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Rahimi R, Saban N, Bar I. Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations. J Phys Chem Lett 2024; 15:3658-3667. [PMID: 38534060 DOI: 10.1021/acs.jpclett.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.
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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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2
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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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Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
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Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
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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] [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 ion Ag + ( benzylamine ) ( L ) .
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Alessandro Maccelli
- 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
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany.,present address: Eagleyard Photonics GmbH, Rudower Chaussee 29, 12489, Berlin, Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany.,present address: Université Lille LASIRE Lab Adv Spect Interact React & Environm Cite Sci, CNRS, UMR 8516, 59000, Lille, France
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany
| | - 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
| | - 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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Rahimi R, Shachar A, Bar I. Experimental/Computational Study on the Impact of Fluorine on the Structure and Noncovalent Interactions in the Monohydrated Cluster of ortho-Fluorinated 2-Phenylethylamine. J Am Chem Soc 2022; 144:8337-8346. [PMID: 35471862 DOI: 10.1021/jacs.2c02480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorine-containing medicinal compounds frequently allow modulation of physical-chemical properties. Here, we address the effect of fluorine, near the ethylamino side chain, on conformational flexibility and noncovalent interactions (NCIs) of the selected jet-cooled monohydrated cluster of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) by mass-selected resonance-enhanced two-photon ionization and ionization-loss stimulated Raman spectroscopies. Our results show that Raman spectral signatures of the 2-FPEA-H2O cluster match the scaled harmonic vibrational Raman frequencies, resulting from density functional theory calculations of the most stable 2-FPEA gauche conformer hydrogen-bonded (HB) to water, confirming the three-dimensional cluster structure. This predicted electronic structure, together with NCI analysis, allows visualization and assessment of the attractive and repulsive interactions. The comparison of the NCIs and revealed red (O-H and N-H stretches) and blue shifts (C-H stretches and CH2 out-of-plane bends) of the cluster to other class members confirm O-H···N, N-H···π, C-H···O, and C-H···F HB formation and their contribution to structure stabilization, uncovering the potential of the approach.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Afik Shachar
- 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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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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Chang X, Sun D, Shi D, Wang G, Chen Y, Zhang K, Tan H, Liu J, Liu B, Ouyang L. Design, synthesis, and biological evaluation of quinazolin-4(3 H)-one derivatives co-targeting poly(ADP-ribose) polymerase-1 and bromodomain containing protein 4 for breast cancer therapy. Acta Pharm Sin B 2021; 11:156-180. [PMID: 33532187 PMCID: PMC7838034 DOI: 10.1016/j.apsb.2020.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/08/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
This study was aimed to design the first dual-target small-molecule inhibitor co-targeting poly (ADP-ribose) polymerase-1 (PARP1) and bromodomain containing protein 4 (BRD4), which had important cross relation in the global network of breast cancer, reflecting the synthetic lethal effect. A series of new BRD4 and PARP1 dual-target inhibitors were discovered and synthesized by fragment-based combinatorial screening and activity assays that together led to the chemical optimization. Among these compounds, 19d was selected and exhibited micromole enzymatic potencies against BRD4 and PARP1, respectively. Compound 19d was further shown to efficiently modulate the expression of BRD4 and PARP1. Subsequently, compound 19d was found to induce breast cancer cell apoptosis and stimulate cell cycle arrest at G1 phase. Following pharmacokinetic studies, compound 19d showed its antitumor activity in breast cancer susceptibility gene 1/2 (BRCA1/2) wild-type MDA-MB-468 and MCF-7 xenograft models without apparent toxicity and loss of body weight. These results together demonstrated that a highly potent dual-targeted inhibitor was successfully synthesized and indicated that co-targeting of BRD4 and PARP1 based on the concept of synthetic lethality would be a promising therapeutic strategy for breast cancer.
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Key Words
- BC, breast cancer
- BET, bromodomain and extra-terminal domain
- BRCA1/2, breast cancer susceptibility gene 1/2
- BRD4
- BRD4, bromodomain 4
- CDK4/6, cyclin-dependent kinase 4/6
- DSB, DNA double-strand break
- Dual-target inhibitor
- EGFR, epidermal growth factor receptor
- ELISA, enzyme linked immunosorbent assay
- ER, estrogen receptor
- ESI-HR-MS, high-resolution mass spectra
- FDA, U.S. Food and Drug Administration
- FITC, fluorescein isothiocyanate isomer I
- HE, hematoxylin-eosin
- HPLC, high-performance liquid chromatography
- HR, homologous recombination
- HRD, homologous recombination deficiency
- IHC, immunohistochemistry
- NHEJ, nonhomologous end-joining
- PARP1
- PARP1, poly(ADP-ribose) polymerase-1
- PI, propidium iodide
- PK, pharmacokinetics
- PPI, protein−protein interaction
- Quinazolin-4(3H)-one derivatives
- SAR, structure–activity relationship
- SOP, standard operation process
- Synthetic lethality
- TCGA, the cancer genome atlas
- TGI, tumor growth inhibition
- TLC, thin-layer chromatography
- TNBC, triple-negative breast cancer
- TR-FRET, time-resolved fluorescence resonance energy transfer.
- shRNA, short hairpin RNA
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Affiliation(s)
| | | | | | | | | | | | | | - Jie Liu
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
| | - Bo Liu
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
| | - Liang Ouyang
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
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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, 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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11
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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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12
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Shachar A, Mayorkas N, Bar I. Structural features of monohydrated 2-(4-fluorophenyl)ethylamine: a combined spectroscopic and computational study. Phys Chem Chem Phys 2017; 19:23999-24008. [PMID: 28831462 DOI: 10.1039/c7cp04195k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A jet-cooled singly hydrated 2-(4-fluorophenyl)ethylamine (4-FPEA-H2O) cluster has been studied by ionization-loss stimulated Raman spectroscopy of the 4-FPEA photofragment and density functional calculations of the parent. Comparison of the measured spectrum of the photofragment to computed scaled harmonic Raman spectra of different conformers of the 4-FPEA-H2O cluster, at the M06-2X/6-311++G(d,p) level of theory, allowed determination of the calculated spectrum that best fits the experimental one. The correlation between them was further supported by the stability of the cluster, as revealed from the calculated energies of the fully optimized geometries of the possible different clusters in the ground electronic state. The corresponding structure consists of a water molecule, which is hydrogen-bonded to the nitrogen lone pair of the folded ethylamino side chain in the most stable gauche conformer of 4-FPEA. The presence of the hydrogen bond and other bonding and non-bonding interactions was also tested by atoms in molecules and noncovalent interaction analyses. The former approach showed no critical points in electron density, while the latter revealed regional topologies of reduced density gradients, indicating the formation of this hydrogen-bond and other attractive and repulsive interactions. The monohydration of 4-FPEA provides an insight into the intra- and inter-molecular interactions that play a role in stabilizing the cluster.
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Affiliation(s)
- Afik Shachar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Shachar A, Mayorkas N, Sachs H, Bar I. The conformational landscape of 2-(4-fluoro-phenyl)-ethylamine: consequences of fluorine substitution at the para position. Phys Chem Chem Phys 2016; 19:510-522. [PMID: 27905592 DOI: 10.1039/c6cp06456f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorination is considered as a possible means for alteration of conformational landscapes in molecules. The effect of fluorine substitution was studied here by measuring the vibronic and vibrational spectra of gas phase 2-(4-fluoro-phenyl)-ethylamine (4-FPEA) by resonant two-photon ionization (R2PI) and by ionization-loss stimulated Raman spectroscopy (ILSRS). The measurement of survey ILSR spectra of 4-FPEA in the amino group region allowed to associate the bands in the R2PI spectrum to origin and vibronic transitions of the ground (S0) to the excited (S1) electronic states of three different conformers. The presence of these conformers of 4-FPEA in the molecular beam was confirmed by measurement of distinctive ILSRS spectral signatures in the 400-1700 and 2750-3500 cm-1 broad spectral range. The interpretation of their structures was assisted by the results of quantum chemical calculations, including a torsional potential energy surface, energies of the fully optimized geometries in the S0 state and harmonic Raman spectra as well as natural bond orbital and atoms in molecule analyses. Comparison of the spectra with the results of scaled harmonic Raman spectra revealed two gauche configurations with folded ethylamino side chains and amino groups aiming to different directions together with a symmetric anti structure with an outward extended chain. The site-specific para-fluorination, at a distant position from the side chain modified the energetic ordering of the conformers, relative to the structure with the fluorine atom at the ortho position, but kept it close to that of PEA.
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Affiliation(s)
- Afik Shachar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - 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.
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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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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