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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 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.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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2
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Pushing the mass limit for intact launch and photoionization of large neutral biopolymers. Commun Chem 2018. [DOI: 10.1038/s42004-018-0095-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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3
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Synthesis, characterization and antibacterial activity of a new calcium complex using sodium 2-mercaptobenzothiazole and 1, 10-phenanthroline as ligands. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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5
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Feketeová L, Khairallah GN, O'Hair RAJ, Nielsen SB. Gas-phase fragmentation of deprotonated tryptophan and its clusters [Trpn -H]- induced by different activation methods. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1395-1402. [PMID: 26147479 DOI: 10.1002/rcm.7233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Non-covalent amino acid clusters are the subject of intense research in diverse areas including peptide bond formation studies or the determination of proton affinities or methylating abilities of amino acids. However, most of the research has focused on positive ions and little is known about anionic clusters. METHODS Fragmentation reactions of deprotonated tryptophan (Trp), [Trp-H](-) and Trp singly deprotonated non-covalently bound clusters [Trp(n) -H](-), n = 2, 3, 4, were investigated using low-energy collision-induced dissociation (CID) with He atoms, high-energy CID with Na atoms, and electron-induced dissociation (EID) with 20-35 eV electrons. Fragmentation of the monomeric Trp anion, where all labile hydrogens were exchanged for deuterium [d(4) -Trp-D](-), was investigated using low-energy CID and EID, in order to shed light on the dissociation mechanisms. RESULTS The main fragmentation channel for Trp cluster anions, [Trp(n) -H](-), n >1, is the loss of the neutral monomer. The fragmentation of the deprotonated Trp monomer induced by electrons resembles the fragmentation induced by high-energy collisions through electronic excitation of the parent. However, the excitation must precede in a different way, shown through only monomer loss from larger clusters, n >1, in case of EID, but intracluster chemistry in the case of high-energy CID. CONCLUSIONS The anion of the indole ring C(8)H(6) N(-) has been identified in the product ion spectra of [Trp(n) -H](-) using all activation methods, thus providing a diagnostic marker ion. No evidence was found for formation of peptide bonds as a route to prebiotic peptides in the fragmentation reactions of these singly deprotonated Trp cluster ions.
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Affiliation(s)
- Linda Feketeová
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
- Université de Lyon, 69003 Lyon, France; Université Claude Bernard Lyon1; Institut de Physique Nucléaire de Lyon, CNRS/IN2P3, UMR5822, 69622 Villeurbanne, France
| | - George N Khairallah
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Richard A J O'Hair
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Steen Brøndsted Nielsen
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Aarhus C, 8000, Denmark
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Sezer U, Schmid P, Felix L, Mayor M, Arndt M. Stability of high-mass molecular libraries: the role of the oligoporphyrin core. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:235-239. [PMID: 25601698 PMCID: PMC4322477 DOI: 10.1002/jms.3526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
Molecular beam techniques are a key to many experiments in physical chemistry and quantum optics. In particular, advanced matter-wave experiments with high-mass molecules profit from the availability of slow, neutral and mass-selected molecular beams that are sufficiently stable to remain intact during laser heating and photoionization mass spectrometry. We present experiments on the photostability with molecular libraries of tailored oligoporphyrins with masses up to 25,000 Da. We compare two fluoroalkylsulfanyl-functionalized libraries based on two different molecular cores that offer the same number of anchor points for functionalization but differ in their geometry and electronic properties. A pentaporphyrin core stabilizes a library of chemically well-defined molecules with more than 1600 atoms. They can be neutrally desorbed with velocities as low as 20 m/s and efficiently analyzed in photoionization mass spectrometry.
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Affiliation(s)
- Uĝur Sezer
- University of Vienna, Faculty of Physics, VCQ and QuNaBioSBoltzmanngasse 5, 1090, Vienna, Austria
| | - Philipp Schmid
- University of Vienna, Faculty of Physics, VCQ and QuNaBioSBoltzmanngasse 5, 1090, Vienna, Austria
| | - Lukas Felix
- Department of Chemistry, University of BaselSt. Johannsring 19, 4056, Basel, Switzerland
| | - Marcel Mayor
- Department of Chemistry, University of BaselSt. Johannsring 19, 4056, Basel, Switzerland
- Karlsruhe Institute of Technology (KIT), Institute of NanotechnologyP.O. Box 3640, 76021, Karlsruhe
| | - Markus Arndt
- University of Vienna, Faculty of Physics, VCQ and QuNaBioSBoltzmanngasse 5, 1090, Vienna, Austria
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Juffmann T, Ulbricht H, Arndt M. Experimental methods of molecular matter-wave optics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:086402. [PMID: 23907707 DOI: 10.1088/0034-4885/76/8/086402] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.
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Stupavska M, Jerigova M, Velic D. Matrix and primary ion-related aspects of tryptophan SIMS analysis. SURF INTERFACE ANAL 2013. [DOI: 10.1002/sia.5085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Stupavska
- Faculty of Natural Sciences; Comenius University in Bratislava; Mlynska dolina; 841 04; Bratislava; Slovakia
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Stupavska M, Aranyosiova M, Velic D. Alkaline earth metal salts of CaCO 3
, BaCO 3
, and SrCO 3
as matrix for tryptophan SIMS analysis. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Feketeová L, Khairallah GN, Brunet C, Lemoine J, Antoine R, Dugourd P, O'Hair RAJ. Fragmentation of the tryptophan cluster [Trp9-2H]2- induced by different activation methods. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3255-3260. [PMID: 20972999 DOI: 10.1002/rcm.4763] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electrospray ionization (ESI) of tryptophan gives rise to multiply charged, non-covalent tryptophan cluster anions, [Trp(n)-xH](x-), in a linear ion trap mass spectrometer, as confirmed by high-resolution experiments performed on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The smallest multiply charged clusters that can be formed in the linear ion trap as a function of charge state are: x = 2, n = 7; x = 3, n = 16; x = 4, n = 31. The fragmentation of the dianionic cluster [Trp(9)-2H](2-) was examined via low-energy collision-induced dissociation (CID), ultraviolet photodissociation (UVPD) at 266 nm and electron-induced dissociation (EID) at electron energies ranging from >0 to 30 eV. CID proceeds mostly via charge separation and evaporation of neutral tryptophan. The smallest doubly charged cluster that can be formed via evaporation of neutral tryptophans is [Trp(7)-2H](2-), consistent with the observation of this cluster in the ESI mass spectrum. UVPD gives singly charged tryptophan clusters ranging from n = 2 to n = 9. The latter ion arises from ejection of an electron to give the radical anion cluster, [Trp(9)-2H](-·). The types of gas-phase EID reactions observed are dependent on the energy of the electrons. Loss of neutral tryptophan is an important channel at lower energies, with the smallest doubly charged ion, [Trp(7)-2H](2-), being observed at 19.8 eV. Coulomb explosion starts to occur at 19.8 eV to form the singly charged cluster ions [Trp(x)-H](-) (x = 1-8) via highly asymmetric fission. At 21.8 eV a small amount of [Trp(2)-H-NH(3)](-) is observed. Thus CID, UVPD and EID are complementary techniques for the study of the fragmentation reactions of cluster ions.
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Affiliation(s)
- Linda Feketeová
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
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11
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Akhmetov A, Moore JF, Gasper GL, Koin PJ, Hanley L. Laser desorption postionization for imaging MS of biological material. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:137-45. [PMID: 20146224 PMCID: PMC2827192 DOI: 10.1002/jms.1716] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Vacuum ultraviolet single photon ionization (VUV SPI) is a soft ionization technique that has the potential to address many of the limitations of matrix-assisted laser desorption/ionization (MALDI) for imaging MS. Laser desorption postionization (LDPI) uses VUV SPI for postionization and is experimentally analogous to a MALDI instrument with the addition of a pulsed VUV light source. This review discusses progress in LDPI-MS over the last decade, with an emphasis on imaging MS of bacterial biofilms, analytes whose high salt environment make them particularly resistant to imaging by MALDI-MS. This review first considers fundamental aspects of VUV SPI including ionization mechanisms, cross sections, quantum yields of ionization, dissociation and potential mass limits. The most common sources of pulsed VUV radiation are then described along with a newly constructed LDPI-MS instrument with imaging capabilities. Next, the detection and imaging of small molecules within intact biofilms is demonstrated by LDPI-MS using 7.87 eV (157.6 nm) VUV photons from a molecular fluorine excimer laser, followed by the use of aromatic tags for detection of selected species within the biofilm. The final section considers the future prospects for imaging intact biological samples by LDPI-MS.
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Affiliation(s)
- Artem Akhmetov
- Department of Chemistry, m/c 111, University of Illinois at Chicago, Chicago, IL 60607-7061
| | - Jerry F. Moore
- MassThink, 500 East Ogden Avenue, Suite 200, Naperville, IL 60563-3281
| | - Gerald L. Gasper
- Department of Chemistry, m/c 111, University of Illinois at Chicago, Chicago, IL 60607-7061
| | - Peter J. Koin
- Department of Bioengineering, m/c 111, University of Illinois at Chicago, Chicago, IL 60607-7061
| | - Luke Hanley
- Department of Chemistry, m/c 111, University of Illinois at Chicago, Chicago, IL 60607-7061
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Juffmann T, Truppe S, Geyer P, Major AG, Deachapunya S, Ulbricht H, Arndt M. Wave and particle in molecular interference lithography. PHYSICAL REVIEW LETTERS 2009; 103:263601. [PMID: 20366311 DOI: 10.1103/physrevlett.103.263601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Indexed: 05/29/2023]
Abstract
The wave-particle duality of massive objects is a cornerstone of quantum physics and a key property of many modern tools such as electron microscopy, neutron diffraction or atom interferometry. Here we report on the first experimental demonstration of quantum interference lithography with complex molecules. Molecular matter-wave interference patterns are deposited onto a reconstructed Si(111) 7x7 surface and imaged using scanning tunneling microscopy. Thereby both the particle and the quantum wave character of the molecules can be visualized in one and the same image. This new approach to nanolithography therefore also represents a sensitive new detection scheme for quantum interference experiments.
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Affiliation(s)
- Thomas Juffmann
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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13
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Marksteiner M, Divochiy A, Sclafani M, Haslinger P, Ulbricht H, Korneev A, Semenov A, Gol'tsman G, Arndt M. A superconducting NbN detector for neutral nanoparticles. NANOTECHNOLOGY 2009; 20:455501. [PMID: 19822928 DOI: 10.1088/0957-4484/20/45/455501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a proof-of-principle study of superconducting single photon detectors (SSPD) for the detection of individual neutral molecules/nanoparticles at low energies. The new detector is applied to characterize a laser desorption source for biomolecules and allows retrieval of the arrival time distribution of a pulsed molecular beam containing the amino acid tryptophan, the polypeptide gramicidin as well as insulin, myoglobin and hemoglobin. We discuss the experimental evidence that the detector is actually sensitive to isolated neutral particles.
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Marksteiner M, Haslinger P, Sclafani M, Ulbricht H, Arndt M. UV and VUV Ionization of Organic Molecules, Clusters, and Complexes. J Phys Chem A 2009; 113:9952-7. [DOI: 10.1021/jp905039f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Marksteiner
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Haslinger
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michele Sclafani
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Hendrik Ulbricht
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Markus Arndt
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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Hanley L, Zimmermann R. Light and molecular ions: the emergence of vacuum UV single-photon ionization in MS. Anal Chem 2009; 81:4174-82. [PMID: 19476385 DOI: 10.1021/ac8013675] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thanks to recent technological advances and single-photon ionization's (SPI's) ability to detect all organics, the technique could become the long-sought universal soft ionization method. (To listen to a podcast about this feature, please go to the Analytical Chemistry Web site at pubs.acs.org/journal/ancham.).
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