1
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Skitnevskaya AD, Gokhberg K, Trofimov AB, Grigoricheva EK, Kuleff AI, Cederbaum LS. Two-Sided Impact of Water on the Relaxation of Inner-Valence Vacancies of Biologically Relevant Molecules. J Phys Chem Lett 2023; 14:1418-1426. [PMID: 36731025 DOI: 10.1021/acs.jpclett.2c03654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
After ionization of an inner-valence electron of molecules, the resulting cation-radicals store substantial internal energy which, if sufficient, can trigger ejection of an additional electron in an Auger decay usually followed by molecule fragmentation. In the environment, intermolecular Coulombic decay (ICD) and electron-transfer mediated decay (ETMD) are also operative, resulting in one or two electrons being ejected from a neighbor, thus preventing the fragmentation of the initially ionized molecule. These relaxation processes are investigated theoretically for prototypical heterocycle-water complexes of imidazole, pyrrole, and pyridine. It is found that the hydrogen-bonding site of the water molecule critically influences the nature and energetics of the electronic states involved, opening or closing certain relaxation processes of the inner-valence ionized system. Our results indicate that the relaxation mechanisms of biologically relevant systems with inner-valence vacancies on their carbon atoms can strongly depend on the presence of the electron-density donating or accepting neighbor, either water or another biomolecule.
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Affiliation(s)
- Anna D Skitnevskaya
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
| | - Kirill Gokhberg
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander B Trofimov
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
- Favorsky's Institute of Chemistry, SB RAS, Favorsky Str. 1, 664033 Irkutsk, Russia
| | - Emma K Grigoricheva
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
| | - Alexander I Kuleff
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Lorenz S Cederbaum
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
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2
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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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3
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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4
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Fischer TLL, Bödecker MADI, Zehnacker A, Mata RA, Suhm MA. Setting up the HyDRA blind challenge for the microhydration of organic molecules. Phys Chem Chem Phys 2022; 24:11442-11454. [DOI: 10.1039/d2cp01119k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...
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5
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Martinelli A, Otero-Mato JM, Garaga MN, Elamin K, Rahman SMH, Zwanziger JW, Werner-Zwanziger U, Varela LM. A New Solid-State Proton Conductor: The Salt Hydrate Based on Imidazolium and 12-Tungstophosphate. J Am Chem Soc 2021; 143:13895-13907. [PMID: 34406757 PMCID: PMC8414554 DOI: 10.1021/jacs.1c06656] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
We report the structure
and charge transport properties of a novel
solid-state proton conductor obtained by acid–base chemistry
via proton transfer from 12-tungstophosphoric acid to imidazole. The
resulting material (henceforth named Imid3WP) is a solid
salt hydrate that, at room temperature, includes four water molecules
per structural unit. To our knowledge, this is the first attempt to
tune the properties of a heteropolyacid-based solid-state proton conductor
by means of a mixture of water and imidazole, interpolating between
water-based and ionic liquid-based proton conductors of high thermal
and electrochemical stability. The proton conductivity of Imid3WP·4H2O measured at truly anhydrous conditions
reads 0.8 × 10–6 S cm–1 at
322 K, which is higher than the conductivity reported for any other
related salt hydrate, despite the lower hydration. In the pseudoanhydrous
state, that is, for Imid3WP·2H2O, the proton
conductivity is still remarkable and, judging from the low activation
energy (Ea = 0.26 eV), attributed to structural
diffusion of protons. From complementary X-ray diffraction data, vibrational
spectroscopy, and solid-state NMR experiments, the local structure
of this salt hydrate was resolved, with imidazolium cations preferably
orienting flat on the surface of the tungstophosphate anions, thus
achieving a densely packed solid material, and water molecules of
hydration that establish extremely strong hydrogen bonds. Computational
results confirm these structural details and also evidence that the
path of lowest energy for the proton transfer involves primarily imidazole
and water molecules, while the proximate Keggin anion contributes
with reducing the energy barrier for this particular pathway.
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Affiliation(s)
- Anna Martinelli
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - José M Otero-Mato
- Grupo de Nanomateriais, Fotónica e Materia Branda, Departamento de Física de Partículas, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Mounesha N Garaga
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Khalid Elamin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | | | - Josef W Zwanziger
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | | | - Luis M Varela
- Grupo de Nanomateriais, Fotónica e Materia Branda, Departamento de Física de Partículas, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
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6
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D'mello VC, Wategaonkar S. Characterization and Photofragmentation Studies of the Benzimidazole Homodimer: Evidence for Excited-State Charge-Coupled Proton Transfer. J Phys Chem A 2021; 125:4967-4975. [PMID: 34101459 DOI: 10.1021/acs.jpca.1c01591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The spectroscopic characterization of the benzimidazole (BIM) homodimer was carried out in a molecular beam in the ground state as well as in the cationic state using the R2PI and RIDIR methods. Primarily, interest in the dimer was due to the observation of a proton-transferred BIM fragment at energies well below its thermodynamic threshold (i.e., barely above the ionization energy of the dimer where fragmentation was not expected). The detailed photofragmentation studies of the homodimer combined with spectroscopic observations and quantum chemical computations of the excited states established that the proton transfer from one subunit to the other occurs via conical intersections connecting the locally excited state, the charge-transfer state, and the ground state. In this study, we have also determined the N-H···N hydrogen bond dissociation energy in the ground state and in the cationic state to be 10.36 ± 0.14 and 27.55 ± 0.20 kcal mol-1, respectively. Incidentally, this happens to be the first such report on the dissociation energy of the N-H···N hydrogen bond.
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Affiliation(s)
- Viola Caroline D'mello
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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7
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Kamerin BS, Niman JW, Kresin VV. Electric deflection of imidazole dimers and trimers in helium nanodroplets: Dipole moments, structure, and fragmentation. J Chem Phys 2020; 153:081101. [DOI: 10.1063/5.0020844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Benjamin S. Kamerin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
| | - John W. Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
| | - Vitaly V. Kresin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
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8
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Gougoula E, Cole DJ, Walker NR. Bifunctional Hydrogen Bonding of Imidazole with Water Explored by Rotational Spectroscopy and DFT Calculations. J Phys Chem A 2020; 124:2649-2659. [PMID: 32141751 DOI: 10.1021/acs.jpca.0c00544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laser vaporization of imidazole in the presence of an argon buffer gas has allowed the generation and isolation of two isomers of an imidazole monohydrate complex, denoted herein as imid···H2O and H2O···imid, within a gas sample undergoing supersonic expansion. Imidazole and water are respectively proton-accepting and proton-donating in imid···H2O, but these roles are reversed in the H2O···imid complex. Both isomers have been characterized by chirped-pulse Fourier transform microwave spectroscopy between 7.0 and 18.5 GHz. The ground-state rotational spectra of four isotopologues of imid···H2O and three isotopologues of H2O···imid have been measured. All spectra have been assigned and fitted to determine rotational (A0, B0, C0), centrifugal distortion (DJ, DJK), and nuclear quadrupole coupling constants (χaa(N1), [χbb(N1) - χcc(N1)], χaa(N3), and [χbb(N3) - χcc(N3)]). Structural parameters (r0 and rs) have been accurately determined from measured rotational constants for each isomer. The imid···H2O complex contains a nonlinear hydrogen bond (∠(O-Hb···N3) = 172.1(26)° in the experimentally determined, r0 geometry) between the pyridinic nitrogen of imidazole and a hydrogen atom of H2O. The DFT calculations find that the H2O···imid complex also contains a nonlinear hydrogen bond between the oxygen atom of water and the hydrogen attached to the pyrrolic nitrogen of imidazole (∠(O···H1-N1) = 174.7°). Two states observed in the spectrum of H2O···imid, assigned as 0- and 0+ states, confirm that large amplitude motions occur on the time scale of the molecular rotation. Density functional theory has been performed to characterize these large amplitude motions.
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Affiliation(s)
- Eva Gougoula
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, U.K
| | - Daniel J Cole
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, U.K
| | - Nicholas R Walker
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, U.K
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9
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Niman JW, Kamerin BS, Kranabetter L, Merthe DJ, Suchan J, Slavíček P, Kresin VV. Direct detection of polar structure formation in helium nanodroplets by beam deflection measurements. Phys Chem Chem Phys 2019; 21:20764-20769. [PMID: 31513195 DOI: 10.1039/c9cp04322e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-range intermolecular forces are able to steer polar molecules submerged in superfluid helium nanodroplets into highly polar metastable configurations. We demonstrate that the presence of such special structures can be identified, in a direct and determinative way, by electrostatic deflection of the doped nanodroplet beam. The measurement also establishes the structures' electric dipole moments. In consequence, the introduced approach is complementary to spectroscopic studies of low-temperature molecular assembly reactions. It is enabled by the fact that within the cold superfluid matrix the molecular dipoles become nearly completely oriented by the applied electric field. As a result, the massive (tens of thousands of helium atoms) nanodroplets undergo significant deflections. The method is illustrated here by an application to dimers and trimers of dimethyl sulfoxide (DMSO) molecules. We interpret the experimental results with ab initio theory, mapping the potential energy surface of DMSO complexes and simulating their low temperature aggregation dynamics.
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Affiliation(s)
- John W Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
| | - Benjamin S Kamerin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
| | - Lorenz Kranabetter
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Daniel J Merthe
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
| | - Jiří Suchan
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic.
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic. and J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Vitaly V Kresin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
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10
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Forsting T, Zischang J, Suhm MA, Eckhoff M, Schröder B, Mata RA. Strained hydrogen bonding in imidazole trimer: a combined infrared, Raman, and theory study. Phys Chem Chem Phys 2019; 21:5989-5998. [DOI: 10.1039/c9cp00399a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is not how three imidazole molecules prefer to arrange, as a combined IR, Raman and computational analysis unambiguously shows.
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Affiliation(s)
- Thomas Forsting
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Julia Zischang
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Marco Eckhoff
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Benjamin Schröder
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Ricardo A. Mata
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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11
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Gutiérrez-Quintanilla A, Briant M, Mengesha E, Gaveau MA, Mestdagh JM, Soep B, Crépin C, Poisson L. A HElium NanoDroplet Isolation (HENDI) investigation of the weak hydrogen bonding in the propyne dimer (CH3CCH)2. Phys Chem Chem Phys 2018; 20:28658-28666. [DOI: 10.1039/c8cp04738c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A HElium Nanodroplet Isolation (HENDI) experiment was performed to explore the absorption spectra of the propyne monomer (CH3CCH), dimer and (CH3CCH)≥3 multimers in the vicinity of the CH stretch region ν1 of the monomer.
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Affiliation(s)
| | - M. Briant
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- CEA Saclay
| | - E. Mengesha
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- CEA Saclay
| | | | | | - B. Soep
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- CEA Saclay
| | - C. Crépin
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- UMR 8214
- CNRS
- F-91405 Orsay
- France
| | - L. Poisson
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- CEA Saclay
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12
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 56:15639-15643. [DOI: 10.1002/anie.201709437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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13
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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14
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Min A, Ahn A, Moon CJ, Lee JH, Seong YG, Kim SK, Choi MY. Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study. Phys Chem Chem Phys 2017; 19:4840-4848. [PMID: 28134364 DOI: 10.1039/c6cp06863d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H2O)1, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H2O)1 conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H2O)1 and AAP(CO)-(H2O)1 conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H2O)1, [syn- and anti-AAP(OH)-(H2O)1 and syn- and anti-AAP(CO)-(H2O)1], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H2O)1 conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H2O)1 conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H2O)1 conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H2O)1 have been found in this study.
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Affiliation(s)
- Ahreum Min
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ahreum Ahn
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Cheol Joo Moon
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ji Hoon Lee
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Yeon Guk Seong
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Myong Yong Choi
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
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15
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Mullaney JC, Zaleski DP, Tew DP, Walker NR, Legon AC. Geometry of an Isolated Dimer of Imidazole Characterised by Rotational Spectroscopy and Ab Initio Calculations. Chemphyschem 2016; 17:1154-8. [DOI: 10.1002/cphc.201501179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/07/2022]
Affiliation(s)
- John C. Mullaney
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
| | - Daniel P. Zaleski
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
- Argonne National Laboratory; Chemical Sciences & Engineering; 9700 S. Cass Ave., Bldg. 200 Lemont IL 60439 USA
| | - David P. Tew
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Nicholas R. Walker
- School of Chemistry, Bedson Building; Newcastle University; Newcastle upon Tyne, Tyne and Wear NE1 7RU UK
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16
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Pysanenko A, Habartová A, Svrčková P, Lengyel J, Poterya V, Roeselová M, Fedor J, Fárník M. Lack of Aggregation of Molecules on Ice Nanoparticles. J Phys Chem A 2015. [PMID: 26214577 DOI: 10.1021/acs.jpca.5b05368] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple molecules adsorbed on the surface of nanosized ice particles can either remain isolated or form aggregates, depending on their mobility. Such (non)aggregation may subsequently drive the outcome of chemical reactions that play an important role in atmospheric chemistry or astrochemistry. We present a molecular beam experiment in which the controlled number of guest molecules is deposited on the water and argon nanoparticles in a pickup chamber and their aggregation is studied mass spectrometrically. The studied molecules (HCl, CH3Cl, CH3CH2CH2Cl, C6H5Cl, CH4, and C6H6) form large aggregates on argon nanoparticles. On the other hand, no aggregation is observed on ice nanoparticles. Molecular simulations confirm the experimental results; they reveal a high degree of aggregation on the argon nanoparticles and show that the molecules remain mostly isolated on the water ice surface. This finding will influence the efficiency of ice grain-mediated synthesis (e.g., in outer space) and is also important for the cluster science community because it shows some limitations of pickup experiments on water clusters.
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17
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Zhang J, Chen L, Freund WM, Kong W. Effective doping of low energy ions into superfluid helium droplets. J Chem Phys 2015; 143:074201. [PMID: 26298127 PMCID: PMC4545055 DOI: 10.1063/1.4928689] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/05/2015] [Indexed: 11/14/2022] Open
Abstract
We report a facile method of doping cations from an electrospray ionization (ESI) source into superfluid helium droplets. By decelerating and stopping the ion pulse of reserpine and substance P from an ESI source in the path of the droplet beam, about 10(4) ion-doped droplets (one ion per droplet) can be recorded, corresponding to a pickup efficiency of nearly 1 out of 1000 ions. We attribute the success of this simple approach to the long residence time of the cations in the droplet beam. The resulting size of the doped droplets, on the order of 10(5)/droplet, is measured using deflection and retardation methods. Our method does not require an ion trap in the doping region, which significantly simplifies the experimental setup and procedure for future spectroscopic and diffraction studies.
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Affiliation(s)
- Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Lei Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - William M Freund
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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18
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Chen L, Zhang J, Freund WM, Kong W. Effect of kinetic energy on the doping efficiency of cesium cations into superfluid helium droplets. J Chem Phys 2015; 143:044310. [PMID: 26233132 PMCID: PMC4522010 DOI: 10.1063/1.4927471] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/15/2015] [Indexed: 11/14/2022] Open
Abstract
We present an experimental investigation of the effect of kinetic energy on the ion doping efficiency of superfluid helium droplets using cesium cations from a thermionic emission source. The kinetic energy of Cs(+) is controlled by the bias voltage of a collection grid collinearly arranged with the droplet beam. Efficient doping from ions with kinetic energies from 20 eV up to 480 V has been observed in different sized helium droplets. The relative ion doping efficiency is determined by both the kinetic energy of the ions and the average size of the droplet beam. At a fixed source temperature, the number of doped droplets increases with increasing grid voltage, while the relative ion doping efficiency decreases. This result implies that not all ions are captured upon encountering with a sufficiently large droplet, a deviation from the near unity doping efficiency for closed shell neutral molecules. We propose that this drop in ion doping efficiency with kinetic energy is related to the limited deceleration rate inside a helium droplet. When the source temperature changes from 14 K to 17 K, the relative ion doping efficiency decreases rapidly, perhaps due to the lack of viable sized droplets. The size distribution of the Cs(+)-doped droplet beam can be measured by deflection and by energy filtering. The observed doped droplet size is about 5 × 10(6) helium atoms when the source temperature is between 14 K and 17 K.
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Affiliation(s)
- Lei Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - William M Freund
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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19
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20
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Trachsel MA, Ottiger P, Frey HM, Pfaffen C, Bihlmeier A, Klopper W, Leutwyler S. Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene. J Phys Chem B 2015; 119:7778-90. [DOI: 10.1021/jp512766r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Maria A. Trachsel
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Angela Bihlmeier
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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21
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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22
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Bhattacherjee A, Wategaonkar S. Conformational preferences of monohydrated clusters of imidazole derivatives revisited. Phys Chem Chem Phys 2015; 17:20080-92. [DOI: 10.1039/c5cp02422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR-UV double resonance spectroscopy was used to identify the conformers of monohydrated benzimidazole andN-methylbenzimidazole in a supersonic jet. A new OH–N bound conformer relevant to histidine containing proteins was discovered. The long standing differences in the literature about the relative energies and abundance of the monohydrated imidazole derivatives have also been resolved.
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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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23
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Shenderovich IG, Lesnichin SB, Tu C, Silverman DN, Tolstoy PM, Denisov GS, Limbach HH. NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations. Chemistry 2014; 21:2915-29. [PMID: 25521423 DOI: 10.1002/chem.201404083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/12/2014] [Indexed: 12/24/2022]
Abstract
By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.
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Affiliation(s)
- Ilya G Shenderovich
- University of Regensburg, Universitätsstrasse 31, 93053 Regensburg (Germany).
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24
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Zhang J, He Y, Freund WM, Kong W. Electron Diffraction of Superfluid Helium Droplets. J Phys Chem Lett 2014; 5:1801-1805. [PMID: 24920997 PMCID: PMC4048102 DOI: 10.1021/jz5006829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Abstract
We present experimental results of electron diffraction of superfluid helium droplets and droplets doped with phthalocyanine gallium chloride and discuss the possibility of performing the same experiment with a laser aligned sample. The diffraction profile of pure droplets demonstrates dependence on the nozzle temperature, that is, on the average size of the droplets. Larger clusters demonstrate faster decay with increasing momentum transfer, whereas smaller clusters converge to isolated gas phase molecules at source temperatures of 18 K and higher. Electron diffraction of doped droplets shows similar modified molecular scattering intensity as that of the corresponding gas phase molecules. On the basis of fittings of the scattering profile, the number of remaining helium atoms of the doped droplets is estimated to be on the order of hundreds. This result offers guidance in assessing the possibility of electron diffraction from laser aligned molecules doped in superfluid helium droplets.
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Affiliation(s)
| | | | | | - Wei Kong
- E-mail: . Phone: 541-737-6714. Fax: 541-737-2062
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25
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Kumar S, Mukherjee A, Das A. Structure of Indole···Imidazole Heterodimer in a Supersonic Jet: A Gas Phase Study on the Interaction between the Aromatic Side Chains of Tryptophan and Histidine Residues in Proteins. J Phys Chem A 2012; 116:11573-80. [DOI: 10.1021/jp309167a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Ankita Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
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26
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Altnöder J, Lee JJ, Otto KE, Suhm MA. Molecular recognition in glycolaldehyde, the simplest sugar: two isolated hydrogen bonds win over one cooperative pair. ChemistryOpen 2012; 1:269-75. [PMID: 24551516 PMCID: PMC3922484 DOI: 10.1002/open.201200031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Indexed: 11/19/2022] Open
Abstract
Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C2-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase.
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Affiliation(s)
- Jonas Altnöder
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Juhyon J Lee
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Katharina E Otto
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
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27
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Zischang J, Lee JJ, Suhm MA. Communication: Where does the first water molecule go in imidazole? J Chem Phys 2012; 135:061102. [PMID: 21842918 DOI: 10.1063/1.3624841] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Supersonic jet FTIR spectroscopy supplemented by (18)O substitution shows unambiguously that water prefers to act as an O-H···N hydrogen bond donor towards imidazole, instead of acting as a N-H···O acceptor. Previous matrix isolation, helium droplet, and aromatic substitution experiments had remained ambiguous, as are standard quantum chemical calculations. The finding is supported by a study of the analogous methanol complexes and by higher level quantum chemical calculations.
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Affiliation(s)
- Julia Zischang
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
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28
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Ahn AR, Lee SJ, Lee SK, Min AR, Kim YS, Jung HJ, Hong SM, Lee JH, Choi MY, Miller RE. Imidazole Trimer-Water Complexes in Superfluid Helium Nanodroplets: Water Stretching Modes. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.4.1407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Lee SK, Lee SJ, Ahn AR, Kim YS, Min AR, Choi MY, Miller RE. Infrared Spectroscopy of Imidazole Trimer in Helium Nanodroplets: Free NH Stretch Mode. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.3.885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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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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31
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Min AR, Lee SJ, Choi MY, Miller RE. Electric Field Dependence Experiments and ab Initio Calculations of Three Cytosine Tautomers in Superfluid Helium Nanodroplets. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.12.3039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Crespo-Otero R, Bravo-Rodríguez K, Suardíaz R, Montero LA, García de la Vega JM. Theoretical Study of Imidazole···NO Complexes. J Phys Chem A 2009; 113:14595-605. [DOI: 10.1021/jp9042733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rachel Crespo-Otero
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400 Havana, Cuba, and Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Kenny Bravo-Rodríguez
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400 Havana, Cuba, and Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Reynier Suardíaz
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400 Havana, Cuba, and Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Luis A. Montero
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400 Havana, Cuba, and Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José M. García de la Vega
- Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de la Habana, 10400 Havana, Cuba, and Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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33
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Choi MY, Miller RE. Imidazole dimer and its water complexes formed in superfluid helium nanodroplets: Infrared spectroscopic studies of free OH vibrational stretching modes. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Poterya V, Profant V, Fárník M, Šištík L, Slavíček P, Buck U. Photoinduced Processes in Hydrogen Bonded System: Photodissociation of Imidazole Clusters. J Phys Chem A 2009; 113:14583-90. [DOI: 10.1021/jp904145q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - Udo Buck
- Max-Planck Institut für Dynamik und Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany
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35
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Lee SJ, Choi MY, Miller RE. Vibrational spectroscopy of xanthine in superfluid helium nanodroplets. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Kong W, Pei L, Zhang J. Linear dichroism spectroscopy of gas phase biological molecules embedded in superfluid helium droplets. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350802573678] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Polarization spectroscopy of aluminum phthalocyanine hydroxide embedded in superfluid helium droplets. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Choi MY, Dong F, Han SW, Miller RE. Nonplanarity of Adenine: Vibrational Transition Moment Angle Studies in Helium Nanodroplets. J Phys Chem A 2008; 112:7185-90. [DOI: 10.1021/jp8012688] [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)
- Myong Yong Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Feng Dong
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Sang Woo Han
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Roger E. Miller
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea, and Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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39
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Pei L, Zhang J, Kong W. Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets. J Chem Phys 2008; 127:174308. [PMID: 17994819 DOI: 10.1063/1.2803186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.
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Affiliation(s)
- Linsen Pei
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
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40
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Chang HC, Jiang JC, Su JC, Chang CY, Lin SH. Evidence of Rotational Isomerism in 1-Butyl-3-methylimidazolium Halides: A Combined High-Pressure Infrared and Raman Spectroscopic Study. J Phys Chem A 2007; 111:9201-6. [PMID: 17628046 DOI: 10.1021/jp071055r] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-pressure methods were applied to investigate the rotational isomerism and the hydrogen-bonding structures of 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Conformation changes of the butyl chain were observed above a pressure of 0.3 GPa. Under ambient pressure, Raman spectra indicate that the more thermodynamically stable butyl structure of the cations is the gauche-anti (GA) and all-anti forms for 1-butyl-3-methylimidazolium bromide and 1-butyl-3-methylimidazolium chloride, respectively. Nevertheless, the high-pressure phases arise from the perturbed GA conformer. The imidazolium C-H bands of 1-butyl-3-methylimidazolium chloride display anomalous nonmonotonic pressure-induced frequency shifts. This discontinuity in the frequency shift is related to the modification of the imidazolium C-H---Cl- contacts upon compression. The alkyl C-H---Cl- interactions are suggested to be a compensatory mechanism to provide additional stability. Density-functional-theory-calculated results also support the high-pressure results that the methyl and butyl C-H groups are suitable proton donor sites for the GA conformer.
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Affiliation(s)
- Hai-Chou Chang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974, Taiwan.
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Anharmonic vibrational spectroscopy calculations with electronic structure potentials: comparison of MP2 and DFT for organic molecules. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0299-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Choi MY, Miller RE. Infrared Laser Spectroscopy of Uracil and Thymine in Helium Nanodroplets: Vibrational Transition Moment Angle Study. J Phys Chem A 2007; 111:2475-9. [PMID: 17388352 DOI: 10.1021/jp0674625] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational spectra are reported in the N-H stretching region for uracil and thymine monomers in helium nanodroplets. Each monomer shows only a single isomer, the global minimum, in agreement with previous experimental and theoretical studies. The assignment of the infrared vibrational bands in the spectra is aided by the measurement of the corresponding vibrational transition moment angles (VTMAs) and ab initio frequency calculations. The ambiguity in the VTMA assignment of the N3H band for the uracil monomer is explained by the presence of dimer bands, which are overlapped with the monomer band.
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Affiliation(s)
- Myong Yong Choi
- Department of Chemistry, The University of North Carolina at Chapel Hill, North Carolina 27599, USA.
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