 2017; 47:438-453. [DOI: 10.1080/10408347.2017.1320215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Takeshi Furuhashi
- Department of Natural and Environmental Science, Teikyo University of Science, Adachi, Tokyo, Japan
- Anicom Specialty Medical Institute Inc., Shinjuku-ku, Tokyo, Japan
| | - Koji Okuda
- JEOL USA, Inc., Peabody, Massachusetts, USA
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32
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McDonald DC, Mauney DT, Leicht D, Marks JH, Tan JA, Kuo JL, Duncan MA. Communication: Trapping a proton in argon: Spectroscopy and theory of the proton-bound argon dimer and its solvation. J Chem Phys 2017; 145:231101. [PMID: 28010076 DOI: 10.1063/1.4972581] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ion-molecule complexes of the form H+Arn are produced in pulsed-discharge supersonic expansions containing hydrogen and argon. These ions are analyzed and mass-selected in a reflectron spectrometer and studied with infrared laser photodissociation spectroscopy. Infrared spectra for the n = 3-7 complexes are characterized by a series of strong bands in the 900-2200 cm-1 region. Computational studies at the MP2/aug-cc-pVTZ level examine the structures, binding energies, and infrared spectra for these systems. The core ion responsible for the infrared bands is the proton-bound argon dimer, Ar-H+-Ar, which is progressively solvated by the excess argon. Anharmonic vibrational theory is able to reproduce the vibrational structure, identifying it as arising from the asymmetric proton stretch in combination with multiple quanta of the symmetric argon stretch. Successive addition of argon shifts the proton vibration to lower frequencies, as the charge is delocalized over more ligands. The Ar-H+-Ar core ion has a first solvation sphere of five argons.
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Affiliation(s)
- D C McDonald
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - D T Mauney
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - D Leicht
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - J H Marks
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J A Tan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 10617, People's Republic of China
| | - J-L Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 10617, People's Republic of China
| | - M A Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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33
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Mauney DT, Mosley JD, Madison LR, McCoy AB, Duncan MA. Infrared spectroscopy and theory of the formaldehyde cation and its hydroxymethylene isomer. J Chem Phys 2016; 145:174303. [DOI: 10.1063/1.4966214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. T. Mauney
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J. D. Mosley
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - L. R. Madison
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - A. B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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34
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Brathwaite AD, Abbott-Lyon HL, Duncan MA. Distinctive Coordination of CO vs N2 to Rhodium Cations: An Infrared and Computational Study. J Phys Chem A 2016; 120:7659-7670. [DOI: 10.1021/acs.jpca.6b07749] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. D. Brathwaite
- College
of Science and Mathematics, University of the Virgin Islands, St. Thomas, United States Virgin Islands 00802
| | - H. L. Abbott-Lyon
- Department of Chemistry & Biochemistry, Kennesaw State University, Kennesaw, Georgia 30144, United States
| | - M. A. Duncan
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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35
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Wenthold PG, Koirala D, Somogyi A, Poutsma JC. Infrared spectroscopic confirmation of α-lactone formation in the dissociation of a gaseous amino acid. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paul G. Wenthold
- Department of Chemistry; Purdue University; 560 Oval Drive West Lafayette IN 47907 USA
| | - Damodar Koirala
- Department of Chemistry; Purdue University; 560 Oval Drive West Lafayette IN 47907 USA
| | - Arpad Somogyi
- Campus Chemical Instrumentation Center, Mass Spectrometry and Proteomics Laboratory; The Ohio State University; 460 West 12th Ave Columbus OH 43210 USA
| | - J. C. Poutsma
- The College of William and Mary; Williamsburg VA 23187 USA
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36
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Roithová J, Gray A, Andris E, Jašík J, Gerlich D. Helium Tagging Infrared Photodissociation Spectroscopy of Reactive Ions. Acc Chem Res 2016; 49:223-30. [PMID: 26821086 DOI: 10.1021/acs.accounts.5b00489] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interrogation of reaction intermediates is key for understanding chemical reactions; however their direct observation and study remains a considerable challenge. Mass spectrometry is one of the most sensitive analytical techniques, and its use to study reaction mixtures is now an established practice. However, the information that can be obtained is limited to elemental analysis and possibly to fragmentation behavior, which is often challenging to analyze. In order to extend the available experimental information, different types of spectroscopy in the infrared and visible region have been combined with mass spectrometry. Spectroscopy of mass selected ions usually utilizes the powerful sensitivity of mass spectrometers, and the absorption of photons is not detected as such but rather translated to mass changes. One approach to accomplish such spectroscopy involves loosely binding a tag to an ion that will be removed by absorption of one photon. We have constructed an ion trapping instrument capable of reaching temperatures that are sufficiently low to enable tagging by helium atoms in situ, thus permitting infrared photodissociation spectroscopy (IRPD) to be carried out. While tagging by larger rare gas atoms, such as neon or argon is also possible, these may cause significant structural changes to small and reactive species, making the use of helium highly beneficial. We discuss the "innocence" of helium as a tag in ion spectroscopy using several case studies. It is shown that helium tagging is effectively innocent when used with benzene dications, not interfering with their structure or IRPD spectrum. We have also provided a case study where we can see that despite its minimal size there are systems where He has a huge effect. A strong influence of the He tagging was shown in the IRPD spectra of HCCl(2+) where large spectral shifts were observed. While the presented systems are rather small, they involve the formation of mixtures of isomers. We have therefore implemented two-color experiments where one laser is employed to selectively deplete a mixture by one (or more) isomer allowing helium tagging IRPD spectra of the remaining isomer(s) to be recorded via the second laser. Our experimental setup, based on a linear wire quadrupole ion trap, allows us to deplete almost 100% of all helium tagged ions in the trap. Using this special feature, we have developed attenuation experiments for determination of absolute photofragmentation cross sections. At the same time, this approach can be used to estimate the representation of isomers in a mixture. The ultimate aim is the routine use of this instrument and technique to study a wide range of reaction intermediates in catalysis. To this end, we present a study of hypervalent iron(IV)-oxo complexes ([(L)Fe(O)(NO3)](+)). We show that we can spectroscopically differentiate iron complexes with S = 1 and S = 2 according to the stretching vibrations of a nitrate counterion.
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Affiliation(s)
- Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Andrew Gray
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Erik Andris
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Juraj Jašík
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Dieter Gerlich
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
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37
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Corinti D, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Cisplatin Binding to Biological Ligands Revealed at the Encounter Complex Level by IR Action Spectroscopy. Chemistry 2016; 22:3794-803. [DOI: 10.1002/chem.201504521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Cecilia Coletti
- Dipartimento di Farmacia; Università G. D'Annunzio; Via dei Vestini 31 66100 Chieti Italy
| | - Nazzareno Re
- Dipartimento di Farmacia; Università G. D'Annunzio; Via dei Vestini 31 66100 Chieti Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
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38
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Hendricks NG, Julian RR. Leveraging ultraviolet photodissociation and spectroscopy to investigate peptide and protein three-dimensional structure with mass spectrometry. Analyst 2016; 141:4534-40. [DOI: 10.1039/c6an01020b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in mass spectrometry and lasers have facilitated the development of novel experiments combining the benefits of both technologies.
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Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California
- Riverside
- USA
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39
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Kocak A, Ashraf MA, Metz RB. Vibrational Spectroscopy Reveals Varying Structural Motifs in Cu+(CH4)n and Ag+(CH4)n (n = 1–6). J Phys Chem A 2015; 119:9653-65. [DOI: 10.1021/acs.jpca.5b07079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abdulkadir Kocak
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Muhammad Affawn Ashraf
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Ricardo B. Metz
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
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40
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Wellman SMJ, Jockusch RA. Moving in on the Action: An Experimental Comparison of Fluorescence Excitation and Photodissociation Action Spectroscopy. J Phys Chem A 2015; 119:6333-8. [DOI: 10.1021/acs.jpca.5b04835] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sydney M. J. Wellman
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rebecca A. Jockusch
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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41
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Brathwaite AD, Ward TB, Walters RS, Duncan MA. Cation−π and CH−π Interactions in the Coordination and Solvation of Cu+(acetylene)n Complexes. J Phys Chem A 2015; 119:5658-67. [DOI: 10.1021/acs.jpca.5b03360] [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)
- Antonio D. Brathwaite
- College
of Science and Mathematics, University of the Virgin Islands, St.
Thomas, United States Virgin
Islands 00802
| | - Timothy B. Ward
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Richard S. Walters
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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42
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study. Inorg Chem 2015; 54:3513-22. [PMID: 25798661 DOI: 10.1021/acs.inorgchem.5b00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.
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Affiliation(s)
- Barbara Chiavarino
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy
| | | | - Jean-Yves Salpin
- ∥Université d'Evry Val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Boulevard François Mitterrand, 91025 Evry, France
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43
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De Petris A, Chiavarino B, Crestoni ME, Coletti C, Re N, Fornarini S. Exploring the Conformational Variability in the Heme b Propionic Acid Side Chains through the Effect of a Biological Probe: A Study of the Isolated Ions. J Phys Chem B 2015; 119:1919-29. [DOI: 10.1021/jp5113476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alberto De Petris
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
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44
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Hendricks NG, Julian RR. Two-step energy transfer enables use of phenylalanine in action-EET for distance constraint determination in gaseous biomolecules. Chem Commun (Camb) 2015; 51:12720-3. [DOI: 10.1039/c5cc03779d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-step energy transfer is observed between phenylalanine, tyrosine, and modified cysteine. This gas-phase system enables use of phenylalanine in energy transfer experiments, provides specific distance information for structure determination, and is easily examined with mass spectrometry.
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Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California, Riverside
- Riverside
- USA
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45
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Canon F, Milosavljević AR, Nahon L, Giuliani A. Action spectroscopy of a protonated peptide in the ultraviolet range. Phys Chem Chem Phys 2015; 17:25725-33. [DOI: 10.1039/c4cp04762a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Action spectroscopy of substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV.
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Affiliation(s)
- Francis Canon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- UMR1324 Centre des Sciences du Goût et de l'Alimentation
| | | | - Laurent Nahon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | - Alexandre Giuliani
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- Uar1008
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46
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Mosley JD, Young JW, Duncan MA. Infrared spectroscopy of the acetyl cation and its protonated ketene isomer. J Chem Phys 2014; 141:024306. [DOI: 10.1063/1.4887074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. D. Mosley
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J. W. Young
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - M. A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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47
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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48
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Reishus KN, Brathwaite AD, Mosley JD, Duncan MA. Coordination versus Solvation in Al+(benzene)n Complexes Studied with Infrared Spectroscopy. J Phys Chem A 2014; 118:7516-25. [DOI: 10.1021/jp500778w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kimberly N. Reishus
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Antonio D. Brathwaite
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Jonathan D. Mosley
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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49
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Liu HT, Ning CG, Huang DL, Wang LS. Vibrational Spectroscopy of the Dehydrogenated Uracil Radical by Autodetachment of Dipole-Bound Excited States of Cold Anions. Angew Chem Int Ed Engl 2014; 53:2464-8. [DOI: 10.1002/anie.201310323] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/29/2023]
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50
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Liu HT, Ning CG, Huang DL, Wang LS. Vibrational Spectroscopy of the Dehydrogenated Uracil Radical by Autodetachment of Dipole-Bound Excited States of Cold Anions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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