1
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Si P, Jayanth A, Andreussi O. Soft-sphere continuum solvation models for nonaqueous solvents. J Comput Chem 2024; 45:719-737. [PMID: 38112395 DOI: 10.1002/jcc.27254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023]
Abstract
Solvation effects profoundly influence the characteristics and behavior of chemical systems in liquid solutions. The interaction between solute and solvent molecules intricately impacts solubility, reactivity, stability, and various chemical processes. Continuum solvation models gained prominence in quantum chemistry by implicitly capturing these interactions and enabling efficient investigations of diverse chemical systems in solution. In comparison, continuum solvation models in condensed matter simulation are very recent. Among these, the self-consistent continuum solvation (SCCS) and the soft-sphere continuum solvation models (SSCS) have been among the first to be successfully parameterized and extended to model periodic systems in aqueous solutions and electrolytes. As most continuum approaches, these models depend on a number of parameters that are linked to experimental or theoretical properties of the solvent, or that can be tuned based on reference data. Here, we present a systematic parameterization of the SSCS model for over 100 nonaqueous solvents. We validate the model's efficacy across diverse solvent environments by leveraging experimental solvation-free energies and partition coefficients from comprehensive databases. The average root means square error over all the solvents was calculated as 0.85 kcal/mol which is below the chemical accuracy (1 kcal/mol). Similarly to what has been reported by Hille et al. (J. Chem. Phys. 2019, 150, 041710.) for the SCCS model, a single-parameter model accurately reproduces experimental solvation energies, showcasing the transferability and predictive power of these continuum approaches. Our findings underscore the potential for a unified approach to predict solvation properties, paving the way for enhanced computational studies across various chemical environments.
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Affiliation(s)
- Pradip Si
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - Ajay Jayanth
- Texas Academy of Math and Science, University of North Texas, Denton, Texas, USA
| | - Oliviero Andreussi
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho, USA
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2
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Burevschi E, Chrayteh M, Murugachandran SI, Loru D, Dréan P, Sanz ME. Water Arrangements upon Interaction with a Rigid Solute: Multiconfigurational Fenchone-(H 2O) 4-7 Hydrates. J Am Chem Soc 2024; 146:10925-10933. [PMID: 38588470 PMCID: PMC11027134 DOI: 10.1021/jacs.4c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Insight into the arrangements of water molecules around solutes is important to understand how solvation proceeds and to build reliable models to describe water-solute interactions. We report the stepwise solvation of fenchone, a biogenic ketone, with 4-7 water molecules. Multiple hydrates were observed using broadband rotational spectroscopy, and the configurations of four fenchone-(H2O)4, three fenchone-(H2O)5, two fenchone-(H2O)6, and one fenchone-(H2O)7 complexes were characterized from the analysis of their rotational spectra in combination with quantum-chemical calculations. Interactions with fenchone deeply perturb water configurations compared with the pure water tetramer and pentamer. In two fenchone-(H2O)4 complexes, the water tetramer adopts completely new arrangements, and in fenchone-(H2O)5, the water pentamer is no longer close to being planar. The water hexamer interacts with fenchone as the least abundant book isomer, while the water heptamer adopts a distorted prism structure, which forms a water cube when including the fenchone oxygen in the hydrogen bonding network. Differences in hydrogen bonding networks compared with those of pure water clusters show the influence of fenchone's topology. Specifically, all observed hydrates except one show two water molecules binding to fenchone through each oxygen lone pair. The observation of several water arrangements for fenchone-(H2O)4-7 complexes highlights water adaptability and provides insight into the solvation process.
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Affiliation(s)
| | - Mhamad Chrayteh
- PhLAM—Physique
des Lasers, Atomes et Molécules, University of Lille, CNRS, UMR 8523, F-59000 Lille, France
| | | | - Donatella Loru
- Department
of Chemistry, King’s College London, London SE1 1DB, U.K.
| | - Pascal Dréan
- PhLAM—Physique
des Lasers, Atomes et Molécules, University of Lille, CNRS, UMR 8523, F-59000 Lille, France
| | - M. Eugenia Sanz
- Department
of Chemistry, King’s College London, London SE1 1DB, U.K.
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3
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Miyazaki M, Ono M, Otsuka R, Dopfer O, Fujii M. Electronic and vibrational spectroscopies of aromatic clusters with He in a supersonic jet: The case of neutral and cationic phenol-Hen (n = 1 and 2). J Chem Phys 2023; 159:134303. [PMID: 37787127 DOI: 10.1063/5.0169716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023] Open
Abstract
Van der Waals clusters composed of He and aromatic molecules provide fundamental information about intermolecular interactions in weakly bound systems. In this study, phenol-helium clusters (PhOH-Hen with n ≤ 2) are characterized for the first time by UV and IR spectroscopies. The S1 ← S0 origin and ionization energy both show small but additive shifts, suggesting π-bound structures of these clusters, a conclusion supported by rotational contour analyses of the S1 origin bands. The OH stretching vibrations of the PhOH moiety in the clusters match with those of bare PhOH in both the S0 and D0 states, illustrating the negligible perturbation of the He atoms on the molecular vibration. Matrix shifts induced by He attachment are discussed based on the observed band positions with the help of complementary quantum chemical calculations. For comparison, the UV and ionization spectra of PhOH-Ne are reported as well.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Megumi Ono
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Remina Otsuka
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
- International Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- International Research Frontiers Initiative (IRFI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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4
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Roy TK, Liu T, Qian Y, Sojdak CA, Kozlowski MC, Lester MI. A five-carbon unsaturated Criegee intermediate: synthesis, spectroscopic identification, and theoretical study of 3-penten-2-one oxide. Chem Sci 2023; 14:10471-10477. [PMID: 37800006 PMCID: PMC10548502 DOI: 10.1039/d3sc03993e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/03/2023] [Indexed: 10/07/2023] Open
Abstract
Biogenic alkenes, such as isoprene and α-pinene, are the predominant source of volatile organic compounds (VOCs) emitted into the atmosphere. Atmospheric processing of alkenes via reaction with ozone leads to formation of zwitterionic reactive intermediates with a carbonyl oxide functional group, known as Criegee intermediates (CIs). CIs are known to exhibit a strong absorption (π* ← π) in the near ultraviolet and visible (UV-vis) region due to the carbonyl oxide moiety. This study focuses on the laboratory identification of a five-carbon CI with an unsaturated substituent, 3-penten-2-one oxide, which can be produced upon atmospheric ozonolysis of substituted isoprenes. 3-Penten-2-one oxide is generated in the laboratory by photolysis of a newly synthesized precursor, (Z)-2,4-diiodopent-2-ene, in the presence of oxygen. The electronic spectrum of 3-penten-2-one oxide was recorded by UV-vis induced depletion of the VUV photoionization signal on the parent m/z 100 mass channel using a time-of-flight mass spectrometer. The resultant electronic spectrum is broad and unstructured with peak absorption at ca. 375 nm. To complement the experimental findings, electronic structure calculations are performed at the CASPT2(12,10)/aug-cc-pVDZ level of theory. The experimental spectrum shows good agreement with the calculated electronic spectrum and vertical excitation energy obtained for the lowest energy conformer of 3-penten-2-one oxide. In addition, OH radical products resulting from unimolecular decay of energized 3-penten-2-oxide CIs are detected by UV laser-induced fluorescence. Finally, the experimental electronic spectrum is compared with that of a four-carbon, isoprene-derived CI, methyl vinyl ketone oxide, to understand the effects of an additional methyl group on the associated electronic properties.
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Affiliation(s)
- Tarun Kumar Roy
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Tianlin Liu
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Yujie Qian
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Christopher A Sojdak
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Marisa C Kozlowski
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
| | - Marsha I Lester
- Department of Chemistry, University of Pennsylvania Philadelphia PA 19104-6323 USA
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5
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Wallbridge SP, Archer S, Elsegood MRJ, Wagner JL, Christie JK, Dann SE. An investigation into the adsorption mechanism of n-butanol by ZIF-8: a combined experimental and ab initio molecular dynamics approach. Phys Chem Chem Phys 2023; 25:19911-19922. [PMID: 37458457 DOI: 10.1039/d3cp02493h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The zeolitic imidazolate framework, ZIF-8, has been shown by experimental methods to have a maximum saturation adsorption capacity of 0.36 g g-1 for n-butanol from aqueous solution, equivalent to a loading of 14 butanol molecules per unit cell or 7 molecules per sodalite β-cage. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) shows the presence of hydrogen bonding between adsorbed butanol molecules within the cage; the presence of three different O-H stretching modes indicates the formation of butanol clusters of varying size. Ab initio molecular dynamics simulations show the formation of intermolecular hydrogen bonding between the butanol molecules, with an average hydrogen-bond coordination number of 0.9 after 15 ps simulation time. The simulations also uniquely demonstrate the presence of weaker interactions between the alcohol O-H group and the π-orbital of the imidazole ring on the internal surface of the cage during early stages of adsorption. The calculated adsorption energy per butanol molecule is -33.7 kJ mol-1, confirming that the butanol is only weakly bound, driven primarily by the hydrogen bonding. Solid-state MAS NMR spectra suggest that the adsorbed butanol molecules possess a reasonable degree of mobility in their adsorbed state, rather than being rigidly held in specific sites. 2D 13C-1H heteronuclear correlation (HETCOR) experiments show interactions between the butanol aliphatic chain and the ZIF-8 framework experimentally, suggesting that O-H interactions with the π-orbital are only short lived. The insight gained from these results will allow the design of more efficient ways of recovering and isolating n-butanol, an important biofuel, from low-concentration solutions.
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Affiliation(s)
| | - Stuart Archer
- Department of Chemistry, Loughborough University, Loughborough, UK.
| | | | - Jonathan L Wagner
- Department of Chemical Engineering, Loughborough University, Loughborough, UK
| | | | - Sandra E Dann
- Department of Chemistry, Loughborough University, Loughborough, UK.
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6
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Feng JY, Lee YP, Hsu PJ, Kuo JL, Ebata T. Structures of (Pyrazine) 2 and (Pyrazine)(Benzene) Dimers Investigated with Infrared-Vacuum Ultraviolet Spectroscopy and Quantum-Chemical Calculations: Competition among π-π, CH···π, and CH···N Interactions. J Phys Chem A 2023; 127:4291-4301. [PMID: 37145887 DOI: 10.1021/acs.jpca.3c01767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The structures of a pyrazine dimer (pyrazine)2 and (pyrazine)(benzene) hetero-dimer cooled in a supersonic beam were investigated by the measurement of the infrared spectra in the C-H stretching region with infrared-vacuum ultraviolet (IR-VUV) spectroscopy and quantum-chemical calculations. The stabilization energy calculation at the CCSD(T)/aug-cc-pVTZ level of theory predicted three isomers for (pyrazine)2 and three for (pyrazine)(benzene) with energy within 6 kJ/mol. Among them, the cross-displaced π-π stacked structure is the most stable in both dimers. In the observed IR spectra, both dimers exhibited two intense bands near 3065 cm-1, with intervals of 8 cm-1 in (pyrazine)2 and 11 cm-1 in (pyrazine)(benzene), while only one band appeared in the monomer. For (pyrazine)(benzene), we also measured the IR spectrum of (pyrazine)(benzene-d6), where the interval of the two bands was unchanged. The analysis of the observed IR spectra with anharmonic calculations suggested the coexistence of three isomers of (pyrazine)2 and (pyrazine)(benzene) in a supersonic jet. For (pyrazine)2, the two isomers which were previously assigned to the H-bonded planar and the π-π stacked structures respectively were reassigned to the cross-displaced π-π stacked and T-shaped structures, respectively. In addition, the quantum chemical calculation and IR-VUV spectral measurement suggested the coexistence of the H-bonded planar isomer in the jet. For (pyrazine)(benzene), the IR spectrum of the (pyrazine) site showed a similar spectral pattern to that of (pyrazine)2, especially the split at ∼3065 cm-1. However, the anharmonic analysis suggested that they are assigned to the different vibrational motions of (pyrazine). The anharmonic vibrational analysis is essential to associate the observed IR spectra with the correct structures of the dimer.
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Affiliation(s)
- Jun-Ying Feng
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Emergent Functional Matter Sciences, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617 Taiwan
| | - Takayuki Ebata
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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7
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Bartalucci E, Malär AA, Mehnert A, Kleine Büning JB, Günzel L, Icker M, Börner M, Wiebeler C, Meier BH, Grimme S, Kersting B, Wiegand T. Probing a Hydrogen-π Interaction Involving a Trapped Water Molecule in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202217725. [PMID: 36630178 DOI: 10.1002/anie.202217725] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/12/2023]
Abstract
The detection and characterization of trapped water molecules in chemical entities and biomacromolecules remains a challenging task for solid materials. We herein present proton-detected solid-state Nuclear Magnetic Resonance (NMR) experiments at 100 kHz magic-angle spinning and at high static magnetic-field strengths (28.2 T) enabling the detection of a single water molecule fixed in the calix[4]arene cavity of a lanthanide complex by a combination of three types of non-covalent interactions. The water proton resonances are detected at a chemical-shift value close to zero ppm, which we further confirm by quantum-chemical calculations. Density Functional Theory calculations pinpoint to the sensitivity of the proton chemical-shift value for hydrogen-π interactions. Our study highlights how proton-detected solid-state NMR is turning into the method-of-choice in probing weak non-covalent interactions driving a whole branch of molecular-recognition events in chemistry and biology.
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Affiliation(s)
- Ettore Bartalucci
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | | | - Anne Mehnert
- Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Lennart Günzel
- Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Maik Icker
- Institute of Organic Chemistry, Leipzig University Linnéstraße 3, 04103, Leipzig, Germany
| | - Martin Börner
- Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Christian Wiebeler
- Institute of Analytic Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany.,Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 2, 04103, Leipzig, Germany
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Berthold Kersting
- Institute of Inorganic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Thomas Wiegand
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany.,previous address: Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
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8
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Arildii D, Matsumoto Y, Dopfer O. Microhydration of the Pyrrole Cation (Py +) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py +(H 2O) 2. J Phys Chem A 2023; 127:2523-2535. [PMID: 36898005 DOI: 10.1021/acs.jpca.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py+) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py+(H2O)2 and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py+(H2O)2 is formed by stepwise hydration of the acidic NH group of Py+ by a hydrogen-bonded (H2O)2 chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py+H2O and (H2O)2, respectively. The linear chain structure of the Py+(H2O)2 cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H2O)2 global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py+ and the π-bonded OH hydrogen of (H2O)2, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.
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Affiliation(s)
- Dashjargal Arildii
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
- International Research Frontiers Initiative, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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9
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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10
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Ito Y, Kominato M, Nakashima Y, Ohshimo K, Misaizu F. Fragment imaging in the infrared photodissociation of the Ar-tagged protonated water clusters H 3O +-Ar and H +(H 2O) 2-Ar. Phys Chem Chem Phys 2023; 25:9404-9412. [PMID: 36928842 DOI: 10.1039/d3cp00469d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Infrared photodissociation of protonated water clusters with an Ar atom, namely H3O+-Ar and H+(H2O)2-Ar, was investigated by an imaging technique for mass-selected ions, to reveal the intra- and intermolecular vibrational dynamics. The presented system has the advantage of achieving fragment ion images with the cluster size- and mode-selective photoexcitation of each OH stretching vibration. Translational energy distributions of photofragments were obtained from the images upon the excitation of the bound (νb) and free (νf) OH stretching vibrations. The energy fractions in the translational motion were compared between νbI and νfI in H3O+-Ar or between νbII and νfII in H+(H2O)2-Ar, where the labels "I" and "II" represent H3O+-Ar and H+(H2O)2-Ar, respectively. In H3O+-Ar, the νfI excitation exhibited a smaller translational energy than νbI. This result can be explained by the higher vibrational energy of νfI, which enabled it to produce bending (ν4) excited H3O+ fragments that should be favored according to the energy-gap model. In contrast to H3O+-Ar, the νbII excitation of an Ar-tagged H2O subunit and the νfII excitation of an untagged H2O subunit resulted in very similar translational energy distributions in H+(H2O)2-Ar. The similar energy fractions independent of the excited H2O subunits suggested that the νbII and νfII excited states relaxed into a common intermediate state, in which the vibrational energy was delocalized within the H2O-H+-H2O moiety. However, the translational energy distributions for H+(H2O)2-Ar did not agree with a statistical dissociation model, which implied another aspect of the process, that is, Ar dissociation via incomplete energy randomization in the whole H+(H2O)2-Ar cluster.
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Affiliation(s)
- Yuri Ito
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
| | - Mizuhiro Kominato
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
| | - Yuji Nakashima
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
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11
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Akman F, Demirpolat A, Kazachenko AS, Kazachenko AS, Issaoui N, Al-Dossary O. Molecular Structure, Electronic Properties, Reactivity (ELF, LOL, and Fukui), and NCI-RDG Studies of the Binary Mixture of Water and Essential Oil of Phlomis bruguieri. Molecules 2023; 28:molecules28062684. [PMID: 36985656 PMCID: PMC10056484 DOI: 10.3390/molecules28062684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil–water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6–31 G (d, p). Molecular structures, HOMO–LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described.
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Affiliation(s)
- Feride Akman
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
- Correspondence: (F.A.); or (A.S.K.)
| | - Azize Demirpolat
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
| | - Aleksandr S. Kazachenko
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Pr. Svobodny 79, 660041 Krasnoyarsk, Russia
- Siberian Branch, FRC “Krasnoyarsk Scientific Center”, Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, Akademgorodok 50, Bld. 24, 660036 Krasnoyarsk, Russia
- Department of Biological Chemistry with Courses in Medical, Pharmaceutical and Toxicological Chemistry, Krasnoyarsk State Medical University, St. Partizan Zheleznyak, Bld. 1, 660022 Krasnoyarsk, Russia
- Correspondence: (F.A.); or (A.S.K.)
| | - Anna S. Kazachenko
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Pr. Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Noureddine Issaoui
- Laboratory of Quantum and Statistical Physics, LR18ES18, Faculty of Sciences, University of Monastir, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Departement of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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12
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Asiamah M, Raston PL. Laser Spectroscopy of Helium Solvated Clusters of Methanol and Methanol-Water in the Symmetric Methyl Stretching Band. J Phys Chem A 2023; 127:946-955. [PMID: 36668688 DOI: 10.1021/acs.jpca.2c08327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mid-infrared spectra of methanol and methanol-water clusters have been investigated in the symmetric CD3 stretching band of CD3OH and CD3OD. We find that the position of this band provides a useful signature of the general type of hydrogen-bonded cluster it is associated with. Our results are consistent with those previously reported in the OH stretching region (Sulaiman, M. I.; Yang, S.; Ellis, A. M. J. Phys. Chem. A 2017, 121, 771-776) in that methanol clusters from the trimer to the pentamer are cyclic and that mixed clusters with one water molecule (and at least two methanol molecules) are also cyclic. We additionally provide evidence that the methanol trimer adopts a chair-like structure (as opposed to bowl-like), that mixed clusters with a larger number of water molecules are also cyclic, and that branched methanol clusters contribute to the depletion signal in larger methanol clusters. We performed double-hybrid DFT calculations which support these interpretations.
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Affiliation(s)
- Maameyaa Asiamah
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Paul L Raston
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.,Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
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13
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Das S, Chakraborty A. Computational investigation of the conformer selective complexes of 1,2,3,4-tetrahydroisoquinoline: Ammonia (THIQ: NH3) in S0. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Das S, Chakraborty A. Non-covalent interactions in the monohydrated complexes of 1,2,3,4-tetrahydroisoquinoline. J Mol Model 2023; 29:37. [PMID: 36629924 DOI: 10.1007/s00894-022-05438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The eleven monohydrates of 1, 2, 3, 4-tetrahydroisoquinoline (THIQ) are analyzed through natural bond orbital (NBO) analysis and QTAIM methods employing M06-2X functional in DFT and MP2 methods. Here, the role of OH bonds as an acceptor and donor is critically analyzed. The role of lone pairs of O is critically monitored in two of the complexes, where N-H···O hydrogen bonds are present. The relative contributions of rehybridisation and hyperconjugation are compared in detail. Popelier criteria are satisfied in all the complexes barring a few exceptions involving weak hydrogen bonds. At the bond critical points (BCP), four monohydrates show higher values of electron density (ρC) and negative values of total electron energy density (HC), while Laplacian [Formula: see text] remains positive. These complexes satisfy the criteria of partial covalency. All these are O-H⋅⋅⋅N-type bonds. Remaining h-bonds are weaker in nature. These are also confirmed by the smaller values of ρC at the respective BCP. The variation of potential energy density (VC) among the complexes seems to be the most important factor in determining the nature of non-covalent interactions.
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Affiliation(s)
- Santu Das
- Department of Physics, Government General Degree College, Hooghly, Singur, 712409, India
- Department of Physics, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India
| | - Abhijit Chakraborty
- Department of Physics, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India.
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15
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Li H. The solvation of SOH group in hydrated HSO 4−(H 2O) n clusters. JOURNAL OF CHEMICAL RESEARCH 2023. [DOI: 10.1177/17475198231153994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The S=O stretching and SOH bending peaks in the vibrational spectra of HSO4−(H2O) n, with n up to 6, are analyzed by both harmonic analysis and ab initio molecular dynamics simulation. The SOH bending mode is found to be much more sensitive to the extent of hydration and to the fluctuation of hydrogen bonds than the S=O stretching mode. The SOH donor hydrogen bond is gradually stabilized by n = 4, and further shortened up to n = 6, which is the key factor to understand the trend of evolution observed in the infrared multiple photon dissociation spectra.
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Affiliation(s)
- Huiyan Li
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, China
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16
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Panwaria P, Juanes M, Mishra KK, Saragi R, Borish K, Usabiaga I, Camiruaga A, Fernández JA, Lesarri A, Das A. Microhydration of Phenyl Formate: Gas-Phase Laser Spectroscopy, Microwave Spectroscopy, and Quantum Chemistry Calculations. Chemphyschem 2022; 23:e202200330. [PMID: 35984348 DOI: 10.1002/cphc.202200330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/17/2022] [Indexed: 01/04/2023]
Abstract
Herein, we have investigated the structure of phenyl formate⋅⋅⋅water (PhOF⋅⋅⋅H2 O) dimer and various non-covalent interactions present there using gas-phase laser spectroscopy and microwave spectroscopy combined with quantum chemistry calculations. Two conformers of PhOF⋅⋅⋅H2 O (C1 and T1), built on the two cis/trans conformers of the bare molecule, have been observed in the experiment. In cis-PhOF, there is an nCO → π A r * ${{{\rm \pi }}_{{\rm A}{\rm r}}^{{\rm {^\ast}}}}$ interaction between the lone-pair orbital of the carbonyl oxygen atom and the π* orbital of the phenyl ring, which persists in the monohydrated C1 conformer of PhOF⋅⋅⋅H2 O according to the NBO and NCI analyses. On the other hand, this interaction is absent in the trans-PhOF conformer as the C=O group is away from the phenyl ring. The C1 conformer is primarily stabilized by an interplay between O-H⋅⋅⋅O=C hydrogen bond and O-H⋅⋅⋅π interactions, while the stability of the T1 conformer is primarily governed by the O-H⋅⋅⋅O=C hydrogen bond. The most important finding of the present work is that the conformational preference of the PhOF monomer is retained in its monohydrated complex.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.,Present address: Department of Chemistry, University of Kentucky, Lexington, Kentucky, 40503, USA
| | - Rizalina Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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17
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Onvlee J, Trippel S, Küpper J. Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water. Nat Commun 2022; 13:7462. [PMID: 36460654 PMCID: PMC9718776 DOI: 10.1038/s41467-022-33901-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/04/2022] [Indexed: 12/05/2022] Open
Abstract
Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible - paving the way for the complete chemical-reactivity experiment.
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Affiliation(s)
- Jolijn Onvlee
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany ,grid.5590.90000000122931605Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Sebastian Trippel
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jochen Küpper
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Baweja S, Panchagnula S, Sanz ME, Evangelisti L, Pérez C, West C, Pate BH. Competition between In-Plane vs Above-Plane Configurations of Water with Aromatic Molecules: Non-Covalent Interactions in 1,4-Naphthoquinone-(H 2O) 1-3 Complexes. J Phys Chem Lett 2022; 13:9510-9516. [PMID: 36200782 PMCID: PMC9575146 DOI: 10.1021/acs.jpclett.2c02618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Non-covalent interactions between aromatic molecules and water are fundamental in many chemical and biological processes, and their accurate description is essential to understand molecular relative configurations. Here we present the rotational spectroscopy study of the water complexes of the polycyclic aromatic hydrocarbon 1,4-naphthoquinone (1,4-NQ). In 1,4-NQ-(H2O)1,2, water molecules bind through O-H···O and C-H···O hydrogen bonds and are located on the plane of 1,4-NQ. For 1,4-NQ-(H2O)3, in-plane and above-plane water configurations are observed exhibiting O-H···O, C-H···O, and lone pair···π-hole interactions. The observation of different water arrangements for 1,4-NQ-(H2O)3 allows benchmarking theoretical methods and shows that they have great difficulty in predicting energy orderings due to the strong competition of C-H···O binding with π and π-hole interactions. This study provides important insight into water interactions with aromatic systems and the challenges in their modeling.
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Affiliation(s)
- Shefali Baweja
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Sanjana Panchagnula
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - M. Eugenia Sanz
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Luca Evangelisti
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
| | - Cristóbal Pérez
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
| | - Channing West
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
| | - Brooks H. Pate
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
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19
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Watanabe T, Ohashi K. Similarity and dissimilarity between water and methanol in solvent effects on the spectroscopic properties of aniline: Molecular dynamics and time-dependent DFT studies. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Wang C, Fu L, Yang S, Zheng H, Wang T, Gao J, Su M, Yang J, Wu G, Zhang W, Zhang Z, Li G, Zhang DH, Jiang L, Yang X. Infrared Spectroscopy of Stepwise Hydration Motifs of Sulfur Dioxide. J Phys Chem Lett 2022; 13:5654-5659. [PMID: 35708351 DOI: 10.1021/acs.jpclett.2c01472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Experimental characterization of microscopic events and behaviors of SO2-H2O interactions is crucial to understanding SO2 atmospheric chemistry but has been proven to be very challenging due to the difficulty in size selection. Here, size-dependent development of SO2 hydrate structure and cluster growth in the SO2(H2O)n (n = 1-16) complexes was probed by infrared spectroscopy based on threshold photoionization using a tunable vacuum ultraviolet free electron laser. Spectral changes with cluster size demonstrate that the sandwich structure initially formed at n = 1 develops into cycle structures with the sulfur and oxygen atoms in a two-dimensional plane (n = 2 and 3) and then into three-dimensional cage structures (n ≥ 4). SO2 is favorably bound to the surface of larger water clusters. These stepwise features of SO2 hydration on various sized water clusters contribute to understanding the reactive sites and electrophilicity of SO2 on cloud droplets, which may have important atmospheric implications for studying the SO2-containing aerosol systems.
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Affiliation(s)
- Chong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Liangfei Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huijun Zheng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Tiantong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jiao Gao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingzhi Su
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jiayue Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weiqing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhaojun Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Gang Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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21
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Fischer JL, Blodgett KN, Harrilal CP, Walsh PS, Davis ZS, Choi S, Choi SH, Zwier TS. Conformer-Specific Spectroscopy and IR-Induced Isomerization of a Model γ-Peptide: Ac-γ 4-Phe-NHMe. J Phys Chem A 2022; 126:1837-1847. [PMID: 35275624 DOI: 10.1021/acs.jpca.2c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-conformation IR and UV spectroscopy of the prototypical capped γ-peptide Ac-γ4-Phe-NHMe (γ4F) was carried out under jet-cooled conditions in the gas phase in order to understand its innate conformational preferences in the absence of a solvent. We obtained conformer-specific IR and UV spectra and compared the results with calculations to make assignments and explore the differences between the γ2- and γ4-substituted molecules. We found four conformers of γ4F in our experiment. Three conformers form nine-membered hydrogen-bonded rings (C9) enclosed by an NH···O═C H-bond but differing in their phenyl ring positions (a, g+, and g-). The fourth conformer forms a strained seven-membered hydrogen-bonded ring in which the amide groups lie in a nominally anti-parallel arrangement stacked on top of one another (labeled S7). This conformer is a close analogue of the amide-stacked conformer (S) found previously in γ2F, in which the Phe side chain is substituted at the γ2 position, Ac-γ2-Phe-NHMe (J. Am. Chem. Soc. 2009, 131, 14243-14245). IR population transfer spectroscopy was used to determine the fractional abundances of the γ4F conformers in the expansion. A combination of force field and density functional theory calculations is used to map out the conformational potential energy surfaces for γ4F and compare it with its γ2F counterpart. Based on this analysis, the phenyl ring prefers to take up structures that facilitate NH···π interactions in γ4F or avoid phenyl interactions with the C═O group in γ2F. The disconnectivity graph for γ4F reveals separate basins associated with the C9 and amide-stacked conformational families, which are separated by a barrier of about 42 kJ/mol. The overall shape of the potential energy surface bears a resemblance to peptides and proteins that have a misfolding pathway that competes with the formation of the native structure.
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Affiliation(s)
- Joshua L Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S Walsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Zachary S Davis
- Department of Chemistry, Wofford College, Spartanburg, South Carolina 29303, United States
| | - Sunglim Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States.,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
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22
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Shi L, Yang D. The alkoxylation effects on the excited‐state intramolecular proton transfer behaviors for 2,6‐bis(benzothiazolyl‐2‐yl)phenol fluorophore: A theoretical research. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lijuan Shi
- Division of General Education Zhongyuan Institute of Science and Technology Zhengzhou China
| | - Dapeng Yang
- College of Physics and Electronics North China University of Water Resources and Electric Power Zhengzhou China
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23
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Giri N, Mahapatra S. Optimal control of photodissociation of phenol using genetic algorithm. J Chem Phys 2022; 156:094305. [DOI: 10.1063/5.0081282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photodissociation dynamics of the OH bond of phenol is studied with an optimally shaped laser pulse. The theoretical model consists of three electronic states (the ground electronic state, ππ* state, and πσ* state) in two nuclear coordinates (the OH stretching coordinate as a reaction coordinate, r, and the CCOH dihedral angle as a coupling coordinate, θ). The optimal UV laser pulse is designed using the genetic algorithm, which optimizes the total dissociative flux of the wave packet. The latter is calculated in the adiabatic asymptotes of the S0 and S1 electronic states of phenol. The initial state corresponds to the vibrational levels of the electronic ground state and is defined as | n r, n θ⟩, where n r and n θ represent the number of nodes along r and θ, respectively. The optimal UV field excites the system to the optically dark πσ* state predominantly over the optically bright ππ* state with the intensity borrowing effect for the |0, 0⟩ and |0, 1⟩ initial states. For the |0, 0⟩ initial condition, the photodissociation to the S1 asymptotic channel is favored slightly over the S0 asymptotic channel. Addition of one quantum of energy along the coupling coordinate increases the dissociation probability in the S1 channel. This is because the wave packet spreads along the coupling coordinate on the πσ* state and follows the adiabatic path. Hence, the S1 asymptotic channel gets more ([Formula: see text]11%) dissociative flux as compared to the S0 asymptotic channel for the |0, 1⟩ initial condition. The |1, 0⟩ and |1, 1⟩ states are initially excited to both the ππ* and πσ* states in the presence of the optimal UV pulse. For these initial conditions, the S1 channel gets more dissociative flux as compared to the S0 channel. This is because the high energy components of the wave packet readily reach the S1 channel. The central frequency of the optimal UV pulse for the |0, 0⟩ and |0, 1⟩ initial states has a higher value as compared to the |1, 0⟩ and |1, 1⟩ initial states. This is explained with the help of an excitation mechanism of a given initial state in relation to its energy.
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Affiliation(s)
- Nitai Giri
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - S. Mahapatra
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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24
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow J, Feng G, Puzzarini C, Barone V. Gestapelt, nicht geklebt: Enthüllung der π→π*‐Wechselwirkung mithilfe des Benzofuran‐Formaldehyd‐Komplexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Lorenzo Spada
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
| | - Silvia Alessandrini
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Yang Zheng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Gang Feng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
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25
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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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26
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Miyazaki M, Sakata Y, Ono M, Otsuka R, Ohara R, Dopfer O, Fujii M. Isomer-Selective Spectroscopy and Dynamics of Phenol-Ar n ( n ≤ 5) Clusters. J Phys Chem A 2021; 125:9969-9981. [PMID: 34761924 DOI: 10.1021/acs.jpca.1c04815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures and ionization-induced solvation dynamics of phenol-(argon)n clusters, PhOH-Arn (n ≤ 5), were studied by using a variety of isomer-selective photoionization and vibrational spectroscopic techniques. Several higher-energy isomers were found and assigned for the first time by systematically controlling the experimental conditions of the supersonic expansion. This behavior is also confirmed for the PhOH-Kr2 cluster. Solvation structures are elucidated by evaluating systematic shifts in the S1 ← S0 origin and ionization energies obtained by resonance-enhanced photoionization, in addition to the OH stretching frequency obtained by IR photodissociation. Isomer-selective picosecond time-resolved IR spectroscopy for the n = 2 clusters revealed that the dynamics for the ionization-induced intermolecular π → H site-switching reaction strongly depends on the initial isomeric structure. In particular, the reaction time for the (1|1) isomer is 7 ps, while that for (2|0) is <3 ps. This difference shows that the switching time is determined by the distance of the reaction coordinate between the initial π-site and the final OH-site.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yuri Sakata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Megumi Ono
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Remina Otsuka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Ryuhei Ohara
- 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.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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27
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow JU, Feng G, Puzzarini C, Barone V. Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex. Angew Chem Int Ed Engl 2021; 61:e202113737. [PMID: 34697878 PMCID: PMC9298890 DOI: 10.1002/anie.202113737] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/14/2022]
Abstract
The 1:1 benzofuran–formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint “rotational spectroscopy–quantum chemistry” strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low‐energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone‐pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi‐experimental equilibrium structure for a molecular complex of such a dimension.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Yang Zheng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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28
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Saleh Y, Sanjay V, Iske A, Yachmenev A, Küpper J. Active learning of potential-energy surfaces of weakly bound complexes with regression-tree ensembles. J Chem Phys 2021; 155:144109. [PMID: 34654290 DOI: 10.1063/5.0057051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several pool-based active learning (AL) algorithms were employed to model potential-energy surfaces (PESs) with a minimum number of electronic structure calculations. Theoretical and empirical results suggest that superior strategies can be obtained by sampling molecular structures corresponding to large uncertainties in their predictions while at the same time not deviating much from the true distribution of the data. To model PESs in an AL framework, we propose to use a regression version of stochastic query by forest, a hybrid method that samples points corresponding to large uncertainties while avoiding collecting too many points from sparse regions of space. The algorithm is implemented with decision trees that come with relatively small computational costs. We empirically show that this algorithm requires around half the data to converge to the same accuracy in comparison to the uncertainty-based query-by-committee algorithm. Moreover, the algorithm is fully automatic and does not require any prior knowledge of the PES. Simulations on a 6D PES of pyrrole(H2O) show that <15 000 configurations are enough to build a PES with a generalization error of 16 cm-1, whereas the final model with around 50 000 configurations has a generalization error of 11 cm-1.
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Affiliation(s)
- Yahya Saleh
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Vishnu Sanjay
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Armin Iske
- Department of Mathematics, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany
| | - Andrey Yachmenev
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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29
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Chou S, Lin S, Chen H, Wu Y. Infrared absorption spectra of phenoxide anions isolated in solid argon. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sheng‐Lung Chou
- Scientific Research Division National Synchrotron Radiation Research Center Hsinchu Taiwan
| | - Shu‐Yu Lin
- Scientific Research Division National Synchrotron Radiation Research Center Hsinchu Taiwan
- Department of Applied Chemistry National Yang Ming Chiao Tung University Hsinchu Taiwan
| | - Hui‐Fen Chen
- Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung Taiwan
| | - Yu‐Jong Wu
- Scientific Research Division National Synchrotron Radiation Research Center Hsinchu Taiwan
- Department of Applied Chemistry National Yang Ming Chiao Tung University Hsinchu Taiwan
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30
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Maué D, Strebert PH, Bernhard D, Rösel S, Schreiner PR, Gerhards M. Dispersionsgebundene, isolierte Dimere in der Gasphase: Beobachtung des kürzesten intermolekularen C‐H⋅⋅⋅H‐C Abstands mittels stimulierter Raman‐Spektroskopie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dominique Maué
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Patrick H. Strebert
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Dominic Bernhard
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Sören Rösel
- Institut für organische Chemie Justus-Liebig-Universität Gießen Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Peter R. Schreiner
- Institut für organische Chemie Justus-Liebig-Universität Gießen Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Markus Gerhards
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
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31
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Maué D, Strebert PH, Bernhard D, Rösel S, Schreiner PR, Gerhards M. Dispersion-Bound Isolated Dimers in the Gas Phase: Observation of the Shortest Intermolecular CH⋅⋅⋅H-C Distance via Stimulated Raman Spectroscopy. Angew Chem Int Ed Engl 2021; 60:11305-11309. [PMID: 33709534 PMCID: PMC8252503 DOI: 10.1002/anie.202016020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/13/2021] [Indexed: 11/30/2022]
Abstract
The triphenylmethane and all‐meta tert‐butyl triphenylmethane dimers, (TPM)2 and (T tBuPM)2, respectively, were studied with ionization loss stimulated Raman spectroscopy in molecular beam experiments to resolve structure sensitive vibrations. This answers the question whether the recently reported linear head‐to‐head arrangement in (T tBuPM)2 results from crystal packing or prevails also in the gas phase, and therefore must result from extraordinarily strong London dispersion (LD) interactions. Our study clearly demonstrates that the head‐to‐head arrangement is maintained even under isolated molecular beam conditions in the absence of crystal packing effects. The central Raman‐active aliphatic C−D vibration of appropriately deuterated (T tBuPM)2 associated with an unusually short C−D⋅⋅⋅D−C distance exhibits a strong blue‐shift compared to the undisturbed case. As the LD stabilizing tert‐butyl groups are absent in (TPM)2, it displays an approximately S6‐symmetric tail‐to‐tail arrangement.
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Affiliation(s)
- Dominique Maué
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Patrick H Strebert
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Dominic Bernhard
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Sören Rösel
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Markus Gerhards
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
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32
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33
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León I, Montero R, Longarte A, Fernández JA. Revisiting the Spectroscopy of Water Dimer in Jets. J Phys Chem Lett 2021; 12:1316-1320. [PMID: 33535759 PMCID: PMC9157493 DOI: 10.1021/acs.jpclett.0c03001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Laser spectroscopy in jets is one of the main sources of structural data from molecular aggregates. Consequently, numerous and sophisticated experimental systems have been developed to extract precise information, which is usually interpreted in the light of quantum mechanical calculations. However, even with the most sophisticated experiments, it is sometimes difficult to interpret the experimental results. We present here the example of water dimer and how after almost 70 years, the assignment of its mass-resolved IR spectrum still generates controversy that extends toward the mechanism of ionization of water aggregates.
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Affiliation(s)
- Iker León
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Unidad Asociada CSIC, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Raúl Montero
- SGIKER
Laser Facility, University of the Basque
Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Asier Longarte
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - José A. Fernández
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
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34
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Fárník M, Fedor J, Kočišek J, Lengyel J, Pluhařová E, Poterya V, Pysanenko A. Pickup and reactions of molecules on clusters relevant for atmospheric and interstellar processes. Phys Chem Chem Phys 2021; 23:3195-3213. [PMID: 33524089 DOI: 10.1039/d0cp06127a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this perspective, we review experiments with molecules picked up on large clusters in molecular beams with the focus on the processes in atmospheric and interstellar chemistry. First, we concentrate on the pickup itself, and we discuss the pickup cross sections. We measure the uptake of different atmospheric molecules on mixed nitric acid-water clusters and determine the accommodation coefficients relevant for aerosol formation in the Earth's atmosphere. Then the coagulation of the adsorbed molecules on the clusters is investigated. In the second part of this perspective, we review examples of different processes triggered by UV-photons or electrons in the clusters with embedded molecules. We start with the photodissociation of hydrogen halides and Freon CF2Cl2 on ice nanoparticles in connection with the polar stratospheric ozone depletion. Next, we mention reactions following the excitation and ionization of the molecules adsorbed on clusters. The first ionization-triggered reaction observed between two different molecules picked up on the cluster was the proton transfer between methanol and formic acid deposited on large argon clusters. Finally, negative ion reactions after slow electron attachment are illustrated by two examples: mixed nitric acid-water clusters, and hydrogen peroxide deposited on large ArN and (H2O)N clusters. The selected examples are discussed from the perspective of the atmospheric and interstellar chemistry, and several future directions are proposed.
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Affiliation(s)
- Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, v.v.i., The Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Prague, Czech Republic.
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35
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Conformer selective monohydrated clusters of 1,2,3,4 –tetrahydroisoquinoline in S0: I-Potential energy surface studies, vibrational signatures and NBO analysis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Chatterjee K, Roy TK, Khatri J, Schwaab G, Havenith M. Unravelling the microhydration frameworks of prototype PAH by infrared spectroscopy: naphthalene–(water)1–3. Phys Chem Chem Phys 2021; 23:14016-14026. [DOI: 10.1039/d1cp01789f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microhydration structures of the prototypical PAH, naphthalene, are probed by IR spectroscopy in helium droplets. The sequential water addition produces an extended hydrogen-bonded hydration network bound via π hydrogen bond to the aromatic ring.
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Affiliation(s)
- Kuntal Chatterjee
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum
- Bochum
- Germany
| | - Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum
- Bochum
- Germany
| | - Jai Khatri
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum
- Bochum
- Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum
- Bochum
- Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum
- Bochum
- Germany
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37
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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38
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Lei J, Alessandrini S, Chen J, Zheng Y, Spada L, Gou Q, Puzzarini C, Barone V. Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex. Molecules 2020; 25:E4899. [PMID: 33113920 PMCID: PMC7660205 DOI: 10.3390/molecules25214899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023] Open
Abstract
The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions.
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Affiliation(s)
- Juncheng Lei
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Junhua Chen
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China; (J.L.); (J.C.); (Y.Z.)
| | - Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy;
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy;
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39
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Feng JY, Lee YP, Zhu CY, Hsu PJ, Kuo JL, Ebata T. IR-VUV spectroscopy of pyridine dimers, trimers and pyridine-ammonia complexes in a supersonic jet. Phys Chem Chem Phys 2020; 22:21520-21534. [PMID: 32955537 DOI: 10.1039/d0cp03197f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The infrared spectra of the C-H stretching vibrations of (pyridine)m, m = 1-3, and the N-H stretching vibrations of (pyridine)m-(NH3)n, m = 1, 2; n = 1-4, complexes were investigated by infrared (IR)-vacuum ultraviolet (VUV) spectroscopy under jet-cooled conditions. The ionization potential (IP0) of the pyridine monomer was determined to be 74 546 cm-1 (9.242 eV), while its complexes showed only smooth curves of the ionization thresholds at ∼9 eV, indicating large structural changes in the ionic form. The pyridine monomer exhibits five main features with several satellite bands in the C-H stretching region at 3000-3200 cm-1. Anharmonic calculations including Fermi-resonance were carried out to analyze the candidates of the overtone and combination bands which can couple to the C-H stretching fundamentals. For (pyridine)2 and (pyridine)3, most C-H bands are blue-shifted by 3-5 cm-1 from those of the monomer. The structures revealed by random searching algorithms with density functional methods indicate that the π-stacked structure is most stable for (pyridine)2, while (pyridine)3 prefers the structures stabilized by dipole-dipole and C-Hπ interactions. For the (pyridine)m-(NH3)n complexes, the mass spectrum exhibited a wide range distribution of the complexes. The observed IR spectra in the N-H stretching vibrations of the complexes showed four main bands in the 3200-3450 cm-1 region. These features are very similar to those of (NH3)n complexes, and the bands are assigned to the anti-symmetric N-H stretching band (ν3), the symmetric N-H stretching (ν1) band, and the first overtone bands of the N-H bending vibrations (2ν4). The anharmonic calculations including the Fermi-resonance between ν1 and 2ν4 well reproduced the observed spectra.
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Affiliation(s)
- Jun-Ying Feng
- Department of Applied Chemistry and Institute for Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan.
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40
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Bhattacharya I, Sadhukhan J, Biswas S, Chakraborty T. Medium-Dependent Crossover from the Red to Blue Shift of the Donor’s Stretching Fundamental in the Binary Hydrogen-Bonded Complexes of CDCl3 with Ethers and Ketones. J Phys Chem A 2020; 124:7259-7270. [DOI: 10.1021/acs.jpca.0c03946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Indrani Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Jayshree Sadhukhan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Chemistry, Govt. General Degree College, Singur, Hooghly 712409, West Bengal, India
| | - Souvick Biswas
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tapas Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Blodgett KN, Jang G, Kim S, Kim MK, Choi SH, Zwier TS. Coexistence of Left- and Right-Handed 12/10-Mixed Helices in Cyclically Constrained β-Peptides and Directed Formation of Single-Handed Helices upon Site-Specific Methylation. J Phys Chem A 2020; 124:5856-5870. [PMID: 32497433 DOI: 10.1021/acs.jpca.0c03545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The inherent conformational preferences of the neutral β-peptide foldamer series, Ac-(ACHC)n-NHBn, n = 2-4, are studied in the gas phase using conformation-specific IR-UV double resonance methods. The cyclically constrained chiral β-amino acid cis-2-aminocyclohexane carboxylic acid (ACHC) is designed to bring both right- and left-handed helices into close energetic proximity. Comparison of the infrared spectra in the NH stretch and amide I/II regions with the predictions of DFT calculations lead to the unambiguous assignment of four out of the six observed conformations of the molecules in this series, while corroborating computational and spectral evidence, affords tentative assignments of the remaining two conformers for which IR data were not recorded. The observed structures fall into one of two conformational families: a right-handed 12/10-mixed helix or its "cap-disrupted" left-handed helical analogue, which coexist with significant populations. Site-specific and stereospecific methylation on the cyclohexane backbone at the dipeptide (n = 2) level is also tested as a means to sterically lock in a predetermined cyclohexane chair conformation. These substitutions are proven to be a means of selectively driving formation of one helical screw sense or the other. Calculated relative energies and free energies of all possible structures for the molecules provide strong supporting evidence that the rigid nature of the ACHC residue confers unusual stability to the 12/10-mixed helix conformation, regardless of local environment, temperature, or C-terminal capping unit. The simultaneous presence of both handed helices offers unique opportunities for future studies of their interconversion.
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Affiliation(s)
- Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Geunhyuk Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Sojung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Min Kyung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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42
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Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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43
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Gottschalk HC, Poblotzki A, Fatima M, Obenchain DA, Pérez C, Antony J, Auer AA, Baptista L, Benoit DM, Bistoni G, Bohle F, Dahmani R, Firaha D, Grimme S, Hansen A, Harding ME, Hochlaf M, Holzer C, Jansen G, Klopper W, Kopp WA, Krasowska M, Kröger LC, Leonhard K, Mogren Al-Mogren M, Mouhib H, Neese F, Pereira MN, Prakash M, Ulusoy IS, Mata RA, Suhm MA, Schnell M. The first microsolvation step for furans: New experiments and benchmarking strategies. J Chem Phys 2020; 152:164303. [DOI: 10.1063/5.0004465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Hannes C. Gottschalk
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Anja Poblotzki
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Mariyam Fatima
- Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Jens Antony
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Alexander A. Auer
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Leonardo Baptista
- Departamento de Química e Ambiental, Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia, Resende, RJ, Brazil
| | - David M. Benoit
- Department of Physics and Mathematics, E. A. Milne Centre for Astrophysics and G. W. Gray Centre for Advanced Materials Chemistry, University of Hull, Hull HU6 7RX, United Kingdom
| | - Giovanni Bistoni
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Rahma Dahmani
- Université Gustave Eiffel, COSYS/LISIS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Dzmitry Firaha
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, 52062 Aachen, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Michael E. Harding
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/LISIS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Christof Holzer
- Theoretical Chemistry Group, Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Georg Jansen
- Fakultät für Chemie, Universität Duisburg-Essen, Universitätsstr. 5, 45117 Essen, Germany
| | - Wim Klopper
- Theoretical Chemistry Group, Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Wassja A. Kopp
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, 52062 Aachen, Germany
| | - Małgorzata Krasowska
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Leif C. Kröger
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, 52062 Aachen, Germany
| | - Kai Leonhard
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, 52062 Aachen, Germany
| | - Muneerah Mogren Al-Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Halima Mouhib
- Université Gustave Eiffel, COSYS/LISIS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Max N. Pereira
- Departamento de Química e Ambiental, Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia, Resende, RJ, Brazil
| | - Muthuramalingam Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Inga S. Ulusoy
- Theoretical Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Ricardo A. Mata
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
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44
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Matsuda Y, Hirano Y, Mizutani S, Sakai D, Fujii A, Maeda S, Ohno K. Migrations and Catalytic Action of Water Molecules in the Ionized Formamide-(H 2O) 2 Cluster. J Phys Chem A 2020; 124:2802-2807. [PMID: 32187496 DOI: 10.1021/acs.jpca.0c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isomerization dynamics involving the migrations, proton transfer reaction, and catalytic actions of water molecules upon vertical ionization of the formamide (FA)-(H2O)2 cluster is investigated by the infrared spectroscopy and theoretical reaction path search calculation. The infrared spectroscopic result indicates the [FA-(H2O)2]+ cation has the hydrogen-bonded structure of the enol isomer cation of formamide and the water dimer. This structure is formed by proton transfer from the CH bond to the carbonyl group through the catalytic action of the water molecules. The isomerization paths involving this enolization in ionized FA-(H2O)2 are explored by using the anharmonic downward distortion following method. We found multiple enolization paths which accompany proton exchanges among the formamide moiety and water molecules through the catalytic actions of the water molecules.
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Affiliation(s)
- Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Yutaro Hirano
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinichi Mizutani
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Daichi Sakai
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba, 305-0044, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.,Institute for Quantum Chemical Exploration, 13F Area Shinagawa, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan
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45
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Roy TK, Mani D, Schwaab G, Havenith M. A close competition between O–H⋯O and O–H⋯π hydrogen bonding: IR spectroscopy of anisole–methanol complex in helium nanodroplets. Phys Chem Chem Phys 2020; 22:22408-22416. [DOI: 10.1039/d0cp02589e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anisole forms O–H⋯O as well O–H⋯π bound complexes with methanol.
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Affiliation(s)
- Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Devendra Mani
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
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46
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Fatima M, Maué D, Pérez C, Tikhonov DS, Bernhard D, Stamm A, Medcraft C, Gerhards M, Schnell M. Structures and internal dynamics of diphenylether and its aggregates with water. Phys Chem Chem Phys 2020; 22:27966-27978. [DOI: 10.1039/d0cp04104a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report on a detailed multi-spectroscopic analysis of the structures and internal dynamics of diphenylether and its aggregates with up to three water molecules by employing molecular beam experiments.
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Affiliation(s)
- M. Fatima
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Pérez
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. S. Tikhonov
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - D. Bernhard
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - C. Medcraft
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Schnell
- Deutsches Elektronen-Synchrotron (DESY)
- D-22607 Hamburg
- Germany
- Institute of Physical Chemistry
- Christian-Albrechts-Universität zu Kiel
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47
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Ohshimo K, Miyazaki S, Hattori K, Misaizu F. Long-distance proton transfer induced by a single ammonia molecule: ion mobility mass spectrometry of protonated benzocaine reacted with NH3. Phys Chem Chem Phys 2020; 22:8164-8170. [DOI: 10.1039/c9cp06923b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A long-distance proton transfer via the vehicle mechanism in the absence of a hydrogen-bonded solvent-bridge in molecules.
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Affiliation(s)
- Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Shun Miyazaki
- Department of Chemistry, Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Keigo Hattori
- Department of Chemistry, Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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48
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49
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Alessandrini S, Barone V, Puzzarini C. Extension of the “Cheap” Composite Approach to Noncovalent Interactions: The jun-ChS Scheme. J Chem Theory Comput 2019; 16:988-1006. [DOI: 10.1021/acs.jctc.9b01037] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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50
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Robertson PA, Villani L, Robertson EG. Conformer Specific Ultraviolet and Infrared Detection of Nicotine in the Vapor Phase. J Phys Chem A 2019; 123:10152-10157. [PMID: 31644291 DOI: 10.1021/acs.jpca.9b09113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A gas-phase electronic spectrum of nicotine in a supersonic expansion has been recorded using two-color resonant two-photon ionization spectroscopy. Efficient photoionization was achievable only via the pyridine chromophore owing to poor Franck-Condon overlap in the N-methylpyrrolidine moiety. Two conformers of nicotine have been characterized and assigned by infrared-ultraviolet (IR-UV) ion depletion and IR-UV hole-burning spectroscopy, in combination with quantum chemical techniques. Trans-A with nitrogen atoms further apart is more stable by 2 kJ mol-1 and the most populated conformer in the supersonic jet, owing this stability to a stronger inter-ring CH···N hydrogen bond than the trans-B counterpart.
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Affiliation(s)
- Patrick A Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Victoria 3086 , Australia.,School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Luigi Villani
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Victoria 3086 , Australia
| | - Evan G Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Victoria 3086 , Australia
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