1
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Gao H, Xiong M, Kong C, Yang Z, Yang T. A theoretical study on hydrated sodium ion-phenylalanine clusters Na +(Phe)(H 2O) n ( n = 0-6; Phe = phenylalanine). Phys Chem Chem Phys 2023; 25:29576-29584. [PMID: 37877287 DOI: 10.1039/d3cp03144f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The cation-π interaction is of importance in many chemical and biological processes such as those involving protein geometries and functionals and ion channels. In this study, to understand the cation-π interaction between essential ions and protein in the water-aqueous environment, geometries, electronic structures, bonding properties, and dynamic stabilities of hydrated Na+-phenylalanine clusters Na+(Phe)(H2O)n (n = 0-6) were studied using density functional theory calculations and ab initio molecular dynamics simulations. After the addition of water molecules, Na+(Phe)(H2O)n structures change from a tridentate complex to quadridentate or pentadentate complexes while the cation-π interaction always exists. The fluctuation between quadridentate and pentadentate complexes results from the competition between cation-O bonding and hydrogen bonding. The charge analysis reveals that the positive charge is mainly located on the Na ion, whereas the further addition of water reduces the binding energy of water, electron affinity, and ionization potential. As the number of water molecules increases, the bonding interactions between the sodium ion and the remaining phenylalanine-water complex increase and correlate with the coordination number, in which the electrostatic interaction contributes more than the orbital interaction. The important orbital interaction terms come from the donation of the carboxyl and amino groups and water to the Na+ ion. Molecular dynamic simulations revealed that Na+(Phe)(H2O)6 is stable at 300 K.
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Affiliation(s)
- Haiyang Gao
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Mo Xiong
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Chuncai Kong
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Zhimao Yang
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
| | - Tao Yang
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China.
- Xi'an Jiaotong University Suzhou Academy, Suzhou, China
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2
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Rolland AD, Biberic LS, Prell JS. Investigation of Charge-State-Dependent Compaction of Protein Ions with Native Ion Mobility-Mass Spectrometry and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:369-381. [PMID: 35073092 DOI: 10.1021/jasms.1c00351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The precise relationship between native gas-phase protein ion structure, charge, desolvation, and activation remains elusive. Much evidence supports the Charge Residue Model for native protein ions formed by electrospray ionization, but scaling laws derived from it relate only to overall ion size. Closer examination of drift tube CCSs across individual native protein ion charge state distributions (CSDs) reveals deviations from global trends. To investigate whether this is due to structure variation across CSDs or contributions of long-range charge-dipole interactions, we performed in vacuo force field molecular dynamics (MD) simulations of multiple charge conformers of three proteins representing a variety of physical and structural features: β-lactoglobulin, concanavalin A, and glutamate dehydrogenase. Results from these simulated ions indicate subtle structure variation across their native CSDs, although effects of these structural differences and long-range charge-dependent interactions on CCS are small. The structure and CCS of smaller proteins may be more sensitive to charge due to their low surface-to-volume ratios and reduced capacity to compact. Secondary and higher order structure from condensed-phase structures is largely retained in these simulations, supporting the use of the term "native-like" to describe results from native ion mobility-mass spectrometry experiments, although, notably, the most compact structure can be the most different from the condensed-phase structure. Collapse of surface side chains to self-solvate through formation of new hydrogen bonds is a major feature of gas-phase compaction and likely occurs during the desolvation process. Results from these MD simulations provide new insight into the relationship of gas-phase protein ion structure, charge, and CCS.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Lejla S Biberic
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, Oregon 97403-1252, United States
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3
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van Geenen FAMG, Kranenburg RF, van Asten AC, Martens J, Oomens J, Berden G. Isomer-Specific Two-Color Double-Resonance IR 2MS 3 Ion Spectroscopy Using a Single Laser: Application in the Identification of Novel Psychoactive Substances. Anal Chem 2021; 93:2687-2693. [PMID: 33470107 PMCID: PMC7859929 DOI: 10.1021/acs.analchem.0c05042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The capability of
an ion trap mass
spectrometer to store ions for
an arbitrary amount of time allows the use of a single infrared (IR)
laser to perform two-color double resonance IR–IR spectroscopic
experiments on mass-to-charge (m/z) selected ions. In this single-laser IR2MS3 scheme, one IR laser frequency is used to remove a selected set
of isomers from the total trapped ion population and the second IR
laser frequency, from the same laser, is used to record the IR spectrum
of the remaining precursor ions. This yields isomer-specific vibrational
spectra of the m/z-selected ions,
which can reveal the structure and identity of the initially co-isolated
isomeric species. The use of a single laser greatly reduces the experimental
complexity of two-color IR2MS3 and enhances
its application in fields employing analytical MS. In this work, we
demonstrate the methodology by acquiring single-laser IR2MS3 spectra in a forensic context, identifying two previously
unidentified isomeric novel psychoactive substances (NPS) from a sample
that was confiscated by the Amsterdam Police.
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Affiliation(s)
- Fred A M G van Geenen
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Ruben F Kranenburg
- Forensic Laboratory, Unit Amsterdam, Dutch National Police, Kabelweg 25, 1014 BA Amsterdam, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Arian C van Asten
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.,Co van Ledden Hulsebosch Center (CLHC), Amsterdam Center for Forensic Science and Medicine, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
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4
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Martens J, van Outersterp RE, Vreeken RJ, Cuyckens F, Coene KLM, Engelke UF, Kluijtmans LAJ, Wevers RA, Buydens LMC, Redlich B, Berden G, Oomens J. Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective. Anal Chim Acta 2019; 1093:1-15. [PMID: 31735202 DOI: 10.1016/j.aca.2019.10.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 01/21/2023]
Abstract
Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Rob J Vreeken
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Filip Cuyckens
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lutgarde M C Buydens
- Radboud University, Institute for Molecules and Materials, Chemometrics, Heyendaalseweg 135, 6525AJ, Nijmegen, the Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands; van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098XH, Amsterdam, Science Park 908, the Netherlands.
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5
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Walhout EQ, Dorn SE, Martens J, Berden G, Oomens J, Cheong PHY, Kroll JH, O'Brien RE. Infrared Ion Spectroscopy of Environmental Organic Mixtures: Probing the Composition of α-Pinene Secondary Organic Aerosol. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:7604-7612. [PMID: 31184875 DOI: 10.1021/acs.est.9b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Characterizing the chemical composition of organic aerosols can elucidate aging mechanisms as well as the chemical and physical properties of the aerosol. However, the high chemical complexity and often low atmospheric abundance present a difficult analytical challenge. Milligrams or more of material may be needed for speciated spectroscopic analysis. In contrast, mass spectrometry provides a very sensitive platform but limited structural information. Here, we combine the strengths of mass spectrometry and infrared (IR) action spectroscopy to generate characteristic IR spectra of individual, mass-isolated ion populations. Soft ionization combined with in situ infrared ion spectroscopy, using the tunable free-electron laser FELIX, provides detailed information on molecular structures and functional groups. We apply this technique, along with quantum mechanical modeling, to characterize organic molecules in secondary organic aerosol (SOA) formed from the ozonolysis of α-pinene. Spectral overlap with a standard is used to identify cis-pinonic acid. We also demonstrate the characterization of isomers for multiple SOA products using both quantum mechanical computations and analyses of fragment ion spectra. These results demonstrate the detailed structural information on isolated ions obtained by combining mass spectrometry with fingerprint IR spectroscopy.
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Affiliation(s)
- Emma Q Walhout
- Department of Chemistry , College of William and Mary , Williamsburg , Virginia 23185 , United States
| | - Shelby E Dorn
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331-4003 , United States
| | - Jonathan Martens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands
| | - Giel Berden
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands
| | - Jos Oomens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c , 6525ED Nijmegen , The Netherlands
- van't Hoff Institute for Molecular Sciences , University of Amsterdam , 1098XH Amsterdam , Science Park 908 , The Netherlands
| | - Paul H-Y Cheong
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331-4003 , United States
| | - Jesse H Kroll
- Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Rachel E O'Brien
- Department of Chemistry , College of William and Mary , Williamsburg , Virginia 23185 , United States
- Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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6
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Oomens J, Polfer NC, Berden G, Eyler JR. Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:86-96. [PMID: 30205710 DOI: 10.1177/1469066718799175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.
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Affiliation(s)
- Jos Oomens
- 1 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 2 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Nicolas C Polfer
- 3 Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Giel Berden
- 1 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - John R Eyler
- 3 Department of Chemistry, University of Florida, Gainesville, Florida, USA
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7
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Jusko P, Simon A, Banhatti S, Brünken S, Joblin C. Direct Evidence of the Benzylium and Tropylium Cations as the Two Long-Lived Isomers of C 7 H 7. Chemphyschem 2018; 19:3182-3185. [PMID: 30238585 PMCID: PMC6420061 DOI: 10.1002/cphc.201800744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 11/12/2022]
Abstract
Disentangling the isomeric structure of C7 H7 + is a longstanding experimental issue. We report here the full mid-infrared vibrational spectrum of C7 H7 + tagged with Ne obtained with infrared-predissociation spectroscopy at 10 K. Saturation depletion measurements were used to assign the contribution of benzylium and tropylium isomers and demonstrate that no other isomer is involved. Recorded spectral features compare well with density functional theory calculations. This opens perspectives for a better understanding and control of the formation paths leading to either tropylium or benzylium ions.
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Affiliation(s)
- Pavol Jusko
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université de Toulouse (UPS), CNRS, CNES, 9 Av. du Colonel Roche, 31028 Toulouse Cedex 4, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, 31062 Toulouse, France
| | - Shreyak Banhatti
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, 50937 Köln, Germany
| | - Sandra Brünken
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Christine Joblin
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université de Toulouse (UPS), CNRS, CNES, 9 Av. du Colonel Roche, 31028 Toulouse Cedex 4, France
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8
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Smith ZM, Steinmetz V, Martens J, Oomens J, Poutsma JC. Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation †. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 429:158-173. [PMID: 29962900 PMCID: PMC6020040 DOI: 10.1016/j.ijms.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH+, CavLi+, and CavNa+; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK+ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs+ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa+ and ArgK+. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na+, K+, and Cs+. A major difference between the zwitterionic forms of ArgM+ and CavM+ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris Sud, Université Paris Saclay, CNRS, Orsay France
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials FELIX Laboratory, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences University of Amsterdam, Amsterdam, The Netherlands
| | - John C Poutsma
- Department of Chemistry, The College of William and Mary, Williamsburg, VA 23187-8795
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9
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study. Inorg Chem 2017; 56:8793-8801. [PMID: 28718635 DOI: 10.1021/acs.inorgchem.7b00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH3)2(5'-dAMP)]+ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH3)2(5'-dAMP)]+ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH3)2(5'-dAMP)]+ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- LCP, Université Paris Sud Orsay, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Jean-Yves Salpin
- LAMBE, Université d'Evry Val d'Essonne, CEA, CNRS, Université Paris-Saclay , F-91025 Evry, France.,LAMBE, Université Cergy-Pontoise, Université Paris-Seine , F-91025 Evry, France
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10
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Dunbar RC, Martens J, Berden G, Oomens J. Water Microsolvation Can Switch the Binding Mode of Ni(II) with Small Peptides. J Phys Chem Lett 2017; 8:2634-2638. [PMID: 28537749 DOI: 10.1021/acs.jpclett.7b00973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ni(II) ions can be caged by surrounding peptide ligands in two basic binding patterns: the "iminol" (IM) binding pattern, where chelation occurs by deprotonated amide nitrogens, or the charge-solvated (CS) binding pattern, where chelation occurs by amide carbonyl oxygens. Gas-phase observation may clarify the factors affecting this choice in solution and in peptide and protein matrices. Infrared spectroscopic determination of gas-phase structures shows here how microsolvation by just one water molecule switches the balance of this choice from IM to CS for the Ni2+Gly3 complex, in contrast with the always-CS structure of the Ni2+Gly4 complex. Quantum-chemical calculations indicate that CS complexation is even more favored in the aqueous limit. Considering gas-phase conditions as comparable to low-pH solutions can reconcile this prediction with the common observation of IM-type binding in solutions at higher pH. This is likely the first gas-phase observation of solvation-induced IM-to-CS transition in oligopeptide complexes with doubly charged transition-metal ions.
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Jonathan Martens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- University of Amsterdam , Science Park 904, 1098XH Amsterdam, The Netherlands
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11
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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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12
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Seo J, Jang J, Warnke S, Gewinner S, Schöllkopf W, von Helden G. Stacking Geometries of Early Protoporphyrin IX Aggregates Revealed by Gas-Phase Infrared Spectroscopy. J Am Chem Soc 2016; 138:16315-16321. [DOI: 10.1021/jacs.6b08700] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Jinhyeong Jang
- Department
of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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13
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Troć A, Gajewy J, Danikiewicz W, Kwit M. Specific Noncovalent Association of Chiral Large-Ring Hexaimines: Ion Mobility Mass Spectrometry and PM7 Study. Chemistry 2016; 22:13258-64. [PMID: 27534731 DOI: 10.1002/chem.201602515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 02/04/2023]
Abstract
Ion mobility mass spectrometry and PM7 semiempirical calculations are effective complementary methods to study gas phase formation of noncovalent complexes from vaselike macrocycles. The specific association of large-ring chiral hexaimines, derived from enantiomerically pure trans-1,2-diaminocyclohexane and various isophthaldehydes, is driven mostly by CH-π and π-π stacking interactions. The isotrianglimine macrocycles are prone to form two types of aggregates: tail-to-tail and head-to-head (capsule) dimers. The stability of the tail-to-tail dimers is affected by the size and electronic properties of the substituents at the C-5 position of the aromatic ring. Electron-withdrawing groups stabilize the aggregate, whereas bulky or electron-donating groups destabilize the complexes.
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Affiliation(s)
- Anna Troć
- Intitute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Jadwiga Gajewy
- Department of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61 614, Poznań, Poland.,Wielkopolska Centre for Advanced Technologies (WCAT), Umultowska 89C, 61-614, Poznań, Poland
| | - Witold Danikiewicz
- Intitute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Kwit
- Department of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61 614, Poznań, Poland. , .,Wielkopolska Centre for Advanced Technologies (WCAT), Umultowska 89C, 61-614, Poznań, Poland. ,
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14
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Shi L, Holliday AE, Bohrer BC, Kim D, Servage KA, Russell DH, Clemmer DE. "Wet" Versus "Dry" Folding of Polyproline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1037-47. [PMID: 27059978 PMCID: PMC5152579 DOI: 10.1007/s13361-016-1372-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/20/2016] [Accepted: 02/22/2016] [Indexed: 05/06/2023]
Abstract
When the all-cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all-trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all-cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions-indicating that some transitions observed in water (i.e., "wet" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline. Graphical Abstract ᅟ.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Alison E Holliday
- Department of Chemistry, Moravian College, Bethlehem, PA, 18018, USA
| | - Brian C Bohrer
- Department of Chemistry, University of Southern Indiana, Evansville, IN, 47712, USA
| | - Doyong Kim
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Kelly A Servage
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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15
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Bouchet A, Schütz M, Dopfer O. Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate. Chemphyschem 2015; 17:232-43. [PMID: 26584245 DOI: 10.1002/cphc.201500939] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 01/29/2023]
Abstract
Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany.
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16
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Masson A, Williams ER, Rizzo TR. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine. J Chem Phys 2015; 143:104313. [DOI: 10.1063/1.4930196] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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17
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Riffet V, Bouchoux G, Frison G. Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach. J Phys Chem B 2015; 119:11527-39. [PMID: 26252717 DOI: 10.1021/acs.jpcb.5b05581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.
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Affiliation(s)
- Vanessa Riffet
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique and CNRS , 91128 Palaiseau cedex, France
| | - Guy Bouchoux
- 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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18
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Cooper RJ, Heiles S, Williams ER. Effects of electronic structure on the hydration of PbNO3(+) and SrNO3(+) ion pairs. Phys Chem Chem Phys 2015; 17:15963-75. [PMID: 26028325 DOI: 10.1039/c5cp01859e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration of PbNO3(+) and SrNO3(+) with up to 30 water molecules was investigated with infrared photodissociation (IRPD) spectroscopy and with theory. These ions are the same size, yet the IRPD spectra of these ion pairs for n = 2-8 are significantly different. Bands in the bonded O-H region (∼3000-3550 cm(-1)) indicate that the onset of a second hydration shell begins at n = 5 for PbNO3(+) and n = 6 for SrNO3(+). Spectra for [PbNO3](+)(H2O)2-5 and [SrNO3](+)(H2O)3-6 indicate that the structures of clusters with Pb(ii) are hemidirected with a void in the coordinate sphere. A natural bond orbital analysis of [PbNO3](+)(H2O)5 indicates that the anisotropic solvation of the ion is due to a region of asymmetric electron density on Pb(ii) that can be explained by charge transfer from the nitrate and water ligands into unoccupied p-orbitals on Pb(ii). There are differences in the IRPD spectra of PbNO3(+) and SrNO3(+) with up to 25 water molecules attached. IR intensity in the bonded O-H region is blue-shifted by ∼50 cm(-1) in nanodrops containing SrNO3(+) compared to those containing PbNO3(+), indicative of a greater perturbation of the water H-bond network by strontium. The free O-H stretches of surface water molecules in nanodrops containing 10, 15, 20, and 25 water molecules are red-shifted by ∼3-8 cm(-1) for PbNO3(+) compared to those for SrNO3(+), consistent with more charge transfer between water molecules and Pb(ii). These results demonstrate that the different electronic structure of these ions significantly influences how they are solvated.
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Affiliation(s)
- Richard J Cooper
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
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19
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Servage KA, Silveira JA, Fort KL, Russell DH. From Solution to Gas Phase: The Implications of Intramolecular Interactions on the Evaporative Dynamics of Substance P During Electrospray Ionization. J Phys Chem B 2015; 119:4693-8. [DOI: 10.1021/jp512708u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua A. Silveira
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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20
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Fort KL, Silveira JA, Pierson NA, Servage KA, Clemmer DE, Russell DH. From Solution to the Gas Phase: Factors That Influence Kinetic Trapping of Substance P in the Gas Phase. J Phys Chem B 2014; 118:14336-44. [DOI: 10.1021/jp5103687] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua A. Silveira
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nicholas A. Pierson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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21
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Cooper RJ, Heiles S, DiTucci MJ, Williams ER. Hydration of Guanidinium: Second Shell Formation at Small Cluster Size. J Phys Chem A 2014; 118:5657-66. [DOI: 10.1021/jp506429a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Richard J. Cooper
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Sven Heiles
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew J. DiTucci
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
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22
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Chang TM, Chakrabarty S, Williams ER. Hydration of gaseous m-aminobenzoic acid: ionic vs neutral hydrogen bonding and water bridges. J Am Chem Soc 2014; 136:10440-9. [PMID: 24971758 DOI: 10.1021/ja5045874] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hydration of a protonated amine and a neutral carboxylic acid were investigated for protonated m-aminobenzoic acid (MABAH(+)) with up to 15 water molecules attached using infrared photodissociation spectroscopy, laser-induced dissociation kinetics, and computational chemistry. A free COO-H stretch in the spectra of MABAH(+)·(H2O)1-5 indicates that water does not bind to the carboxylic acid H atom. This band is absent in the spectrum of MABAH(+) with six or more water molecules attached, and there is a hydrogen-bonded (HB) COO-H stretch indicating that water hydrogen bonds to the carboxylic acid H atom for these larger clusters. Photodissociation kinetic data for MABAH(+)·(H2O)6 indicate that greater than 74 ± 13% of the ion population consists of the HB COO-H isomer, consistent with this isomer being ≥0.5 kJ mol(-1) lower in energy than isomers where the carboxylic acid H atom does not donate a hydrogen bond. Calculations at the B3LYP/6-31+G** and MP2/6-31+G**//B3LYP/6-31+G** levels of theory indicate that this energy difference is 3-5 kJ mol(-1), in agreement with the experimental results. Lower effective ion heating rates, either by attenuation of the laser power or irradiation of the ions at a lower frequency, result in more time for interconversion between the free and HB COO-H isomers. These data suggest that the barrier to dissociation for the free COO-H isomer is less than that for the HB COO-H isomer but greater than the barrier for interconversion between the two isomers. These results show the competition between hydration of a primary protonated amine vs that of a neutral carboxylic acid and the effect of water bridging between the two functional groups, which provide valuable insight into the hydration of protonated amino acids and establish rigorous benchmarks for theoretical modeling of water-biomolecule interactions.
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Affiliation(s)
- Terrence M Chang
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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23
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Wei Z, Chen D, Zhao H, Li Y, Zhu J, Liu B. Ab initio investigation of the first hydration shell of protonated glycine. J Chem Phys 2014; 140:085103. [DOI: 10.1063/1.4862985] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Silveira JA, Fort KL, Kim D, Servage KA, Pierson NA, Clemmer DE, Russell DH. From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide Conformations. J Am Chem Soc 2013; 135:19147-53. [DOI: 10.1021/ja4114193] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Joshua A. Silveira
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - DoYong Kim
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nicholas A. Pierson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Abstract
The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.
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Affiliation(s)
- Terrence M Chang
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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28
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Milosavljević AR, Cerovski VZ, Canon F, Nahon L, Giuliani A. Nanosolvation-Induced Stabilization of a Protonated Peptide Dimer Isolated in the Gas Phase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Milosavljević AR, Cerovski VZ, Canon F, Nahon L, Giuliani A. Nanosolvation-Induced Stabilization of a Protonated Peptide Dimer Isolated in the Gas Phase. Angew Chem Int Ed Engl 2013; 52:7286-90. [DOI: 10.1002/anie.201301667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/05/2013] [Indexed: 11/07/2022]
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30
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Schmidt J, Kass SR. Zwitterion vs Neutral Structures of Amino Acids Stabilized by a Negatively Charged Site: Infrared Photodissociation and Computations of Proline–Chloride Anion. J Phys Chem A 2013; 117:4863-9. [DOI: 10.1021/jp402267c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jacob Schmidt
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steven R. Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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31
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WEI JING, WANG JINYUN, ZHANG MINYI, CHAI GUOLIANG, LIN CHENSHENG, CHENG WENDAN. A THEORETICAL STUDY ON SECOND HARMONIC GENERATION HYPERPOLARIZABILITIES OF PHENYLALANINE POLYPEPTIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633612501180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The second harmonic generation (SHG) hyperpolarizabilities of phenylalanine and homopolypeptides are investigated by configuration interaction among singly excited configurations (CIS) technique combined with the sum-over-states (SOS) method. The geometries of peptides containing phenylalanine ( Phe )n(n = 1–8) are optimized by B3LYP/6-31g(d) method, and they form the special structures like β-sheet (a common protein secondary structure). It is found that the energy gaps of various peptides are reduced and the hyperpolarizabilities are increased with the peptide chains lengthened. We discuss the origin of the second-order nonlinear optical response in phenylalanine homopolypeptides and confirm that the π → π* transitions in the aromatic residue of phenylalanine make the most important contributions to the second-order polarizability. Our results strongly suggest that the hyperpolarizabilities are dominated from the propagation direction of peptide chains.
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Affiliation(s)
- JING WEI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - JIN-YUN WANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - MIN-YI ZHANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - GUO-LIANG CHAI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - CHEN-SHENG LIN
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - WEN-DAN CHENG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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32
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Wang C, Lin Z, Zhang R. Zwitterions are the most stable form for neutral arginylglycine in gas phase: Clear theoretical evidence. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Silveira JA, Servage KA, Gamage CM, Russell DH. Cryogenic Ion Mobility-Mass Spectrometry Captures Hydrated Ions Produced During Electrospray Ionization. J Phys Chem A 2013; 117:953-61. [DOI: 10.1021/jp311278a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua A. Silveira
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - Kelly A. Servage
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - Chaminda M. Gamage
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - David H. Russell
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
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34
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Chutia S, Rossi M, Blum V. Water Adsorption at Two Unsolvated Peptides with a Protonated Lysine Residue: From Self-Solvation to Solvation. J Phys Chem B 2012; 116:14788-804. [DOI: 10.1021/jp3098268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sucismita Chutia
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
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35
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Chang TM, Prell JS, Warrick ER, Williams ER. Where’s the Charge? Protonation Sites in Gaseous Ions Change with Hydration. J Am Chem Soc 2012; 134:15805-13. [DOI: 10.1021/ja304929h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Terrence M. Chang
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - James S. Prell
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Erika R. Warrick
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
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36
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Demireva M, O’Brien JT, Williams ER. Water-Induced Folding of 1,7-Diammoniumheptane. J Am Chem Soc 2012; 134:11216-24. [DOI: 10.1021/ja303313p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Demireva
- Department of Chemistry, University of California, Berkeley 94720-1460, United States
| | - Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley 94720-1460, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley 94720-1460, United States
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37
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Nagornova NS, Rizzo TR, Boyarkin OV. Interplay of Intra- and Intermolecular H-Bonding in a Progressively Solvated Macrocyclic Peptide. Science 2012; 336:320-3. [DOI: 10.1126/science.1218709] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Takis PG, Melissas VS, Troganis AN. A “hidden” role of amino and imino groups is unveiled during the micro-solvation study of three biomolecule groups in water. NEW J CHEM 2012. [DOI: 10.1039/c2nj40390k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Purushotham U, Vijay D, Narahari Sastry G. A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine. J Comput Chem 2011; 33:44-59. [DOI: 10.1002/jcc.21942] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 07/16/2011] [Indexed: 11/10/2022]
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40
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Shi X, Ren J, Parks JH. Aldehyde complexes with protonated peptides in the gas phase. J Phys Chem B 2011; 115:11183-92. [PMID: 21834583 DOI: 10.1021/jp112037a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This Article presents a study of aldehyde complexes with peptide ions formed by bimolecular collisions in the gas phase. Desolvated ions generated by electrospray ionization are stored within a radio frequency (RF) ion trap and exposed to aldehyde vapor. Mass spectrometry measurements were performed on the resulting aldehyde complexes formed with single amino acids (LysH(+), HisH(+), and ArgH(+)) and polypeptides [Pro(n)-Lys+2H](2+) and [(Gly-Ser)(m)-Lys+2H](2+). These data identify several interesting and unexpected aspects of the aldehyde complex kinetics. It is observed that the formation of stable complexes requires the presence of water vapor. The formation kinetics of aldehyde-peptide complexes exhibits multiexponential time dependence that is modeled by interactions in the presence of structural heterogeneity. Aldehyde binding appears to involve a competition between conformers with unhindered access to protonation sites and conformers with intramolecular solvation of these sites. Proton transfer to the aldehyde ligand is responsible for the loss of the complexes. This is supported by proton affinity calculations and identified by reaction products exhibiting loss of protonation by the parent ion accompanied by the appearance of aldehyde cations.
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Affiliation(s)
- Xiangguo Shi
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, USA
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41
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Wang D, Gulyuz K, Stedwell CN, Polfer NC. Diagnostic NH and OH vibrations for oxazolone and diketopiperazine structures: b2 from protonated triglycine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1197-1203. [PMID: 21953102 DOI: 10.1007/s13361-011-0147-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/03/2011] [Accepted: 04/04/2011] [Indexed: 05/31/2023]
Abstract
We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b(2) from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H(+) stretch of the protonated carbonyl group at 3585 cm(-1). Conversely, b(2) from protonated triglycine exhibits a strong band at 3345 cm(-1), associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH(2) and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.
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Affiliation(s)
- Da Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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42
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Prell JS, Chang TM, Biles JA, Berden G, Oomens J, Williams ER. Isomer Population Analysis of Gaseous Ions From Infrared Multiple Photon Dissociation Kinetics. J Phys Chem A 2011; 115:2745-51. [DOI: 10.1021/jp2004166] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Terrence M. Chang
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Jeffrey A. Biles
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Giel Berden
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
- University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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43
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Prell JS, O’Brien JT, Williams ER. Structural and Electric Field Effects of Ions in Aqueous Nanodrops. J Am Chem Soc 2011; 133:4810-8. [DOI: 10.1021/ja108341t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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44
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Polfer NC. Infrared multiple photon dissociation spectroscopy of trapped ions. Chem Soc Rev 2011; 40:2211-21. [DOI: 10.1039/c0cs00171f] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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45
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Patzer A, Zimmermann M, Alata I, Jouvet C, Dopfer O. Electronic Spectra of Protonated Benzaldehyde Clusters with Ar and N2: Effect of ππ* Excitation on the Intermolecular Potential. J Phys Chem A 2010; 114:12600-4. [DOI: 10.1021/jp109949y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander Patzer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Max Zimmermann
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Ivan Alata
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Christophe Jouvet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, and Centre Laser de l’Université Paris Sud (EA. 4127) and Institut des Sciences Moleculaires d’Orsay CNRS (FRE 3363), Universite Paris-Sud 11, 91405 Orsay Cedex, France
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46
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Prell JS, Correra TC, Chang TM, Biles JA, Williams ER. Entropy Drives an Attached Water Molecule from the C- to N-Terminus on Protonated Proline. J Am Chem Soc 2010; 132:14733-5. [DOI: 10.1021/ja106167d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Thiago C. Correra
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Terrence M. Chang
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Jeffrey A. Biles
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460
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