1
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Lemmens AK, Ferrari P, Loru D, Batra G, Steber AL, Redlich B, Schnell M, Martinez-Haya B. Wetting of a Hydrophobic Surface: Far-IR Action Spectroscopy and Dynamics of Microhydrated Naphthalene. J Phys Chem Lett 2023; 14:10794-10802. [PMID: 38013434 DOI: 10.1021/acs.jpclett.3c02854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The interaction of water and polycyclic aromatic hydrocarbons is of fundamental importance in areas as diverse as materials science and atmospheric and interstellar chemistry. The interplay between hydrogen bonding and dipole-π interactions results in subtle dynamics that are challenging to describe from first principles. Here, we employ far-IR action vibrational spectroscopy with the infrared free-electron laser FELIX to investigate naphthalene with one to three water molecules. We observe diffuse bands associated with intermolecular vibrational modes that serve as direct probes of the loose binding of water to the naphthalene surface. These signatures are poorly reproduced by static DFT or Møller-Plesset computations. Instead, a rationalization is achieved through Born-Oppenheimer Molecular Dynamics simulations, revealing the active mobility of water over the surface, even at low temperatures. Therefore, our work provides direct insights into the wetting interactions associated with shallow potential energy surfaces while simultaneously demonstrating a solid experimental-computational framework for their investigation.
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Affiliation(s)
- Alexander K Lemmens
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Radboud University, Institute of Molecules and Materials, HFML-FELIX, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Piero Ferrari
- Radboud University, Institute of Molecules and Materials, HFML-FELIX, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Donatella Loru
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gayatri Batra
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Amanda L Steber
- Department of Physical and Inorganic Chemistry, Faculty of Science, University of Valladolid, 47011 Valladolid, Spain
| | - Britta Redlich
- Radboud University, Institute of Molecules and Materials, HFML-FELIX, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
| | - Bruno Martinez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
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2
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Kotobi A, Schwob L, Vonbun-Feldbauer GB, Rossi M, Gasparotto P, Feiler C, Berden G, Oomens J, Oostenrijk B, Scuderi D, Bari S, Meißner RH. Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble. Commun Chem 2023; 6:46. [PMID: 36869192 PMCID: PMC9984374 DOI: 10.1038/s42004-023-00835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.
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Affiliation(s)
- Amir Kotobi
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | | | - Mariana Rossi
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Piero Gasparotto
- Scientific Computing Division, Paul Scherrer Institute, Villigen, Switzerland
| | - Christian Feiler
- Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands
| | - Bart Oostenrijk
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Debora Scuderi
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Saclay, Orsay, France
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Robert H Meißner
- Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany.
- Hamburg University of Technology, Institute of Polymers and Composites, Hamburg, Germany.
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3
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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4
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Bakels S, Stroganova I, Rijs AM. Probing the formation of isolated cyclo-FF peptide clusters by far-infrared action spectroscopy. Phys Chem Chem Phys 2021; 23:20945-20956. [PMID: 34545387 DOI: 10.1039/d1cp03237b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Small cyclic peptides containing phenylalanine residues are prone to aggregate in the gas phase into highly hydrophobic chains. A combination of laser desorption, mass spectrometry and conformational selective IR-UV action spectroscopy allows us to obtain detailed structural insights into the formation processes of the cyclic L-phenylalanyl-L-phenylalanine dipeptide (named cyclo-FF) aggregates. The rigid properties of cyclo-FF result in highly resolved IR spectra for the smaller clusters (n ≤ 3) and corresponding conformational assignments. For the higher order clusters (n > 3) the spectra are less resolved, however the observed ratios, peak positions and trends in IR shifts are key to make predictions on their structural details. Whereas the mid-IR spectral region between 1000-1800 cm-1 turns out to be undiagnostic for these small aggregates and the 3 μm region only for specific calculated structures, the far-IR contains valuable information that allows for clear assignments.
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Affiliation(s)
- Sjors Bakels
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Iuliia Stroganova
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands. .,Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M Rijs
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands.
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5
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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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6
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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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7
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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8
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Galimberti DR, Bougueroua S, Mahé J, Tommasini M, Rijs AM, Gaigeot MP. Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment. Faraday Discuss 2019; 217:67-97. [DOI: 10.1039/c8fd00211h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.
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Affiliation(s)
| | | | - Jérôme Mahé
- LAMBE UMR8587
- Univ Evry
- Université Paris-Saclay
- CNRS
- 91025 Evry
| | - Matteo Tommasini
- Department of Chemistry, Materials, Chemical Engineering “G. Natta” Politecnico di Milano
- 20133 Milano
- Italy
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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9
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Roy TK, Kopysov V, Pereverzev A, Šebek J, Gerber RB, Boyarkin OV. Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy. Phys Chem Chem Phys 2018; 20:24894-24901. [PMID: 30234204 DOI: 10.1039/c8cp03989e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu 181143, India
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10
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Hassan I, Donati L, Stensitzki T, Keller BG, Heyne K, Imhof P. The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Jiang Z, Biczysko M, Moriarty NW. Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations. Proteins 2018; 86:273-278. [DOI: 10.1002/prot.25451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/16/2017] [Accepted: 01/01/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Zhongming Jiang
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division; Lawrence Berkeley National Laboratory; Berkeley California 94720
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12
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Kalanoor B, Ronen M, Oren Z, Gerber D, Tischler YR. New Method to Study the Vibrational Modes of Biomolecules in the Terahertz Range Based on a Single-Stage Raman Spectrometer. ACS OMEGA 2017; 2:1232-1240. [PMID: 28393138 PMCID: PMC5377281 DOI: 10.1021/acsomega.6b00547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/14/2017] [Indexed: 05/04/2023]
Abstract
The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times. We show that this method enables LFV mode characterization of biomolecules even in a hydrated environment. The measured spectra exhibit distinct features originating from intra- and/or intermolecular collective motion and lattice modes. The observed modes are highly sensitive to the overall structure, size, long-range order, and configuration of the molecules, as well as to their environment. Thus, the LFV Raman spectrum acts as a fingerprint of the molecular structure and conformational state of a biomolecule. The comprehensive method we present here is widely applicable, thus enabling high-throughput study of LFV modes of biomolecules.
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Affiliation(s)
- Basanth
S. Kalanoor
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Ronen
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ziv Oren
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Department
of Biotechnology, Israel Institute of Biological
Research, Nes-Ziona 7410001, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (D.G.)
| | - Yaakov R. Tischler
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (Y.R.T.)
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13
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Yatsyna V, Bakker DJ, Feifel R, Rijs AM, Zhaunerchyk V. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide. J Chem Phys 2017; 145:104309. [PMID: 27634262 DOI: 10.1063/1.4962360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.
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Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Daniël J Bakker
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M Rijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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14
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Bakker DJ, Dey A, Tabor DP, Ong Q, Mahé J, Gaigeot MP, Sibert EL, Rijs AM. Fingerprints of inter- and intramolecular hydrogen bonding in saligenin–water clusters revealed by mid- and far-infrared spectroscopy. Phys Chem Chem Phys 2017; 19:20343-20356. [DOI: 10.1039/c7cp01951c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saligenin (2-(hydroxymethyl)phenol) exhibits both strong and weak intramolecular electrostatic interactions.
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Affiliation(s)
- Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Arghya Dey
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Daniel P. Tabor
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Qin Ong
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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15
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Mahé J, Bakker DJ, Jaeqx S, Rijs AM, Gaigeot MP. Mapping gas phase dipeptide motions in the far-infrared and terahertz domain. Phys Chem Chem Phys 2017; 19:13778-13787. [DOI: 10.1039/c7cp00369b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vibrational signatures of Ac-Phe-AA-NH2 dipeptides are recorded and analysed in the far IR/THz spectral domain (100–800 cm−1, 3–24 THz), with the ‘AA’ amino acid chosen within the series ‘AA’ = Gly, Ala, Pro, Cys, Ser, Val. Phe stands for phenylalanine.
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Affiliation(s)
- Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
| | - Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Sander Jaeqx
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
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16
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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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17
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Bakker DJ, Peters A, Yatsyna V, Zhaunerchyk V, Rijs AM. Far-Infrared Signatures of Hydrogen Bonding in Phenol Derivatives. J Phys Chem Lett 2016; 7:1238-43. [PMID: 26982390 DOI: 10.1021/acs.jpclett.6b00016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
One of the most direct ways to study the intrinsic properties of the hydrogen-bond interaction is by gas-phase far-infrared (far-IR) spectroscopy because the modes involving hydrogen-bond deformation are excited in this spectral region; however, the far-IR regime is often ignored in molecular structure identification due to the absence of strong far-IR light sources and difficulty in assigning the observed modes by quantum chemical calculations. Far-IR/UV ion-dip spectroscopy using the free electron laser FELIX was applied to directly probe the intramolecular hydrogen-bond interaction in a family of phenol derivatives. Three vibrational modes have been identified, which are expected to be diagnostic for the hydrogen-bond strength: hydrogen-bond stretching and hydrogen-bond-donating and -accepting OH torsion vibrations. Their position is evaluated with respect to the hydrogen bond strength, that is, the length of the hydrogen-bonded OH length. This shows that the hydrogen bond stretching frequency is diagnostic for the size of the ring that is closed by the hydrogen bond, while the strength of the hydrogen bond can be determined from the hydrogen-bond-donating OH torsion frequency. The combination of these two normal modes allows the direct probing of intramolecular hydrogen-bond characteristics using conformation-selective far-IR vibrational spectroscopy.
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Affiliation(s)
- Daniël J Bakker
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Atze Peters
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Vasyl Yatsyna
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
- University of Gothenburg , Department of Physics, 412 96 Gothenburg, Sweden
| | - Vitali Zhaunerchyk
- University of Gothenburg , Department of Physics, 412 96 Gothenburg, Sweden
| | - Anouk M Rijs
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
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18
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Yatsyna V, Bakker DJ, Feifel R, Rijs AM, Zhaunerchyk V. Aminophenol isomers unraveled by conformer-specific far-IR action spectroscopy. Phys Chem Chem Phys 2016; 18:6275-83. [DOI: 10.1039/c5cp07426f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Far-infrared action spectroscopy of aminophenol in the gas-phase revealed isomer- and conformer-specific vibrational signatures and provided the heights of NH2 inversion barrier.
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Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- 412 96 Gotheburg
- Sweden
- Radboud University
| | - Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Raimund Feifel
- University of Gothenburg
- Department of Physics
- 412 96 Gotheburg
- Sweden
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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19
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Seoudi RS, Dowd A, Smith BJ, Mechler A. Structural analysis of bioinspired nano materials with synchrotron far IR spectroscopy. Phys Chem Chem Phys 2016; 18:11467-73. [DOI: 10.1039/c6cp01355d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Synchrotron far-infrared spectroscopy was used in conjunction with density functional theory vibrational analysis to ascertain the core structure of self-assembled fibrous superstructures formed by unnatural β3-tripeptides.
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Affiliation(s)
- Rania S. Seoudi
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Annette Dowd
- School of Mathematical and Physical Sciences
- University of Technology Sydney
- Australia
| | - Brian J. Smith
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Adam Mechler
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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20
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Lepere V, Le Barbu-Debus K, Clavaguéra C, Scuderi D, Piani G, Simon AL, Chirot F, MacAleese L, Dugourd P, Zehnacker A. Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies. Phys Chem Chem Phys 2015; 18:1807-17. [PMID: 26679547 DOI: 10.1039/c5cp06768e] [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
Ion mobility experiments are combined with Infra-Red Multiple Photon Dissociation (IRMPD) spectroscopy and quantum chemical calculations for assessing the role of chirality in the structure of protonated and sodiated di- or tetra-peptides. Sodiated systems show a strong chirality dependence of the competition between Na(+)O and Na(+)π interactions. Chirality effects are more subtle in protonated systems and manifest themselves by differences in the secondary interactions such hydrogen bonds between neutral groups or those involving the aromatic rings.
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Affiliation(s)
- Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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