1
|
Otaki H, Ishiuchi SI, Fujii M, Sugita Y, Yagi K. Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Phys Chem Chem Phys 2024; 26:9906-9914. [PMID: 38477212 DOI: 10.1039/d4cp00064a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.
Collapse
Affiliation(s)
- Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo, Nagasaki, Nagasaki 852-8521, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Preitschopf T, Sturm F, Stroganova I, Lemmens AK, Rijs AM, Fischer I. IR/UV Double Resonance Study of the 2-Phenylallyl Radical and its Pyrolysis Products. Chemistry 2023; 29:e202202943. [PMID: 36479856 DOI: 10.1002/chem.202202943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Isolated 2-phenylallyl radicals (2-PA), generated by pyrolysis from a nitrite precursor, have been investigated by IR/UV ion dip spectroscopy using free electron laser radiation. 2-PA is a resonance-stabilized radical that is considered to be involved in the formation of polycyclic aromatic hydrocarbons (PAH) in combustion, but also in interstellar space. The radical is identified based on its gas-phase IR spectrum. Furthermore, a number of bimolecular reaction products are identified, showing that the self-reaction as well as reactions with unimolecular decomposition products of 2-PA form several PAH efficiently. Possible mechanisms are discussed and the chemistry of 2-PA is compared with the one of the related 2-methylallyl and phenylpropargyl radicals.
Collapse
Affiliation(s)
- Tobias Preitschopf
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Floriane Sturm
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Iuliia Stroganova
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Alexander K Lemmens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED, Nijmegen, The Netherlands
| | - Anouk M Rijs
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
4
|
Krüger P, Both JH, Linne U, Chirot F, Weitzel KM. Photoelectron Circular Dichroism of Electrosprayed Gramicidin Anions. J Phys Chem Lett 2022; 13:6110-6116. [PMID: 35759344 DOI: 10.1021/acs.jpclett.2c01437] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many sophisticated approaches for analyzing properties of chiral matter have been developed in recent years. But in general, the available chiroptical methods are limited to either solvated or small gaseous molecules. Studying the chirality of large biopolymers in the gas phase, including aspects of the secondary structure, becomes accessible by combining the electrospray ionization technique with chiroptical detection protocols. Here, laser-induced photodetachment from gramicidin anions, a peptide consisting of 15 amino acids has been investigated. The angular distribution of photoelectrons is demonstrated to be sensitive to the substitution of protons by cesium ions, which is accompanied by a conformational change. The photoelectron circular dichroism (PECD) is -0.5% for bare gramicidin, whereas gramicidin with several Cs+ ions attached exhibits a PECD of +0.5%. The results are complemented and supported by ion mobility studies. The presented approach offers the prospect of studying chirality and the secondary structure of various biopolymers.
Collapse
Affiliation(s)
- Peter Krüger
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Jon Henrik Both
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Fabien Chirot
- Institut Lumière Matière, UMR5306 Université de Lyon, Université Lyon 1, CNRS, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Karl-Michael Weitzel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| |
Collapse
|
5
|
Lemmens AK, Rap DB, Brünken S, Buma WJ, Rijs AM. Polycyclic aromatic hydrocarbon growth in a benzene discharge explored by IR-UV action spectroscopy. Phys Chem Chem Phys 2022; 24:14816-14824. [PMID: 35695165 PMCID: PMC9215700 DOI: 10.1039/d2cp01631a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infrared signatures of polycyclic aromatic hydrocarbons (PAHs) are detected towards many phases of stellar evolution. PAHs are major players in the carbon chemistry of the interstellar medium, forming the connection between small hydrocarbons and large fullerenes. However, as details on the formation of PAHs in these environments are still unclear, modeling their abundance and chemistry has remained far from trivial. By combining molecular beam mass-selective IR spectroscopy and calculated IR spectra, we analyze the discharge of benzene and identify resulting products including larger PAHs, radicals and intermediates that serve as promising candidates for radio astronomical searches. The identification of various reaction products indicates that different gas-phase reaction mechanisms leading to PAH growth must occur under the same conditions to account for all observed PAH-related species, thereby revealing the complex and interconnected network of PAH formation pathways. The results of this study highlight key (exothermic) reactions that need to be included in astrochemical models describing the carbon chemistry in our universe.
Collapse
Affiliation(s)
- Alexander K. Lemmens
- Van't Hoff Institute for Molecular Sciences, University of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands,Institute for Molecules and Materials, FELIX Laboratory, Radboud UniversityToernooiveld 76525 EDNijmegenThe Netherlands
| | - Daniël B. Rap
- Institute for Molecules and Materials, FELIX Laboratory, Radboud UniversityToernooiveld 76525 EDNijmegenThe Netherlands
| | - Sandra Brünken
- Institute for Molecules and Materials, FELIX Laboratory, Radboud UniversityToernooiveld 76525 EDNijmegenThe Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences, University of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands,Institute for Molecules and Materials, FELIX Laboratory, Radboud UniversityToernooiveld 76525 EDNijmegenThe Netherlands
| | - Anouk M. Rijs
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit AmsterdamDe Boelelaan 11081081 HV AmsterdamThe Netherlands
| |
Collapse
|
6
|
Dit Fouque KJ, Scutelnic V, Hegemann JD, Rebuffat S, Maître P, Rizzo TR, Fernandez-Lima F. Structural Insights from Tandem Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Infrared/Ultraviolet Spectroscopy on Sphingonodin I: Lasso vs Branched-Cyclic Topoisomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1096-1104. [PMID: 33765377 DOI: 10.1021/jasms.1c00041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lasso peptides form a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked topology, where the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Sphingonodin I is a lasso peptide that has not yet been structurally characterized using the traditional structural biology tools (e.g., NMR and X-ray crystallography), and its biological function has not yet been elucidated. In the present work, we describe structural signatures characteristic of the class II lasso peptide sphingonodin I and its branched-cyclic analogue using a combination of gas-phase ion tools (e.g., tandem mass spectrometry, MS/MS, trapped ion mobility spectrometry, TIMS, and infrared, IR, and ultraviolet, UV, spectroscopies). Tandem MS/MS CID experiments on sphingonodin I yielded mechanically interlocked species with associated bi and yj fragments demonstrating the presence of a lasso topology, while tandem MS/MS ECD experiments on sphingonodin I showed a significant increase in hydrogen migration in the loop region when compared to the branched-cyclic analogue. The high-mobility resolving power of TIMS permitted the separation of both topoisomers, where sphingonodin I adopted a more compact structure than its branched-cyclic analogue. Cryogenic and room-temperature IR spectroscopy experiments evidenced a different hydrogen bond network between the two topologies, while cryogenic UV spectroscopy experiments clearly demonstrated a distinct phenylalanine environment for the lasso peptide.
Collapse
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
| | - Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS, 57 rue Cuvier, CP-54, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex France
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
| |
Collapse
|
7
|
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
|
8
|
XRD structure and vibrational analysis of DL-β-Leucine, as aided by DFT tetramer model and characterized by NBO, AIM and NCI calculations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Lemmens AK, Rap DB, Thunnissen JMM, Willemsen B, Rijs AM. Polycyclic aromatic hydrocarbon formation chemistry in a plasma jet revealed by IR-UV action spectroscopy. Nat Commun 2020; 11:269. [PMID: 31937755 PMCID: PMC6959308 DOI: 10.1038/s41467-019-14092-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022] Open
Abstract
Large polycyclic aromatic hydrocarbons (PAHs) are the most abundant complex molecules in the interstellar medium; however, their possible formation pathways from small molecular species are still elusive. In the present work, we follow and characterize the formation of PAHs in an electrical discharge, specifically the PAH naphthalene in a molecular beam of argon. The fragments, products and reaction intermediates are unambiguously structurally identified by mass-selective IR-UV spectroscopy combined with quantum chemical calculations. This experiment provides evidence of the formation of larger PAHs containing up to four cyclic rings in the gas phase originating from a non-radical PAH molecule as a precursor. In addition to PAH formation, key resonance stabilized radical intermediates and intermediates containing di-acetylenic side groups are unambiguously identified in our experiment. We thereby not only reveal competing formation pathways to larger PAHs, but also identify intermediate species to PAH formation that are candidates for detection in radio-astronomy. Polycyclic aromatic hydrocarbons (PAHs) are present in the interstellar medium but their origin is unclear. Here the authors investigate large PAH formation from smaller PAHs in a plasma jet by mass-selective IR and UV laser spectroscopy, uncovering diacetylene radical addition as formation mechanism.
Collapse
Affiliation(s)
- Alexander K Lemmens
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Daniël B Rap
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Johannes M M Thunnissen
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Bryan Willemsen
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Anouk M Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands.
| |
Collapse
|
11
|
|
12
|
Fischer JL, Elvir BR, DeLucia SA, Blodgett KN, Zeller M, Kubasik MA, Zwier TS. Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation. J Phys Chem A 2019; 123:4178-4187. [PMID: 30973730 DOI: 10.1021/acs.jpca.9b01698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Joshua L. Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brayan R. Elvir
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Sally-Ann DeLucia
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Karl N. Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthew A. Kubasik
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
13
|
León I, Lesarri A, Fernández JA. Evaluation of the aggregation process in a mixture of propofol and benzocaine. Phys Chem Chem Phys 2019; 21:3537-3544. [PMID: 30137107 DOI: 10.1039/c8cp04386h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a mass-resolved IR spectrosopic study on propofol-benzocaine aggregates. This is a complex system due to the several conformational isomers that both monomers may adopt and to the combination of functional groups they present, which allow the molecules to interact in many possible ways. However, our results demonstrate that a single conformation is favored for each stoichiometry. In the heterodimer, propofol acts as a proton donor to the ester group of benzocaine, while the whole cluster is stabilized by dispersive forces. These dispersive forces account for an important part of the system's stabilization energy as the calculations suggest. Propofol does not show any affinity for the amino group of benzocaine, even when a second molecule of propofol is introduced. These results demonstrate the difficulty in anticipating the aggregation preferences of even small organic molecules.
Collapse
Affiliation(s)
- I León
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country, Barrio Sarriena s/n, 48940 Leioa, Spain.
| | | | | |
Collapse
|
14
|
Affiliation(s)
- Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
15
|
Hirsch F, Reusch E, Constantinidis P, Fischer I, Bakels S, Rijs AM, Hemberger P. Self-Reaction of ortho-Benzyne at High Temperatures Investigated by Infrared and Photoelectron Spectroscopy. J Phys Chem A 2018; 122:9563-9571. [PMID: 30444617 DOI: 10.1021/acs.jpca.8b09640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ortho-Benzyne, a Kekulé-type biradical is considered to be a key intermediate in the formation of polycyclic aromatic hydrocarbons (PAH) and soot. In the present work we study the ortho-benzyne self-reactions in a hot microreactor and identify the high-temperature products by IR/UV spectroscopy and by photoion mass-selected threshold photoelectron spectroscopy (ms-TPES) in a free jet. Ms-TPES confirms formation of ortho-benzyne as generated from benzocyclobutenedione, as well as benzene, biphenylene, diacetylene, and acetylene, originating from the reaction o-C6H4 → HCC-CCH + C2H2, and CH3. PAH molecules like naphthalene, 2-ethynylnaphthalene, fluorene, phenanthrene, and triphenylene are identified based on their IR/UV spectra. By comparison with recent computations their formation starting from o-benzyne can be readily understood and supports the importance of the biradical addition (1,4-cycloaddition followed by fragmentation) pathway to PAH molecules, recently proposed by Comandini et al.
Collapse
Affiliation(s)
- Florian Hirsch
- Institute of Physical and Theoretical Chemistry , University of Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Engelbert Reusch
- Institute of Physical and Theoretical Chemistry , University of Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Philipp Constantinidis
- Institute of Physical and Theoretical Chemistry , University of Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry , University of Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Sjors Bakels
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Anouk M Rijs
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Patrick Hemberger
- Laboratory for Femtochemistry and Synchrotron Radiation , Paul Scherrer Institut (PSI) , CH-5232 Villigen , Switzerland
| |
Collapse
|
16
|
Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophys J 2017; 112:1185-1197. [PMID: 28355546 DOI: 10.1016/j.bpj.2017.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/11/2017] [Accepted: 01/30/2017] [Indexed: 10/19/2022] Open
Abstract
Integral membrane protein function can be modulated by the host bilayer. Because biological membranes are diverse and nonuniform, we explore the consequences of lipid diversity using gramicidin A channels embedded in phosphatidylcholine (PC) bilayers composed of equimolar mixtures of di-oleoyl-PC and di-erucoyl-PC (dC18:1+dC22:1, respectively), di-palmitoleoyl-PC and di-nervonoyl-PC (dC16:1+dC24:1, respectively), and di-eicosenoyl-PC (pure dC20:1), all of which have the same average bilayer chain length. Single-channel lifetime experiments, molecular dynamics simulations, and a simple lipid compression model are used in tandem to gain insight into lipid redistribution around the channel, which partially alleviates the bilayer deformation energy associated with channel formation. The average single-channel lifetimes in the two-component bilayers (95 ± 10 ms for dC18:1+dC22:1 and 195 ± 20 ms for dC16:1+dC24:1) were increased relative to the single-component dC20:1 control bilayer (65 ± 10 ms), implying lipid redistribution. Using a theoretical treatment of thickness-dependent changes in channel lifetimes, the effective local enrichment of lipids around the channel was estimated to be 58 ± 4% dC18:1 and 66 ± 2% dC16:1 in the dC18:1+dC22:1 and dC16:1+dC24:1 bilayers, respectively. 3.5-μs molecular dynamics simulations show 66 ± 2% dC16:1 in the first lipid shell around the channel in the dC16:1+dC24:1 bilayer, but no significant redistribution (50 ± 4% dC18:1) in the dC18:1+dC22:1 bilayer; these simulated values are within the 95% confidence intervals of the experimental averages. The strong preference for the better matching lipid (dC16:1) near the channel in the dC16:1+dC24:1 mixture and lesser redistribution in the dC18:1+dC22:1 mixture can be explained by the energetic cost associated with compressing the lipids to match the channel's hydrophobic length.
Collapse
Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Andreia M Maer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Huan Rui
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
| |
Collapse
|
17
|
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
|
18
|
Constantinidis P, Hirsch F, Fischer I, Dey A, Rijs AM. Products of the Propargyl Self-Reaction at High Temperatures Investigated by IR/UV Ion Dip Spectroscopy. J Phys Chem A 2016; 121:181-191. [DOI: 10.1021/acs.jpca.6b08750] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Constantinidis
- Institute
of Physical and Theoretical Chemistry, University of Würzburg, Am
Hubland, D-97074 Würzburg, Germany
| | - F. Hirsch
- Institute
of Physical and Theoretical Chemistry, University of Würzburg, Am
Hubland, D-97074 Würzburg, Germany
| | - I. Fischer
- Institute
of Physical and Theoretical Chemistry, University of Würzburg, Am
Hubland, D-97074 Würzburg, Germany
| | - A. Dey
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - A. M. Rijs
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| |
Collapse
|
19
|
Otaki H, Yagi K, Ishiuchi SI, Fujii M, Sugita Y. Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations. J Phys Chem B 2016; 120:10199-10213. [DOI: 10.1021/acs.jpcb.6b06672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yuji Sugita
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Quantitative Biology Center, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
20
|
Jeanne Dit Fouque K, Lavanant H, Zirah S, Steinmetz V, Rebuffat S, Maître P, Afonso C. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers. J Phys Chem A 2016; 120:3810-6. [DOI: 10.1021/acs.jpca.6b04496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Sylvie Rebuffat
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| |
Collapse
|
21
|
Muhammad SA, Ali A, Naz A, Hassan A, Riaz N, Saeed-ul-Hassan S, Andleeb S, Barh D. A New Broad-Spectrum Peptide Antibiotic Produced by Bacillus brevis Strain MH9 Isolated from Margalla Hills of Islamabad, Pakistan. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-015-9508-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Roy TK, Sharma R, Gerber RB. First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments. Phys Chem Chem Phys 2016; 18:1607-14. [DOI: 10.1039/c5cp05979h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data.
Collapse
Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- Central University of Rajasthan
| | - Rahul Sharma
- Department of Chemistry
- Indian Institute of Technology
- Roorkee
- India
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- University of California
| |
Collapse
|
23
|
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.
Collapse
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
| | | |
Collapse
|
24
|
Schmitt M, Spiering F, Zhaunerchyk V, Jongma RT, Jaeqx S, Rijs AM, van der Zande WJ. Far-infrared spectra of the tryptamine A conformer by IR-UV ion gain spectroscopy. Phys Chem Chem Phys 2016; 18:32116-32124. [DOI: 10.1039/c6cp02358d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-far-infrared photon excited tryptamine has structured resonance enhanced multi-photon ionization UV spectra, revealing the mode composition of the S1-state. Upon multiple-far-infrared photon absorption, the UV spectrum broadens allowing ion gain spectroscopy to be performed.
Collapse
Affiliation(s)
- Michael Schmitt
- Heinrich-Heine-Universität Institut für Physikalische Chemie
- D-40225 Düsseldorf
- Germany
| | - Frans Spiering
- Radboud University
- Institute for Molecules and Materials
- Felix Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Vitali Zhaunerchyk
- Radboud University
- Institute for Molecules and Materials
- Felix Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Rienk T. Jongma
- 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
| | - Wim J. van der Zande
- Radboud University
- Institute for Molecules and Materials
- Felix Laboratory
- 6525 ED Nijmegen
- The Netherlands
| |
Collapse
|
25
|
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
|
26
|
Roy TK, Kopysov V, Nagornova NS, Rizzo TR, Boyarkin OV, Gerber RB. Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy. Chemphyschem 2015; 16:1374-8. [DOI: 10.1002/cphc.201500085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
|
27
|
Mahé J, Jaeqx S, Rijs AM, Gaigeot MP. Can far-IR action spectroscopy combined with BOMD simulations be conformation selective? Phys Chem Chem Phys 2015; 17:25905-14. [DOI: 10.1039/c5cp01518a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The combination of conformation selective far-IR/UV double resonance spectroscopy with Born–Oppenheimer molecular dynamics (BOMD) simulations is presented here for the structural characterization of the Ac-Phe-Pro-NH2 peptide in the far-infrared spectral domain, i.e. for radiation below 800 cm−1.
Collapse
Affiliation(s)
- Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
| | - 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
- Institut Universitaire de France
| |
Collapse
|
28
|
Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014; 53:3663-6. [DOI: 10.1002/anie.201311189] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Indexed: 11/11/2022]
|
29
|
Jaeqx S, Oomens J, Cimas A, Gaigeot MP, Rijs AM. Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born-Oppenheimer Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
30
|
Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
31
|
Aguado E, León I, Millán J, Cocinero EJ, Jaeqx S, Rijs AM, Lesarri A, Fernández JA. Unraveling the Benzocaine–Receptor Interaction at Molecular Level Using Mass-Resolved Spectroscopy. J Phys Chem B 2013; 117:13472-80. [DOI: 10.1021/jp4068944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Edurne Aguado
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Iker León
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Judith Millán
- Departamento
de Química, Facultad de
Ciencias, Estudios Agroalimentarios
e Informática, Universidad de La Rioja, Madre de Dios,
51, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Sander Jaeqx
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M. Rijs
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Alberto Lesarri
- Departamento de Química Física y Química
Inorgánica, Facultad de
Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| |
Collapse
|
32
|
Nei YW, Crampton KT, Berden G, Oomens J, Rodgers MT. Infrared multiple photon dissociation action spectroscopy of deprotonated RNA mononucleotides: gas-phase conformations and energetics. J Phys Chem A 2013; 117:10634-49. [PMID: 24053133 DOI: 10.1021/jp4039495] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5'-monophosphate (A5'p), guanosine-5'-monophosphate (G5'p), cytidine-5'-monophosphate (C5'p), and uridine-5'-monophosphate (U5'p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570-1900 cm(-1), that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G(d,p) level of theory finds that the most stable conformations of the deprotonated forms of A5'p, C5'p, and U5'p are accessed in the experiments, and these conformers adopt the C3' endo conformation of the ribose moiety and the anti conformation of the nucleobase. In the case of deprotonated G5'p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the syn rather than anti conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2'-hydroxyl group on their structure, stability, and fragmentation behavior.
Collapse
Affiliation(s)
- Y-w Nei
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | | | | | | | | |
Collapse
|
33
|
Volkov V, Bonn M. Structural Properties of gp41 Fusion Peptide at a Model Membrane Interface. J Phys Chem B 2013; 117:15527-35. [DOI: 10.1021/jp405852r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- V. Volkov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - M. Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
34
|
|
35
|
Buchanan EG, Dean JC, Zwier TS, Sibert EL. Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane. J Chem Phys 2013; 138:064308. [DOI: 10.1063/1.4790163] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
Jaeqx S, Du W, Meijer EJ, Oomens J, Rijs AM. Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding. J Phys Chem A 2012; 117:1216-27. [DOI: 10.1021/jp3053339] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Weina Du
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | - Evert Jan Meijer
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | | | | |
Collapse
|