1
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Arildii D, Matsumoto Y, Dopfer O. Microhydration of the Pyrrole Cation (Py +) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py +(H 2O) 2. J Phys Chem A 2023; 127:2523-2535. [PMID: 36898005 DOI: 10.1021/acs.jpca.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py+) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py+(H2O)2 and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py+(H2O)2 is formed by stepwise hydration of the acidic NH group of Py+ by a hydrogen-bonded (H2O)2 chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py+H2O and (H2O)2, respectively. The linear chain structure of the Py+(H2O)2 cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H2O)2 global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py+ and the π-bonded OH hydrogen of (H2O)2, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.
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Affiliation(s)
- Dashjargal Arildii
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
- International Research Frontiers Initiative, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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2
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Miyazaki M, Kamiya T, Wohlgemuth M, Chatterjee K, Mitrić R, Dopfer O, Fujii M. Real-time observation of photoionization-induced water migration dynamics in 4-methylformanilide-water by picosecond time-resolved infrared spectroscopy and ab initio molecular dynamics simulations. Phys Chem Chem Phys 2021; 24:73-85. [PMID: 34633007 DOI: 10.1039/d1cp03327a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel time-resolved pump-probe spectroscopic approach that enables to keep high resolution in both the time and energy domain, nanosecond excitation-picosecond ionization-picosecond infrared probe (ns-ps-ps TRIR) spectroscopy, has been applied to the trans-4-methylformanilide-water (4MetFA-W) cluster. Water migration dynamics from the CO to the NH binding site in a peptide linkage triggered by photoionization of 4MetFA-W is directly monitored by the ps time evolution of IR spectra, and the presence of an intermediate state is revealed. The time evolution is analyzed by rate equations based on a four-state model of the migration dynamics. Time constants for the initial to the intermediate and hot product and to the final product are obtained. The acceleration of the dynamics by methyl substitution and the strong contribution of intracluster vibrational energy redistribution in the termination of the solvation dynamics is suggested. This picture is well confirmed by the ab initio on-the-fly molecular dynamics simulations. Vibrational assignments of 4MetFA and 4MetFA-W in the neutral (S0 and S1) and ionic (D0) electronic states measured by ns IR dip and electron-impact IR photodissociation spectroscopy are also discussed prior to the results of time-resolved spectroscopy.
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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
| | - Tairiku Kamiya
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany.
| | - Kuntal Chatterjee
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany. .,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-15, 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.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
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3
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Huang X, Aranguren JP, Ehrmaier J, Noble JA, Xie W, Sobolewski AL, Dedonder-Lardeux C, Jouvet C, Domcke W. Photoinduced water oxidation in pyrimidine-water clusters: a combined experimental and theoretical study. Phys Chem Chem Phys 2020; 22:12502-12514. [PMID: 32452507 DOI: 10.1039/d0cp01562h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photocatalytic oxidation of water with molecular or polymeric N-heterocyclic chromophores is a topic of high current interest in the context of artificial photosynthesis, that is, the conversion of solar energy to clean fuels. Hydrogen-bonded clusters of N-heterocycles with water molecules in a molecular beam are simple model systems for which the basic mechanisms of photochemical water oxidation can be studied under well-defined conditions. In this work, we explored the photoinduced H-atom transfer reaction in pyrimidine-water clusters yielding pyrimidinyl and hydroxyl radicals with laser spectroscopy, mass spectrometry and trajectory-based ab initio molecular dynamics simulations. The oxidation of water by photoexcited pyrimidine is unequivocally confirmed by the detection of the pyrimidinyl radical. The dynamics simulations provide information on the time scales and branching ratios of the reaction. While relaxation to local minima of the S1 potential-energy surface is the dominant reaction channel, the H-atom transfer reaction occurs on ultrafast time scales (faster than about 100 fs) with a branching ratio of a few percent.
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Affiliation(s)
- Xiang Huang
- Department of Chemistry, Technical University of Munich, Garching, Germany.
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4
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Matsuda Y, Hirano Y, Mizutani S, Sakai D, Fujii A, Maeda S, Ohno K. Migrations and Catalytic Action of Water Molecules in the Ionized Formamide-(H 2O) 2 Cluster. J Phys Chem A 2020; 124:2802-2807. [PMID: 32187496 DOI: 10.1021/acs.jpca.0c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isomerization dynamics involving the migrations, proton transfer reaction, and catalytic actions of water molecules upon vertical ionization of the formamide (FA)-(H2O)2 cluster is investigated by the infrared spectroscopy and theoretical reaction path search calculation. The infrared spectroscopic result indicates the [FA-(H2O)2]+ cation has the hydrogen-bonded structure of the enol isomer cation of formamide and the water dimer. This structure is formed by proton transfer from the CH bond to the carbonyl group through the catalytic action of the water molecules. The isomerization paths involving this enolization in ionized FA-(H2O)2 are explored by using the anharmonic downward distortion following method. We found multiple enolization paths which accompany proton exchanges among the formamide moiety and water molecules through the catalytic actions of the water molecules.
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Affiliation(s)
- Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Yutaro Hirano
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinichi Mizutani
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Daichi Sakai
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba, 305-0044, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.,Institute for Quantum Chemical Exploration, 13F Area Shinagawa, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan
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5
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Wu JY, Cheng PY. Ultrafast Protonation of an Amide: Photoionization-Induced Proton Transfer in Phenol-Dimethylformamide Complex Cation. J Phys Chem A 2019; 123:10700-10713. [DOI: 10.1021/acs.jpca.9b09651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jun-Yi Wu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan, R.
O. C
| | - Po-Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan, R.
O. C
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Miyazaki M, Chatterjee K, Hattori K, Otsuka R, Ishiuchi SI, Dopfer O, Fujii M. Ionization-Induced π → H Site Switching in Resorcinol-Ar n ( n = 1 and 2) Clusters Probed by Infrared Spectroscopy. J Phys Chem A 2019; 123:6828-6839. [PMID: 31304754 DOI: 10.1021/acs.jpca.9b04460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectra of resorcinol (Rs)-Arn clusters (n = 1 and 2) have been measured in the neutral and cationic ground states (S0 and D0) by IR dip and resonance-enhanced multiphoton ionization (REMPI)-IR spectroscopy. The OH stretching vibrations in S0 keep their frequency regardless of the number of Ar atoms and the conformation of the OH groups in Rs (rotamers RsI and RsII), demonstrating that the Ar atoms are attached to the aromatic π-ring (π-bound structure) in S0. In the D0 state, the IR spectra of Rs+-Arn reflect the difference in the Rs conformations (RsI+ and RsII+). For n = 1, the IR spectra of both rotamers are almost the same as those of the corresponding monomer cations, indicating that Ar ligands essentially remain π-bonded after ionization. In contrast, the IR spectra of Rs+-Ar2 show hydrogen-bonded and free OH stretching vibrations, demonstrating that for a significant fraction of the clusters, the Ar atoms migrate from the π-bound site to the OH groups. The ionization-induced π → H migration yields are not unity for both rotamers RsI+-Ar2 and RsII+-Ar2. This result is in sharp contrast to phenol+-Ar2, in which one of the Ar atoms migrates to the OH site with 100% yield. The mechanism leading to the nonunity yield in Rs+-Ar2 is discussed in terms of the number of OH binding sites and Franck-Condon factors. The ionization excess energy dependence of the IR spectra of Rs+-Ar2 and its Rs+-Ar fragments is discussed in terms of the Ar binding energies estimated from the photoionization and photodissociation efficiency spectra.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Institut für Optik und Atomare Physik , Technische Universität Berlin , Hardenbergstrasse 36 , 10623 Berlin , Germany
| | - Kuntal Chatterjee
- Institut für Optik und Atomare Physik , Technische Universität Berlin , Hardenbergstrasse 36 , 10623 Berlin , Germany
| | | | | | | | - Otto Dopfer
- Institut für Optik und Atomare Physik , Technische Universität Berlin , Hardenbergstrasse 36 , 10623 Berlin , Germany
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7
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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8
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Klyne J, Dopfer O. Microhydration of protonated 5-hydroxyindole revealed by infrared spectroscopy. Phys Chem Chem Phys 2019; 21:2706-2718. [PMID: 30663737 DOI: 10.1039/c8cp06950f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Controlled microsolvation of protonated aromatic biomolecules with water is fundamental to understand proton transfer reactions in aqueous environments. We measured infrared photodissociation (IRPD) spectra of mass-selected microhydrates of protonated 5-hydroxyindole (5HIH+-Wn, W = H2O, n = 1-3) in the OH and NH stretch ranges (2700-3800 cm-1), which are sensitive to the spectroscopic characteristics of interior solvation, water network formation, and proton transfer to solvent. Analysis of the IRPD spectra by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) reveals the coexistence of C3- and C4-protonated carbenium ions, 5HIH+(C3) and 5HIH+(C4), as well as the O-protonated oxonium ion, 5HIH+(O). Monohydrated 5HIH+-W clusters are formed by hydrogen-bonding (H-bonding) of the first water to the most acidic functional group, namely, the NH group in the case of 5HIH+(C3), the OH group for 5HIH+(C4), and the OH2 group for 5HIH+(O). The latter benefits from its twofold degeneracy and the outstandingly high binding energy of D0 ∼ 100 kJ mol-1. Larger 5HIH+-W2/3 clusters preferably grow (i) by H-bonding of the second water to the remaining vacant functional group and and/or (ii) by formation of W2 water chains at the respective most acidic functional group. Our IRPD spectra of 5HIH+-Wn do not indicate any proton transfer to the solvent up to n = 3, in line with the proton affinities of 5HI and Wn. Comparison of 5HIH+-Wn to neutral 5HI-W and cationic 5HI+-Wn clusters elucidates the impact of different charge states on the topology of the initial solvation shell. Furthermore, to access the influence of the size of the arene ion and a second functional group, we draw a comparison to microhydration of protonated phenol.
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Affiliation(s)
- Johanna Klyne
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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9
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Chatterjee K, Dopfer O. Switching of binding site from nonpolar to polar ligands toward cationic benzonitrile revealed by infrared spectroscopy. J Chem Phys 2018; 149:174315. [DOI: 10.1063/1.5057430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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10
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Yang N, Duong CH, Kelleher PJ, Johnson MA. Unmasking Rare, Large-Amplitude Motions in D 2-Tagged I -·(H 2O) 2 Isotopomers with Two-Color, Infrared-Infrared Vibrational Predissociation Spectroscopy. J Phys Chem Lett 2018; 9:3744-3750. [PMID: 29924622 DOI: 10.1021/acs.jpclett.8b01485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We describe a two-color, isotopomer-selective infrared-infrared population-labeling method that can monitor very slow spectral diffusion of OH oscillators in H-bonded networks and apply it to the I-·(HDO)·(D2O) and I-·(H2O)·(D2O) systems, which are cryogenically cooled and D2-tagged at an ion trap temperature of 15 K. These measurements reveal very large (>400 cm-1), spontaneous spectral shifts despite the fact that the predissociation spectra in the OH stretching region of both isotopologues are sharp and readily assigned to four fundamentals of largely decoupled OH oscillators held in a cyclic H-bonded network. This spectral diffusion is not observed in the untagged isotopologues of the dihydrate clusters that are generated under the same source conditions but does become apparent at about 75 K. These results are discussed in the context of the large-amplitude "jump" mechanism for H-bond relaxation dynamics advanced by Laage and Hynes in an experimental scenario where rare events can be captured by following the migration of OH groups among the four available positions in the quasi-rigid equilibrium structure.
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Affiliation(s)
- Nan Yang
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Chinh H Duong
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Patrick J Kelleher
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory , Yale University , New Haven , Connecticut 06520 , United States
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11
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Chatterjee K, Dopfer O. Microhydration of PAH + cations: evolution of hydration network in naphthalene +-(H 2O) n clusters ( n ≤ 5). Chem Sci 2018; 9:2301-2318. [PMID: 29719704 PMCID: PMC5903421 DOI: 10.1039/c7sc05124g] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022] Open
Abstract
The interaction of polycyclic aromatic hydrocarbon molecules with water (H2O = W) is of fundamental importance in chemistry and biology. Herein, size-selected microhydrated naphthalene cation nanoclusters, Np+-W n (n ≤ 5), are characterized by infrared photodissociation (IRPD) spectroscopy in the C-H and O-H stretch range to follow the stepwise evolution of the hydration network around this prototypical PAH+ cation. The IRPD spectra are highly sensitive to the hydration structure and are analyzed by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) to determine the predominant structural isomers. For n = 1, W forms a bifurcated CH···O ionic hydrogen bond (H-bond) to two acidic CH protons of the bicyclic ring. For n ≥ 2, the formation of H-bonded solvent networks dominates over interior ion solvation, because of strong cooperativity in the former case. For n ≥ 3, cyclic W n solvent structures are attached to the CH protons of Np+. However, while for n = 3 the W3 ring binds in the CH···O plane to Np+, for n ≥ 4 the cyclic W n clusters are additionally stabilized by stacking interactions, leading to sandwich-type configurations. No intracluster proton transfer from Np+ to the W n solvent is observed in the studied size range (n ≤ 5), because of the high proton affinity of the naphthyl radical compared to W n . This is different from microhydrated benzene+ clusters, (Bz-W n )+, for which proton transfer is energetically favorable for n ≥ 4 due to the much lower proton affinity of the phenyl radical. Hence, because of the presence of polycyclic rings, the interaction of PAH+ cations with W is qualitatively different from that of monocyclic Bz+ with respect to interaction strength, structure of the hydration shell, and chemical reactivity. These differences are rationalized and quantified by quantum chemical analysis using the natural bond orbital (NBO) and noncovalent interaction (NCI) approaches.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik , Technische Universität Berlin , Hardenbergstr. 36 , 10623 Berlin , Germany . ; Tel: +49 30 31423018
| | - Otto Dopfer
- Institut für Optik und Atomare Physik , Technische Universität Berlin , Hardenbergstr. 36 , 10623 Berlin , Germany . ; Tel: +49 30 31423018
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12
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Miyazaki M, Naito A, Ikeda T, Klyne J, Sakota K, Sekiya H, Dopfer O, Fujii M. Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole-water cluster by time-resolved IR spectroscopy. Phys Chem Chem Phys 2018; 20:3079-3091. [PMID: 29143839 DOI: 10.1039/c7cp06127g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation plays an essential role in controlling the mechanism and dynamics of chemical reactions in solution. The present study reveals that changes in the local solute-solvent interaction have a great impact on the timescale of solvent rearrangement dynamics. Time-resolved IR spectroscopy has been applied to a hydration rearrangement reaction in the monohydrated 5-hydroxyindole-water cluster induced by photoionization of the solute molecule. The water molecule changes the stable hydration site from the indolic NH site to the substituent OH site, both of which provide a strongly attractive potential for hydration. The rearrangement time constant amounts to 8 ± 2 ns, and is further slowed down by a factor of more than five at lower excess energy. These rearrangement times are slower by about three orders of magnitude than those reported for related systems where the water molecule is repelled from a repulsive part of the interaction potential toward an attractive well. The excess energy dependence of the time constant is well reproduced by RRKM theory. Differences in the reaction mechanism are discussed on the basis of energy relaxation dynamics.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
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13
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Klyne J, Schmies M, Miyazaki M, Fujii M, Dopfer O. Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide +-(H 2O) n clusters (n ≤ 3). Phys Chem Chem Phys 2018; 20:3148-3164. [PMID: 28913535 DOI: 10.1039/c7cp04659f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA+, N-phenylacetamide), AA+-(H2O)n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (νOH, νNH, νCH, amide A, 2800-3800 cm-1) and fingerprint (amide I-II, 1000-1900 cm-1) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA+-(H2O)n structures, the H2O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H2O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH3) on the shape of the intermolecular potential and the structure of the hydration shell.
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Affiliation(s)
- Johanna Klyne
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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Esteves-López N, Coussan S, Dedonder-Lardeux C, Jouvet C. Photoinduced water splitting in pyridine water clusters. Phys Chem Chem Phys 2018; 18:25637-25644. [PMID: 27711521 DOI: 10.1039/c6cp04398d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio calculations predict that pyridine (Py) can act as a photo-catalyst to split water by the absorption of a UV photon following the reaction Py-H2O + hν → PyH˙ + OH˙. To test this prediction, we performed two types of experiments: in the first, we characterize the electronic spectroscopy of the PyH˙ radical in the gas phase. In the second, we evidence the reaction through the UV excitation of molecular Py-(H2O)n clusters obtained in a supersonic expansion and monitoring the PyH˙ reaction product. The results show unambiguously that PyH˙ is produced, and thus that water is split using pyridine as a photo-catalyst.
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Affiliation(s)
- Natalia Esteves-López
- CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaires (PIIM) UMR-7345, Marseille, France.
| | - Stephane Coussan
- CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaires (PIIM) UMR-7345, Marseille, France.
| | - Claude Dedonder-Lardeux
- CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaires (PIIM) UMR-7345, Marseille, France.
| | - Christophe Jouvet
- CNRS, Aix-Marseille Université, Physique des Interactions Ioniques et Moléculaires (PIIM) UMR-7345, Marseille, France.
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15
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Klyne J, Miyazaki M, Fujii M, Dopfer O. Sequential microhydration of cationic 5-hydroxyindole (5HI+): infrared photodissociation spectra of 5HI+–Wn clusters (W = H2O, n ≤ 4). Phys Chem Chem Phys 2018; 20:3092-3108. [DOI: 10.1039/c7cp06132c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding properties of the acidic OH and NH groups of the 5-hydroxyindole cation are probed by infrared spectroscopy and DFT calculations of its microhydrated clusters.
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Affiliation(s)
- Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Mitsuhiko Miyazaki
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
- Laboratory for Chemistry and Life Science
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
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16
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Bernhard D, Holzer C, Dietrich F, Stamm A, Klopper W, Gerhards M. The Structure of Diphenyl Ether-Methanol in the Electronically Excited and Ionic Ground States: A Combined IR/UV Spectroscopic and Theoretical Study. Chemphyschem 2017; 18:3634-3641. [PMID: 29024275 DOI: 10.1002/cphc.201700722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/24/2017] [Indexed: 11/06/2022]
Abstract
Diphenyl ether offers competing docking sites for methanol: the ether oxygen acts as a common hydrogen-bond acceptor and the π system of each phenyl ring allows for OH-π interactions driven by electrostatic, induction, and dispersion forces. Based on investigations in the electronic ground state (S0 ), we present a detailed study of the electronically excited state (S1 ) and the ionic ground state (D0 ), in which an impact on the structural preference is expected compared with the S0 state. Dispersion forces in the electronically excited state were analyzed by comparing the computed binding energies at the coupled-cluster-singles (CCS) and approximate coupled-cluster-singles-doubles levels of theory (CC2 approximation). By applying UV/IR/UV spectroscopy, we found a more strongly bound OH-π structure in the S1 state compared with the S0 state, in agreement with spin-component-scaled CC2 calculations. A structural rearrangement into a non-hydrogen-bonded structure takes places upon ionization in the D0 state, which was revealed by using IR photodissociation spectroscopy and confirmed by theory.
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Affiliation(s)
- Dominic Bernhard
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Christof Holzer
- Institut für Physikalische Chemie, Abteilung für Theoretische Chemie, Karlsruher Institut für Technologie, KIT, Fritz-Haber-Weg 2, D-76131, Karlsruhe, Germany
| | - Fabian Dietrich
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Anke Stamm
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Wim Klopper
- Institut für Physikalische Chemie, Abteilung für Theoretische Chemie, Karlsruher Institut für Technologie, KIT, Fritz-Haber-Weg 2, D-76131, Karlsruhe, Germany
| | - Markus Gerhards
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
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17
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Ikeda T, Sakota K, Sekiya H. Elevation of the Energy Threshold for Isomerization of 5-Hydroxyindole-(tert-butyl alcohol)1 Cluster Cations. J Phys Chem A 2017; 121:5809-5816. [DOI: 10.1021/acs.jpca.7b05434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takamasa Ikeda
- Department
of Chemistry, Faculty of Science, and Department of Molecular Chemistry,
Graduate School of Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, Japan, 819-0395
| | - Kenji Sakota
- Division
of Molecular Material Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka, Japan, 558-8585
| | - Hiroshi Sekiya
- Department
of Chemistry, Faculty of Science, and Department of Molecular Chemistry,
Graduate School of Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, Japan, 819-0395
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18
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Schütz M, Matsumoto Y, Bouchet A, Öztürk M, Dopfer O. Microsolvation of the pyrrole cation (Py+) with nonpolar and polar ligands: infrared spectra of Py+–Ln with L = Ar, N2, and H2O (n ≤ 3). Phys Chem Chem Phys 2017; 19:3970-3986. [DOI: 10.1039/c6cp07251h] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR spectra and dispersion-corrected density functional calculations of pyrrole cluster ions with Ar, N2, and H2O reveal the competition between H-bonding and π-stacking motifs of this prototypical heterocyclic aromatic cation in a hydrophobic and hydrophilic solvent.
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Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | | | - Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Murat Öztürk
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
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19
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Gu Q, Su P, Xia Y, Yang Z, Trindle CO, Knee JL. Quantitative probing of subtle interactions among H-bonds in alpha hydroxy carboxylic acid complexes. Phys Chem Chem Phys 2017; 19:24399-24411. [DOI: 10.1039/c7cp03917d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alpha OH stretching frequency may be affected upon complexing with water and formic acid.
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Affiliation(s)
- Quanli Gu
- School of Basic Medical Sciences
- Xinxiang Medical University
- Xinxiang
- China
- Chemistry Department
| | - Peifeng Su
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Yong Xia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Zhijun Yang
- School of Basic Medical Sciences
- Xinxiang Medical University
- Xinxiang
- China
| | - Carl O. Trindle
- Chemistry Department
- University of Virginia
- Charlottesville
- USA
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20
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Wohlgemuth M, Miyazaki M, Tsukada K, Weiler M, Dopfer O, Fujii M, Mitrić R. Deciphering environment effects in peptide bond solvation dynamics by experiment and theory. Phys Chem Chem Phys 2017; 19:22564-22572. [DOI: 10.1039/c7cp03992a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Probing solvation dynamics at the molecular level: different water migration pathways around a peptide bond.
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Affiliation(s)
- Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| | - Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Kohei Tsukada
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Martin Weiler
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
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21
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Chatterjee K, Dopfer O. Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+–water. Phys Chem Chem Phys 2017; 19:32262-32271. [DOI: 10.1039/c7cp06893j] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combination of infrared spectroscopy and quantum chemical calculations unravels the salient properties of the bifurcated CH⋯O ionic hydrogen bond typical for the PAH+–H2O interaction.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
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22
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Gu Q, Tang Z, Su P, Wu W, Yang Z, Trindle CO, Knee JL. Communication: Physical origins of ionization potential shifts in mixed carboxylic acids and water complexes. J Chem Phys 2016; 145:051101. [DOI: 10.1063/1.4959970] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Quanli Gu
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Chemistry Department, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Zhen Tang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhijun Yang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Carl O. Trindle
- Chemistry Department, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Joseph L. Knee
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
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24
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Bouchet A, Schütz M, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction. Phys Chem Chem Phys 2016; 17:25742-54. [PMID: 25757357 DOI: 10.1039/c5cp00221d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, D-10623 Berlin, Germany.
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25
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Dopfer O, Fujii M. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level. Chem Rev 2016; 116:5432-63. [DOI: 10.1021/acs.chemrev.5b00610] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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26
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Ikeda T, Sakota K, Sekiya H. Rearrangements of a Water Molecule in Both Directions between Two Hydrogen-Bonding Sites of 5-Hydroxyindole Cation: Experimental Determination of the Energy Threshold for the Rearrangement. J Phys Chem A 2016; 120:1825-32. [DOI: 10.1021/acs.jpca.5b12111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takamasa Ikeda
- Department of Chemistry,
Faculty of Science, and Department of Molecular Chemistry, Graduate
School of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kenji Sakota
- Department of Chemistry,
Faculty of Science, and Department of Molecular Chemistry, Graduate
School of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroshi Sekiya
- Department of Chemistry,
Faculty of Science, and Department of Molecular Chemistry, Graduate
School of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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27
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Dunbar RC, Martens J, Berden G, Oomens J. Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate. Phys Chem Chem Phys 2016; 18:26923-26932. [DOI: 10.1039/c6cp03974j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Giel Berden
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
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28
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Miyazaki M, Sakata Y, Schütz M, Dopfer O, Fujii M. Photoionization-induced π ↔ H site switching dynamics in phenol+–Rg (Rg = Ar, Kr) dimers probed by picosecond time-resolved infrared spectroscopy. Phys Chem Chem Phys 2016; 18:24746-54. [DOI: 10.1039/c6cp05016f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Picosecond time-resolved infrared spectroscopy of phenol–rare gas dimer cations reveal delocalization of a wavepacket of the single rare gas atom above and below phenol in around 100 ps.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Yuri Sakata
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
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29
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Bouchet A, Schütz M, Dopfer O. Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate. Chemphyschem 2015; 17:232-43. [PMID: 26584245 DOI: 10.1002/cphc.201500939] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 01/29/2023]
Abstract
Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany.
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30
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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31
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Schütz M, Sakota K, Moritz R, Schmies M, Ikeda T, Sekiya H, Dopfer O. Simultaneous Interaction of Hydrophilic and Hydrophobic Solvents with Ethylamino Neurotransmitter Radical Cations: Infrared Spectra of Tryptamine+-(H2O)m-(N2)n Clusters (m,n ≤ 3). J Phys Chem A 2015; 119:10035-51. [DOI: 10.1021/acs.jpca.5b07408] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markus Schütz
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Kenji Sakota
- Department
of Chemistry, Faculty of Sciences, and Department of Molecular Chemistry,
Graduate School of Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Raphael Moritz
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Matthias Schmies
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Takamasa Ikeda
- Department
of Chemistry, Faculty of Sciences, and Department of Molecular Chemistry,
Graduate School of Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hiroshi Sekiya
- Department
of Chemistry, Faculty of Sciences, and Department of Molecular Chemistry,
Graduate School of Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, D-10623 Berlin, Germany
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32
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Otto Dopfer. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201411127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Otto Dopfer. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Klyne J, Schmies M, Fujii M, Dopfer O. Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide+–(H2O)n Clusters (n ≤ 5). J Phys Chem B 2015; 119:1388-406. [DOI: 10.1021/jp511421h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Johanna Klyne
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Matthias Schmies
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Masaaki Fujii
- Chemical
Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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35
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Miyazaki M, Nakamura T, Wohlgemuth M, Mitrić R, Dopfer O, Fujii M. Single water solvation dynamics in the 4-aminobenzonitrile–water cluster cation revealed by picosecond time-resolved infrared spectroscopy. Phys Chem Chem Phys 2015; 17:29969-77. [DOI: 10.1039/c5cp05400a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excess energy of photoionization can control the time scale of single water solvent orientation dynamics from picoseconds to infinitely long trapping in a local minimum.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Takashi Nakamura
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Matthias Wohlgemuth
- Institut für Theoretische und Physikalische Chemie
- Julius-Maximilians-Universität Würzburg
- 97070 Würzburg
- Germany
| | - Roland Mitrić
- Institut für Theoretische und Physikalische Chemie
- Julius-Maximilians-Universität Würzburg
- 97070 Würzburg
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Masaaki Fujii
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
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36
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Bouchet A, Klyne J, Piani G, Dopfer O, Zehnacker A. Diastereo-specific conformational properties of neutral, protonated and radical cation forms of (1R,2S)-cis- and (1R,2R)-trans-amino-indanol by gas phase spectroscopy. Phys Chem Chem Phys 2015; 17:25809-21. [DOI: 10.1039/c5cp00576k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of ionisation and protonation on the geometric and electronic structure of a prototypical aromatic amino-alcohol with two chiral centres are revealed by IR and UV spectroscopy.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Giovanni Piani
- CNRS
- Institut des Sciences Moléculaires d’Orsay (ISMO/UMR8214) and Univ. Paris Sud
- Orsay
- France
- CLUPS (Centre Laser de l’Université Paris Sud/LUMAT FR 2764)
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Anne Zehnacker
- CNRS
- Institut des Sciences Moléculaires d’Orsay (ISMO/UMR8214) and Univ. Paris Sud
- Orsay
- France
- CLUPS (Centre Laser de l’Université Paris Sud/LUMAT FR 2764)
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37
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Wohlgemuth M, Miyazaki M, Weiler M, Sakai M, Dopfer O, Fujii M, Mitrić R. Aufklärung der Solvatationsdynamik eines einzelnen Wassermoleküls durch Infrarotspektroskopie: Theorie und Experiment. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Schmies M, Miyazaki M, Fujii M, Dopfer O. Microhydrated aromatic cluster cations: Binding motifs of 4-aminobenzonitrile-(H2O)n cluster cations with n ≤ 4. J Chem Phys 2014; 141:214301. [DOI: 10.1063/1.4901893] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthias Schmies
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Mitsuhiko Miyazaki
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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39
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Wohlgemuth M, Miyazaki M, Weiler M, Sakai M, Dopfer O, Fujii M, Mitrić R. Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra-Theory Meets Experiment. Angew Chem Int Ed Engl 2014; 53:14601-4. [DOI: 10.1002/anie.201409047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 11/09/2022]
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40
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Stamm A, Schwing K, Gerhards M. Investigation of the hydrated 7-hydroxy-4-methylcoumarin dimer by combined IR/UV spectroscopy. J Chem Phys 2014; 141:194304. [DOI: 10.1063/1.4900893] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Stamm
- TU Kaiserslautern, Fachbereich Chemie and Research Center Optimas, Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - K. Schwing
- TU Kaiserslautern, Fachbereich Chemie and Research Center Optimas, Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - M. Gerhards
- TU Kaiserslautern, Fachbereich Chemie and Research Center Optimas, Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
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41
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Lorenz UJ, Rizzo TR. Structural melting of an amino acid dimer upon intersystem crossing. J Am Chem Soc 2014; 136:14974-80. [PMID: 25250642 DOI: 10.1021/ja507981p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a spectroscopic investigation of the excited-state dynamics of the phenylalanine (Phe)/serine (Ser) protonated dimer in the gas phase. Using an ultraviolet (UV) laser pulse, we promote individual isomers to the S1 state and probe their fate with an infrared (IR) pulse. We find that the S1 state has a lifetime of ~70 ns and undergoes intersystem crossing (ISC) to the T1 state. Time-resolved IR spectra allow us to follow the structural evolution of the dimer. In the S1 state, the different isomers retain the hydrogen-bonding pattern of the ground state. Intersystem crossing triggers a sudden increase of the vibrational energy, so that the dimers can overcome isomerization barriers and explore large parts of the potential energy surface (PES). Their broad IR spectra largely resemble one another and indicate that the dimers adopt a molten structure.
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Affiliation(s)
- Ulrich J Lorenz
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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42
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Leavitt CM, Moore KB, Raston PL, Agarwal J, Moody GH, Shirley CC, Schaefer HF, Douberly GE. Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide. J Phys Chem A 2014; 118:9692-700. [DOI: 10.1021/jp5092653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul L. Raston
- Department
of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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43
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Gu Q, Trindle CO, Knee JL. Electronic and Cationic Spectroscopy of 9-Hydroxy-9-fluorene Carboxylic Acid. J Phys Chem A 2014; 118:4982-7. [DOI: 10.1021/jp5045578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quanli Gu
- R. J. Reynolds
Tobacco Company, Winston Salem, North Carolina 27105, United States
| | - Carl O. Trindle
- Chemistry
Department, University of Virginia, Charlottesville, Virginia 22903, United States
| | - J. L. Knee
- Chemistry
Department, Wesleyan University, Middletown, Connecticut 06459, United States
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44
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Dopfer O, Patzer A, Chakraborty S, Alata I, Omidyan R, Broquier M, Dedonder C, Jouvet C. Electronic and vibrational spectra of protonated benzaldehyde-water clusters, [BZ-(H2O)n≤5]H+: Evidence for ground-state proton transfer to solvent for n ≥ 3. J Chem Phys 2014; 140:124314. [DOI: 10.1063/1.4869341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Klyne J, Schmies M, Dopfer O. Microsolvation of the Formanilide Cation (FA+) in a Nonpolar Solvent: Infrared Spectra of FA+–Ln Clusters (L = Ar, N2; n ≤ 8). J Phys Chem B 2014; 118:3005-17. [DOI: 10.1021/jp5011988] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johanna Klyne
- Institut für Optik
und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse
36, 10623 Berlin, Germany
| | - Matthias Schmies
- Institut für Optik
und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse
36, 10623 Berlin, Germany
| | - Otto Dopfer
- Institut für Optik
und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse
36, 10623 Berlin, Germany
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46
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Wolk AB, Leavitt CM, Garand E, Johnson MA. Cryogenic ion chemistry and spectroscopy. Acc Chem Res 2014; 47:202-10. [PMID: 23972279 DOI: 10.1021/ar400125a] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The use of mass spectrometry in macromolecular analysis is an incredibly important technique and has allowed efficient identification of secondary and tertiary protein structures. Over 20 years ago, Chemistry Nobelist John Fenn and co-workers revolutionized mass spectrometry by developing ways to non-destructively extract large molecules directly from solution into the gas phase. This advance, in turn, enabled rapid sequencing of biopolymers through tandem mass spectrometry at the heart of the burgeoning field of proteomics. In this Account, we discuss how cryogenic cooling, mass selection, and reactive processing together provide a powerful way to characterize ion structures as well as rationally synthesize labile reaction intermediates. This is accomplished by first cooling the ions close to 10 K and condensing onto them weakly bound, chemically inert small molecules or rare gas atoms. This assembly can then be used as a medium in which to quench reactive encounters by rapid evaporation of the adducts, as well as provide a universal means for acquiring highly resolved vibrational action spectra of the embedded species by photoinduced mass loss. Moreover, the spectroscopic measurements can be obtained with readily available, broadly tunable pulsed infrared lasers because absorption of a single photon is sufficient to induce evaporation. We discuss the implementation of these methods with a new type of hybrid photofragmentation mass spectrometer involving two stages of mass selection with two laser excitation regions interfaced to the cryogenic ion source. We illustrate several capabilities of the cryogenic ion spectrometer by presenting recent applications to peptides, a biomimetic catalyst, a large antibiotic molecule (vancomycin), and reaction intermediates pertinent to the chemistry of the ionosphere. First, we demonstrate how site-specific isotopic substitution can be used to identify bands due to local functional groups in a protonated tripeptide designed to stereoselectively catalyze bromination of biaryl substrates. This procedure directly reveals the particular H-bond donor and acceptor groups that enforce the folded structure of the bare ion as well as provide contact points for noncovalent interaction with substrates. We then show how photochemical hole-burning involving only vibrational excitations can be used in a double-resonance mode to systematically disentangle overlapping spectra that arise when several conformers of a dipeptide are prepared in the ion source. Finally, we highlight our ability to systematically capture reaction intermediates and spectroscopically characterize their structures. Through this method, we can identify the pathway for water-network-mediated, proton-coupled transformation of nitrosonium, NO(+) to HONO, a key reaction controlling the cations present in the ionosphere. Through this work, we reveal the critical role played by water molecules occupying the second solvation shell around the ion, where they stabilize the emergent product ion in a fashion reminiscent of the solvent coordinate responsible for the barrier to charge transfer in solution. Looking to the future, we predict that the capture and characterization of fleeting intermediate complexes in the homogeneous catalytic activation of small molecules like water, alkanes, and CO2 is a likely avenue rich with opportunity.
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Affiliation(s)
- Arron B. Wolk
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
| | - Christopher M. Leavitt
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P. O. Box 208107, New Haven, Connecticut 06520, United States
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47
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Nakamura T, Schmies M, Patzer A, Miyazaki M, Ishiuchi SI, Weiler M, Dopfer O, Fujii M. Solvent Migration in Microhydrated Aromatic Aggregates: Ionization-Induced Site Switching in the 4-Aminobenzonitrile-Water Cluster. Chemistry 2014; 20:2031-9. [DOI: 10.1002/chem.201303321] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/02/2013] [Indexed: 01/29/2023]
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48
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Miyazaki M, Takeda A, Schmies M, Sakai M, Misawa K, Ishiuchi SI, Michels F, Müller-Dethlefs K, Dopfer O, Fujii M. Ionization-induced π → H site-switching in phenol–CH4complexes studied using IR dip spectroscopy. Phys Chem Chem Phys 2014; 16:110-6. [DOI: 10.1039/c3cp53533a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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49
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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50
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Schmies M, Patzer A, Schütz M, Miyazaki M, Fujii M, Dopfer O. Microsolvation of the acetanilide cation (AA+) in a nonpolar solvent: IR spectra of AA+–Lnclusters (L = He, Ar, N2; n ≤ 10). Phys Chem Chem Phys 2014; 16:7980-95. [DOI: 10.1039/c4cp00401a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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