1
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Tikhonov DS, Scutelnic V, Sharapa DI, Krotova AA, Dmitrieva AV, Obenchain DA, Schnell M. Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations. Struct Chem 2022. [DOI: 10.1007/s11224-022-02053-4] [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
AbstractHere, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$
+
ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$
2
H
+
and (Imidazole)$$_{3}\mathrm{H}^{+}$$
3
H
+
the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.
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2
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Chatterjee K, Dopfer O. Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine. Phys Chem Chem Phys 2020; 22:17275-17290. [PMID: 32685941 DOI: 10.1039/d0cp02919j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.
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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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3
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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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4
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Tesler LF, Cismesia AP, Bell MR, Bailey LS, Polfer NC. Operation and Performance of a Mass-Selective Cryogenic Linear Ion Trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2115-2124. [PMID: 30062479 PMCID: PMC6301008 DOI: 10.1007/s13361-018-2026-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
We report on the performance of a cryogenic 2D linear ion trap (cryoLIT) that is shown to be mass-selective in the temperature range of 17-295 K. As the cryoLIT is cooled, the ejection voltages during the mass instability scan decrease, which results in an effective mass shift to lower m/z relative to room temperature. This is attributed to a decrease in trap radius caused by thermal contraction. Additionally, the cryoLIT generates reproducible mass spectra from day-to-day, and is capable of performing stored waveform inverse Fourier transform (SWIFT) mass isolation of fragile N2-tagged ions for the purpose of background-free infrared dissociation spectroscopy. Graphical Abstract ᅟ.
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Affiliation(s)
- Larry F Tesler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Adam P Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Matthew R Bell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Laura S Bailey
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, USA.
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5
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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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6
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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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7
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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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8
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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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9
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Rojek T, Goldeman W, Ślepokura K, Duczmal M, Wojciechowska A, Matczak-Jon E. Two isomorphous Co(ii) coordination polymers based on new α,α-disubstituted derivatives of zoledronic acid: synthesis, structures and properties. Dalton Trans 2017; 46:6900-6911. [DOI: 10.1039/c7dt00410a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1D Co(ii) coordination polymers based on new derivatives of zoledronic acid. Spectroscopic and magnetic characterization.
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Affiliation(s)
- Tomasz Rojek
- Department of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Waldemar Goldeman
- Department of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | | | - Marek Duczmal
- Department of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | | | - Ewa Matczak-Jon
- Department of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
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10
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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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11
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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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12
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Bhattacherjee A, Wategaonkar S. Water bridges anchored by a C–H⋯O hydrogen bond: the role of weak interactions in molecular solvation. Phys Chem Chem Phys 2016; 18:27745-27749. [DOI: 10.1039/c6cp05469b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonded water bridges are re-directed from a polar NH bond to a weakly activated C(2)–H bond upon N-methylation. Infrared spectra, supported by ab initio calculations, provide direct evidence of the role of the C(2)–H donor in the solvation of the imidazole ring.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
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13
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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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14
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Sakota K, Schütz M, Schmies M, Moritz R, Bouchet A, Ikeda T, Kouno Y, Sekiya H, Dopfer O. Weak hydrogen bonding motifs of ethylamino neurotransmitter radical cations in a hydrophobic environment: infrared spectra of tryptamine+–(N2)n clusters (n ≤ 6). Phys Chem Chem Phys 2014; 16:3798-806. [DOI: 10.1039/c3cp54127d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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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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16
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Schmies M, Patzer A, Kruppe S, Miyazaki M, Ishiuchi S, Fujii M, Dopfer O. Microsolvation of the 4‐Aminobenzonitrile Cation (ABN
+
) in a Nonpolar Solvent: IR Spectra of ABN
+
L
n
(L=Ar and N
2
,
n
≤4). Chemphyschem 2012. [DOI: 10.1002/cphc.201200790] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Schmies
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany)
| | - Alexander Patzer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany)
| | - Sarah Kruppe
- 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)
| | - Shun‐ichi Ishiuchi
- 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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17
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Fujii M, Dopfer O. Ionisation-induced site switching dynamics in solvated aromatic clusters: phenol–(rare gas)nclusters as prototypical example. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.656013] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Ishiuchi SI. Static and Dynamic Structures of Phenol/Ar Clusters Studied by Multiresonance Laser Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20110167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Ishiuchi SI, Miyazaki M, Sakai M, Fujii M, Schmies M, Dopfer O. Ionization-induced π → H site switching dynamics in phenol–Ar3. Phys Chem Chem Phys 2011; 13:2409-16. [DOI: 10.1039/c0cp01926g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Gerardi HK, Gardenier GH, Viswanathan U, Auerbach SM, Johnson MA. Vibrational predissociation spectroscopy and theory of Ar-tagged, protonated Imidazole (Im) Im1–3H+·Ar clusters. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.10.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Schmies M, Patzer A, Fujii M, Dopfer O. Structures and IR/UV spectra of neutral and ionic phenol–Arn cluster isomers (n≤ 4): competition between hydrogen bonding and stacking. Phys Chem Chem Phys 2011; 13:13926-41. [DOI: 10.1039/c1cp20676a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase. Phys Chem Chem Phys 2011; 13:15644-56. [DOI: 10.1039/c1cp21681c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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23
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Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared Spectra of Protonated Neurotransmitters: Serotonin. J Phys Chem A 2010; 114:13268-76. [DOI: 10.1021/jp109337a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anita Lagutschenkov
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Judith Langer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Giel Berden
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Jos Oomens
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany, FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, and University of Amsterdam, Science Park 904, Amsterdam 1098XH, The Netherlands
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24
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Chakraborty S, Patzer A, Dopfer O. IR spectra of protonated benzaldehyde clusters, C7H7O+–Ln (L=Ar,N2;n≤2): Ion-ligand binding motifs of the cis and trans oxonium isomers. J Chem Phys 2010; 133:044307. [DOI: 10.1063/1.3460458] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Walter C, Kritzer R, Schubert A, Meier C, Dopfer O, Engel V. Dissipative Wave Packet Dynamics of Hydrophobic → Hydrophilic Site Switching in Phenol-Ar Clusters. J Phys Chem A 2010; 114:9743-8. [DOI: 10.1021/jp101964e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ch. Walter
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Laboratoire de Collisions, Agrégats et Reactivité, IRSAMC, Université Paul Sabatier, 31062 Toulouse, France, and Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
| | - R. Kritzer
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Laboratoire de Collisions, Agrégats et Reactivité, IRSAMC, Université Paul Sabatier, 31062 Toulouse, France, and Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
| | - A. Schubert
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Laboratoire de Collisions, Agrégats et Reactivité, IRSAMC, Université Paul Sabatier, 31062 Toulouse, France, and Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany
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IR spectra of resorcinol+–Arn cluster cations (n=1, 2): Evidence for photoionization-induced π→H isomerization. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Adesokan AA, Gerber RB. Anharmonic Vibrational Spectroscopy Calculations for Proton-Bound Amino Acid Dimers. J Phys Chem A 2008; 113:1905-12. [DOI: 10.1021/jp807106h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adeyemi A. Adesokan
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - R. B. Gerber
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Patzer A, Knorke H, Langer J, Dopfer O. IR spectra of phenol+–(O2)n cation clusters (n=1–4): Hydrogen bonding versus stacking interactions. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Ishiuchi SI, Sakai M, Tsuchida Y, Takeda A, Kawashima Y, Dopfer O, Müller-Dethlefs K, Fujii M. IR signature of the photoionization-induced hydrophobic→hydrophilic site switching in phenol-Arn clusters. J Chem Phys 2007; 127:114307. [PMID: 17887837 DOI: 10.1063/1.2775935] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IR spectra of phenol-Arn (PhOH-Arn) clusters with n=1 and 2 were measured in the neutral and cationic electronic ground states in order to determine the preferential intermolecular ligand binding motifs, hydrogen bonding (hydrophilic interaction) versus pi bonding (hydrophobic interaction). Analysis of the vibrational frequencies of the OH stretching motion, nuOH, observed in nanosecond IR spectra demonstrates that neutral PhOH-Ar and PhOH-Ar2 as well as cationic PhOH+-Ar have a pi-bound structure, in which the Ar atoms bind to the aromatic ring. In contrast, the PhOH+-Ar2 cluster cation is concluded to have a H-bound structure, in which one Ar atom is hydrogen-bonded to the OH group. This pi-->H binding site switching induced by ionization was directly monitored in real time by picosecond time-resolved IR spectroscopy. The pi-bound nuOH band is observed just after the ionization and disappears simultaneously with the appearance of the H-bound nuOH band. The analysis of the picosecond IR spectra demonstrates that (i) the pi-->H site switching is an elementary reaction with a time constant of approximately 7 ps, which is roughly independent of the available internal vibrational energy, (ii) the barrier for the isomerization reaction is rather low(<100 cm(-1)), (iii) both the position and the width of the H-bound nuOH band change with the delay time, and the time evolution of these spectral changes can be rationalized by intracluster vibrational energy redistribution occurring after the site switching. The observation of the ionization-induced switch from pi bonding to H bonding in the PhOH+-Ar2 cation corresponds to the first manifestation of an intermolecular isomerization reaction in a charged aggregate.
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Affiliation(s)
- Shun-ichi Ishiuchi
- Chemical Resources Laboratory, Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
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Takeda A, Andrei HS, Miyazaki M, Ishiuchi SI, Sakai M, Fujii M, Dopfer O. IR spectra of phenol+–Krn cluster cations (n=1,2): Evidence for photoionization-induced π→H isomerization. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.06.103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Adesokan AA, Chaban GM, Dopfer O, Gerber RB. Vibrational Spectroscopy of Protonated Imidazole and its Complexes with Water Molecules: Ab Initio Anharmonic Calculations and Experiments. J Phys Chem A 2007; 111:7374-81. [PMID: 17500546 DOI: 10.1021/jp070785w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH+), and its complexes with water (ImH+)(H2O)n, are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH+)(H2O)N2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH+)H2O and (ImH+)(H2O)2 show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH+ shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH+ have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.
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Affiliation(s)
- Adeyemi A Adesokan
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, USA
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Wang X, Lee JS, Yang DS. Electron Spectroscopy, Molecular Structures, and Binding Energies of Al- and Cu-Imidazole. J Phys Chem A 2006; 110:12777-84. [PMID: 17125291 DOI: 10.1021/jp0649605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Al- and Cu-imidazole are produced in laser-vaporization supersonic molecular beams and studied with pulsed field ionization-zero electron kinetic energy (ZEKE) spectroscopy and second-order Møller-Plesset (MP2) theory. The sigma and pi structures of these complexes are predicted by MP2 calculations, but only the sigma structures are identified by the experimental measurements. For these sigma structures, adiabatic ionization energies and several vibrational frequencies are measured from the ZEKE spectra, the ground electronic states of the neutral and ionized complexes are determined by comparing the observed and calculated spectra, and the metal-ligand bond dissociation energies of the neutral states are derived by using a thermochemical relation. The measured vibrational modes include the metal-ligand stretch and bend and ligand ring distortions. The metal-ligand stretch frequencies of these transient complexes are compared with those of coordinately saturated, stable metal compounds, and the ligand-based distortion frequencies are compared with those of the free ligand. Al-imidazole has a larger bond dissociation energy than Cu-imidazole, although the opposite order was previously found for the corresponding ions. The weaker bonding of the Cu complex is attributed to the antibonding interaction and the electron repulsion between the Cu 4s and N lone-pair electrons.
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Affiliation(s)
- Xu Wang
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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Pasker FM, Solcà N, Dopfer O. Spectroscopic Identification of Carbenium and Ammonium Isomers of Protonated Aniline (AnH+): IR Spectra of Weakly Bound AnH+−Ln Clusters (L = Ar, N2). J Phys Chem A 2006; 110:12793-804. [PMID: 17125293 DOI: 10.1021/jp064571a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared photodissociation (IRPD) spectra of mass-selected clusters composed of protonated aniline (C6H8N+ = AnH+) and a variable number of neutral ligands (L = Ar, N2) are obtained in the N-H stretch range. The AnH+ -Ln complexes (n < or = 3) are produced by chemical ionization in a supersonic expansion of An, H2, and L. The IRPD spectra of AnH+-Ln feature the unambiguous fingerprints of at least two different AnH+ nucleation centers, namely, the ammonium isomer (5) and the carbenium ions (1 and/or 3) corresponding to protonation at the N atom and at the C atoms in the para and/or ortho positions, respectively. Protonation at the meta and ipso positions is not observed. Both classes of observed AnH+-Ln isomers exhibit very different photofragmentation behavior upon vibrational excitation arising from the different interaction strengths of the AnH+ cores with the surrounding neutral ligands. Analysis of the incremental N-H stretch frequency shifts as a function of cluster size shows that microsolvation of both 5 and 1/3 in Ar and N2 starts with the formation of intermolecular H bonds of the ligands to the acidic NH protons and proceeds by intermolecular pi bonding to the aromatic ring. The analysis of both the photofragmentation branching ratios and the N-H stretch frequencies demonstrates that the N-H bonds in 5 are weaker and more acidic than those in 1/3, leading to stronger intermolecular H bonds with L. The interpretation of the spectroscopic data is supported by density functional calculations conducted at the B3LYP level using the 6-31G* and 6-311G(2df,2pd) basis sets. Comparison with clusters of neutral aniline and the aniline radical cation demonstrates the drastic effect of protonation and ionization on the acidity of the N-H bonds and the topology of the intermolecular potential, in particular on the preferred aromatic substrate-nonpolar ligand recognition motif.
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Affiliation(s)
- Felix M Pasker
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, D-10623 Berlin, Germany
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Chiavarino B, Crestoni ME, Fornarini S, Dopfer O, Lemaire J, Maître P. IR Spectroscopic Features of Gaseous C7H7O+ Ions: Benzylium versus Tropylium Ion Structures. J Phys Chem A 2006; 110:9352-60. [PMID: 16869683 DOI: 10.1021/jp0628380] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gaseous [C7H7O]+ ions have been formed by protonation of benzaldehyde or tropone (2,4,6-cycloheptatrienone) in the cell of an FT-ICR mass spectrometer using C2H5(+) as a Brønsted acid. The so-formed species have been assayed by infrared multiphoton dissociation (IRMPD) using the free electron laser (FEL) at the CLIO (Centre Laser Infrarouge Orsay) facility. The IRMPD features are quite distinct for ions from the two different precursors, pointing to two different isomers. A number of potential structures for [C7H7O]+ ions have been optimized at the B3LYP/6-31+G(d,p) level of theory, and their relative energies and IR spectra are reported. On this basis, the IRMPD spectra of [C7H7O]+ ions are found to display features characteristic of O-protonated species, with no evidence of any further skeletal rearrangements. The so-formed ions are thus hydroxy-substituted benzylium and tropylium ions, respectively, representative members of the benzylium/tropylium ion family. The IRMPD assay using the FEL laser light has allowed their unambiguous discrimination where other mass spectrometric techniques have yielded a less conclusive answer.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy.
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Andrei HS, Solcà N, Dopfer O. Microhydration of Protonated Biomolecular Building Blocks: IR Spectra of Protonated Imidazole-Watern Complexes. Chemphyschem 2006; 7:107-10. [PMID: 16317795 DOI: 10.1002/cphc.200500432] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Horia-Sorin Andrei
- Institut für Physikalische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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Hobza P, Zahradník R, Müller-Dethlefs K. The World of Non-Covalent Interactions: 2006. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060443] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.
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Solcà N, Dopfer O. Hydrogen-Bonded Networks in Ethanol Proton Wires: IR Spectra of (EtOH)qH+−Ln Clusters (L = Ar/N2, q ≤ 4, n ≤ 5). J Phys Chem A 2005; 109:6174-86. [PMID: 16833957 DOI: 10.1021/jp0514776] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Isolated and microsolvated protonated ethanol clusters, (EtOH)qH+-Ln with L = Ar and N2, are characterized by infrared photodissociation (IRPD) spectroscopy in the 3 microm range and quantum chemical calculations. For comparison, also the spectrum of the protonated methanol dimer, (MeOH)2H+, is presented. The IRPD spectra carry the signature of H-bonded (EtOH)qH+ chain structures, in which the excess proton is either strongly localized on one or (nearly) equally shared between two EtOH molecules, corresponding to Eigen-type ion cores (EtOH2+ for q = 1, 3) or Zundel-type ion cores (EtOH-H+-HOEt for q = 2, 4), respectively. In contrast to neutral (EtOH)q clusters, no cyclic (EtOH)qH+ isomers are detected in the size range investigated (q < or = 4), indicative of the substantial impact of the excess proton on the properties of the H-bonded ethanol network. The acidity of the two terminal OH groups in the (EtOH)qH+ chains decreases with the length of the chain (q). Comparison between (ROH)qH+ with R = CH3 and C2H5 shows that the acidity of the terminal O-H groups increases with the length of the aliphatic rest (R). The most stable (EtOH)qH+-Ln clusters with n < or = 2 feature intermolecular H-bonds between the inert ligands and the two available terminal OH groups of the (EtOH)qH+ chain. Asymmetric microsolvation of (EtOH)qH+ with q = 2 and 4 promotes a switch from Zundel-type to Eigen-type cores, demonstrating that the fundamental structural motif of the (EtOH)qH+ proton wire sensitively depends on the environment. The strength of the H-bonds between L and (EtOH)qH+ is shown to provide a rather sensitive probe of the acidity of the terminal OH groups.
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Affiliation(s)
- Nicola Solcà
- Institute for Physical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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