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Terry LM, Klumb MK, Nemchick DJ, Hodyss R, Maiwald F, Weber JM. Cryogenic Ion Vibrational Spectroscopy of Protonated Valine: Messenger Tag Effects. J Phys Chem A 2024; 128:7137-7144. [PMID: 39150465 DOI: 10.1021/acs.jpca.4c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
We report the infrared photodissociation spectrum of tagged protonated valine in the range 1000-1900 cm-1, prepared in a cryogenic ion trap. Comparison of experimental results with calculated infrared spectra based on density functional theory shows that the hydroxyl group of the carboxylic acid functionality and the protonated amine group adopt a trans configuration. Nitrogen and methane molecules were used as messenger tags with optimal tagging temperatures of 30 K for N2 and 60 K for CH4. While the calculated infrared spectra of the tagged ion suggest only a weak influence of the messenger tag on the frequency positions of ValH+, the measured intensities for N2-tagged ValH+ appear strongly suppressed for all but the highest frequency feature at 1773 cm-1. We trace this behavior to the binding energy of the N2 tag, which is significantly higher than that of CH4, based on density functional and coupled cluster calculations and rate estimates for photoinduced unimolecular dissociation from statistical theory.
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Affiliation(s)
- Lane M Terry
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - Maddie K Klumb
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - Deacon J Nemchick
- California Institute of Technology, NASA Jet Propulsion Laboratory, Pasadena, California 91109, United States
| | - Robert Hodyss
- California Institute of Technology, NASA Jet Propulsion Laboratory, Pasadena, California 91109, United States
| | - Frank Maiwald
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
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2
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Harville PA, Moss OC, Rana A, Snowden EA, Johnson MA. Demonstration of Capture, Cooling, Tagging, and Spectroscopic Characterization of UV Photoproduct Ions in a Cryogenic Ion Trap: Application to 266 nm Photofragment Ions from Rhodamine 6G. J Phys Chem A 2024. [PMID: 39194345 DOI: 10.1021/acs.jpca.4c04283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
We demonstrate a method to determine the structures of the primary photodissociation products from a cryogenically cooled parent ion. In this approach, a target ion is cooled by a pulse of buffer gas and tagged in a 20 K Paul trap. The cold ion is then photodissociated by pulsed (∼5 ns) UV laser excitation, and the ionic products are trapped, cooled, and tagged by introduction of a second buffer gas pulse in the same trap. The tagged fragments are then ejected into a triple focusing, UV/vis/IR time-of-flight photofragmentation mass spectrometer which yields vibrational and electronic spectra of the mass-selected photofragments. These methods are demonstrated by application to the 266 nm photodissociation of the Rhodamine 6G cation to yield the R575 fragment ion based on loss of ethene as well as to a weaker secondary fragment arising from loss of m/z 43.
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Affiliation(s)
- Payten A Harville
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Olivia C Moss
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Abhijit Rana
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elizabeth A Snowden
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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3
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Ozeki M, Orito M, Ishikawa H. Observation of the Infrared-Induced Structural Change in the Microscopic Hydrogen Bond Network of Phenol-Methanol Cluster Cations in a Cold-Ion Trap. J Phys Chem A 2024; 128:5873-5882. [PMID: 38996183 DOI: 10.1021/acs.jpca.4c01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
To gain insight into microscopic hydrogen bond networks, we measured ultraviolet photodissociation (UVPD) spectra of the phenol-methanol 1:3 cluster cation, [PhOH(MeOH)3]+ trapped in a variable temperature ion trap. At low temperatures, an isomer with a ring-type hydrogen bond structure dominates, whereas at higher temperatures the chain-type isomers become dominant due to the flexibility of their hydrogen bond structures. We also found a clear temperature dependence of the spectral features, such as band position and width. In addition to the above measurement, we observed the infrared (IR) induced isomerization of [PhOH(MeOH)3]+ to study the dynamical aspects of hydrogen bond networks. We succeeded in observing IR-induced isomerization from the ring to chain forms of [PhOH(MeOH)3]+ at low temperature. The isomerization was clearly identified as a change in the UVPD spectra. The time evolution of the UVPD spectra after IR excitation indicated that the IR-induced isomerization occurs within a nanosecond. The chain-type isomers produced by the IR-induced isomerization are then converted back to the ring-type form by collisions with cold He buffer gas in the trap. This backward isomerization proceeds with a time constant of 100 μs under our experimental conditions. In this study, we evaluated the temperatures of the chain isomers during the backward isomerization on the basis of the spectral features.
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Affiliation(s)
- Masayoshi Ozeki
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Masataka Orito
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
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4
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Yoo IT, Jeong J, Eun HJ, Yun J, Heo J, Kim NJ. Conformation-Selective Ultraviolet-Ultraviolet Hole Burning Spectra of Ubiquitin Ions in a Cryogenic Ion Trap. J Phys Chem Lett 2024; 15:7398-7402. [PMID: 38995855 DOI: 10.1021/acs.jpclett.4c01385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Understanding the structural variations of conformational isomers in proteins is crucial for elucidating protein folding mechanisms. Here, we present a novel method for obtaining conformation-selective ultraviolet (UV)-UV hole burning (HB) spectra of ubiquitin ions ((Ubi+zH)+z, z = 7-10) produced via electrospray ionization. Our approach involves binding multiple N2 molecules to ubiquitin ions ((Ubi+zH)+z(N2)m, m = 1-55) within a cryogenic ion trap. Upon exposure to UV irradiation, efficient fragmentation of (Ubi+zH)+z(N2)m occurs, primarily yielding bare (Ubi+zH)+z ions as fragments. The significant mass difference between the parent and fragment ions facilitates the acquisition of UV-UV HB spectra, which reveal the presence of at least two distinct conformers. Molecular dynamics simulations suggest that these conformers correspond to A-state structures, differing only in the interactions of a tyrosine residue with neighboring residues. Our findings underscore UV-UV HB spectroscopy of protein ions as a powerful tool for exploring diverse protein isomers.
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Affiliation(s)
- Il Tae Yoo
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Jinho Jeong
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Han Jun Eun
- Gas Metrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Jiyeon Yun
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Jiyoung Heo
- Department of Green Chemical Engineering, Sangmyung University, Chungnam 31066, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
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5
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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6
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Bergmeister S, Ganner L, Ončák M, Gruber E. Gas-Phase Electronic Structure of Phthalocyanine Ions: A Study of Symmetry and Solvation Effects. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307816. [PMID: 38225692 DOI: 10.1002/advs.202307816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/19/2023] [Indexed: 01/17/2024]
Abstract
Research into and applications of phthalocyanines (Pc) are mostly connected to their intriguing electronic properties. Here, messenger-type UV-vis spectroscopy of two metal-free ions from the phthalocyanine family, cationic H2Pc+ and H2PcD+, along with their hydrates is performed. They show that the electronic properties of both ions can be traced to those in the conjugate base, Pc2-, however, they are affected by state splitting due to the reduced symmetry; in the H2Pc+ radical cation, a new band appears due to excitations into the singly-occupied molecular orbital. Quantum chemical spectra modeling reproduces all important features of the measured spectra and provides insight into the nature of electronic transitions. Hydration of the ions has only a mild effect on the electronic spectra, showing the stability of the electronic structure with respect to solvation effects.
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Affiliation(s)
- Stefan Bergmeister
- Institute for Ion and Applied Physics, University of Innsbruck, Technikerstraße 25, Innsbruck, 6020, Austria
| | - Lisa Ganner
- Institute for Ion and Applied Physics, University of Innsbruck, Technikerstraße 25, Innsbruck, 6020, Austria
| | - Milan Ončák
- Institute for Ion and Applied Physics, University of Innsbruck, Technikerstraße 25, Innsbruck, 6020, Austria
| | - Elisabeth Gruber
- Institute for Ion and Applied Physics, University of Innsbruck, Technikerstraße 25, Innsbruck, 6020, Austria
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7
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Uleanya KO, Anstöter CS, Dessent CEH. Photodissociative decay pathways of the flavin mononucleotide anion and its complexes with tryptophan and glutamic acid. Phys Chem Chem Phys 2023; 25:30697-30707. [PMID: 37934009 DOI: 10.1039/d3cp04359b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Flavin mononucleotide (FMN) is a highly versatile biological chromophore involved in a range of biochemical pathways including blue-light sensing proteins and the control of circadian rhythms. Questions exist about the effect of local amino acids on the electronic properties and photophysics of the chromophore. Using gas-phase anion laser photodissociation spectroscopy, we have measured the intrinsic electronic spectroscopy (3.1-5.7 eV) and accompanying photodissociative decay pathways of the native deprotonated form of FMN, i.e. [FMN-H]- complexed with the amino acids tryptophan (TRP) and glutamic acid (GLU), i.e. [FMN-H]-·TRP and [FMN-H]-·GLU, to investigate the extent to which these amino acids perturb the electronic properties and photodynamics of the [FMN-H]- chromophore. The overall photodepletion profiles of [FMN-H]-·TRP and [FMN-H]-·GLU are similar to that of the monomer, revealing that amino acid complexation occurs without significant spectral shifting of the [FMN-H]- electronic excitations over this region. Both [FMN-H]-·TRP and [FMN-H]-·GLU are observed to decay by non-statistical photodecay pathways, although the behaviour of [FMN-H]-·TRP is closer to statistical fragmentation. Long-lived FMN excited states (triplet) are therefore relatively quenched when TRP binds to [FMN-H]-. Importantly, we find that [FMN-H]-, [FMN-H]-·TRP and [FMN-H]-·GLU all decay predominantly via electron detachment following photoexcitation of the flavin chromophore, with amino acid complexation appearing not to inhibit this decay channel. The strong propensity for electron detachment is attributed to excited-state proton transfer within FMN, with proton transfer from a ribose alcohol to the phosphate preceding electron detachment.
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Affiliation(s)
- Kelechi O Uleanya
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Cate S Anstöter
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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8
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Fries DV, Klein MP, Straßner A, Huber ME, Luczak M, Wiehn C, Niedner-Schatteburg G. Cryo IR spectroscopy and cryo kinetics of dinitrogen activation and cleavage by small tantalum cluster cations. J Chem Phys 2023; 159:164303. [PMID: 37873960 DOI: 10.1063/5.0157217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
We investigate small tantalum clusters Tan+, n = 2-4, for their capability to cleave N2 adsorption spontaneously. We utilize infrared photon dissociation (IR-PD) spectroscopy of isolated and size selected clusters under cryogenic conditions within a buffer gas filled ion trap, and we augment our experiments by quantum chemical simulations (at DFT level). All Tan+ clusters, n = 2-4, seem to cleave N2 efficiently. We confirm and extend a previous study under ambient conditions on Ta2+ cluster [Geng et al., Proc. Natl. Acad. Sci. U. S. A. 115, 11680-11687 (2018)]. Our cryo studies and the concomitant DFT simulations of the tantalum trimer Ta3+ suggest cleavage of the first and activation of the second and third N2 molecule across surmountable barriers and along much-involved multidimensional reaction paths. We unravel the underlying reaction processes and the intermediates involved. The study of the N2 adsorbate complexes of Ta4+ presented here extends our earlier study and previously published spectra from (4,m), m = 1-5 [Fries et al., Phys. Chem. Chem. Phys. 23(19), 11345-11354 (2021)], up to m = 12. We confirm the priory published double activation and nitride formation, succeeded by single side-on N2 coordination. Significant red shifts of IR-PD bands from these side-on coordinated μ2-κN:κN,N N2 ligands correlate with the degree of tilting towards the second coordinating Ta center. All subsequently attaching N2 adsorbates onto Ta4+ coordinate in an end-on fashion, and we find clear evidence for co-existence of end-on coordination isomers. The study of stepwise N2 adsorption revealed adsorption limits m(max) of [Tan(N2)m]+ which increase with n, and kinetic fits revealed significant N2 desorption rates upon higher N2 loads. The enhanced absolute rate constants of the very first adsorbate steps kabs(n,0) of the small Ta3+ and Ta4+ clusters independently suggest dissociative N2 adsorption and likely N2 cleavage into Ta nitrides.
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Affiliation(s)
- Daniela V Fries
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Matthias P Klein
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Annika Straßner
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Maximilian E Huber
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Maximilian Luczak
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Christopher Wiehn
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Gereon Niedner-Schatteburg
- Department of Chemistry and State Research Center OPTIMAS, Rheinland-Pfälzische Technische Universität (RPTU) Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
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9
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Miyazaki M, Ono M, Otsuka R, Dopfer O, Fujii M. Electronic and vibrational spectroscopies of aromatic clusters with He in a supersonic jet: The case of neutral and cationic phenol-Hen (n = 1 and 2). J Chem Phys 2023; 159:134303. [PMID: 37787127 DOI: 10.1063/5.0169716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023] Open
Abstract
Van der Waals clusters composed of He and aromatic molecules provide fundamental information about intermolecular interactions in weakly bound systems. In this study, phenol-helium clusters (PhOH-Hen with n ≤ 2) are characterized for the first time by UV and IR spectroscopies. The S1 ← S0 origin and ionization energy both show small but additive shifts, suggesting π-bound structures of these clusters, a conclusion supported by rotational contour analyses of the S1 origin bands. The OH stretching vibrations of the PhOH moiety in the clusters match with those of bare PhOH in both the S0 and D0 states, illustrating the negligible perturbation of the He atoms on the molecular vibration. Matrix shifts induced by He attachment are discussed based on the observed band positions with the help of complementary quantum chemical calculations. For comparison, the UV and ionization spectra of PhOH-Ne are reported as well.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Megumi Ono
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Remina Otsuka
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
- International Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- International Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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10
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Foreman MM, Hirsch RJ, Weber JM. Influence of Metal Identity in Bipyridine-Based Metal-4N Complexes With Formate. J Phys Chem A 2023; 127:7586-7593. [PMID: 37647595 DOI: 10.1021/acs.jpca.3c04496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
We present the vibrational spectra of a series of dicationic, organometallic complexes consisting of a transition metal center (Co, Ni, or Cu) coordinated by 4,4'-di(tert-butyl)-2,2'-bipyridine (DTBbpy) ligands and a formate adduct. Spectral features are analyzed and assigned through comparison with density functional theory calculations, and structures are reported. Natural population analysis shows that the DTBbpy ligands serve as flexible charge reservoirs in each complex. Shifts in the vibrational signatures of the formate moiety reveal that the nature of the metal center plays a crucial role in the charge distribution and formate-metal binding motif in each complex, illustrating the impact of the metal center on the structural and electronic properties of these complexes.
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Affiliation(s)
- Madison M Foreman
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Rebecca J Hirsch
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309-0440, United States
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11
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Wu X, Pan Z, Steglich M, Ascher P, Bodi A, Bjelić S, Hemberger P. A direct liquid sampling interface for photoelectron photoion coincidence spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:034103. [PMID: 37012765 DOI: 10.1063/5.0136665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/19/2023] [Indexed: 06/19/2023]
Abstract
We introduce an effective and flexible high vacuum interface to probe the liquid phase with photoelectron photoion coincidence (liq-PEPICO) spectroscopy at the vacuum ultraviolet (VUV) beamline of the Swiss Light Source. The interface comprises a high-temperature sheath gas-driven vaporizer, which initially produces aerosols. The particles evaporate and form a molecular beam, which is skimmed and ionized by VUV radiation. The molecular beam is characterized using ion velocity map imaging, and the vaporization parameters of the liq-PEPICO source have been optimized to improve the detection sensitivity. Time-of-flight mass spectra and photoion mass-selected threshold photoelectron spectra (ms-TPES) were recorded for an ethanolic solution of 4-propylguaiacol, vanillin, and 4-hydroxybenzaldehyde (1 g/l of each). The ground state ms-TPES band of vanillin reproduces the reference, room-temperature spectrum well. The ms-TPES for 4-propylguaiacol and 4-hydroxybenzaldehyde are reported for the first time. Vertical ionization energies obtained by equation-of-motion calculations reproduce the photoelectron spectral features. We also investigated the aldol condensation dynamics of benzaldehyde with acetone using liq-PEPICO. Our direct sampling approach, thus, enables probing reactions at ambient pressure during classical synthesis procedures and microfluidic chip devices.
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Affiliation(s)
- Xiangkun Wu
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Zeyou Pan
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | | | | | - Andras Bodi
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Saša Bjelić
- Paul Scherrer Institute, 5232 Villigen, Switzerland
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12
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Kocheril GS, Gao HW, Wang LS. Vibrationally- and rotationally-resolved photoelectron imaging of cryogenically-cooled SbO 2–. Mol Phys 2023. [DOI: 10.1080/00268976.2023.2182610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Affiliation(s)
| | - Han-Wen Gao
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, RI, USA
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13
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Tureček F. UV-vis spectroscopy of gas-phase ions. MASS SPECTROMETRY REVIEWS 2023; 42:206-226. [PMID: 34392556 DOI: 10.1002/mas.21726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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14
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Sherman SL, Fischer KC, Garand E. Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues. J Phys Chem A 2022; 126:4036-4045. [PMID: 35700447 DOI: 10.1021/acs.jpca.2c02584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR-IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. These observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.
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Affiliation(s)
- Summer L Sherman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kaitlyn C Fischer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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15
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Töpfer K, Upadhyay M, Meuwly M. Quantitative molecular simulations. Phys Chem Chem Phys 2022; 24:12767-12786. [PMID: 35593769 PMCID: PMC9158373 DOI: 10.1039/d2cp01211a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022]
Abstract
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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16
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Zelenka J, Pereverzev A, Jahn U, Roithová J. Sulfonyl Nitrene and Amidyl Radical: Structure and Reactivity. Chemistry 2022; 28:e202104493. [PMID: 35266598 PMCID: PMC9323475 DOI: 10.1002/chem.202104493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 11/10/2022]
Abstract
Photocatalytic generation of nitrenes and radicals can be used to tune or even control their reactivity. Photocatalytic activation of sulfonyl azides leads to the elimination of N2 and the resulting reactive species initiate C−H activations and amide formation reactions. Here, we present reactive radicals that are generated from sulfonyl azides: sulfonyl nitrene radical anion, sulfonyl nitrene and sulfonyl amidyl radical, and test their gas phase reactivity in C−H activation reactions. The sulfonyl nitrene radical anion is the least reactive and its reactivity is governed by the proton coupled electron transfer mechanism. In contrast, sulfonyl nitrene and sulfonyl amidyl radicals react via hydrogen atom transfer pathways. These reactivities and detailed characterization of the radicals with vibrational spectroscopy and with DFT calculations provide information necessary for taking control over the reactivity of these intermediates.
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Affiliation(s)
- Jan Zelenka
- Department of Spectroscopy and Catalysis Institute for Molecules and Materials Radboud University Nijmegen, Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Aleksandr Pereverzev
- Department of Spectroscopy and Catalysis Institute for Molecules and Materials Radboud University Nijmegen, Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague 6 Czech Republic
| | - Jana Roithová
- Department of Spectroscopy and Catalysis Institute for Molecules and Materials Radboud University Nijmegen, Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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17
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Pereverzev A, Roithová J. Experimental techniques and terminology in gas-phase ion spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4826. [PMID: 35434805 PMCID: PMC9285946 DOI: 10.1002/jms.4826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 06/01/2023]
Abstract
This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.
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Affiliation(s)
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityNijmegenThe Netherlands
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18
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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19
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Zviagin A, Kopysov V, Nagornova NS, Boyarkin OV. Tracking local and global structural changes in a protein by cold ion spectroscopy. Phys Chem Chem Phys 2022; 24:8158-8165. [PMID: 35332911 DOI: 10.1039/d2cp00217e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated protein ubiquitin and its microhydrated complexes prepared in the gas phase in a range of charge states under different ionization conditions. The UV spectra appear vibrationally resolved for the unfolded protein, but become redshifted and smooth for the native-like structures of ubiquitin. This spectroscopic change results from the H-bonding of the hydroxyl of Tyr to the amide group of Glu-51 in the compact structures; the minimum length of this bond was estimated to be ∼1.7 Å. IR spectroscopy reflects the global structural change by observing redshifts of free NH/OH-stretch vibrational transitions. Evaporative cooling of microhydrated complexes of ubiquitin keeps the protein chilly during ionization, enabling native-like conformers with up to eight protons to survive in the gas phase.
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Affiliation(s)
- Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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20
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Buntine JT, Carrascosa E, Bull JN, Jacovella U, Cotter MI, Watkins P, Liu C, Scholz MS, Adamson BD, Marlton SJP, Bieske EJ. An ion mobility mass spectrometer coupled with a cryogenic ion trap for recording electronic spectra of charged, isomer-selected clusters. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043201. [PMID: 35489918 DOI: 10.1063/5.0085680] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Infrared and electronic spectra are indispensable for understanding the structural and energetic properties of charged molecules and clusters in the gas phase. However, the presence of isomers can potentially complicate the interpretation of spectra, even if the target molecules or clusters are mass-selected beforehand. Here, we describe an instrument for spectroscopically characterizing charged molecular clusters that have been selected according to both their isomeric form and their mass-to-charge ratio. Cluster ions generated by laser ablation of a solid sample are selected according to their collision cross sections with helium buffer gas using a drift tube ion mobility spectrometer and their mass-to-charge ratio using a quadrupole mass filter. The mobility- and mass-selected target ions are introduced into a cryogenically cooled, three-dimensional quadrupole ion trap where they are thermalized through inelastic collisions with an inert buffer gas (He or He/N2 mixture). Spectra of the molecular ions are obtained by tagging them with inert atoms or molecules (Ne and N2), which are dislodged following resonant excitation of an electronic transition, or by photodissociating the cluster itself following absorption of one or more photons. An electronic spectrum is generated by monitoring the charged photofragment yield as a function of wavelength. The capacity of the instrument is illustrated with the resonance-enhanced photodissociation action spectra of carbon clusters (Cn +) and polyacetylene cations (HC2nH+) that have been selected according to the mass-to-charge ratio and collision cross section with He buffer gas and of mass-selected Au2 + and Au2Ag+ clusters.
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Affiliation(s)
- Jack T Buntine
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Eduardo Carrascosa
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - James N Bull
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Ugo Jacovella
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Mariah I Cotter
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Patrick Watkins
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Chang Liu
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Michael S Scholz
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Brian D Adamson
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Samuel J P Marlton
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Evan J Bieske
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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21
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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22
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Roy TK. Performance of Vibrational Self-Consistent Field Theory for Accurate Potential Energy Surfaces: Fundamentals, Excited States, and Intensities. J Phys Chem A 2022; 126:608-622. [PMID: 35050620 DOI: 10.1021/acs.jpca.1c09989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of vibrational structure calculations beyond harmonic approximation in the framework of the vibrational self-consistent field method with second-order perturbation corrections (VSCF-PT2) is investigated in conjunction with very accurate potential energy surfaces (PESs) given by various coupled-cluster electronic structure theories. The quality of anharmonic calculations depends on the accuracy of the underlying multidimensional PES obtained from its functional form, which is given by the level of electronic structure theory. Two such highest levels of typical coupled-cluster electronic structure methods, CCSD and the ″gold standard″ CCSD(T), along with their variants such as CCD, CR-CCL (completely renormalized CR-CC(2,3) approach), and CCSD(TQ) are tested for the construction of accurate anharmonic potentials without any fitting or ad hoc scaling and using cc-pVTZ basis sets. The accuracy of VSCF-PT2 theory in comparison to experimental values is tested for a series of 16 molecules with 135 fundamental bands, 64 overtones, and combination bands and also for 39 intensities. It is found that CCD and CCSD bind the potential tighter than CCSD(T) and the computed VSCF-PT2 transitions are more blue-shifted showing higher deviation from the experiment. In general, VSCF-PT2 results computed at the CCSD(T) potential offer a good cost/accuracy ratio, with the mean absolute deviation and the mean absolute percentage error with the experiment being ∼16 cm-1 and 1.38, respectively, for fundamentals. Additionally, while the CR-CCL and CCSD(TQ) methods offer similar levels of accuracies as compared to CCSD(T), the former offers a better accuracy/cost ratio than the latter and is a suitable alternative to CCSD(T).
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Samba, Jammu and Kashmir 181143, India
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23
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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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24
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Marlton SJP, Trevitt A. Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers. Chem Commun (Camb) 2022; 58:9451-9467. [DOI: 10.1039/d2cc02101c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...
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25
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Kregel SJ, Thompson BJ, Nathanson GM, Bertram TH. The Wisconsin Oscillator: A Low-Cost Circuit for Powering Ion Guides, Funnels, and Traps. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2821-2826. [PMID: 34730958 DOI: 10.1021/jasms.1c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, we present the Wisconsin Oscillator, a small, inexpensive, low-power circuit for powering ion-guiding devices such as multipole ion guides, ion funnels, active ion-mobility devices, and non-mass-selective ion traps. The circuit can be constructed for under $30 and produces two antiphase RF waveforms of up to 250 Vp-p in the high kilohertz to low megahertz range while drawing less than 1 W of power. The output amplitude is determined by a 0-6.5 VDC drive voltage, and voltage amplification is achieved using a resonant LC circuit, negating the need for a large RF transformer. The Wisconsin Oscillator automatically oscillates with maximum amplitude at the resonant frequency defined by the onboard capacitors, inductors, and the capacitive load of the ion-guiding device. We show that our circuit can replace larger and more expensive RF power supplies without degradation of the ion signal and expect this circuit to be of use in miniature and portable mass spectrometers as well as in home-built systems utilizing ion-guiding devices.
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Affiliation(s)
- Steven J Kregel
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Blaise J Thompson
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Gilbert M Nathanson
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Timothy H Bertram
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
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26
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Käser S, Meuwly M. Transfer learned potential energy surfaces: accurate anharmonic vibrational dynamics and dissociation energies for the formic acid monomer and dimer. Phys Chem Chem Phys 2021; 24:5269-5281. [PMID: 34792523 PMCID: PMC8890265 DOI: 10.1039/d1cp04393e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational dynamics of the formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PESMP2) and transfer-learned (PESTL) to the CCSD(T) levels of theory. The normal mode (MAEs of 17.6 and 25.1 cm−1) and second order vibrational perturbation theory (VPT2, MAEs of 6.7 and 17.1 cm−1) frequencies from PESTL for all modes below 2000 cm−1 for FAM and FAD agree favourably with experiment. For the OH stretch mode the experimental frequencies are overestimated by more than 150 cm−1 for both FAM and FAD from normal mode calculations. Conversely, VPT2 calculations on PESTL for FAM reproduce the experimental OH frequency to within 22 cm−1. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011 cm−1, compared with an experimentally reported, broad (∼100 cm−1) absorption band with center frequency estimated at ∼3050 cm−1. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PESTL. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yields a dissociation energy of D0 = −14.23 ± 0.08 kcal mol−1 compared with an experimentally determined value of −14.22 ± 0.12 kcal mol−1. Neural network based PESs are constructed for formic acid monomer and dimer at the MP2 and transfer learned to the CCSD(T) level of theory. The PESs are used to study the vibrational dynamics and dissociation energy of the molecules.![]()
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Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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27
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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28
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Harrilal CP, DeBlase AF, McLuckey SA, Zwier TS. Two-Color IRMPD Applied to Conformationally Complex Ions: Probing Cold Ion Structure and Hot Ion Unfolding. J Phys Chem A 2021; 125:9394-9404. [PMID: 34644093 DOI: 10.1021/acs.jpca.1c08388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two-color infrared multiphoton dissociation (2C-IRMPD) spectroscopy is a technique that mitigates spectral distortions due to nonlinear absorption that is inherent to one-color IRMPD. We use a 2C-IRMPD scheme that incorporates two independently tunable IR sources, providing considerable control over the internal energy content and type of spectrum obtained by varying the trap temperature, the time delays and fluences of the two infrared lasers, and whether the first or second laser wavelength is scanned. In this work, we describe the application of this variant of 2C-IRMPD to conformationally complex peptide ions. The 2C-IRMPD technique is used to record near-linear action spectra of both cations and anions with temperatures ranging from 10 to 300 K. We also determine the conditions under which it is possible to record IR spectra of single conformers in a conformational mixture. Furthermore, we demonstrate the capability of the technique to explore conformational unfolding by recording IR spectra with widely varying internal energy in the ion. The protonated peptide ions YGGFL (NH3+-Tyr-Gly-Gly-Phe-Leu, Leu-enkephalin) and YGPAA (NH3+-Tyr-Gly-Pro-Ala-Ala) are used as model systems for exploring the advantages and disadvantages of the method when applied to conformationally complex ions.
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Affiliation(s)
- Christopher P Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Andrew F DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States.,Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
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29
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Rabus JM, Pellegrinelli RP, Khodr AHA, Bythell BJ, Rizzo TR, Carrascosa E. Unravelling the structures of sodiated β-cyclodextrin and its fragments. Phys Chem Chem Phys 2021; 23:13714-13723. [PMID: 34128027 PMCID: PMC8220536 DOI: 10.1039/d1cp01058a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/05/2021] [Indexed: 12/29/2022]
Abstract
We present cryogenic infrared spectra of sodiated β-cyclodextrin [β-CD + Na]+, a common cyclic oligosaccharide, and its main dissociation products upon collision-induced dissociation (CID). We characterize the parent ions using high-resolution ion mobility spectrometry and cryogenic infrared action spectroscopy, while the fragments are characterized by their mass and cryogenic infrared spectra. We observe sodium-cationized fragments that differ in mass by 162 u, corresponding to Bn/Zm ions. For the m/z 347 product ion, electronic structure calculations are consistent with formation of the lowest energy 2-ketone B2 ion structure. For the m/z 509 product ion, both the calculated 2-ketone B3 and the Z3 structures show similarities with the experimental spectrum. The theoretical structure most consistent with the spectrum of the m/z 671 ions is a slightly higher energy 2-ketone B4 structure. Overall, the data suggest a consistent formation mechanism for all the observed fragments.
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Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Ali Hassan Abi Khodr
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
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30
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Müller D, Dopfer O. Interaction of Alkali Ions with Flavins: Infrared and Optical Spectra of Metal–Riboflavin Complexes. J Phys Chem A 2021; 125:3146-3158. [DOI: 10.1021/acs.jpca.1c01846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- David Müller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
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31
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Affiliation(s)
- Martin Mayer
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
| | - Knut R. Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
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32
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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33
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Carrà A, Spezia R. In Silico
Tandem Mass Spectrometer: an Analytical and Fundamental Tool. ACTA ACUST UNITED AC 2021. [DOI: 10.1002/cmtd.202000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Andrea Carrà
- Agilent Technologies Italia Via Piero Gobetti 2/C 20063 Cernusco SN, Milano Italy
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique Sorbonne Université, UMR 7616 CNRS 4, Place Jussieu 75005 Paris France
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34
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Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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35
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Tiefenthaler L, Ončák M, Kollotzek S, Kočišek J, Scheier P. Dissociation of Valine Cluster Cations. J Phys Chem A 2020; 124:8439-8445. [PMID: 32931273 PMCID: PMC7569673 DOI: 10.1021/acs.jpca.0c07208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Independently
of the preparation method, for cluster cations of
aliphatic amino acids, the protonated form MnH+ is always the dominant species. This is a surprising
fact considering that in the gas phase, they dissociate primarily
by the loss of 45 Da, i.e., the loss of the carboxylic group. In the
present study, we explore the dissociation dynamics of small valine
cluster cations Mn+ and their protonated counterparts MnH+ via collision-induced dissociation
experiments and ab initio calculations with the aim to elucidate the
formation of MnH+-type cations
from amino acid clusters. For the first time, we report the preparation
of valine cluster cations Mn+ in laboratory conditions, using
a technique of cluster ion assembly inside He droplets. We show that
the Mn+ cations cooled down to He droplet temperature can dissociate
to form both Mn-1H+ and
[Mn–COOH]+ ions. With
increasing internal energy, the Mn-1H+ formation channel becomes dominant. Mn-1H+ ions then fragment nearly exclusively
by monomer loss, describing the high abundance of protonated clusters
in the mass spectra of amino acid clusters.
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Affiliation(s)
- Lukas Tiefenthaler
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, Innsbruck A-6020, Austria
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, Innsbruck A-6020, Austria
| | - Siegfried Kollotzek
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, Innsbruck A-6020, Austria
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, Prague 18223, Czech Republic
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, Innsbruck A-6020, Austria
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36
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Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J Am Chem Soc 2020; 142:17372-17383. [PMID: 32866376 DOI: 10.1021/jacs.0c05365] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of ΔCp as well as ΔG, ΔH, and ΔS for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Wen Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zane Baird
- Baxter Healthcare Corporation, 927 South Curry Pike, Bloomington, Indiana 47403, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, United States
| | - Arthur Laganowsky
- 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
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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37
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Kwon JH, Lee MJ, Song G, Tsuruta K, Ishiuchi SI, Fujii M, Kang H. Cryogenic Ion Spectroscopy of a Singly Protonated Peptide DYYVVR: Locating Phosphorylation Sites of a Kinase Domain. J Phys Chem Lett 2020; 11:7103-7108. [PMID: 32787320 DOI: 10.1021/acs.jpclett.0c01802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cryogenic ion spectroscopy (CIS) was applied to singly protonated DYYVVR, a tryptic peptide that contains the two active tyrosine residues (Y980 and Y981) of the Janus kinase 3 (JAK3) kinase domain, together with its point mutants (Y980F and Y981F) and phosphorylated peptides (pY980, pY981, and pY980pY981). The two tyrosine chromophores showed distinguishable UV absorption bands at around 35 200 and 35 450 cm-1, respectively. By comparing with the point mutants, the lower electronic band was assigned to the absorption of Y981, and the higher one was assigned to Y980. When phosphorylated, the UV absorption of the phosphorylated chromophore shifts to higher energy above 36 500 cm-1 but the unphosphorylated chromophore gives the absorption in the same region. Conformer-specific IR spectroscopy and density functional theory (DFT) calculations were used to tentatively assign the structure of DYYVVR. Two conformations were found, where Y981 is solvated by the protonated side chain of arginine R984, and the orientation of the carboxylic OH of D979 was different between the two. It is demonstrated that CIS can be used to distinguish the two tyrosine chromophores and to locate the phosphorylation site of a kinase domain.
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Affiliation(s)
- Jang Han Kwon
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Min Ji Lee
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Gyeongok Song
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | | | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | | | - Hyuk Kang
- Department of Chemistry, Ajou University, Suwon 16499, Korea
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38
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Leicht D, Rittgers BM, Douberly GE, Wagner JP, McDonald DC, Mauney DT, Tsuge M, Lee YP, Duncan MA. Infrared spectroscopy of H+(CO)2 in the gas phase and in para-hydrogen matrices. J Chem Phys 2020; 153:084305. [DOI: 10.1063/5.0019731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Leicht
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | | | - Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - J. Philipp Wagner
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - David C. McDonald
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Daniel T. Mauney
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Masashi Tsuge
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Yuan-Pern Lee
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Atomic and Molecular Sciences Academia Sinica, Taipei 10617, Taiwan
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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39
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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40
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Anstöter CS, Verlet JRR. Gas-Phase Synthesis and Characterization of the Methyl-2,2-dicyanoacetate Anion Using Photoelectron Imaging and Dipole-Bound State Autodetachment. J Phys Chem Lett 2020; 11:6456-6462. [PMID: 32687376 DOI: 10.1021/acs.jpclett.0c02036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The methyl-2,2-dicyanoacetate anion is synthesized in an electrospray ionization source through a gas-phase reaction involving tetracyanoethylene and methanol. Photoelectron imaging is used to determine the isomeric form of the product. The photoelectron spectra and angular distributions are consistent with only a single isomer. Additionally, mode-specific vibrational autodetachment is observed. This can be correlated with the emission from a photoexcited dipole-bound state by considering the IR spectrum of the neutral molecule, adding further confirmation of the isomeric form and providing a binding energy of the dipole-bound state. Our experiments show how conventional photoelectron imaging can be used to determine detailed information about gas-phase reaction products.
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Affiliation(s)
- Cate S Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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41
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Zhang Y, Tang Y, Tan C, Xu W. Toward Nanopore Electrospray Mass Spectrometry: Nanopore Effects in the Analysis of Bacteria. ACS CENTRAL SCIENCE 2020; 6:1001-1008. [PMID: 32607447 PMCID: PMC7318062 DOI: 10.1021/acscentsci.0c00622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 05/13/2023]
Abstract
The shape and structure analyses capability of nanopore is powerful and complementary to mass spectrometry analysis. It is extremely attractive but challenging to integrate these two techniques. The feasibility of combining nanopore electrospray with mass spectrometry was explored in this study. A nanopore effect was observed during the nano-electrospray of single bacterium, through which the shape and dimension of a single bacterium could be obtained. Molecular information on these bacteria was then acquired by analyzing these bacteria deposited on the counter electrode through laser spray ionization mass spectrometry experiments. Proof-of-concept experiments were carried out for four types of bacteria. Results show that the combination of nanopore results with mass spectrum data could effectively improve the identification accuracy of these bacteria from 72.5% to 100%. Although initial experiments were demonstrated in this work, results showed that it is feasible and promising to integrate nanopore technology with mass spectrometry for large biomolecule studies in the near future.
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Affiliation(s)
| | | | | | - Wei Xu
- . Web: http://www.escience.cn/people/weixu
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42
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Zelenka J, Roithová J. Mechanistic Investigation of Photochemical Reactions by Mass Spectrometry. Chembiochem 2020; 21:2232-2240. [DOI: 10.1002/cbic.202000072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/23/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Jan Zelenka
- Department of Spectroscopy and CatalysisInstitute for Molecules and MaterialsRadboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen (The Netherlands
| | - Jana Roithová
- Department of Spectroscopy and CatalysisInstitute for Molecules and MaterialsRadboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen (The Netherlands
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43
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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44
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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45
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Carnegie PD, Marks JH, Brathwaite AD, Ward TB, Duncan MA. Microsolvation in V +(H 2O) n Clusters Studied with Selected-Ion Infrared Spectroscopy. J Phys Chem A 2020; 124:1093-1103. [PMID: 31961153 DOI: 10.1021/acs.jpca.9b11275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gas-phase ion-molecule clusters of the form V+(H2O)n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit redshifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V+ ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of acceptor-acceptor-donor (AAD)-coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly charged or doubly charged cation-water clusters. This indicates that cation identity and charge-site location in the cluster can produce discernable spectral differences for clusters in this size range.
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Affiliation(s)
- Prosser D Carnegie
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Joshua H Marks
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Antonio D Brathwaite
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Timothy B Ward
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Michael A Duncan
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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Cirri A, Hernández HM, Johnson CJ. High Precision Electronic Spectroscopy of Ligand-Protected Gold Nanoclusters: Effects of Composition, Environment, and Ligand Chemistry. J Phys Chem A 2020; 124:1467-1479. [PMID: 31916764 DOI: 10.1021/acs.jpca.9b09164] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Atomically precise gold nanoclusters (AuNCs) are a class of nanomaterials valued for their electronic properties and diverse structural features. While the advent of X-ray crystallography of AuNCs has revealed their geometric structures with high precision, detailed electronic structure analysis is challenged by environmental, compositional, and thermal averaging effects present in electronic spectra of typical samples. To circumvent these challenges, we have adapted mass spectrometer-based electronic absorption spectroscopy techniques to acquire high-resolution electronic spectra of atomically precisely defined nanoclusters separated from a synthetic mixture. Here we discuss recent results using this approach to link the surface chemistry of triphenylphosphine-protected AuNCs to their electronic structure and expand on key elements of the experiment and the link between these gas-phase measurements and solution-phase behavior of AuNCs. Chemically derivatized Au8(P(p-X-Ph)3)72+ and Au9(P(p-X-Ph)3)83+ clusters, where X = -H, -CH3, or -OCH3, are used to derive systematic trends in the response of the electronic spectrum to the electron-donating character of the ligand shell. We find a linear relationship between the substituent Hammett parameter σp and the transition energy between both sets of clusters' highest occupied and lowest unoccupied molecular orbitals, a transition that is localized in the metal core within the limits of the superatomic model. The similarity of the mass-selective and solution-phase UV/vis spectra of Au9(PPh3)83+ indicates that the interpretation of these experiments is transferable to the condensed phase. He and N2 environments are introduced to a series of isovalent clusters as a subtle probe of discrete environmental effects over electronic structure. Strikingly, select bands in the UV/vis spectrum respond strongly to the identity of the environment, which we interpret as a state-selective indicator of interfacially relevant electronic transitions. Physically predictable trends such as these will aid in building molecular design principles necessary for the development of novel materials based on nanoclusters.
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Affiliation(s)
- Anthony Cirri
- Department of Chemistry , Stony Brook University , 100 Nicolls Road , Stony Brook , New York 11794-3400 , United States
| | - Hanna Morales Hernández
- Department of Chemistry , Stony Brook University , 100 Nicolls Road , Stony Brook , New York 11794-3400 , United States
| | - Christopher J Johnson
- Department of Chemistry , Stony Brook University , 100 Nicolls Road , Stony Brook , New York 11794-3400 , United States
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Noble JA, Marceca E, Dedonder C, Jouvet C. Influence of the N atom and its position on electron photodetachment of deprotonated indole and azaindole. Phys Chem Chem Phys 2020; 22:27290-27299. [DOI: 10.1039/d0cp03609a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dipole bound state and its vibrational structure observed in deprotonated 7-azaindole by recording the signal of 7-azaindolyl stable neutral radical.
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Affiliation(s)
- Jennifer A. Noble
- CNRS
- Aix Marseille Univ
- PIIM
- Physique des Interactions Ioniques et Moléculaires
- UMR 7345
| | - Ernesto Marceca
- INQUIMAE (CONICET – Universidad de Buenos Aires)
- DQIAQF (Facultad de Ciencias Exactas y Naturales
- Universidad de Buenos Aires)
- Ciudad Universitaria
- 1428 Buenos Aires
| | - Claude Dedonder
- CNRS
- Aix Marseille Univ
- PIIM
- Physique des Interactions Ioniques et Moléculaires
- UMR 7345
| | - Christophe Jouvet
- CNRS
- Aix Marseille Univ
- PIIM
- Physique des Interactions Ioniques et Moléculaires
- UMR 7345
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48
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Bergmann TG, Welzel MO, Jacob CR. Towards theoretical spectroscopy with error bars: systematic quantification of the structural sensitivity of calculated spectra. Chem Sci 2019; 11:1862-1877. [PMID: 34123280 PMCID: PMC8148348 DOI: 10.1039/c9sc05103a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular spectra calculated with quantum-chemical methods are subject to a number of uncertainties (e.g., errors introduced by the computational methodology) that hamper the direct comparison of experiment and computation. Judging these uncertainties is crucial for drawing reliable conclusions from the interplay of experimental and theoretical spectroscopy, but largely relies on subjective judgment. Here, we explore the application of methods from uncertainty quantification to theoretical spectroscopy, with the ultimate goal of providing systematic error bars for calculated spectra. As a first target, we consider distortions of the underlying molecular structure as one important source of uncertainty. We show that by performing a principal component analysis, the most influential collective distortions can be identified, which allows for the construction of surrogate models that are amenable to a statistical analysis of the propagation of uncertainties in the molecular structure to uncertainties in the calculated spectrum. This is applied to the calculation of X-ray emission spectra of iron carbonyl complexes, of the electronic excitation spectrum of a coumarin dye, and of the infrared spectrum of alanine. We show that with our approach it becomes possible to obtain error bars for calculated spectra that account for uncertainties in the molecular structure. This is an important first step towards systematically quantifying other relevant sources of uncertainty in theoretical spectroscopy. Uncertainty quantification is applied in theoretical spectroscopy to obtain error bars accounting for the structural sensitivity of calculated spectra.![]()
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Affiliation(s)
- Tobias G Bergmann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Michael O Welzel
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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50
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Chand A, Biswal HS. Hydrogen Bonds with Chalcogens: Looking Beyond the Second Row of the Periodic Table. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00140-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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