1
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Fischer JL, Blodgett KN, Harrilal CP, Walsh PS, Davis ZS, Choi S, Choi SH, Zwier TS. Conformer-Specific Spectroscopy and IR-Induced Isomerization of a Model γ-Peptide: Ac-γ 4-Phe-NHMe. J Phys Chem A 2022; 126:1837-1847. [PMID: 35275624 DOI: 10.1021/acs.jpca.2c00112] [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
Single-conformation IR and UV spectroscopy of the prototypical capped γ-peptide Ac-γ4-Phe-NHMe (γ4F) was carried out under jet-cooled conditions in the gas phase in order to understand its innate conformational preferences in the absence of a solvent. We obtained conformer-specific IR and UV spectra and compared the results with calculations to make assignments and explore the differences between the γ2- and γ4-substituted molecules. We found four conformers of γ4F in our experiment. Three conformers form nine-membered hydrogen-bonded rings (C9) enclosed by an NH···O═C H-bond but differing in their phenyl ring positions (a, g+, and g-). The fourth conformer forms a strained seven-membered hydrogen-bonded ring in which the amide groups lie in a nominally anti-parallel arrangement stacked on top of one another (labeled S7). This conformer is a close analogue of the amide-stacked conformer (S) found previously in γ2F, in which the Phe side chain is substituted at the γ2 position, Ac-γ2-Phe-NHMe (J. Am. Chem. Soc. 2009, 131, 14243-14245). IR population transfer spectroscopy was used to determine the fractional abundances of the γ4F conformers in the expansion. A combination of force field and density functional theory calculations is used to map out the conformational potential energy surfaces for γ4F and compare it with its γ2F counterpart. Based on this analysis, the phenyl ring prefers to take up structures that facilitate NH···π interactions in γ4F or avoid phenyl interactions with the C═O group in γ2F. The disconnectivity graph for γ4F reveals separate basins associated with the C9 and amide-stacked conformational families, which are separated by a barrier of about 42 kJ/mol. The overall shape of the potential energy surface bears a resemblance to peptides and proteins that have a misfolding pathway that competes with the formation of the native structure.
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Affiliation(s)
- Joshua L Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S Walsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Zachary S Davis
- Department of Chemistry, Wofford College, Spartanburg, South Carolina 29303, United States
| | - Sunglim Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States.,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
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2
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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3
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Lemmens A, Rap DB, Thunnissen JMM, Gruet S, Steber AL, Panchagnula S, Tielens AGGM, Schnell M, Buma WJ, Rijs AM. Far-IR Absorption of Neutral Polycyclic Aromatic Hydrocarbons (PAHs): Light on the Mechanism of IR-UV Ion Dip Spectroscopy. J Phys Chem Lett 2020; 11:8997-9002. [PMID: 33035060 PMCID: PMC7649846 DOI: 10.1021/acs.jpclett.0c02714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Gas-phase IR-UV double-resonance laser spectroscopy is an IR absorption technique that bridges the gap between experimental IR spectroscopy and theory. The IR experiments are used to directly evaluate predicted frequencies and potential energy surfaces as well as to probe the structure of isolated molecules. However, a detailed understanding of the underlying mechanisms is, especially in the far-IR regime, still far from complete, even though this is crucial for properly interpreting the recorded IR absorption spectra. Here, events occurring upon excitation to vibrational levels of polycyclic aromatic hydrocarbons by far-IR radiation from the FELIX free electron laser are followed using resonance-enhanced multiphoton ionization spectroscopy. These studies provide detailed insight into how ladder climbing and anharmonicity influence IR-UV spectroscopy and therefore the resulting IR signatures in the far-IR region. Moreover, the potential energy surfaces of these low-frequency delocalized modes are investigated and shown to have a strong harmonic character.
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Affiliation(s)
- Alexander
K. Lemmens
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Daniël B. Rap
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Johannes M. M. Thunnissen
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Sébastien Gruet
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Amanda L. Steber
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Sanjana Panchagnula
- Leiden
Observatory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | | | - Melanie Schnell
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Wybren Jan Buma
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Anouk M. Rijs
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
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4
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Ishiuchi SI, Wako H, Xantheas SS, Fujii M. Probing the selectivity of Li + and Na + cations on noradrenaline at the molecular level. Faraday Discuss 2019; 217:396-413. [PMID: 31115392 DOI: 10.1039/c8fd00186c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although several mechanisms concerning the biological function of lithium salts, drugs having tranquilizing abilities, have been proposed so far, the key mechanism for its selectivity and subsequent interaction with neurotransmitters has not been established yet. We report ultraviolet (UV) and infrared (IR) spectra under ultra-cold conditions of Li+ and Na+ complexes of noradrenaline (NAd, norepinephrine), a neurotransmitter responsible for the body's response to stress or danger, in an effort to provide a molecular level understanding of the conformational changes of NAd due to its interactions with these two cations. A detailed analysis of the IR spectra, aided by quantum chemical calculations, reveals that the Li+-noradrenaline (NAd-Li+) complex forms only an extended structure, while the NAd-Na+ and protonated (NAd-H+) complexes form both folded and extended structures. This conformational preference of the NAd-Li+ complex is further explained by considering specific conformational distributions in solution. Our results clearly discern the unique structural motifs that NAd adopts when interacting with Li+ compared with other abundant cations in the human body (Na+) and can form the basis of a molecular level understanding of the selectivity of Li+ in biological systems.
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Affiliation(s)
- Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Hiromichi Wako
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, WA 99352, USA. and Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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5
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Sohn WY, Kim JJ, Jeon M, Aoki T, Ishiuchi SI, Fujii M, Kang H. Entropic effects make a more tightly folded conformer of a β-amino acid less stable: UV-UV hole burning and IR dip spectroscopy of l-β3-homotryptophan using a laser desorption supersonic jet technique. Phys Chem Chem Phys 2018; 20:19979-19986. [DOI: 10.1039/c8cp02106f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gas-phase spectroscopy of homotryptophan was done to understand conformations of β-peptides.
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Affiliation(s)
- Woon Yong Sohn
- Department of Applied Chemistry
- Faculty of Science and Engineering
- Chuo University
- Tokyo 112-8551
- Japan
| | - Jeong Jin Kim
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Myeongwon Jeon
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
| | - Takuma Aoki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Hyuk Kang
- Department of Chemistry
- Department of Energy Systems Research
- Ajou University
- Suwon 16499
- Korea
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6
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Robertson PA, Lobo IA, Wilson DJ, Robertson EG. Nitriles as directionally tolerant hydrogen bond acceptors: IR-UV ion depletion spectroscopy of benzenepropanenitrile and its hydrate clusters. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.08.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
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Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
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9
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Szczepaniak M, Moc J. Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study. J Phys Chem A 2015; 119:10946-58. [DOI: 10.1021/acs.jpca.5b07720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Szczepaniak
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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10
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Alauddin M, Gloaguen E, Brenner V, Tardivel B, Mons M, Zehnacker‐Rentien A, Declerck V, Aitken DJ. Intrinsic Folding Proclivities in Cyclic β‐Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer‐Selective Spectroscopy and Quantum Chemistry. Chemistry 2015; 21:16479-93. [DOI: 10.1002/chem.201501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
- Current address: Department of Chemistry, University of Dhaka, Dhaka‐1000 (Bangladesh)
| | - Eric Gloaguen
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Valérie Brenner
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Benjamin Tardivel
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Michel Mons
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | | | - Valérie Declerck
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
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11
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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12
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Walsh PS, Buchanan EG, Gord JR, Zwier TS. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H2O)n clusters, n = 2-4. J Chem Phys 2015; 142:154303. [PMID: 25903886 DOI: 10.1063/1.4917305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Patrick S. Walsh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Joseph R. Gord
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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13
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Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Phys Chem Chem Phys 2015; 16:9876-91. [PMID: 24419903 DOI: 10.1039/c3cp52774c] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
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Affiliation(s)
- R Chaudret
- Sorbonne Universités, UPMC, Laboratoire de Chimie Théorique and CNRS, UMR 7616, 75252 Paris Cedex 05, Paris, France.
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14
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Dean JC, Burke NL, Hopkins JR, Redwine JG, Ramachandran PV, McLuckey SA, Zwier TS. UV Photofragmentation and IR Spectroscopy of Cold, G-Type β-O-4 and β–β Dilignol–Alkali Metal Complexes: Structure and Linkage-Dependent Photofragmentation. J Phys Chem A 2015; 119:1917-32. [PMID: 25695912 DOI: 10.1021/jp512603n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jacob C. Dean
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John R. Hopkins
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - James G. Redwine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - P. V. Ramachandran
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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15
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Carr JK, Zabuga AV, Roy S, Rizzo TR, Skinner JL. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations. J Chem Phys 2014; 140:224111. [PMID: 24929378 PMCID: PMC4187283 DOI: 10.1063/1.4882059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/26/2014] [Indexed: 02/04/2023] Open
Abstract
The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.
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Affiliation(s)
- J K Carr
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - A V Zabuga
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - S Roy
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - T R Rizzo
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - J L Skinner
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
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16
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Gord JR, Walsh PS, Fisher BF, Gellman SH, Zwier TS. Mimicking the First Turn of an α-Helix with an Unnatural Backbone: Conformation-Specific IR and UV Spectroscopy of Cyclically Constrained β/γ-Peptides. J Phys Chem B 2014; 118:8246-56. [PMID: 24694352 DOI: 10.1021/jp5015884] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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17
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Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Dean JC, Walsh PS, Biswas B, Ramachandran PV, Zwier TS. Single-conformation UV and IR spectroscopy of model G-type lignin dilignols: the β–O–4 and β–β linkages. Chem Sci 2014. [DOI: 10.1039/c3sc53260g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Walsh PS, Kusaka R, Buchanan EG, James WH, Fisher BF, Gellman SH, Zwier TS. Cyclic constraints on conformational flexibility in γ-peptides: conformation specific IR and UV spectroscopy. J Phys Chem A 2013; 117:12350-62. [PMID: 24147873 DOI: 10.1021/jp408736t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Single-conformation spectroscopy has been used to study two cyclically constrained and capped γ-peptides: Ac-γACHC-NHBn (hereafter γACHC, Figure 1a), and Ac-γACHC-γACHC-NHBn (γγACHC, Figure 1b), under jet-cooled conditions in the gas phase. The γ-peptide backbone in both molecules contains a cyclohexane ring incorporated across each Cβ-Cγ bond and an ethyl group at each Cα. This substitution pattern was designed to stabilize a (g+, g+) torsion angle sequence across the Cα-Cβ-Cγ segment of each γ-amino acid residue. Resonant two-photon ionization (R2PI), infrared-ultraviolet hole-burning (IR-UV HB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to probe the single-conformation spectroscopy of these molecules. In both γACHC and γγACHC, all population is funneled into a single conformation. With RIDIR spectra in the NH stretch (3200-3500 cm(-1)) and amide I/II regions (1400-1800 cm(-1)), in conjunction with theoretical predictions, assignments have been made for the conformations observed in the molecular beam. γACHC forms a single nearest-neighbor C9 hydrogen-bonded ring whereas γγACHC takes up a next-nearest-neighbor C14 hydrogen-bonded structure. The gas-phase C14 conformation represents the beginning of a 2.614-helix, suggesting that the constraints imposed on the γ-peptide backbone by the ACHC and ethyl groups already impose this preference in the gas-phase di-γ-peptide, in which only a single C14 H-bond is possible, constituting one full turn of the helix. A similar conformational preference was previously documented in crystal structures and NMR analysis of longer γ-peptide oligomers containing the γACHC subunit [Guo, L., et al. Angew. Chem. Int. Ed. 2011, 50, 5843-5846]. In the gas phase, the γACHC-H2O complex was also observed and spectroscopically interrogated in the molecular beam. Here, the monosolvated γACHC retains the C9 hydrogen bond observed in the bare molecule, with the water acting as a bridge between the C-terminal carbonyl and the π-cloud of the UV chromophore. This is in contrast to the unconstrained γ-peptide-H2O complex, which incorporates H2O into both C9 and amide-stacked conformations.
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Affiliation(s)
- Patrick S Walsh
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907 United States
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20
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Kusaka R, Zhang D, Walsh PS, Gord JR, Fisher BF, Gellman SH, Zwier TS. Role of Ring-Constrained γ-Amino Acid Residues in α/γ-Peptide Folding: Single-Conformation UV and IR Spectroscopy. J Phys Chem A 2013; 117:10847-62. [PMID: 24070234 DOI: 10.1021/jp408258w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryoji Kusaka
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Di Zhang
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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21
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Mayorkas N, Bernat A, Izbitski S, Bar I. Vibrational and vibronic spectra of tryptamine conformers. J Chem Phys 2013; 138:124312. [DOI: 10.1063/1.4798218] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Buchanan EG, Sibert EL, Zwier TS. Ground State Conformational Preferences and CH Stretch–Bend Coupling in a Model Alkoxy Chain: 1,2-Diphenoxyethane. J Phys Chem A 2013; 117:2800-11. [PMID: 23480677 DOI: 10.1021/jp400691a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Edwin L. Sibert
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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23
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Çarçabal P, Cocinero EJ, Simons JP. Binding energies of micro-hydrated carbohydrates: measurements and interpretation. Chem Sci 2013. [DOI: 10.1039/c3sc50135c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Dean JC, Buchanan EG, Zwier TS. Mixed 14/16 Helices in the Gas Phase: Conformation-Specific Spectroscopy of Z-(Gly)n, n = 1, 3, 5. J Am Chem Soc 2012; 134:17186-201. [PMID: 23039317 DOI: 10.1021/ja306652c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jacob C. Dean
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084,
United States
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25
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Buchanan EG, James WH, Choi SH, Guo L, Gellman SH, Müller CW, Zwier TS. Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling. J Chem Phys 2012; 137:094301. [DOI: 10.1063/1.4747507] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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26
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Xie Y, Schaefer HF, Silaghi-Dumitrescu R, Peng B, Li QS, Stearns JA, Rizzo TR. Conformational Preferences of Gas-Phase Helices: Experiment and Theory Struggle to Agree: The Seven-Residue Peptide Ac-Phe-(Ala)5-Lys-H+. Chemistry 2012; 18:12941-4. [DOI: 10.1002/chem.201202068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Indexed: 11/12/2022]
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27
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Roy S, Lessing J, Meisl G, Ganim Z, Tokmakoff A, Knoester J, Jansen TLC. Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline. J Chem Phys 2012; 135:234507. [PMID: 22191886 DOI: 10.1063/1.3665417] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.
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Affiliation(s)
- Santanu Roy
- Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Abstract
We review the frontiers of spectroscopy from a historical perspective, starting with the development of atomic spectroscopy about 150 years ago, followed by some comments on selected previous Faraday Discussions. As the spectrum of frontiers at the Faraday Discussion 150 is very broad, we give only a brief survey providing a map of the various frontiers approached today. This is followed by an exemplary discussion of one particular frontier towards the spectroscopic detection of symmetry violations in fundamental physics. In particular the understanding of parity violation in chiral molecules has recently made great progress. We briefly describe the advances made in recent decades as well as the current status of theory and experiments in this exciting field of research. We conclude with an outlook on open questions and frontiers of the future in spectroscopy.
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Affiliation(s)
- Martin Quack
- ETH Zürich, Laboratory of Physical Chemistry, CH-8093 Zürich, Switzerland.
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James WH, Buchanan EG, Müller CW, Dean JC, Kosenkov D, Slipchenko LV, Guo L, Reidenbach AG, Gellman SH, Zwier TS. Evolution of amide stacking in larger γ-peptides: triamide H-bonded cycles. J Phys Chem A 2011; 115:13783-98. [PMID: 21978283 DOI: 10.1021/jp205527e] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.
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Affiliation(s)
- William H James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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Dean JC, Buchanan EG, James WH, Gutberlet A, Biswas B, Ramachandran PV, Zwier TS. Conformation-Specific Spectroscopy and Populations of Diastereomers of a Model Monolignol Derivative: Chiral Effects in a Triol Chain. J Phys Chem A 2011; 115:8464-78. [DOI: 10.1021/jp204367k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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