1
|
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: 38] [Impact Index Per Article: 9.5] [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.
Collapse
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
| |
Collapse
|
2
|
Kumar S, Singh SK, Vaishnav JK, Hill JG, Das A. Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes. Chemphyschem 2017; 18:828-838. [PMID: 28124829 DOI: 10.1002/cphc.201601405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/24/2017] [Indexed: 11/07/2022]
Abstract
π-Hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature, great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study, the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋅⋅⋅methylated benzene (ind⋅⋅⋅n-mb, n=1-6) complexes is probed through a combination of supersonic jet experiments and benchmark-quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant two-photon ionization and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋅⋅⋅π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely to be due to multiple tilted conformations of each dimer possessing similar stabilization energies.
Collapse
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Department of Dynamics at Surfaces, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077, Gottingen, Germany
| | - Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Jamuna K Vaishnav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Indian Institute of Technology (IIT) Indore, Khandwa Rd, Simrol, Madhya, Pradesh, 452020, India
| | - J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Stamm A, Maué D, Schaly A, Schlicher S, Bartl J, Kubik S, Gerhards M. Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues. Phys Chem Chem Phys 2017; 19:10718-10726. [DOI: 10.1039/c6cp08696a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues were performed by applying combined IR/UV spectroscopy in the molecular beam and DFT calculations. The intrinsic structural properties especially with regard to the influence of different amino acid residues are fundamental for optimizing their binding ability.
Collapse
Affiliation(s)
- A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - A. Schaly
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Schlicher
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - J. Bartl
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Kubik
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| |
Collapse
|
5
|
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]
|
6
|
Stamm A, Bernhard D, Gerhards M. Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions. Phys Chem Chem Phys 2016; 18:15327-36. [DOI: 10.1039/c6cp01675h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first molecular beam investigations of an isolated linear depsipeptide are presented. By applying IR/UV spectroscopic methods and DFT calculations three structural arrangements are identified with the most stable structure being only stable by including dispersion interactions.
Collapse
Affiliation(s)
- A. Stamm
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - D. Bernhard
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Yan B, Jaeqx S, van der Zande WJ, Rijs AM. A conformation-selective IR-UV study of the dipeptides Ac-Phe-Ser-NH2 and Ac-Phe-Cys-NH2: probing the SH···O and OH···O hydrogen bond interactions. Phys Chem Chem Phys 2015; 16:10770-8. [PMID: 24756311 DOI: 10.1039/c4cp00810c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conformational preferences of peptides are mainly controlled by the stabilizing effect of intramolecular interactions. In peptides with polar side chains, not only the backbone but also the side chain interactions determine the resulting conformations. In this paper, the conformational preferences of the capped dipeptides Ac-Phe-Ser-NH2 (FS) and Ac-Phe-Cys-NH2 (FC) are resolved under laser-desorbed jet cooling conditions using IR-UV ion dip spectroscopy and density functional theory (DFT) quantum chemistry calculations. As serine (Ser) and cysteine (Cys) only differ in an OH (Ser) or SH (Cys) moiety; this subtle alteration allows us to study the effect of the difference in hydrogen bonding for an OH and SH group in detail, and its effect on the secondary structure. IR absorption spectra are recorded in the NH stretching region (3200-3600 cm(-1)). In combination with quantum chemical calculations the spectra provide a direct view of intramolecular interactions. Here, we show that both FS as FC share a singly γ-folded backbone conformation as the most stable conformer. The hydrogen bond strength of OH···O (FS) is stronger than that of SH···O (FC), resulting in a more compact gamma turn structure. A second conformer is found for FC, showing a β turn interaction.
Collapse
Affiliation(s)
- Bin Yan
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | | | | | | |
Collapse
|
9
|
Lee JJ, Albrecht M, Rice CA, Suhm MA, Stamm A, Zimmer M, Gerhards M. Adaptive Aggregation of Peptide Model Systems. J Phys Chem A 2013; 117:7050-63. [DOI: 10.1021/jp400056n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juhyon J. Lee
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Merwe Albrecht
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Anke Stamm
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Manuel Zimmer
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Markus Gerhards
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| |
Collapse
|
10
|
Wang C, Lin Z, Zhang R. Zwitterions are the most stable form for neutral arginylglycine in gas phase: Clear theoretical evidence. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
11
|
Schwing K, Reyheller C, Schaly A, Kubik S, Gerhards M. Structural Analysis of an Isolated Cyclic Tetrapeptide and its Monohydrate by Combined IR/UV Spectroscopy. Chemphyschem 2011; 12:1981-8. [DOI: 10.1002/cphc.201001055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/07/2011] [Indexed: 11/10/2022]
|
12
|
Plowright RJ, Gloaguen E, Mons M. Compact Folding of Isolated Four-Residue Neutral Peptide Chains: H-Bonding Patterns and Entropy Effects. Chemphyschem 2011; 12:1889-99. [DOI: 10.1002/cphc.201001023] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Indexed: 11/08/2022]
|
13
|
Abo-Riziq A, Grace L, Crews B, Callahan MP, van Mourik T, Vries MSD. Conformational Structure of Tyrosine, Tyrosyl-glycine, and Tyrosyl-glycyl-glycine by Double Resonance Spectroscopy. J Phys Chem A 2011; 115:6077-87. [DOI: 10.1021/jp110601w] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ali Abo-Riziq
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Louis Grace
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bridgit Crews
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael P. Callahan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland, U.K
| | - Mattanjah S. de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| |
Collapse
|
14
|
Arachchilage APW, Wang F, Feyer V, Plekan O, Prince KC. Correlation of electronic structures of three cyclic dipeptides with their photoemission spectra. J Chem Phys 2010; 133:174319. [DOI: 10.1063/1.3499740] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
15
|
Bouteiller Y, Poully JC, Desfrançois C, Grégoire G. Evaluation of MP2, DFT, and DFT-D Methods for the Prediction of Infrared Spectra of Peptides. J Phys Chem A 2009; 113:6301-7. [DOI: 10.1021/jp901570r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yves Bouteiller
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Jean Christophe Poully
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Charles Desfrançois
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| |
Collapse
|
16
|
Kong W, Pei L, Zhang J. Linear dichroism spectroscopy of gas phase biological molecules embedded in superfluid helium droplets. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350802573678] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
17
|
Häber T, Seefeld K, Engler G, Grimme S, Kleinermanns K. IR/UV spectra and quantum chemical calculations of Trp–Ser: Stacking interactions between backbone and indole side-chain. Phys Chem Chem Phys 2008; 10:2844-51. [DOI: 10.1039/b718710f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
18
|
Brenner V, Piuzzi F, Dimicoli I, Tardivel B, Mons M. Spectroscopic Evidence for the Formation of Helical Structures in Gas-Phase Short Peptide Chains. J Phys Chem A 2007; 111:7347-54. [PMID: 17530827 DOI: 10.1021/jp070681l] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminoisobutyric acid (Aib) is a synthetic amino acid known to favor the formation of 3(10) helical structures in condensed phases, namely, crystals. The intrinsic character of these helicogenic properties has been investigated on the Ac-Aib-Phe-Aib-NH2 molecule under isolated conditions, namely, in the gas phase, both experimentally by double-resonance IR/UV spectroscopy and theoretically by quantum chemistry. A convergent set of evidence, based on energetic, IR, and UV spectroscopic data as well as on analogies with the similar peptide Ac-Ala-Phe-Ala-NH2 previously studied, enables us to conclude the formation of an incipient 310 helix in these isolated systems.
Collapse
Affiliation(s)
- Valérie Brenner
- Laboratoire Francis Perrin, URA CEA-CNRS 2453, Service des Photons, Atomes et Molécules, CEA Saclay, bât 522, Gif-sur-Yvette Cedex, France
| | | | | | | | | |
Collapse
|
19
|
Abstract
Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.
Collapse
Affiliation(s)
- Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
| | | |
Collapse
|
20
|
Devereux M, Popelier PLA. The Effects of Hydrogen-Bonding Environment on the Polarization and Electronic Properties of Water Molecules. J Phys Chem A 2007; 111:1536-44. [PMID: 17279739 DOI: 10.1021/jp067922u] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adequate representation of the interactions that take place between water molecules has long been a goal of force field design. A full understanding of how the molecular charge distribution of water is altered by adjacent water molecules and by the hydrogen-bonding environment is a vital step toward achieving this task. For this purpose we generated ab initio electron densities of pure water clusters and hydrated serine and tyrosine. Quantum chemical topology enabled the study of a well-defined water molecule inside these clusters, by means of its volume, energy, and multipole moments. Intra- and intermolecular charge transfer was monitored and related to the polarization of water in hydrogen-bonded networks. Our analysis affords a way to define different types of water molecules in clusters.
Collapse
Affiliation(s)
- M Devereux
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, Great Britain
| | | |
Collapse
|
21
|
Fricke H, Schäfer G, Schrader T, Gerhards M. Secondary structure binding motifs of the jet cooled tetrapeptide model Ac–Leu–Val–Tyr(Me)–NHMe. Phys Chem Chem Phys 2007; 9:4592-7. [PMID: 17690785 DOI: 10.1039/b706519a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this paper the structure of the isolated tetrapeptide model Ac-Leu-Val-Tyr(Me)-NHMe (Leu = leucine, Val = valine, Tyr = tyrosine) is investigated by mass- and isomer-selective IR/UV double resonance spectroscopy. Two isomers of this peptide are observed and in combination with force field, ab initio, and DFT calculations these structures are assigned to folded arrangements presenting two different secondary structure binding motifs: (a) a combined gamma-turn/beta-turn structure and (b) a triple gamma-turn structure, which is described for the first time for an isolated model system in the gas phase.
Collapse
Affiliation(s)
- H Fricke
- Heinrich-Heine Universität Düsseldorf, Institut für Physikalische Chemie I, Universitätsstrasse 26.33.O2, 40225 Düsseldorf, Germany
| | | | | | | |
Collapse
|
22
|
Grégoire G, Gaigeot MP, Marinica DC, Lemaire J, Schermann JP, Desfrançois C. Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car–Parrinello dynamics at 300 K. Phys Chem Chem Phys 2007; 9:3082-97. [PMID: 17612732 DOI: 10.1039/b618094a] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.
Collapse
Affiliation(s)
- G Grégoire
- Laboratoire de Physique des Lasers UMR 7538 Institut Galilée, Université Paris 13, Villetaneuse, France.
| | | | | | | | | | | |
Collapse
|
23
|
|
24
|
Dehareng D, Dive G. Charge Transfer Study through the Determination of the Ionization Energies of Tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the Inclusion of One Glycine in Alanine and Leucine Containing Peptides. J Phys Chem A 2006; 110:11975-87. [PMID: 17064186 DOI: 10.1021/jp064255w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH(2) terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH(2)=CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH(2) terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide.
Collapse
Affiliation(s)
- Dominique Dehareng
- Centre d'Ingéniérie des Protéines, Institut de Chimie B6a, Sart Tilman, B4000, Liège, Belgium.
| | | |
Collapse
|
25
|
|