51
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Liu H, An Z, He J. Nanosheet-enhanced efficiency in amine-catalyzed asymmetric epoxidation of α, β-unsaturated aldehydes via host-guest synergy. MOLECULAR CATALYSIS 2017. [DOI: 10.1016/j.mcat.2017.09.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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52
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Filippi A, Fraschetti C, Guarcini L, Zazza C, Ema T, Speranza M. Spectroscopic Discrimination of Diastereomeric Complexes Involving an Axially Chiral Receptor. Chemphyschem 2017; 18:2475-2481. [DOI: 10.1002/cphc.201700732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Antonello Filippi
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Caterina Fraschetti
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Laura Guarcini
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Costantino Zazza
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
| | - Tadashi Ema
- Graduate School of Natural Sciences and Technology; Okayama University; Tsushima Okayama 700-8530 Japan
| | - Maurizio Speranza
- Università di Roma “La Sapienza”; Dipartimento di Chimica e Tecnologie del Farmaco; P.le A. Moro, 5 Roma 00185 Italy
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53
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Seo J, Warnke S, Pagel K, Bowers MT, von Helden G. Infrared spectrum and structure of the homochiral serine octamer–dichloride complex. Nat Chem 2017; 9:1263-1268. [DOI: 10.1038/nchem.2821] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/06/2017] [Indexed: 01/14/2023]
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54
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Li H, Hu A, Jiang J, Luo Y. Systematic Study on Hydrated Arginine: Clear Theoretical Evidence for the Canonical-to-Zwitterionic Structure Transition. J Phys Chem A 2017; 121:3598-3605. [PMID: 28441493 DOI: 10.1021/acs.jpca.7b02008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive ab initio investigations have been performed to characterize the stable conformers of hydrated arginine (Arg-H2O). Many new low-energy canonical Arg-H2O conformers were identified and they are more stable than previous results. The large energy differences (more than 5.00 kcal mol-1) between the canonical and zwitterionic Arg-H2O isomers calculated by the composite CBS-QB3 method confirmed the dominance of the zwitterions. The micro effects of corrections of the zero-point energy and the basis set superposition error on the stability of hydrated isomers were carefully examined for the first time. The infrared (IR) spectra were simulated at a recommended temperature and the notable spectral differences enable the unambiguous identification of the different hydrated forms. Further transition state calculations revealed that the canonical Arg-H2O can be transformed to the zwitterions using the amino group as a bridge. Our study thus shows valuable insights into the hydration of large flexible molecules and provides solid theoretical evidence for the canonical-to-zwitterionic structure transition of hydrated arginine.
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Affiliation(s)
- Hongbao Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Andong Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China , Hefei, Anhui 230026, China.,Guizhou Provincial Key Laboratory of Computational Nano-Material Science, and Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University , Guiyang, Guizhou 550018, China
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55
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Schindler B, Barnes L, Gray CJ, Chambert S, Flitsch SL, Oomens J, Daniel R, Allouche AR, Compagnon I. IRMPD Spectroscopy Sheds New (Infrared) Light on the Sulfate Pattern of Carbohydrates. J Phys Chem A 2017; 121:2114-2120. [PMID: 28198185 DOI: 10.1021/acs.jpca.6b11642] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
IR spectroscopy of gas-phase ions is proposed to resolve positional isomers of sulfated carbohydrates. Mass spectrometric fingerprints and gas-phase vibrational spectra in the near and mid-IR regions were obtained for sulfated monosaccharides, yielding unambiguous signatures of sulfated isomers. We report the first systematic exploration of the biologically relevant but notoriously challenging deprotonated state in the near IR region. Remarkably, anions displayed very atypical vibrational profiles, which challenge the well-established DFT (Density Functionnal Theory) modeling. The proposed approach was used to elucidate the sulfate patterns in glycosaminoglycans, a ubiquitous class of mammalian carbohydrates, which is regarded as a major challenge in carbohydrate structural analysis. Isomeric glycosaminoglycan disaccharides from heparin and chondroitin sources were resolved, highlighting the potential of infrared multiple photon dissociation spectroscopy as a novel structural tool for carbohydrates.
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Affiliation(s)
- B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - L Barnes
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - C J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - S Chambert
- Univ Lyon, INSA-Lyon, Université Lyon 1, CPE Lyon, ICBMS, UMR 5246 , Bâtiment Jules Verne, 20 avenue Albert Einstein, F-69621 Villeurbanne, France
| | - S L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, Nijmegen 6525ED, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098XH, The Netherlands
| | - R Daniel
- CNRS, UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université Evry-Val-d'Essonne , Evry 91025, France
| | - A R Allouche
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France.,Institut Universitaire de France IUF , 103 Boulevard St Michel, Paris 75005, France
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56
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Yao J, Chen H, Jiang F, Jiao Z, Jin M. Titanium dioxide and cadmium sulfide co-sensitized graphitic carbon nitride nanosheets composite photocatalysts with superior performance in phenol degradation under visible-light irradiation. J Colloid Interface Sci 2017; 490:154-162. [DOI: 10.1016/j.jcis.2016.11.051] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
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57
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Boles GC, Owen CJ, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+and Cd2+. Phys Chem Chem Phys 2017; 19:12394-12406. [DOI: 10.1039/c7cp01786c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD of [Zn(Glu-H)ACN]+was particularly interesting because fragmentation of the amino acid was favored, rather than dissociation of the ACN ligand.
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Affiliation(s)
| | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
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58
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Fu W, Carr PJJ, Lecours MJ, Burt M, Marta RA, Steinmetz V, Fillion E, McMahon TB, Hopkins WS. Intramolecular cation–π interactions in protonated phenylalanine derivatives. Phys Chem Chem Phys 2017; 19:729-734. [DOI: 10.1039/c6cp07337a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.
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Affiliation(s)
- Weiqiang Fu
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | | | | | - Michael Burt
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Rick A. Marta
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | | | - Eric Fillion
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
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59
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Li H, Jiang J, Luo Y. Identification of the protonation site of gaseous triglycine: the cis-peptide bond conformation as the global minimum. Phys Chem Chem Phys 2017; 19:15030-15038. [DOI: 10.1039/c7cp01997a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive ab initio investigations have been performed to characterize stable conformers of protonated triglycine (GGGH) in the gas phase.
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Affiliation(s)
- Hongbao Li
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
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60
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León I, Alonso ER, Mata S, Cabezas C, Rodríguez MA, Grabow JU, Alonso JL. The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2. Phys Chem Chem Phys 2017; 19:24985-24990. [DOI: 10.1039/c7cp03924g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy.
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Affiliation(s)
- I. León
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - E. R. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - S. Mata
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - C. Cabezas
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - M. A. Rodríguez
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - J.-U. Grabow
- Institut für Physikalische Chemie und Elektrochemie
- Lehrgebiet A
- Gottfried-Wilhelm-Leibniz-Universität
- D-30167 Hannover
- Germany
| | - J. L. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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61
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Corinti D, De Petris A, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy. Chemphyschem 2016; 18:318-325. [PMID: 27935248 DOI: 10.1002/cphc.201601172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/07/2016] [Indexed: 11/08/2022]
Abstract
The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH3 )2 (histidine)]+ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Alberto De Petris
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria E Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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62
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Asparagine Complexes with Zn2+ and Cd2+ and Their Deamidation Processes. J Phys Chem B 2016; 120:12486-12500. [DOI: 10.1021/acs.jpcb.6b10326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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63
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Scuderi D, Bodo E, Chiavarino B, Fornarini S, Crestoni ME. Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations. Chemistry 2016; 22:17239-17250. [PMID: 27808437 DOI: 10.1002/chem.201603298] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/02/2023]
Abstract
The redox activity of cysteine sulfur allows numerous post-translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas-phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSOx ]- (x=1, 2, 3, representing the number of S-bound oxygen atoms), which are key intermediates in the redox-switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur-containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO- in [cysSO]- migrates to the carboxylate in [cysSO3 ]- , whereas it turns out to be shared in [cysSO2 ]- . Evidence is gathered that a mixture of close-lying low-energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.
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Affiliation(s)
- Debora Scuderi
- Laboratoire de Chimie Physique d'Orsay, Faculté des Sciences, Université Paris Sud, UMR8000 CNRS, Bât 350, 91405, Orsay Cedex, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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64
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van der Linde C, Tang WK, Siu CK, Beyer MK. Electrons Mediate the Gas-Phase Oxidation of Formic Acid with Ozone. Chemistry 2016; 22:12684-7. [PMID: 27400953 DOI: 10.1002/chem.201603080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Christian van der Linde
- Institut für Ionenphysik und Angewandte Physik; Leopold-Franzens-Universität Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
| | - Wai-Kit Tang
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
| | - Chi-Kit Siu
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
| | - Martin K. Beyer
- Institut für Ionenphysik und Angewandte Physik; Leopold-Franzens-Universität Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
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65
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Paciotti R, Coletti C, Re N, Scuderi D, Chiavarino B, Fornarini S, Crestoni ME. Serine O-sulfation probed by IRMPD spectroscopy. Phys Chem Chem Phys 2016; 17:25891-904. [PMID: 26027702 DOI: 10.1039/c5cp01409c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sulfation of amino acids is a frequent post-translational modification. It is highly labile, though, and characterizing it by mass spectrometry, an otherwise powerful and widely exploited tool in analytical proteomics, is a challenge. The presently reported study is aimed at revealing the O-sulfation of l-serine and elucidating the effects of protonation and deprotonation on the structure and stability of the ensuing ionic species, [sSer + H](+) and [sSer - H](-). These ions are obtained as gaseous, isolated species by electrospray ionization, trapped in a Paul ion-trap, and sampled by IR multiple photon dissociation (IRMPD) spectroscopy in either the 750-1900 cm(-1) fingerprint range, or the 2900 and 3700 cm(-1) range encompassing the N-H and O-H stretching modes. The recorded IRMPD spectra present diagnostic signatures of the sulfate modification which are missing in the spectra of the native serine ions, [Ser + H](+) and [Ser - H](-). The experimental IRMPD features have been interpreted by comparison with the linear IR spectra of the lowest energy structures that are likely candidates for the sampled ions, calculated at the M06-2X/6-311+G(d,p) level of theory. Evidence is gathered that the most stable conformations of [sSer + H](+) are stabilized by hydrogen bonding interactions between the protonated amino group and both the carbonyl and sulfate oxygens. [sSer - H](-) ions possess a negatively charged sulfate group involved in either a S=O···HN or a S=O···HO hydrogen bond. The experimental IRMPD spectra are consistent with the presence of multiple low-lying structures in a thermally equilibrated population of several species particularly in the case of [sSer - H](-) ions, where the high structural flexibility combined with the presence of a negative charge favors the co-existence of several different H-bonding motifs.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
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66
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Kempkes LJM, Martens JK, Grzetic J, Berden G, Oomens J. Deamidation reactions of protonated asparagine and glutamine investigated by ion spectroscopy. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:483-490. [PMID: 26777678 DOI: 10.1002/rcm.7464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Deamidation of Asn and Gln residues is a primary route for spontaneous post-translational protein modification. Several structures have been proposed for the deamidation products of the protonated amino acids. Here we verify these structures by ion spectroscopy, as well as the structures of parallel and sequential fragmentation products. METHODS Infrared ion spectroscopy using the free electron laser FELIX has been applied to the reaction products from deamidation of protonated glutamine and asparagine in a tandem mass spectrometer. IR spectra were recorded over the 800-1900 cm(-1) spectral range by infrared multiple-photon dissociation (IRMPD) spectroscopy. Molecular structures of the fragment ions are derived from comparison of the experimental spectra with spectra predicted for different candidate structures by density functional theory (DFT) calculations. RESULTS [AsnH(+) -NH3](+) is found to possess a 3-aminosuccinic anhydride structure protonated on the amino group. The dissociation reaction involving loss of H2O and CO forms a linear immonium ion. For [GlnH(+)-NH3](+), the N-terminal nitrogen acts as the nucleophile leading to an oxo-proline product ion structure. For [GlnH(+)-NH3](+), a sequential loss of [CO + H2O] is found, leading to a pyrolidone-like structure. We also confirm by IR spectroscopy that dehydration of protonated aspartic acid (AspH(+)) and glutamic acid (GluH(+)) leads to identical structures as to those found for the loss of NH3 from AsnH(+) and GlnH(+). CONCLUSIONS The structure determined for AsnH(+) is in agreement with the suggested structure derived from measured and computed activation energies. IR ion spectra for the NH3 -loss product from GlnH(+) establish that a different reaction mechanism occurs for this species as compared to AsnH(+). For both amino acids, loss of NH3 occurs from the side chain.
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Affiliation(s)
- Lisanne J M Kempkes
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jonathan K Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Josipa Grzetic
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for 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
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67
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Heiles S, Cooper RJ, Berden G, Oomens J, Williams ER. Hydrogen bond mediated stabilization of the salt bridge structure for the glycine dimer anion. Phys Chem Chem Phys 2016; 17:30642-7. [PMID: 26524433 DOI: 10.1039/c5cp06120b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of a salt bridge in deprotonated glycine dimer anions in a solvent-free environment is investigated using both infrared multiple photon dissociation spectroscopy between 600 and 1800 cm(-1) and theory. The zwitterionic and nonzwitterionic forms of glycine in this complex are computed to be nearly iso-energetic, yet predominantly the zwitterionic form is observed experimentally. The zwitterion stability is attributed to both the Coulombic attraction and the high stabilization from intramolecular hydrogen bonding that drives the energetic cost of proton transfer in a solvent free environment. These results show that there is a fine balance between the stabilities of these two forms of the anion. Elucidating the role of intrinsic factors, such as hydrogen bonding, can lead to a better understanding of the stabilities of salt bridges in the interiors of large proteins or at protein interfaces.
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Affiliation(s)
- S Heiles
- Department of Chemistry, University of California, B42 Hildebrand Hall, Berkeley, CA 94720, USA.
| | - Richard J Cooper
- Department of Chemistry, University of California, B42 Hildebrand Hall, Berkeley, CA 94720, USA.
| | - Giel Berden
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Evan R Williams
- Department of Chemistry, University of California, B42 Hildebrand Hall, Berkeley, CA 94720, USA.
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68
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Andreeva OA, Burkova LA, Podeshvo IV. Fourier transform IR spectroscopic study of substituent effect in aromatic amino acids on the zwitterion–neutral molecule tautomeric equilibrium. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2016. [DOI: 10.1134/s1990793115060147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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69
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Coates RA, Boles GC, McNary CP, Berden G, Oomens J, Armentrout PB. Zn2+ and Cd2+ cationized serine complexes: infrared multiple photon dissociation spectroscopy and density functional theory investigations. Phys Chem Chem Phys 2016; 18:22434-45. [DOI: 10.1039/c6cp03805k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc and cadmium dications bind serine in tridentate structures at the amine and carbonyl groups and side-chain hydroxyl group.
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Affiliation(s)
| | | | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525ED Nijmegen
- The Netherlands
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70
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Ieritano C, Carr PJJ, Hasan M, Burt M, Marta RA, Steinmetz V, Fillion E, McMahon TB, Scott Hopkins W. The structures and properties of proton- and alkali-bound cysteine dimers. Phys Chem Chem Phys 2016; 18:4704-10. [DOI: 10.1039/c5cp07414b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.
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Affiliation(s)
| | | | - Moaraj Hasan
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Michael Burt
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Rick A. Marta
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
| | - Vincent Steinmetz
- Laboratoire Chimie Physique – CLIO
- Campus Universitaire
- d'Orsay
- Orsay
- France
| | - Eric Fillion
- Department of Chemistry
- University of Waterloo
- Waterloo
- Canada
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71
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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72
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Ehsan MU, Bozai Y, Pearson WL, Horenstein NA, Eyler JR. Infrared multiple photon dissociation spectrum of protonated bis(2-methoxyethyl) ether obtained with a tunable CO2 laser. Phys Chem Chem Phys 2015; 17:25877-81. [PMID: 26007681 DOI: 10.1039/c5cp01752a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A moderate-resolution infrared multiple photon dissociation (IRMPD) spectrum of protonated bis(2-methoxyethyl) ether (diglyme) was obtained using a grating-tuned CO2 laser. The experimental spectrum compares well with one calculated theoretically at the MP2 level and exhibits defined peaks over the span of the CO2 laser output lines as opposed to a relatively featureless spectrum over this wavelength range obtained using free electron laser infrared radiation. The lowest energy structure corresponding to the calculated vibrational spectrum is consistent with structures previously calculated at the same level of theory. Alternative structures were calculated at lower levels of theory for comparison and investigation of the energetics of proton-heteroatom interactions. Broadening of the IRMPD action spectrum due to energetic phenomena characteristic of proton bridges was not observed and thus did not obscure the correlation between theoretical calculations and experimentally determined spectra as it may have in previous studies.
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Affiliation(s)
- M U Ehsan
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA.
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73
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Khairallah GN, Maccarone AT, Pham HT, Benton TM, Ly T, da Silva G, Blanksby SJ, O'Hair RAJ. Radical Formation in the Gas-Phase Ozonolysis of Deprotonated Cysteine. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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74
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Khairallah GN, Maccarone AT, Pham HT, Benton TM, Ly T, da Silva G, Blanksby SJ, O'Hair RAJ. Radical Formation in the Gas‐Phase Ozonolysis of Deprotonated Cysteine. Angew Chem Int Ed Engl 2015; 54:12947-51. [DOI: 10.1002/anie.201506019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Indexed: 11/07/2022]
Affiliation(s)
- George N. Khairallah
- School of Chemistry and Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010 (Australia)
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (Australia)
| | - Alan T. Maccarone
- School of Chemistry, University of Wollongong, New South Wales 2522 (Australia)
| | - Huong T. Pham
- School of Chemistry, University of Wollongong, New South Wales 2522 (Australia)
| | - Timothy M. Benton
- School of Chemistry and Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010 (Australia)
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (Australia)
| | - Tony Ly
- School of Chemistry, University of Wollongong, New South Wales 2522 (Australia)
| | - Gabriel da Silva
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, Victoria 3010 (Australia)
| | - Stephen J. Blanksby
- Central Analytical Research Facility, Queensland University of Technology, Queensland 4001 (Australia)
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (Australia)
| | - Richard A. J. O'Hair
- School of Chemistry and Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010 (Australia)
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (Australia)
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75
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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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76
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Plummer CE, Stover ML, Bokatzian SS, Davis JTM, Dixon DA, Cassady CJ. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides. J Phys Chem B 2015. [PMID: 26196065 DOI: 10.1021/acs.jpcb.5b04486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.
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Affiliation(s)
- Chelsea E Plummer
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L Stover
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Samantha S Bokatzian
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - John T M Davis
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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77
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Flick TG, Campuzano IDG, Bartberger MD. Structural Resolution of 4-Substituted Proline Diastereomers with Ion Mobility Spectrometry via Alkali Metal Ion Cationization. Anal Chem 2015; 87:3300-7. [DOI: 10.1021/ac5043285] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tawnya G. Flick
- Department
of Oral Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Iain D. G. Campuzano
- Department
of Molecular Structure and Characterization, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Michael D. Bartberger
- Department
of Molecular Structure and Characterization, Amgen, Inc., Thousand Oaks, California 91320, United States
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78
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Abstract
The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF3-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)2] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.
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Affiliation(s)
- R. A. Cormanich
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
- Chemistry Institute
| | - R. Rittner
- Chemistry Institute
- State University of Campinas
- Campinas
- Brazil
| | - M. Bühl
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
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79
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Cheng F, Wang H, Dong X. The amphoteric properties of g-C3N4 nanosheets and fabrication of their relevant heterostructure photocatalysts by an electrostatic re-assembly route. Chem Commun (Camb) 2015; 51:7176-9. [DOI: 10.1039/c5cc01035g] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A stable colloid of g-C3N4 nanosheets was prepared on a large scale via a H2SO4 exfoliation route.
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Affiliation(s)
- Fuxing Cheng
- Department of Chemistry
- School of Sciences
- Zhejiang Sci-Tech University
- Hangzhou
- China
| | - Hainan Wang
- Department of Chemistry
- School of Sciences
- Zhejiang Sci-Tech University
- Hangzhou
- China
| | - Xiaoping Dong
- Department of Chemistry
- School of Sciences
- Zhejiang Sci-Tech University
- Hangzhou
- China
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80
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Li H, Li L, Jiang J, Lin Z, Luo Y. Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine. Phys Chem Chem Phys 2015; 17:24754-60. [DOI: 10.1039/c5cp03729h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The global minimum of the dipeptide ArgGly is found to be in the canonical form, rather than the zwitterionic form.
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Affiliation(s)
- Hongbao Li
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science and Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
| | - Leilei Li
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- China
| | - Yi Luo
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science and Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
- Hefei National Laboratory for Physical Sciences at the Microscale
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81
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Meyer F, Blum M, Benkert A, Hauschild D, Nagarajan S, Wilks RG, Andersson J, Yang W, Zharnikov M, Bär M, Heske C, Reinert F, Weinhardt L. “Building Block Picture” of the Electronic Structure of Aqueous Cysteine Derived from Resonant Inelastic Soft X-ray Scattering. J Phys Chem B 2014; 118:13142-50. [DOI: 10.1021/jp5089417] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- F. Meyer
- Experimentelle
Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - M. Blum
- Department
of Chemistry, University of Nevada, Las Vegas, 4505 Maryland
Parkway, Las Vegas, Nevada 89154-4003, United States
| | - A. Benkert
- Experimentelle
Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - D. Hauschild
- Experimentelle
Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - S. Nagarajan
- Angewandte
Physikalische Chemie, Universität Heidelberg, INF 253,69120 Heidelberg, Germany
| | - R. G. Wilks
- Solar
Energy Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - J. Andersson
- Department
of Physics and Astronomy, Uppsala University, Box 516, S-751 20 Uppsala, Sweden
| | - W. Yang
- Advanced
Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - M. Zharnikov
- Angewandte
Physikalische Chemie, Universität Heidelberg, INF 253,69120 Heidelberg, Germany
| | - M. Bär
- Department
of Chemistry, University of Nevada, Las Vegas, 4505 Maryland
Parkway, Las Vegas, Nevada 89154-4003, United States
- Solar
Energy Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
- Institut
für Physik und Chemie, Brandenburgische Technische Universität Cottbus-Senftenberg, Platz der Deutschen Einheit 1, 03046 Cottbus, Germany
| | - C. Heske
- Department
of Chemistry, University of Nevada, Las Vegas, 4505 Maryland
Parkway, Las Vegas, Nevada 89154-4003, United States
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 18/20, 76128 Karlsruhe, Germany
| | - F. Reinert
- Experimentelle
Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - L. Weinhardt
- Department
of Chemistry, University of Nevada, Las Vegas, 4505 Maryland
Parkway, Las Vegas, Nevada 89154-4003, United States
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 18/20, 76128 Karlsruhe, Germany
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82
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Bokatzian SS, Stover ML, Plummer CE, Dixon DA, Cassady CJ. An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine. J Phys Chem B 2014; 118:12630-43. [DOI: 10.1021/jp510037c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samantha S. Bokatzian
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Michele L. Stover
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Chelsea E. Plummer
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A. Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Carolyn J. Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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83
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Gregori B, Guidoni L, Chiavarino B, Scuderi D, Nicol E, Frison G, Fornarini S, Crestoni ME. Vibrational Signatures of S-Nitrosoglutathione as Gaseous, Protonated Species. J Phys Chem B 2014; 118:12371-82. [DOI: 10.1021/jp5072742] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Leonardo Guidoni
- Dipartimento
di Scienza Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio 2, Coppito, L’Aquila I-64100, Italy
| | | | - Debora Scuderi
- Laboratoire
de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris-Sud, Batiment 350, 91405 Orsay Cedex, France
| | - Edith Nicol
- Laboratoire
de Chimie Moléculaire, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Frison
- Laboratoire
de Chimie Moléculaire, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
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84
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A fragment based step-by-step strategy for determining the most stable conformers of biomolecules. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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85
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Li C, Monti S, Agren H, Carravetta V. Cysteine on TiO2(110): a theoretical study by reactive dynamics and photoemission spectra simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8819-8828. [PMID: 25020148 DOI: 10.1021/la5014973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Owing to the importance of bioinorganic interface properties for the biocompatibility of implants and for biosensing technology, it has become indispensable to gain understanding of their crucial structure-property relations at the atomistic level. Motivated by this fact, we use cysteine amino acid on perfect and defective TiO2(110) surfaces as model systems and study adsorption by means of classical all-atom reactive molecular dynamics and ab initio O 1s, N 1s, and S 2p photoemission spectra (XPS) simulations of the most relevant adsorbate structures. By analysis of the dynamics results and a detailed comparison with spectra recently collected for this adsorbate, we obtain conclusions of both general and particular character. It is shown that the interaction of cysteine with the TiO2(110) surface has multipoint character involving the carboxylic group as well as the amino and sulfur groups. The proton-transfer reactivity of cysteine is enhanced by the presence of the surface, and different forms of cysteines are confirmed to be present in the adsorbate. A general conclusion is that reactive force field dynamics combined with selected spectroscopy provides a viable path to understanding bioinorganic surfaces with ramifications for the design of such surfaces for future technological applications.
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Affiliation(s)
- Cui Li
- Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , SE-10044 Stockholm, Sweden
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86
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Minkov VS, Boldyreva EV. Contribution of Weak S–H···O Hydrogen Bonds to the Side Chain Motions in d,l-Homocysteine on Cooling. J Phys Chem B 2014; 118:8513-23. [DOI: 10.1021/jp503154x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vasily S. Minkov
- Novosibirsk State University, 2 Pirogov
str., 630090 Novosibirsk, Russian Federation
- Institute
of Solid State Chemistry and Mechanochemistry Siberian Branch of Russian Academy of Sciences, 18 Kutateladze str., 630128 Novosibirsk, Russian Federation
| | - Elena V. Boldyreva
- Novosibirsk State University, 2 Pirogov
str., 630090 Novosibirsk, Russian Federation
- Institute
of Solid State Chemistry and Mechanochemistry Siberian Branch of Russian Academy of Sciences, 18 Kutateladze str., 630128 Novosibirsk, Russian Federation
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87
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88
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Schinle F, Jacob CR, Wolk AB, Greisch JF, Vonderach M, Weis P, Hampe O, Johnson MA, Kappes MM. Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase. J Phys Chem A 2014; 118:8453-63. [PMID: 24884600 DOI: 10.1021/jp501772d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.
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Affiliation(s)
- Florian Schinle
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , 76021 Karlsruhe, Germany
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89
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90
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Puzzarini C, Biczysko M, Barone V, Largo L, Peña I, Cabezas C, Alonso JL. Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue. J Phys Chem Lett 2014; 5:534-540. [PMID: 26276605 DOI: 10.1021/jz402744a] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | | | - Vincenzo Barone
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Laura Largo
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - Isabel Peña
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - Carlos Cabezas
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - José Luis Alonso
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
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91
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DeBlase AF, Kass SR, Johnson MA. On the character of the cyclic ionic H-bond in cryogenically cooled deprotonated cysteine. Phys Chem Chem Phys 2014; 16:4569-75. [DOI: 10.1039/c3cp54117g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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92
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Hu Y, Guan J, Bernstein ER. Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters. MASS SPECTROMETRY REVIEWS 2013; 32:484-501. [PMID: 24122973 DOI: 10.1002/mas.21387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 06/02/2023]
Abstract
Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.
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Affiliation(s)
- Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
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93
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94
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Purushotham U, Sastry GN. A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms. J Comput Chem 2013; 35:595-610. [DOI: 10.1002/jcc.23482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/08/2013] [Accepted: 10/13/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Uppula Purushotham
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
| | - G. Narahari Sastry
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
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95
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Gupta M, da Silva EF, Svendsen HF. Explicit Solvation Shell Model and Continuum Solvation Models for Solvation Energy and pKa Determination of Amino Acids. J Chem Theory Comput 2013; 9:5021-37. [DOI: 10.1021/ct400459y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mayuri Gupta
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eirik F. da Silva
- Department
of Process Technology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway
| | - Hallvard F. Svendsen
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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96
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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.
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Affiliation(s)
- Y-w Nei
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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97
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Guru PS, Dash S. Amino Acid Modified Eggshell Powder (AA-ESP)—A Novel Bio-Solid Scaffold for Adsorption of Some Styrylpyridinium Dyes. J DISPER SCI TECHNOL 2013. [DOI: 10.1080/01932691.2012.737752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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98
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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99
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Fang Y, Liu F, Emre R, Liu J. Guided-Ion-Beam Scattering and Direct Dynamics Trajectory Study on the Reaction of Deprotonated Cysteine with Singlet Molecular Oxygen. J Phys Chem B 2013; 117:2878-87. [DOI: 10.1021/jp4002077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yigang Fang
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65-30 Kissena Boulevard, Queens, New York
11367, United States
| | - Fangwei Liu
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65-30 Kissena Boulevard, Queens, New York
11367, United States
| | - Rifat Emre
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65-30 Kissena Boulevard, Queens, New York
11367, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, 65-30 Kissena Boulevard, Queens, New York
11367, United States
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100
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Piccirillo S, Ciavardini A, Bodo E, Rondino F, Scuderi D, Steinmetz V, Paladini A. Probing the competition among different coordination motifs in metal-ciprofloxacin complexes through IRMPD spectroscopy and DFT calculations. Inorg Chem 2013; 52:103-12. [PMID: 23252622 DOI: 10.1021/ic301299e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The vibrational spectra of ciprofloxacin complexes with monovalent (Li(+), Na(+), K(+), Ag(+)) and polyvalent (Mg(2+), Al(3+)) metal ions are recorded in the range 1000-1900 cm(-1) by means of infrared multiple-photon dissociation (IRMPD) spectroscopy. The IRMPD spectra are analyzed and interpreted in the light of density functional theory (DFT)-based quantum chemical calculations in order to identify the possible structures present under our experimental conditions. For each metal-ciprofloxacin complex, four isomers are predicted, considering different chelation patterns. A good agreement is found between the measured IRMPD spectrum and the calculated absorption spectrum of the most stable isomer for each complex. Metal ion size and charge are found to drive the competition among the different coordination motifs: small size and high charge density metal ions prefer to coordinate the quinolone between the two carbonyl oxygen atoms, whereas large-size metal ions prefer the carboxylate group as a coordination site. In the latter case, an intramolecular hydrogen bond compensates the weaker interaction established by these cations. The role of the metal cation on the stabilization of ionic and nonionic structures of ciprofloxacin is also investigated. It is found that large-size metal ions preferentially stabilize charge separated motifs and that the increase of metal ion charge has a stabilizing effect on the zwitterionic form of ciprofloxacin.
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Affiliation(s)
- Susanna Piccirillo
- Dip. di Scienze e Tecnologie Chimiche, Università di Roma 'Tor Vergata', via della Ricerca Scientifica, 00133 Rome, Italy
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