1
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Elferink H, Remmerswaal WA, Houthuijs KJ, Jansen O, Hansen T, Rijs AM, Berden G, Martens J, Oomens J, Codée JDC, Boltje TJ. Competing C-4 and C-5-Acyl Stabilization of Uronic Acid Glycosyl Cations. Chemistry 2022; 28:e202201724. [PMID: 35959853 PMCID: PMC9825916 DOI: 10.1002/chem.202201724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Indexed: 01/11/2023]
Abstract
Uronic acids are carbohydrates carrying a terminal carboxylic acid and have a unique reactivity in stereoselective glycosylation reactions. Herein, the competing intramolecular stabilization of uronic acid cations by the C-5 carboxylic acid or the C-4 acetyl group was studied with infrared ion spectroscopy (IRIS). IRIS reveals that a mixture of bridged ions is formed, in which the mixture is driven towards the C-1,C-5 dioxolanium ion when the C-5,C-2-relationship is cis, and towards the formation of the C-1,C-4 dioxepanium ion when this relation is trans. Isomer-population analysis and interconversion barrier computations show that the two bridged structures are not in dynamic equilibrium and that their ratio parallels the density functional theory computed stability of the structures. These studies reveal how the intrinsic interplay of the different functional groups influences the formation of the different regioisomeric products.
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Affiliation(s)
- Hidde Elferink
- Institute for Molecules and MaterialsSynthetic Organic ChemistryRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
| | - Wouter A. Remmerswaal
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Kas J. Houthuijs
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Oscar Jansen
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Thomas Hansen
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands,Departament de Química Inorgànica i Orgànica & IQTUBUniversitat de Barcelona08028BarcelonaSpain
| | - Anouk M. Rijs
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands,Division of BioAnalytical ChemistryDepartment of Chemistry and Pharmaceutical SciencesAIMMS Amsterdam Institute of Molecular and Life SciencesVrije Univeristeit AmsterdamDe Boelelaan 10851081 HVAmsterdam (TheNetherlands
| | - Giel Berden
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jonathan Martens
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jos Oomens
- Institute for Molecules and MaterialsFELIX LaboratoryRadboud University NijmegenToernooiveld 76525 EDNijmegen (TheNetherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Thomas J. Boltje
- Institute for Molecules and MaterialsSynthetic Organic ChemistryRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
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2
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Remmerswaal WA, Houthuijs KJ, van de Ven R, Elferink H, Hansen T, Berden G, Overkleeft HS, van der Marel GA, Rutjes FPJT, Filippov DV, Boltje TJ, Martens J, Oomens J, Codée JDC. Stabilization of Glucosyl Dioxolenium Ions by "Dual Participation" of the 2,2-Dimethyl-2-( ortho-nitrophenyl)acetyl (DMNPA) Protection Group for 1,2- cis-Glucosylation. J Org Chem 2022; 87:9139-9147. [PMID: 35748115 PMCID: PMC9295149 DOI: 10.1021/acs.joc.2c00808] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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The stereoselective
introduction of glycosidic bonds is of paramount
importance to oligosaccharide synthesis. Among the various chemical
strategies to steer stereoselectivity, participation by either neighboring
or distal acyl groups is used particularly often. Recently, the use
of the 2,2-dimethyl-2-(ortho-nitrophenyl)acetyl (DMNPA)
protection group was shown to offer enhanced stereoselective steering
compared to other acyl groups. Here, we investigate the origin of
the stereoselectivity induced by the DMNPA group through systematic
glycosylation reactions and infrared ion spectroscopy (IRIS) combined
with techniques such as isotopic labeling of the anomeric center and
isomer population analysis. Our study indicates that the origin of
the DMNPA stereoselectivity does not lie in the direct participation
of the nitro moiety but in the formation of a dioxolenium ion that
is strongly stabilized by the nitro group.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Roel van de Ven
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Hidde Elferink
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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3
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McNary CP, Demireva M, Martens J, Berden G, Oomens J, Hamlow LA, Rodgers MT, Armentrout PB. Infrared multiple photon dissociation action spectroscopy of protonated unsymmetrical dimethylhydrazine and proton-bound dimers of hydrazine and unsymmetrical dimethylhydrazine. Phys Chem Chem Phys 2021; 23:25877-25885. [PMID: 34766618 DOI: 10.1039/d1cp03781a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser and an optical parametric oscillator laser system. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP-GD3BJ/6-311+G(d,p) level of theory. These comparisons show that protonated UDMH binds the proton at the methylated nitrogen atom (α) with two low-lying α conformers probably being populated. For (UDMH)2H+, the proton is shared between the methylated nitrogen atoms with several low-lying α conformers likely to be populated. Higher-lying conformers of (UDMH)2H+ in which the proton is shared between α and β (unmethylated) nitrogen atoms cannot be ruled out on the basis of the IRPMD spectrum. For (N2H4)2H+, there are four low-lying conformers that all reproduce the IRMPD spectrum reasonably well. As hydrazine and UDMH see usage as fuels for rocket engines, such spectra are potentially useful as a means of remotely monitoring rocket launches, especially in cases of unsuccessful launches where environmental hazards need to be assessed.
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Affiliation(s)
| | - Maria Demireva
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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4
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van Outersterp RE, Martens J, Peremans A, Lamard L, Cuyckens F, Oomens J, Berden G. Evaluation of table-top lasers for routine infrared ion spectroscopy in the analytical laboratory. Analyst 2021; 146:7218-7229. [PMID: 34724520 PMCID: PMC8607882 DOI: 10.1039/d1an01406d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/20/2021] [Indexed: 01/12/2023]
Abstract
Infrared ion spectroscopy is increasingly recognized as a method to identify mass spectrometry-detected analytes in many (bio)chemical areas and its integration in analytical laboratories is now on the horizon. Commercially available quadrupole ion trap mass spectrometers are attractive ion spectroscopy platforms but operate at relatively high pressures. This promotes collisional deactivation which directly interferes with the multiple-photon excitation process required for ion spectroscopy. To overcome this, infrared lasers having a high instantaneous power are required and therefore a majority of analytical studies have been performed at infrared free electron laser facilities. Proliferation of the technique to routine use in analytical laboratories requires table-top infrared lasers and optical parametric oscillators (OPOs) are the most suitable candidates, offering both relatively high intensities and reasonable spectral tuning ranges. Here, we explore the potential of a range of commercially available high-power OPOs for ion spectroscopy, comparing systems with repetition rates of 10 Hz, 20 kHz, 80 MHz and a continuous-wave (cw) system. We compare the performance for various molecular ions and show that the kHz and MHz repetition-rate systems outperform cw and 10 Hz systems in photodissociation efficiency and offer several advantages in terms of cost-effectiveness and practical implementation in an analytical laboratory not specialized in laser spectroscopy.
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Affiliation(s)
- Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - André Peremans
- Laboratoire Physique de la Matière et du Rayonnement (P.M.R), Université de Namur, 5000 Namur, Belgium
| | | | - Filip Cuyckens
- Drug Metabolism & Pharmacokinetics, Janssen R&D, Beerse, Belgium
| | - 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, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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5
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Boles GC, Kempkes LJM, Martens J, Berden G, Oomens J, Armentrout PB. Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:786-805. [PMID: 33570934 DOI: 10.1021/jasms.0c00468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Deamidation of asparaginyl (Asn) peptides is a spontaneous post-translational modification that plays a significant role in degenerative diseases and other biological processes under physiological conditions. In the gas phase, deamidation of protonated peptides is a major fragmentation channel upon activation by collision-induced dissociation. Here, we present a full description of the deamidation process from protonated asparagine-serine, [AsnSer+H]+, via infrared (IR) action spectroscopy and threshold collision-induced dissociation (TCID) experiments in combination with theoretical calculations. The IR results demonstrate that deamidation proceeds via bifurcating reaction pathways leading to furanone- and succinimide-type product ion structures, with a population analysis indicating the latter product dominates. Theory demonstrates that nucleophilic attack of the peptidyl amide oxygen onto the Asn side chain leads to furanone formation, whereas nucleophilic attack by the peptidyl amide nitrogen onto the Asn side-chain carbonyl carbon leads to the formation of the succinimide product structure. TCID experiments find that furanone formation has a threshold energy of 145 ± 12 kJ/mol and succinimide formation occurs with a threshold energy of 131 ± 12 kJ/mol, consistent with theoretical energies and with the spectroscopic results indicating that succinimide dominates. The results provide information regarding the inductive and steric effects of the Ser side chain on the deamidation process. The other major channel observed in the TCID experiments of [AsnSer+H]+ is dehydration, where a threshold energy of 104 ± 10 kJ/mol is determined. A complete IR and theoretical analysis of this pathway is also provided. As for deamidation, a bifurcating pathway is found with both dominant oxazoline and minor diketopiperazine products identified. Here, the Ser side chain is directly involved in both pathways.
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Affiliation(s)
- Georgia C Boles
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Lisanne J M Kempkes
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- 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, Science Park 904, 1098 XH 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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6
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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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7
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Andersson Å, Poline M, Kodambattil M, Rebrov O, Loire E, Maître P, Zhaunerchyk V. Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations. J Phys Chem A 2020; 124:2408-2415. [PMID: 32106670 PMCID: PMC7307929 DOI: 10.1021/acs.jpca.9b11811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
structures of three proton-bound dimers (Met2H+, MetTrpH+, and Trp2H+) are
investigated in the gas phase with infrared multiple photon disassociation
(IRMPD) spectroscopy in combination with quantum chemical calculations.
Their IRMPD spectra in the range of 600–1850 cm–1 are obtained experimentally using an FT-ICR mass spectrometer and
the CLIO free electron laser as an IR light source. The most abundant
conformers are elucidated by comparing the IRMPD spectra with harmonic
frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory.
Discrepancies between the experimental and theoretical data in the
region of 1500–1700 cm–1 are attributed to
the anharmonicity of the amino bending modes. We confirm the result
of a previous IRMPD study that the structure of gas-phase Trp2H+ is charge-solvated but find that there are more
stable structures than originally reported (Feng, R.; Yin, H.; Kong,
X. Rapid Commun. Mass Spectrom.2016, 30, 24–28). In addition, gas-phase Met2H+ and MetTrpH+ have been revealed to
have charge-solvated structures. For all three dimers, the most stable
conformer is found to be of type A. The spectrum of Met2H+, however, cannot be explained without some abundance
of type B charge-solvated conformers as well as salt-bridged structures.
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Affiliation(s)
- Åke Andersson
- Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Mathias Poline
- Department of Physics, Stockholm University, 114 19 Stockholm, Sweden
| | - Meena Kodambattil
- Department of Physics, University of Gothenburg, 405 30 Gothenburg, Sweden.,International School of Photonics, Cochin University of Science and Technology, Kochi, Kerala 682022, India
| | - Oleksii Rebrov
- Department of Physics, Stockholm University, 114 19 Stockholm, Sweden
| | - Estelle Loire
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, Orsay 91405, France
| | - Philippe Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, Orsay 91405, France
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 405 30 Gothenburg, Sweden
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8
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Munshi MU, Martens J, Berden G, Oomens J. Protoisomerization of Indigo and Isoindigo Dyes Confirmed by Gas-Phase Infrared Ion Spectroscopy. J Phys Chem A 2019; 123:8226-8233. [PMID: 31490692 PMCID: PMC6767361 DOI: 10.1021/acs.jpca.9b06858] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Gas-phase
infrared multiple-photon dissociation (IRMPD) spectra
are recorded for the protonated dye molecules indigo and isoindigo
by using a quadrupole ion trap (QIT) mass spectrometer coupled to
the free electron laser for infrared experiments (FELIX). From their
fingerprint IR spectra (600—1800 cm–1) and
comparison with quantum-chemical calculations at the density functional
level of theory (B3LYP/6-31++G(d,p)), we derive their structures.
We focus particularly on the question of whether trans-to-cis isomerization occurs upon protonation and
transfer to the gas phase. The trans-configuration
is energetically favored in the neutral forms of the dyes in solution
and in the gas phase. Instead, the cis-isomer is
lower in energy for the protonated forms of both species, but indigo
is also notorious for not undergoing double-bond trans-to-cis isomerization, in contrast to many other
conjugated systems. The IR spectra suggest that protoisomerization
from trans to cis indeed occurs
for both dyes. To estimate the extent of isomerization, on-resonance
kinetics are measured on diagnostic and common vibrational frequencies
to determine the ratio of cis-to-trans isomers. We find ratios of 65–70% cis and
30–35% trans for indigo versus 75–80% cis and 20–25% trans for isoindigo.
Transition-state calculations for the isomerization reactions have
been carried out, which indeed suggest a lower barrier for protonated
isoindigo, qualitatively explaining the more efficient isomerization.
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Affiliation(s)
- Musleh Uddin Munshi
- Institute for Molecules and Materials, FELIX Laboratory , Radboud University , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory , Radboud University , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory , Radboud University , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory , Radboud University , Toernooiveld 7 , 6525 ED Nijmegen , The Netherlands.,University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
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9
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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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10
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Corinti D, Paciotti R, Re N, Coletti C, Chiavarino B, Crestoni ME, Fornarini S. Binding motifs of cisplatin interaction with simple biomolecules and aminoacid targets probed by IR ion spectroscopy. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2019-0110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
The primary intermediates resulting from the interaction of cisplatin, cis-(PtCl2(NH3)2], most widespread antitumor drug, with biomolecular targets are characterized. Electrospray ionization is used to deliver ions formed in solution into the gas phase where they are structurally interrogated by vibrational “action” spectroscopy in conjunction with quantum chemical calculations. The aquation products, cis-[PtX(NH3)2(H2O)]+ (X = Cl, OH), lying along the path responsible for biological activity, are shown to display distinctive features responding to ligation pattern and optimized geometry. The IR spectra of trans-[PtX(NH3)2(H2O)]+ are different, testifying that cis and trans complexes are stable, non interconverting species both in solution and in the gas phase. Ligand substitution by simple nucleophiles (L = pyridine, 4(5)-methylimidazole, thioanisole, trimethylphosphate, acetamide, dimethylacetamide, urea and thiourea) yields cis-[PtCl(NH3)2(L)]+ complexes displaying remarkable regioselectivity whenever L presents multiple candidate platination sites. The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. The isomer and conformer population of the ensuing cis-[PtCl(NH3)2(Met/His)]+ complexes, sampled in the gas phase, can be ascertained by photofragmentation kinetics on isomer/conformer specific resonances.
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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 , Roma I-00185 , Italy
| | - Roberto Paciotti
- Dipartimento di Farmacia , Università G. D’Annunzio Chieti-Pescara , Via dei Vestini 31 , Chieti I-66100 , Italy
| | - Nazzareno Re
- Dipartimento di Farmacia , Università G. D’Annunzio Chieti-Pescara , Via dei Vestini 31 , Chieti I-66100 , Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia , Università G. D’Annunzio Chieti-Pescara , Via dei Vestini 31 , Chieti I-66100 , Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco , Università degli Studi di Roma La Sapienza , P.le A. Moro 5 , Roma I-00185 , Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco , Università degli Studi di Roma La Sapienza , P.le A. Moro 5 , Roma I-00185 , Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco , Università degli Studi di Roma La Sapienza , P.le A. Moro 5 , Roma I-00185 , Italy
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11
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Heller J, Ončák M, Bersenkowitsch NK, van der Linde C, Beyer MK. Infrared multiple photon dissociation of cesium iodide clusters doped with mono-, di- and triglycine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:122-132. [PMID: 30284923 PMCID: PMC7100558 DOI: 10.1177/1469066718803307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Charged cesium iodide clusters doped with mono-, di- and triglycine serve as a model system for sea salt aerosols containing biological molecules. Here, we investigate reactions of these complexes under infrared irradiation, with spectra obtained by infrared multiple photon dissociation. The cluster ions are generated via electrospray ionization and analyzed in the cell of a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Depending on the cluster size and peptide length, loss of HI or loss of a glycine unit is observed. The experimental measurements are supported by quantum chemical calculations. We show that N-H and O-H stretching modes dominate the spectrum, with large shifts depending on local interactions, namely due to interaction with iodide anions or intramolecular hydrogen bonding. Both experiment and theory indicate that several isomers are present in the experimental mixture, with different infrared fingerprints as well as dissociation pathways.
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Affiliation(s)
- Jakob Heller
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Nina K Bersenkowitsch
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | | | - Martin K Beyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
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12
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Molano-Arevalo JC, Gonzalez W, Jeanne Dit Fouque K, Miksovska J, Maitre P, Fernandez-Lima F. Insights from ion mobility-mass spectrometry, infrared spectroscopy, and molecular dynamics simulations on nicotinamide adenine dinucleotide structural dynamics: NAD +vs. NADH. Phys Chem Chem Phys 2018; 20:7043-7052. [PMID: 29473073 DOI: 10.1039/c7cp05602h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy. NAD solution time decay studies showed a two-component distribution, assigned to changes from a "close" to "open" conformation with the increase of the organic content. NAD gas-phase studies using nESI-TIMS-MS displayed two ion mobility bands for NAD+ protonated and sodiated species, while four and two ion mobility bands were observed for NADH protonated and sodiated species, respectively. Changes in the mobility profiles were observed for NADH as a function of the starting solution conditions and the time after desolvation, while NAD+ profiles showed no dependence. IRMPD spectroscopy of NAD+ and NADH protonated species in the 800-1800 and 3200-3700 cm-1 spectral regions showed common and signature bands between the NAD forms. Candidate structures were proposed for NAD+ and NADH kinetically trapped intermediates of the protonated and sodiated species, based on their collision cross sections and IR profiles. Results showed that NAD+ and NADH species exist in open, stack, and closed conformations and that the driving force for conformational dynamics is hydrogen bonding of the N-H-O and O-H-O forms with ribose rings.
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13
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Fraschetti C, Guarcini L, Zazza C, Mannina L, Circi S, Piccirillo S, Chiavarino B, Filippi A. Real time evolution of unprotected protonated galactosamine probed by IRMPD spectroscopy. Phys Chem Chem Phys 2018. [PMID: 29536991 DOI: 10.1039/c7cp07642h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conformational characterization of single α- and β-epimers of galactosamine in solution still remains an intriguing task because of their flexibility and ability to interconvert. This difficulty was circumvented by recording several "snapshots" of the epimerization process by means of fast ESI vaporization of a galactosamine·HCl sample solution at different times. Consequently, the so generated gaseous mixtures were spectroscopically investigated and the specific conformational features of both α- and β-epimers were assigned, despite the overlapping of several IR signals. Interestingly, from a comparison with time-resolved 1H-NMR data obtained for the same solutions, the catalyzing effect of the applied ESI technique in the anomerization process clearly emerges. Finally, the experimental data were supported using both the Density Functional Theory (DFT) and Block-Localized Wavefunction (BLW) approaches: the latter method was applied here for the first time for the investigation of charged species.
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Affiliation(s)
- C Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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14
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Lee SS, Park S, Hong Y, Lee JU, Kim JH, Yoon D, Kong X, Lee S, Oh HB. Chiral differentiation of d- and l-alanine by permethylated β-cyclodextrin: IRMPD spectroscopy and DFT methods. Phys Chem Chem Phys 2018; 19:14729-14737. [PMID: 28540941 DOI: 10.1039/c7cp01085k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gaseous chiral differentiation of alanine by permethylated β-cyclodextrin was studied using IRMPD spectroscopy and density functional theory calculations. The protonated non-covalent complexes of permethylated β-cyclodextrin and d- or l-alanine were mass-selected and investigated by IR laser pulses in the wavelength region of 2650-3800 cm-1. The remarkably different features of the IRMPD spectra for d- and l-alanine are described, and their origin is elucidated by quantum chemical calculations. We show that the differentiation of the experimentally observed spectral features is the result of different local interactions of d- and l-alanine with permethylated β-cyclodextrin. We also assign the extremely high-frequency (>3700 cm-1) bands in the observed spectra to the stretch motions of completely isolated alanine -OH groups.
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Affiliation(s)
- Sung-Sik Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 446-701, Republic of Korea.
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15
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Esser TK, Knorke H, Siro-Brigiano F, Galimberti DR, Asmis KR, Gaigeot MP, Lisy JM. Influence of argon and D2 tagging on the hydrogen bond network in Cs+(H2O)3; kinetic trapping below 40 K. Phys Chem Chem Phys 2018; 20:28476-28486. [DOI: 10.1039/c8cp06020g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tuning cluster ion conformations between 12 and 21 K.
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Affiliation(s)
- Tim K. Esser
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- D-04103 Leipzig
- Germany
| | - Harald Knorke
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- D-04103 Leipzig
- Germany
| | | | | | - Knut R. Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- D-04103 Leipzig
- Germany
| | | | - James M. Lisy
- Department of Chemistry
- University of Illinois at Urbana-Champaign, Urbana
- Illinois 61801
- USA
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16
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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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17
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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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18
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Patrick AL, Cismesia AP, Tesler LF, Polfer NC. Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 418:148-155. [PMID: 28781574 PMCID: PMC5542407 DOI: 10.1016/j.ijms.2016.09.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH2 stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.
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19
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Paciotti R, Corinti D, De Petris A, Ciavardini A, Piccirillo S, Coletti C, Re N, Maitre P, Bellina B, Barran P, Chiavarino B, Elisa Crestoni M, Fornarini S. Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes. Phys Chem Chem Phys 2017; 19:26697-26707. [DOI: 10.1039/c7cp05203k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
IRMPD spectroscopy discloses N- versus S-platination.
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20
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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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21
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Jeanne Dit Fouque K, Lavanant H, Zirah S, Steinmetz V, Rebuffat S, Maître P, Afonso C. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers. J Phys Chem A 2016; 120:3810-6. [DOI: 10.1021/acs.jpca.6b04496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Hélène Lavanant
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Séverine Zirah
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Sylvie Rebuffat
- Muséum national d’Histoire naturelle, Sorbonne Universités, Centre national de la Recherche scientifique, Laboratoire Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014, FR 3038; Univ Rouen; INSA Rouen; CNRS, 1 Rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
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22
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Nelson CR, Abutokaikah MT, Harrison AG, Bythell BJ. Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:487-497. [PMID: 26602904 DOI: 10.1007/s13361-015-1298-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.
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Affiliation(s)
- Carissa R Nelson
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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23
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Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies. Met Ions Life Sci 2016; 16:103-31. [DOI: 10.1007/978-3-319-21756-7_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Dunbar RC, Berden G, Martens JK, Oomens J. Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor. J Phys Chem A 2015; 119:9901-9. [PMID: 26325483 DOI: 10.1021/acs.jpca.5b06315] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan K Martens
- 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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25
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Yin H, Kong X. Structure of Protonated Threonine Dimers in the Gas Phase: Salt-Bridged or Charge-Solvated? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1455-1461. [PMID: 26111520 DOI: 10.1007/s13361-015-1194-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/04/2015] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
For homodimers of amino acids, their salt-bridged structures are gradually stabilized as the proton affinity of the component amino acid increases. Threonine has a proton affinity value located in the middle of the list of 20 natural amino acids. Thus, identifying whether the most stable isomer of protonated threonine dimer (Thr(2)H(+)) has a charge-solvated or salt-bridged structure is important and helpful for understanding the structures of other homodimers. By combining infrared photodissociation (IRPD) spectroscopy and theoretical calculations, the structures of Thr(2)H(+) were investigated. Based on calculations at the M062X/6-311++G(d,p)//M062X/6-311++G(d,p) level, the most stable isomer of Thr(2)H(+) was computed to be a charge-solvated structure, with an energy 3.87 kcal/mol lower than the most stable salt-bridged isomer. The predicted infrared spectrum is in good agreement with the experimental spectrum. To evaluate the temperature effect on the distribution of different isomers, the relative concentrations of the six isomers of Thr(2)H(+) were calculated at different temperatures, according to their partition functions and enthalpies. The results show that the isomers are dominated by charge-solvated structures at a temperature of 300 K.
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Affiliation(s)
- Hong Yin
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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26
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Brites V, Lisy JM, Gaigeot MP. Infrared Predissociation Vibrational Spectroscopy of Li+(H2O)3–4Ar0,1 Reanalyzed Using Density Functional Theory Molecular Dynamics. J Phys Chem A 2015; 119:2468-74. [DOI: 10.1021/jp508699m] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V. Brites
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement,
LAMBE UMR 8587 CNRS, Université d’Evry Val d’Essonne, 91025 Evry, France
| | - J. M. Lisy
- Department
of Chemistry, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - M.-P. Gaigeot
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement,
LAMBE UMR 8587 CNRS, Université d’Evry Val d’Essonne, 91025 Evry, France
- Institut Universitaire de France IUF, 103 Blvd St Michel, 75005 Paris, France
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27
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Berdakin M, Steinmetz V, Maitre P, Pino GA. On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory. Phys Chem Chem Phys 2015; 17:25915-24. [DOI: 10.1039/c5cp02221e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single water molecule hydration stabilizes two quasi-isoenergetic complexes of cytosine⋯Ag+.
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Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Philippe Maitre
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
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28
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Zehnacker A. Optical spectroscopy coupled with mass spectrometry methods. Phys Chem Chem Phys 2015; 17:25672-5. [DOI: 10.1039/c5cp90155c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This themed issue reports on recent progress in the fast developing field of spectroscopy of ions by means of mass spectrometry coupled with optical spectroscopy. It focuses on both the experimental and theoretical aspects of this topic.
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Affiliation(s)
- Anne Zehnacker
- CNRS
- Institut des Sciences Moléculaires d’Orsay (ISMO/UMR8214) and Univ. Paris Sud
- Orsay
- France
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29
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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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30
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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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31
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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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32
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Zhao J, Lau JKC, Grzetic J, Verkerk UH, Oomens J, Siu KWM, Hopkinson AC. Structures of a(n)* ions derived from protonated pentaglycine and pentaalanine: results from IRMPD spectroscopy and DFT calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1957-1968. [PMID: 24026976 DOI: 10.1007/s13361-013-0728-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
Infrared multiple-photon dissociation (IRMPD) spectroscopy and DFT calculations have been used to probe the most stable structures of a3(*) and a4(*) ions derived from both protonated pentaglycine (denoted G5) and pentaalanine (A5). The a3(*) and a4(*) ions derived from protonated A5 feature a CHR=N-CHR'- group at the N-terminus and an oxazolone ring at the C-terminus, as proposed previously [J. Am. Soc. Mass Spectrom. 19, 1788-1798 (2008)]. The isomeric a4(*) ion derived from A5 with a 3,5-dihydro-4H-imidazol-4-one ring structure was calculated to have a slightly better energy than the oxazolone, but the barrier to its formation is higher and there was no evidence of this ion in the IRMPD spectrum. By contrast, the a4(*) and [a4 - H2O](+) (denoted a4(0)) ions from G5 gave strikingly similar IRMPD spectra and both have the 3,5-dihydro-4H-imidazol-4-one ring structure similar to that recently reported for the [GGGG + H - H2O](+) ion [Int. J. Mass Spectrom. 316-318, 268-272 (2012)]. In the absence of a solvent molecule, the pathway to the oxazolone is calculated to be lower than those to thermodynamically more stable products, the a4(0) and the a4(*) with the 3,5-dihydro-4H-imidazol-4-one ring structure. Incorporation of one water molecule is sufficient to reduce the barrier to formation of the a4(0) of G5 to below that for formation of the oxazolone. On the equivalent potential energy surface for protonated A5 the barrier to formation of the a4(0) ion is 12.3 kcal mol(-1) higher than that for oxazolone formation and the a4(0) ion is not observed experimentally.
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Affiliation(s)
- Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, ON, M3J 1P3, Canada
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33
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Walker M, Sen A, Harvey AJ, Dessent CE. Complexation of anions to gas-phase amino acids: Conformation is critical in determining if the global minimum is canonical or zwitterionic. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Luxford TF, Milner EM, Yoshikawa N, Bullivant C, Dessent CE. Complexation of carboxylate anions with the arginine gas-phase amino acid: Effects of chain length on the geometry of extended ion binding. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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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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36
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Schröder D, Buděšínský M, Roithová J. Deprotonation of p-Hydroxybenzoic Acid: Does Electrospray Ionization Sample Solution or Gas-Phase Structures? J Am Chem Soc 2012; 134:15897-905. [DOI: 10.1021/ja3060589] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Detlef Schröder
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2,
16610 Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2,
16610 Prague 6, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry,
Faculty of Sciences, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
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37
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Crestoni ME, Chiavarino B, Scuderi D, Di Marzio A, Fornarini S. Discrimination of 4-hydroxyproline diastereomers by vibrational spectroscopy of the gaseous protonated species. J Phys Chem B 2012; 116:8771-9. [PMID: 22764742 DOI: 10.1021/jp302382p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of proline is a prominent oxidative post-translational modification (oxPTM) in animals, characterized by site specificity and stereochemical control. The presence of this irreversible modification and the ensuing generation of a chiral center have been assayed in (2S,4R)-4-hydroxyproline and (2S,4S)-4-hydroxyproline forming the protonated species by electrospray ionization and sampling them by infrared multiple photon dissociation (IRMPD) spectroscopy. IRMPD spectra, recorded both in the 950-1950 cm(-1) (using the CLIO free electron laser) and in the 3200-3700 cm(-1) [using a tabletop parametric oscillator/amplifier (OPO/OPA) laser] regions, have been interpreted by comparison with the absorbance spectra of the lowest energy structures calculated at MP2/6-311+G** level of theory. Remarkable spectral differences have emerged in the fingerprint region, pointing to the unambiguous discrimination between S,R and S,S diastereomers. The main differences arise from the position of the carbonyl stretching mode, a signature of nonzwitterionic structures, moving from 1750 cm(-1) for the S,R form to 1770 cm(-1) for the S,S diastereomer. Furthermore, a well-defined band associated with the NH(2) wagging mode at 1333 cm(-1) is a distinct mark of the S,S isomer. Each gaseous protonated epimer comprises a population of at least three conformers, stabilized by intramolecular hydrogen bonds linking the two hydrogens of protonated secondary amine group with the 4-hydroxy substituent and with an oxygen atom of the carboxylic group, respectively. Interestingly, a tendency to adopt either C(4)-exo (up) or C(4)-endo (down) pyrrolidine puckering upon proline 4(R)- or 4(S)-hydroxylation, respectively, is observed here. The same bias is found in neutral hydroxyprolines and in collagen model peptides. In the protonated species under examination, this bias originates chirality-induced vibrational features revealed by IRMPD spectroscopy.
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Affiliation(s)
- Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, P. le A. Moro 5, I-00185 Roma, Italy.
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38
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Filippi A, Fraschetti C, Piccirillo S, Rondino F, Botta B, D'Acquarica I, Calcaterra A, Speranza M. Chirality effects on the IRMPD spectra of basket resorcinarene/nucleoside complexes. Chemistry 2012; 18:8320-8. [PMID: 22696428 DOI: 10.1002/chem.201200614] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Indexed: 11/12/2022]
Abstract
The IRMPD spectra of the ESI-formed proton-bound complexes of the R,R,R,R- and S,S,S,S-enantiomers of a bis(diamido)-bridged basket resorcin[4]arene (R and S) with cytosine (1), cytidine (2), and cytarabine (3) were measured in the region 2800-3600 cm(-1). Comparison of the IRMPD spectra with the corresponding ONIOM (B3LYP/6-31(d):UFF)-calculated absorption frequencies allowed the assessment of the vibrational modes that are responsible for the observed spectroscopic features. All of the complexes investigated, apart from [R⋅H⋅3](+), showed similar IRMPD spectra, which points to similar structural and conformational landscapes. Their IRMPD spectra agree with the formation of several isomeric structures in the ESI source, wherein the N(3)-protonated guest establishes noncovalent interactions with the host amidocarbonyl groups that are either oriented inside the host cavity or outside it between one of the bridged side-chains and the upper aromatic nucleus. The IRMPD spectrum of the [R⋅H⋅3](+) complex was clearly different from the others. This difference is attributed to the effect of intramolecular hydrogen-bonding interactions between the C(2')-OH group and the aglycone oxygen atom of the nucleosidic guest upon repulsive interactions between the same oxygen atom and the aromatic rings of the host.
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Affiliation(s)
- Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, 00185 Roma, Italy
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Verkerk UH, Zhao J, Saminathan IS, Lau JKC, Oomens J, Hopkinson AC, Siu KWM. Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes. Inorg Chem 2012; 51:4707-10. [PMID: 22455512 DOI: 10.1021/ic2026973] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative.
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Affiliation(s)
- Udo H Verkerk
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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40
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Gillis EAL, Demireva M, Nanda K, Beran G, Williams ER, Fridgen TD. Structures and energetics of electrosprayed uracilnCa2+clusters (n = 14–4) in the gas phase. Phys Chem Chem Phys 2012; 14:3304-15. [DOI: 10.1039/c1cp22984b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Barylyuk K, Fritsche L, Balabin RM, Nieckarz R, Zenobi R. Gas-phase basicity of several common MALDI matrices measured by a simple experimental approach. RSC Adv 2012. [DOI: 10.1039/c1ra01117k] [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] Open
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