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Schütz M, Bouchet A, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. Effects of Aromatic Fluorine Substitution on Protonated Neurotransmitters: The Case of 2-Phenylethylamine. Chemistry 2016; 22:8124-36. [DOI: 10.1002/chem.201600798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Otto Dopfer
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
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2
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Kaledin M, Adedeji DT. Driven molecular dynamics studies of the shared proton motion in the H5O2+·Ar cluster: the effect of argon tagging and deuteration on vibrational spectra. J Phys Chem A 2015; 119:1875-84. [PMID: 25686318 DOI: 10.1021/jp511305c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report IR spectra of H5O2(+) and H5O2(+)·Ar and their deuterium isotopologues using ab initio molecular dynamics. The trajectories were propagated as microcanonical (NVE) ensembles at energies corresponding to temperatures 50 and 100 K. The potential energy surface is calculated on-the-fly at the MP2/aug-cc-pVDZ level of theory. The calculations show that adding an argon atom to H5O2(+) introduces symmetry breaking in the Zundel core ion, causes blueshift in the shared proton vibration by about 200 cm(-1), and leads to the splitting of the OH stretch vibrations into four bands. Driven molecular dynamics (DMD) method is used to assign the spectrum by coupling the dipole moment to an external electric field oscillating at frequency ω. The broad feature at 1100 cm(-1) in the H5O2(+)·Ar spectrum is ascribed to the large amplitude shared proton vibration coupled with torsion and wag modes. MD MP2 simulations predict the H/D redshift in the shared proton vibration and water bending vibration to be about 280 and 460 cm(-1), respectively, in good agreement with experimental observations.
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Affiliation(s)
- Martina Kaledin
- Kennesaw State University , Chemistry & Biochemistry, 370 Paulding Avenue NW, Box No. 1203, Kennesaw, Georgia 30144, United States
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3
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Chiavarino B, Crestoni ME, Schütz M, Bouchet A, Piccirillo S, Steinmetz V, Dopfer O, Fornarini S. Cation-π interactions in protonated phenylalkylamines. J Phys Chem A 2014; 118:7130-8. [PMID: 25061749 DOI: 10.1021/jp505037n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza , P. le A. Moro 5, I-00185 Roma, Italy
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4
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Vaden TD, de Boer TSJA, Simons JP, Snoek LC, Suhai S, Paizs B. Vibrational spectroscopy and conformational structure of protonated polyalanine peptides isolated in the gas phase. J Phys Chem A 2013; 112:4608-16. [PMID: 18444632 DOI: 10.1021/jp800069n] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.
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Affiliation(s)
- Timothy D Vaden
- Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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WEI JING, WANG JINYUN, ZHANG MINYI, CHAI GUOLIANG, LIN CHENSHENG, CHENG WENDAN. A THEORETICAL STUDY ON SECOND HARMONIC GENERATION HYPERPOLARIZABILITIES OF PHENYLALANINE POLYPEPTIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633612501180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The second harmonic generation (SHG) hyperpolarizabilities of phenylalanine and homopolypeptides are investigated by configuration interaction among singly excited configurations (CIS) technique combined with the sum-over-states (SOS) method. The geometries of peptides containing phenylalanine ( Phe )n(n = 1–8) are optimized by B3LYP/6-31g(d) method, and they form the special structures like β-sheet (a common protein secondary structure). It is found that the energy gaps of various peptides are reduced and the hyperpolarizabilities are increased with the peptide chains lengthened. We discuss the origin of the second-order nonlinear optical response in phenylalanine homopolypeptides and confirm that the π → π* transitions in the aromatic residue of phenylalanine make the most important contributions to the second-order polarizability. Our results strongly suggest that the hyperpolarizabilities are dominated from the propagation direction of peptide chains.
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Affiliation(s)
- JING WEI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - JIN-YUN WANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - MIN-YI ZHANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - GUO-LIANG CHAI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - CHEN-SHENG LIN
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - WEN-DAN CHENG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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6
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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7
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Filippi A, Fraschetti C, Piccirillo S, Rondino F, Botta B, D'Acquarica I, Calcaterra A, Speranza M. Chirality effects on the IRMPD spectra of basket resorcinarene/nucleoside complexes. Chemistry 2012; 18:8320-8. [PMID: 22696428 DOI: 10.1002/chem.201200614] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Indexed: 11/12/2022]
Abstract
The IRMPD spectra of the ESI-formed proton-bound complexes of the R,R,R,R- and S,S,S,S-enantiomers of a bis(diamido)-bridged basket resorcin[4]arene (R and S) with cytosine (1), cytidine (2), and cytarabine (3) were measured in the region 2800-3600 cm(-1). Comparison of the IRMPD spectra with the corresponding ONIOM (B3LYP/6-31(d):UFF)-calculated absorption frequencies allowed the assessment of the vibrational modes that are responsible for the observed spectroscopic features. All of the complexes investigated, apart from [R⋅H⋅3](+), showed similar IRMPD spectra, which points to similar structural and conformational landscapes. Their IRMPD spectra agree with the formation of several isomeric structures in the ESI source, wherein the N(3)-protonated guest establishes noncovalent interactions with the host amidocarbonyl groups that are either oriented inside the host cavity or outside it between one of the bridged side-chains and the upper aromatic nucleus. The IRMPD spectrum of the [R⋅H⋅3](+) complex was clearly different from the others. This difference is attributed to the effect of intramolecular hydrogen-bonding interactions between the C(2')-OH group and the aglycone oxygen atom of the nucleosidic guest upon repulsive interactions between the same oxygen atom and the aromatic rings of the host.
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Affiliation(s)
- Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, 00185 Roma, Italy
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8
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Jin L, Gerber RB. Migration and chemical reaction of H+ in protonated β-galactose. Phys Chem Chem Phys 2012; 14:13522-6. [DOI: 10.1039/c2cp41766a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Leavitt CM, Wolk AB, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Characterizing the intramolecular H-bond and secondary structure in methylated GlyGlyH+ with H2 predissociation spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1941-1952. [PMID: 21952771 DOI: 10.1007/s13361-011-0228-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH(+)•(H(2))(1,2), GlySarH(+)•(D(2))(2), SarGlyH(+)•(H(2))(2), and SarSarH(+)•(D(2))(2), generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H(2) (D(2)) molecules in a linear action regime throughout the 700-4200 cm(-1) range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110°) about the peptide backbone.
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Affiliation(s)
- Christopher M Leavitt
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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10
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of protonated neurotransmitters: dopamine. Phys Chem Chem Phys 2011; 13:2815-23. [DOI: 10.1039/c0cp02133d] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Spectroscopy of mobility-selected biomolecular ions. Faraday Discuss 2011; 150:243-55; discussion 257-92. [DOI: 10.1039/c0fd00004c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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12
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase. Phys Chem Chem Phys 2011; 13:15644-56. [DOI: 10.1039/c1cp21681c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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13
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Gaigeot MP. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. Phys Chem Chem Phys 2010; 12:10198-209. [PMID: 20539891 DOI: 10.1039/c003485a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
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Prell JS, O'Brien JT, Williams ER. IRPD spectroscopy and ensemble measurements: effects of different data acquisition and analysis methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:800-9. [PMID: 20185332 DOI: 10.1016/j.jasms.2010.01.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/06/2010] [Accepted: 01/10/2010] [Indexed: 05/17/2023]
Abstract
Three different commonly used infrared photodissociation (IRPD) spectroscopy acquisition and analysis methods are described, and results from these methods are compared using the same dataset for an extensively hydrated metal cation, La(3+)(H(2)O)(36). Using the first-order laser-induced photodissociation rate constant as an IRPD intensity has several advantages over photodissociation yield and depletion/appearance methods in that intensities can be more directly compared with calculated infrared absorption spectra, and the intensities can be readily corrected for changes in laser power or irradiation times used for optimum data acquisition at each frequency. Extending IRPD spectroscopy to large clusters can be complicated when blackbody infrared radiative dissociation competes strongly with laser-induced photodissociation. A new method to obtain IRPD spectra of single precursor ions or ensembles of precursor ions that is nearly equivalent to the photodissociation rate constant method for single precursor ions is demonstrated. The ensemble IRPD spectra represent the "average" structure of clusters of a given size range, and this method has the advantage that spectra with improved signal-to-noise ratios can be obtained with no increase in data acquisition time. Results using this new method for a precursor ensemble consisting of La(3+)(H(2)O)(35-37) are compared with results for La(3+)(H(2)O)(36).
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Affiliation(s)
- James S Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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Gaigeot MP. Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. Phys Chem Chem Phys 2010; 12:3336-59. [PMID: 20336243 DOI: 10.1039/b924048a] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France.
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16
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Cimas A, Gaigeot MP. DFT-MD and vibrational anharmonicities of a phosphorylated amino acid. Success and failure. Phys Chem Chem Phys 2010; 12:3501-10. [DOI: 10.1039/b924025j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Prell JS, Flick TG, Oomens J, Berden G, Williams ER. Coordination of Trivalent Metal Cations to Peptides: Results from IRMPD Spectroscopy and Theory. J Phys Chem A 2009; 114:854-60. [DOI: 10.1021/jp909366a] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Tawnya G. Flick
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Giel Berden
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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18
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Zhao D, Langer J, Oomens J, Dopfer O. Infrared spectra of protonated polycyclic aromatic hydrocarbon molecules: Azulene. J Chem Phys 2009; 131:184307. [DOI: 10.1063/1.3262720] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fung Y, Besson T, Lemaire J, Maitre P, Zubarev R. Room-Temperature Infrared Spectroscopy Combined with Mass Spectrometry Distinguishes Gas-Phase Protein Isomers. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Fung Y, Besson T, Lemaire J, Maitre P, Zubarev R. Room-Temperature Infrared Spectroscopy Combined with Mass Spectrometry Distinguishes Gas-Phase Protein Isomers. Angew Chem Int Ed Engl 2009; 48:8340-2. [DOI: 10.1002/anie.200901516] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Cimas A, Maitre P, Ohanessian G, Gaigeot MP. Molecular Dynamics and Room Temperature Vibrational Properties of Deprotonated Phosphorylated Serine. J Chem Theory Comput 2009; 5:2388-400. [DOI: 10.1021/ct900179d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- A. Cimas
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - P. Maitre
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - G. Ohanessian
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - M.-P. Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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22
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Prell JS, O’Brien JT, Steill JD, Oomens J, Williams ER. Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges. J Am Chem Soc 2009; 131:11442-9. [DOI: 10.1021/ja901870d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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23
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Fridgen TD. Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes. MASS SPECTROMETRY REVIEWS 2009; 28:586-607. [PMID: 19343731 DOI: 10.1002/mas.20224] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long-awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry.
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Affiliation(s)
- Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada A1B 3X7.
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24
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Rizzo TR, Stearns JA, Boyarkin OV. Spectroscopic studies of cold, gas-phase biomolecular ions. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350903069931] [Citation(s) in RCA: 242] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Wu R, McMahon TB. Protonation Sites and Conformations of Peptides of Glycine (Gly1−5H+) by IRMPD Spectroscopy. J Phys Chem B 2009; 113:8767-75. [DOI: 10.1021/jp811468q] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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26
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Polfer NC, Oomens J. Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance. MASS SPECTROMETRY REVIEWS 2009; 28:468-494. [PMID: 19241457 DOI: 10.1002/mas.20215] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
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Affiliation(s)
- Nick C Polfer
- Chemistry Department, University of Florida, Gainesville, Florida 32611, USA.
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27
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Cimas A, Vaden TD, de Boer TSJA, Snoek LC, Gaigeot MP. Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy. J Chem Theory Comput 2009; 5:1068-78. [DOI: 10.1021/ct900057s] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- A. Cimas
- LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France, and Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - T. D. Vaden
- LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France, and Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - T. S. J. A. de Boer
- LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France, and Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - L. C. Snoek
- LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France, and Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - M.-P. Gaigeot
- LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France, and Physical and Theoretical Chemistry Laboratory, Chemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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28
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Kabelác M, Hobza P, Spirko V. The ab initio assigning of the vibrational probing modes of tryptophan: linear shifting of approximate anharmonic frequencies vs. multiplicative scaling of harmonic frequencies. Phys Chem Chem Phys 2009; 11:3921-6. [PMID: 19440620 DOI: 10.1039/b823373j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To gain insight into the prospects for a few-dimensional ab initio quantum-mechanical description of the vibrational motions of conformationally flexible molecular systems, the NH-, NH(2)-, CO- and OH-stretching and COH-bending vibrations of the most stable tryptophan conformations have been probed using simple one- and two-dimensional anharmonic Hamiltonians and potential energy functions evaluated by means of the standard RI-MP2, CCSD(T) and DFT-D quantum chemical procedures. Although strongly dependent on the procedure used, the calculated vibrational spectral patterns have been found to be in a robust one-to-one harmony with their experimental counterparts, thus proving the adequacy of the theory used for the reliable assignment of the experimental data. Therefore, the approach appears to be a suitable tool for assigning the vibrational probing modes even of systems which are too large to be tractable by the standard normal-coordinate analysis.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, v.v.i, Academy of Sciences of the Czech Republic, Flemingovo, Prague 6, Czech Republic
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29
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Gaigeot MP. Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations. J Phys Chem A 2009; 112:13507-17. [PMID: 19053558 DOI: 10.1021/jp807550j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?
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Affiliation(s)
- M-P Gaigeot
- LAMBE UMR8587 Laboratoire Analyse et Modelisation pour la Biologie et l'Environnement, Universite d'Evry val d'Essonne, Boulevard F. Mitterrand, Batiment Maupertuis, 91025 Evry, France.
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30
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Stearns JA, Seaiby C, Boyarkin OV, Rizzo TR. Spectroscopy and conformational preferences of gas-phase helices. Phys Chem Chem Phys 2009; 11:125-32. [DOI: 10.1039/b814143f] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Prell JS, Demireva M, Oomens J, Williams ER. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J Am Chem Soc 2008; 131:1232-42. [DOI: 10.1021/ja808177z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Maria Demireva
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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32
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Correia CF, Clavaguera C, Erlekam U, Scuderi D, Ohanessian G. IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide. Chemphyschem 2008; 9:2564-73. [DOI: 10.1002/cphc.200800469] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Vaden TD, Gowers SAN, de Boer TSJA, Steill JD, Oomens J, Snoek LC. Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe. J Am Chem Soc 2008; 130:14640-50. [PMID: 18844349 DOI: 10.1021/ja804213s] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.
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Affiliation(s)
- Timothy D Vaden
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
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34
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Wu R, McMahon TB. An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy. Chemphyschem 2008; 9:2826-35. [DOI: 10.1002/cphc.200800543] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples. ACTA ACUST UNITED AC 2008. [DOI: 10.1135/cccc20081261] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Our previous benchmark CCSD(T)/ complete basis set limit calculations were collected into a database named begdb - Benchmark Energy and Geometry DataBase. Web-based interface to this database was prepared and is available at www.begdb.com. Users can browse, search and plot the data online or download structures and energy tables.
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