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Fries DV, Klein MP, Straßner A, Huber ME, Luczak M, Wiehn C, Niedner-Schatteburg G. Cryo IR spectroscopy and cryo kinetics of dinitrogen activation and cleavage by small tantalum cluster cations. J Chem Phys 2023; 159:164303. [PMID: 37873960 DOI: 10.1063/5.0157217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
We investigate small tantalum clusters Tan+, n = 2-4, for their capability to cleave N2 adsorption spontaneously. We utilize infrared photon dissociation (IR-PD) spectroscopy of isolated and size selected clusters under cryogenic conditions within a buffer gas filled ion trap, and we augment our experiments by quantum chemical simulations (at DFT level). All Tan+ clusters, n = 2-4, seem to cleave N2 efficiently. We confirm and extend a previous study under ambient conditions on Ta2+ cluster [Geng et al., Proc. Natl. Acad. Sci. U. S. A. 115, 11680-11687 (2018)]. Our cryo studies and the concomitant DFT simulations of the tantalum trimer Ta3+ suggest cleavage of the first and activation of the second and third N2 molecule across surmountable barriers and along much-involved multidimensional reaction paths. We unravel the underlying reaction processes and the intermediates involved. The study of the N2 adsorbate complexes of Ta4+ presented here extends our earlier study and previously published spectra from (4,m), m = 1-5 [Fries et al., Phys. Chem. Chem. Phys. 23(19), 11345-11354 (2021)], up to m = 12. We confirm the priory published double activation and nitride formation, succeeded by single side-on N2 coordination. Significant red shifts of IR-PD bands from these side-on coordinated μ2-κN:κN,N N2 ligands correlate with the degree of tilting towards the second coordinating Ta center. All subsequently attaching N2 adsorbates onto Ta4+ coordinate in an end-on fashion, and we find clear evidence for co-existence of end-on coordination isomers. The study of stepwise N2 adsorption revealed adsorption limits m(max) of [Tan(N2)m]+ which increase with n, and kinetic fits revealed significant N2 desorption rates upon higher N2 loads. The enhanced absolute rate constants of the very first adsorbate steps kabs(n,0) of the small Ta3+ and Ta4+ clusters independently suggest dissociative N2 adsorption and likely N2 cleavage into Ta nitrides.
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Affiliation(s)
- Daniela V Fries
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Matthias P Klein
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Annika Straßner
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Maximilian E Huber
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Maximilian Luczak
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Christopher Wiehn
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Gereon Niedner-Schatteburg
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
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Rahimi R, Saban N, Bar I. Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration. J Am Chem Soc 2023; 145:18455-18467. [PMID: 37561882 DOI: 10.1021/jacs.3c04762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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3
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Yamaguchi K, Hirata K, Ishiuchi SI, Fujii M. Ultraviolet and infrared spectra of mono-, di- and tri-hydrated clusters of protonated noradrenaline – Solvation and conformational variations. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Corinti D, Maccelli A, Chiavarino B, Schütz M, Bouchet A, Dopfer O, Crestoni ME, Fornarini S. Cation-π Interactions between a Noble Metal and a Polyfunctional Aromatic Ligand: Ag + (benzylamine). Chemistry 2022; 28:e202200300. [PMID: 35412692 PMCID: PMC9325466 DOI: 10.1002/chem.202200300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Indexed: 12/21/2022]
Abstract
The structure of an isolated Ag+ (benzylamine) complex is investigated by infrared multiple photon dissociation (IRMPD) spectroscopy complemented with quantum chemical calculations of candidate geometries and their vibrational spectra, aiming to ascertain the role of competing cation-N and cation-π interactions potentially offered by the polyfunctional ligand. The IRMPD spectrum has been recorded in the 800-1800 cm-1 fingerprint range using the IR free electron laser beamline coupled with an FT-ICR mass spectrometer at the Centre Laser Infrarouge d'Orsay (CLIO). The resulting IRMPD pattern points toward a chelate coordination (N-Ag+ -π) involving both the amino nitrogen atom and the aromatic π-system of the phenyl ring. The gas-phase reactivity of Ag+ (benzylamine) with a neutral molecular ligand (L) possessing either an amino/aza functionality or an aryl group confirms N- and π-binding affinity and suggests an augmented silver coordination in the product adduct ionAg + ( benzylamine ) ( L ) .
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del FarmacoUniversità degli studi di Roma La SapienzaP.le A. Moro 5I-00185RomaItaly
| | - Alessandro Maccelli
- Dipartimento di Chimica e Tecnologie del FarmacoUniversità degli studi di Roma La SapienzaP.le A. Moro 5I-00185RomaItaly
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del FarmacoUniversità degli studi di Roma La SapienzaP.le A. Moro 5I-00185RomaItaly
| | - Markus Schütz
- Institut für Optik und Atomare PhysikTechnische Universität BerlinHardenbergstr. 3610623BerlinGermany
- present address: Eagleyard Photonics GmbHRudower Chaussee 2912489BerlinGermany
| | - Aude Bouchet
- Institut für Optik und Atomare PhysikTechnische Universität BerlinHardenbergstr. 3610623BerlinGermany
- present address: Université Lille LASIRE Lab Adv Spect Interact React & Environm Cite Sci, CNRS, UMR 851659000LilleFrance
| | - Otto Dopfer
- Institut für Optik und Atomare PhysikTechnische Universität BerlinHardenbergstr. 3610623BerlinGermany
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del FarmacoUniversità degli studi di Roma La SapienzaP.le A. Moro 5I-00185RomaItaly
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del FarmacoUniversità degli studi di Roma La SapienzaP.le A. Moro 5I-00185RomaItaly
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Ocean Acidification Amplifies the Olfactory Response to 2-Phenylethylamine: Altered Cue Reception as a Mechanistic Pathway? J Chem Ecol 2021; 47:859-876. [PMID: 34014453 PMCID: PMC8613125 DOI: 10.1007/s10886-021-01276-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
With carbon dioxide (CO2) levels rising dramatically, climate change threatens marine environments. Due to increasing CO2 concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century. There is an urgent need to understand the impact of ocean acidification on chemical-ecological processes. To date, the extent and mechanisms by which the decreasing ocean pH influences chemical communication are unclear. Combining behaviour assays with computational chemistry, we explore the function of the predator related cue 2-phenylethylamine (PEA) for hermit crabs (Pagurus bernhardus) in current and end-of-the-century oceanic pH. Living in intertidal environments, hermit crabs face large pH fluctuations in their current habitat in addition to climate-change related ocean acidification. We demonstrate that the dietary predator cue PEA for mammals and sea lampreys is an attractant for hermit crabs, with the potency of the cue increasing with decreasing pH levels. In order to explain this increased potency, we assess changes to PEA’s conformational and charge-related properties as one potential mechanistic pathway. Using quantum chemical calculations validated by NMR spectroscopy, we characterise the different protonation states of PEA in water. We show how protonation of PEA could affect receptor-ligand binding, using a possible model receptor for PEA (human TAAR1). Investigating potential mechanisms of pH-dependent effects on olfactory perception of PEA and the respective behavioural response, our study advances the understanding of how ocean acidification interferes with the sense of smell and thereby might impact essential ecological interactions in marine ecosystems.
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Beyond templating: Electronic structure impacts of aromatic cations in organic–inorganic antimony chlorides. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202000484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Müller D, Dopfer O. Interaction of Alkali Ions with Flavins: Infrared and Optical Spectra of Metal–Riboflavin Complexes. J Phys Chem A 2021; 125:3146-3158. [DOI: 10.1021/acs.jpca.1c01846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- David Müller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
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8
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Xu C, Xu L, Han R, Zhu Y, Zhang J. Blood circulation stable doxorubicin prodrug nanoparticles containing hydrazone and thioketal moieties for antitumor chemotherapy. Colloids Surf B Biointerfaces 2021; 201:111632. [PMID: 33667865 DOI: 10.1016/j.colsurfb.2021.111632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/26/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
Prodrug nanoparticles with cleavable moieties sensitive to intracellular stimuli have drawn great attention on cancer chemotherapy. Herein, a reactive oxygen species (ROS)-responsive doxorubicin prodrug mPEG-Phe-TK-Phe-hyd-DOX was synthesized, in which hydrophilic methoxy poly(ethylene glycol) (mPEG) and hydrophobic anticancer drug doxorubicin (DOX) were conjugated with hydrazone (hyd) and ROS-responsive thioketal (TK) moieties. The ROS-responsiveness of prodrug was confirmed by proton nuclear magnetic resonance (1H NMR) and dynamic light scattering (DLS). Unexpectedly, the results of in vitro drug release indicated that the hydrazone bond of prodrug nanoparticles was insensitive to pH, which may be due to the strong hydrophobicity, π-π interactions and cation-π interactions jointly inhibited the hydrolysis of hydrazone bonds under acidic conditions. The cellular uptake and in vitro anticancer study showed that ROS-responsive prodrug nanoparticles exhibited faster cellular uptake and better anticancer efficacy. The in vivo experiments showed that the ROS-responsive prodrug nanoparticles had comparable antitumor efficacy with free anticancer drug DOX and reduced organ toxicity. Our results provide novel idea of successfully design multi-stimuli-responsive nano-drug carrier.
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Affiliation(s)
- Caidie Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Long Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
| | - Renlu Han
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yabin Zhu
- Medical School of Ningbo University, Ningbo, 315211, China
| | - Jianfeng Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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Singh VB. Spectroscopic Signatures and the Cation-π Interaction in Conformational Preferences of the Neurotransmitter Dopamine in Aqueous Solution. ACS Chem Neurosci 2021; 12:613-625. [PMID: 33523624 DOI: 10.1021/acschemneuro.0c00597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The precise determination of the neurotransmitter dopamine's conformational preferences in aqueous solution is crucial for understanding its neurobiological function. The first principle Møller-Plesset perturbation theory (MP2) and dispersion corrected density functional theory (DFT-D3) methods, employing the basis set aug-cc-pVDZ(/pVTZ), are used to reinvestigate the nine lowest-energy (isolated) structures of protonated dopamine (DAH+) in both gas and aqueous phases. DAH+ trans isomer t1 is found higher in energy than lowest-energy gauche isomer g+1 (g + 1) by 6.4 and 5.7 kJ mol-1, at the MP2 and B3LYP-D3 levels of theory, respectively, in the aqueous environment within the polarizable continuum model (PCM). We found that the solvated cation, NH3+, retains its attractive character, which supports the previous report that agonist DAH+ can be involved in cation (NH3+)-π interaction in the active states of the D2 dopamine receptor. The dispersion corrected DFT evaluation of anharmonicity allows us to confirm the most experimental frequencies and suggest some new interpretations. The IR and Raman spectra's influential band for both gauche and the trans conformers observed at 1287/1288 cm-1 were enhanced in aqueous solution. The experimental Raman spectrum for dopamine was compared with the conformer-specific computed Raman spectrum of protonated dopamine (DAH+). The intense Raman band at 1451 cm-1 indicates the necessity of DAH+ calculated values in interpreting the Raman spectra. The most intense Raman band at 750 cm-1 arises due to the trans DAH+, t1, revealed by MP2/aug-cc-pVDZ Raman spectra, indicating trans DAH+ dominance in the bulk DAH+ of extracellular fluid.
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Chiavarino B, Sinha RK, Crestoni ME, Corinti D, Filippi A, Fraschetti C, Scuderi D, Maitre P, Fornarini S. Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay. Chemistry 2021; 27:2348-2360. [PMID: 33175428 DOI: 10.1002/chem.202003555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Indexed: 11/06/2022]
Abstract
The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]+ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]+ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Rajeev K Sinha
- Department of Atomic and Molecular Physics, Manipal University, Manipal, 576104, Karnataka, India
| | - 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
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Debora Scuderi
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Philippe Maitre
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:E692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]-, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
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Kwon JH, Lee MJ, Song G, Tsuruta K, Ishiuchi SI, Fujii M, Kang H. Cryogenic Ion Spectroscopy of a Singly Protonated Peptide DYYVVR: Locating Phosphorylation Sites of a Kinase Domain. J Phys Chem Lett 2020; 11:7103-7108. [PMID: 32787320 DOI: 10.1021/acs.jpclett.0c01802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cryogenic ion spectroscopy (CIS) was applied to singly protonated DYYVVR, a tryptic peptide that contains the two active tyrosine residues (Y980 and Y981) of the Janus kinase 3 (JAK3) kinase domain, together with its point mutants (Y980F and Y981F) and phosphorylated peptides (pY980, pY981, and pY980pY981). The two tyrosine chromophores showed distinguishable UV absorption bands at around 35 200 and 35 450 cm-1, respectively. By comparing with the point mutants, the lower electronic band was assigned to the absorption of Y981, and the higher one was assigned to Y980. When phosphorylated, the UV absorption of the phosphorylated chromophore shifts to higher energy above 36 500 cm-1 but the unphosphorylated chromophore gives the absorption in the same region. Conformer-specific IR spectroscopy and density functional theory (DFT) calculations were used to tentatively assign the structure of DYYVVR. Two conformations were found, where Y981 is solvated by the protonated side chain of arginine R984, and the orientation of the carboxylic OH of D979 was different between the two. It is demonstrated that CIS can be used to distinguish the two tyrosine chromophores and to locate the phosphorylation site of a kinase domain.
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Affiliation(s)
- Jang Han Kwon
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Min Ji Lee
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Gyeongok Song
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | | | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | | | - Hyuk Kang
- Department of Chemistry, Ajou University, Suwon 16499, Korea
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Rodrigues-Oliveira AF, Batista PR, Ducati LC, Correra TC. Analyzing the N–H+…π interactions of protonated tryptophan and phenylalkylamines using QTAIM, NCI, and NBO. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02643-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Chiavarino B, Dopfer O, Crestoni ME, Corinti D, Maître P, Fornarini S. IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions. Chemphyschem 2020; 21:749-761. [PMID: 31951044 DOI: 10.1002/cphc.202000041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 11/09/2022]
Abstract
Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH+ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH+ and m-OH-BZH+ only cis conformers are present in the ion population analyzed. For o-OH-BZH+ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH+ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH+ , m-OH-BZH+ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.
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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, 00185, Roma, Italy
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Philippe Maître
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
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Corinti D, Maccelli A, Chiavarino B, Maitre P, Scuderi D, Bodo E, Fornarini S, Crestoni ME. Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy. J Chem Phys 2019; 150:165101. [PMID: 31042893 DOI: 10.1063/1.5086666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]+, and as a Cu(ii) complex, [Cu(Cur - H)]+, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm-1) and hydrogen stretching (3100-3750 cm-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]+ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH3 groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]+ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Alessandro Maccelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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Corinti D, Crestoni ME, Fornarini S, Pieper M, Niehaus K, Giampà M. An integrated approach to study novel properties of a MALDI matrix (4-maleicanhydridoproton sponge) for MS imaging analyses. Anal Bioanal Chem 2018; 411:953-964. [DOI: 10.1007/s00216-018-1531-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 02/02/2023]
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17
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Corinti D, Catone D, Turchini S, Rondino F, Crestoni ME, Fornarini S. Photoionization mass spectrometry of ω-phenylalkylamines: Role of radical cation-π interaction. J Chem Phys 2018; 148:164307. [DOI: 10.1063/1.5027786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza,” P.le A. Moro 5, I-00185 Roma, Italy
| | - Daniele Catone
- CNR-ISM, Area della Ricerca di Roma Tor Vergata, Via del Fosso del Cavaliere 100, Roma, Italy
| | - Stefano Turchini
- CNR-ISM, Area della Ricerca di Roma Tor Vergata, Via del Fosso del Cavaliere 100, Roma, Italy
| | - Flaminia Rondino
- C. R. ENEA Frascati, FSN-TECFIS, Via E. Fermi 45, 00044 Frascati, 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
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Jašíková L, Roithová J. Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules. Chemistry 2018; 24:3374-3390. [PMID: 29314303 DOI: 10.1002/chem.201705692] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 01/07/2023]
Abstract
Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.
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Affiliation(s)
- Lucie Jašíková
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
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19
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Corinti D, Gregori B, Guidoni L, Scuderi D, McMahon TB, Chiavarino B, Fornarini S, Crestoni ME. Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy. Phys Chem Chem Phys 2018; 20:4429-4441. [PMID: 29372198 DOI: 10.1039/c7cp06657k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The binding motifs in the halide adducts with tyrosine ([Tyr + X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]- and [nitroTyr + X]-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]-, where the anion is placed above the face of the aromatic ring.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy.
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20
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Corinti D, Coletti C, Re N, Piccirillo S, Giampà M, Crestoni ME, Fornarini S. Hydrolysis of cis- and transplatin: structure and reactivity of the aqua complexes in a solvent free environment. RSC Adv 2017. [DOI: 10.1039/c7ra01182b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Vibrational spectroscopy and ligand exchange reactivity allows unambiguous discrimination of singly and doubly aquated species from cis- and transplatin, highlighting elementary events at the basis of anticancer action.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco
- Università degli Studi di Roma “La Sapienza”
- I-00185 Roma
- Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia
- Università G. D'Annunzio
- I-66100 Chieti
- Italy
| | - Nazzareno Re
- Dipartimento di Farmacia
- Università G. D'Annunzio
- I-66100 Chieti
- Italy
| | - Susanna Piccirillo
- Dip. di Scienze e Tecnologie Chimiche
- Università di Roma “Tor Vergata”
- 00133 Rome
- Italy
| | - Marco Giampà
- Dipartimento di Chimica e Tecnologie del Farmaco
- Università degli Studi di Roma “La Sapienza”
- I-00185 Roma
- Italy
- Proteom- und Metabolomforschung
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco
- Università degli Studi di Roma “La Sapienza”
- I-00185 Roma
- Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco
- Università degli Studi di Roma “La Sapienza”
- I-00185 Roma
- Italy
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21
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Paciotti R, Corinti D, De Petris A, Ciavardini A, Piccirillo S, Coletti C, Re N, Maitre P, Bellina B, Barran P, Chiavarino B, Elisa Crestoni M, Fornarini S. Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes. Phys Chem Chem Phys 2017; 19:26697-26707. [DOI: 10.1039/c7cp05203k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
IRMPD spectroscopy discloses N- versus S-platination.
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22
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Bouchet A, Klyne J, Ishiuchi SI, Fujii M, Dopfer O. Conformation of protonated glutamic acid at room and cryogenic temperatures. Phys Chem Chem Phys 2017; 19:10767-10776. [DOI: 10.1039/c6cp08553a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear infrared spectroscopy of protonated glutamic acid in a cryogenic ion trap allows for the clear-cut and quantitative identification of the two conformers of this fundamental biomolecule.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
- Laboratory for Chemistry and Life Science
| | - Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
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23
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Wako H, Ishiuchi SI, Kato D, Féraud G, Dedonder-Lardeux C, Jouvet C, Fujii M. A conformational study of protonated noradrenaline by UV–UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method. Phys Chem Chem Phys 2017; 19:10777-10785. [DOI: 10.1039/c6cp08426e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In protonated noradrenaline, 3 folded and 2 extended conformers were identified under the ultra-cold condition.
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Affiliation(s)
- Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Daichi Kato
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Géraldine Féraud
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Claude Dedonder-Lardeux
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Christophe Jouvet
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
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24
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Nieto P, Günther A, Berden G, Oomens J, Dopfer O. IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions. J Phys Chem A 2016; 120:8297-8308. [PMID: 27690438 DOI: 10.1021/acs.jpca.6b08281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800-1830 cm-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs+LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M+-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.
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Affiliation(s)
- Pablo Nieto
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Alan Günther
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
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25
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Voronina L, Masson A, Kamrath M, Schubert F, Clemmer D, Baldauf C, Rizzo T. Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase. J Am Chem Soc 2016; 138:9224-33. [DOI: 10.1021/jacs.6b04550] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Liudmila Voronina
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Antoine Masson
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Kamrath
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Franziska Schubert
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - David Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - Thomas Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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26
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Bouchet A, Schütz M, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction. Phys Chem Chem Phys 2016; 17:25742-54. [PMID: 25757357 DOI: 10.1039/c5cp00221d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, D-10623 Berlin, Germany.
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27
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Paciotti R, Coletti C, Re N, Scuderi D, Chiavarino B, Fornarini S, Crestoni ME. Serine O-sulfation probed by IRMPD spectroscopy. Phys Chem Chem Phys 2016; 17:25891-904. [PMID: 26027702 DOI: 10.1039/c5cp01409c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sulfation of amino acids is a frequent post-translational modification. It is highly labile, though, and characterizing it by mass spectrometry, an otherwise powerful and widely exploited tool in analytical proteomics, is a challenge. The presently reported study is aimed at revealing the O-sulfation of l-serine and elucidating the effects of protonation and deprotonation on the structure and stability of the ensuing ionic species, [sSer + H](+) and [sSer - H](-). These ions are obtained as gaseous, isolated species by electrospray ionization, trapped in a Paul ion-trap, and sampled by IR multiple photon dissociation (IRMPD) spectroscopy in either the 750-1900 cm(-1) fingerprint range, or the 2900 and 3700 cm(-1) range encompassing the N-H and O-H stretching modes. The recorded IRMPD spectra present diagnostic signatures of the sulfate modification which are missing in the spectra of the native serine ions, [Ser + H](+) and [Ser - H](-). The experimental IRMPD features have been interpreted by comparison with the linear IR spectra of the lowest energy structures that are likely candidates for the sampled ions, calculated at the M06-2X/6-311+G(d,p) level of theory. Evidence is gathered that the most stable conformations of [sSer + H](+) are stabilized by hydrogen bonding interactions between the protonated amino group and both the carbonyl and sulfate oxygens. [sSer - H](-) ions possess a negatively charged sulfate group involved in either a S=O···HN or a S=O···HO hydrogen bond. The experimental IRMPD spectra are consistent with the presence of multiple low-lying structures in a thermally equilibrated population of several species particularly in the case of [sSer - H](-) ions, where the high structural flexibility combined with the presence of a negative charge favors the co-existence of several different H-bonding motifs.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
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28
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Schütz M, Bouchet A, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. Effects of Aromatic Fluorine Substitution on Protonated Neurotransmitters: The Case of 2-Phenylethylamine. Chemistry 2016; 22:8124-36. [DOI: 10.1002/chem.201600798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Otto Dopfer
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
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Corinti D, Mannina L, Chiavarino B, Steinmetz V, Fornarini S, Crestoni ME. IRMPD signature of protonated pantothenic acid, an ubiquitous nutrient. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Schütz M, Bouchet A, Dopfer O. Infrared spectrum of the cold ortho-fluorinated protonated neurotransmitter 2-phenylethylamine: competition between NH+⋯π and NH+⋯F interactions. Phys Chem Chem Phys 2016; 18:26980-26989. [DOI: 10.1039/c6cp05915e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IR spectra of cold rare-gas tagged ions reveal the switch of the preferred conformation of the highly flexible side chain of a prototypical protonated neurotransmitter induced by site-specific aromatic fluorination.
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Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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31
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Mayorkas N, Sachs H, Schütz M, Ishiuchi SI, Fujii M, Dopfer O, Bar I. Structural motifs of 2-(2-fluoro-phenyl)-ethylamine conformers. Phys Chem Chem Phys 2016; 18:1191-201. [DOI: 10.1039/c5cp06131h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibronic and vibrational spectra of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) conformers were measured in a molecular beam by resonant two-photon ionization (R2PI), ultraviolet–ultraviolet hole burning (UV–UV HB) spectroscopy, and ionization-loss stimulated Raman spectroscopy (ILSRS).
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Affiliation(s)
- Nitzan Mayorkas
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Hanan Sachs
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Shun-ichi Ishiuchi
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Ilana Bar
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
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32
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Bouchet A, Schütz M, Dopfer O. Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate. Chemphyschem 2015; 17:232-43. [PMID: 26584245 DOI: 10.1002/cphc.201500939] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 01/29/2023]
Abstract
Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany.
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33
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Su P, Chen Z, Wu W. An energy decomposition analysis study for intramolecular non-covalent interaction. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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34
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Sinha RK, Scuderi D, Maitre P, Chiavarino B, Crestoni ME, Fornarini S. Elusive Sulfurous Acid: Gas-Phase Basicity and IR Signature of the Protonated Species. J Phys Chem Lett 2015; 6:1605-1610. [PMID: 26263321 DOI: 10.1021/acs.jpclett.5b00450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres.
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Affiliation(s)
- Rajeev K Sinha
- †Faculté des Sciences, Laboratoire de Chimie Physique, UMR8000 CNRS, Université Paris-Sud, Batiment 349, 91405 Orsay Cedex, France
- ∥Department of Atomic and Molecular Physics, Manipal University, Manipal, 576104 Karnataka, India
| | - Debora Scuderi
- †Faculté des Sciences, Laboratoire de Chimie Physique, UMR8000 CNRS, Université Paris-Sud, Batiment 349, 91405 Orsay Cedex, France
| | - Philippe Maitre
- †Faculté des Sciences, Laboratoire de Chimie Physique, UMR8000 CNRS, Université Paris-Sud, Batiment 349, 91405 Orsay Cedex, France
| | - Barbara Chiavarino
- ‡Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Maria Elisa Crestoni
- ‡Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- ‡Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
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35
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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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Laakia J, Kauppila TJ, Adamov A, Sysoev AA, Kotiaho T. Separation of isomeric amines with ion mobility spectrometry. Talanta 2015; 132:889-93. [DOI: 10.1016/j.talanta.2014.10.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022]
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37
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Bouchet A, Klyne J, Piani G, Dopfer O, Zehnacker A. Diastereo-specific conformational properties of neutral, protonated and radical cation forms of (1R,2S)-cis- and (1R,2R)-trans-amino-indanol by gas phase spectroscopy. Phys Chem Chem Phys 2015; 17:25809-21. [DOI: 10.1039/c5cp00576k] [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
The effects of ionisation and protonation on the geometric and electronic structure of a prototypical aromatic amino-alcohol with two chiral centres are revealed by IR and UV spectroscopy.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Giovanni Piani
- CNRS
- Institut des Sciences Moléculaires d’Orsay (ISMO/UMR8214) and Univ. Paris Sud
- Orsay
- France
- CLUPS (Centre Laser de l’Université Paris Sud/LUMAT FR 2764)
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Anne Zehnacker
- CNRS
- Institut des Sciences Moléculaires d’Orsay (ISMO/UMR8214) and Univ. Paris Sud
- Orsay
- France
- CLUPS (Centre Laser de l’Université Paris Sud/LUMAT FR 2764)
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