1
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Du W, Gao F, Cui P, Yu Z, Tong W, Wang J, Ren Z, Song C, Xu J, Ma H, Dang L, Zhang D, Lu Q, Jiang J, Wang J, Pi L, Sheng Z, Lu Q. Twisting, untwisting, and retwisting of elastic Co-based nanohelices. Nat Commun 2023; 14:4426. [PMID: 37481654 PMCID: PMC10363140 DOI: 10.1038/s41467-023-40001-w] [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: 09/30/2022] [Accepted: 07/07/2023] [Indexed: 07/24/2023] Open
Abstract
The reversible transformation of a nanohelix is one of the most exquisite and important phenomena in nature. However, nanomaterials usually fail to twist into helical crystals. Considering the irreversibility of the previously studied twisting forces, the reverse process (untwisting) is more difficult to achieve, let alone the retwisting of the untwisted crystalline nanohelices. Herein, we report a new reciprocal effect between molecular geometry and crystal structure which triggers a twisting-untwisting-retwisting cycle for tri-cobalt salicylate hydroxide hexahydrate. The twisting force stems from competition between the condensation reaction and stacking process, different from the previously reported twisting mechanisms. The resulting distinct nanohelices give rise to unusual structure elasticity, as reflected in the reversible change of crystal lattice parameters and the mutual transformation between the nanowires and nanohelices. This study proposes a fresh concept for designing reversible processes and brings a new perspective in crystallography.
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Affiliation(s)
- Wei Du
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 211816, Nanjing, P. R. China
| | - Feng Gao
- Department of Materials Science and Engineering, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, College of Engineering and Applied Science, Nanjing University, 210023, Nanjing, P. R. China.
| | - Peng Cui
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
| | - Zhiwu Yu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Wei Tong
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Jihao Wang
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Zhuang Ren
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Chuang Song
- Department of Materials Science and Engineering, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, College of Engineering and Applied Science, Nanjing University, 210023, Nanjing, P. R. China
| | - Jiaying Xu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Haifeng Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Liyun Dang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Di Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Qingyou Lu
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China.
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China.
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China.
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China.
| | - Li Pi
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Zhigao Sheng
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Qingyi Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China.
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2
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Kumar M, Song HS, Lee J, Park D, Suk H, Hur MS. Intense multicycle THz pulse generation from laser-produced nanoplasmas. Sci Rep 2023; 13:4233. [PMID: 36918732 PMCID: PMC10015041 DOI: 10.1038/s41598-023-31427-9] [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: 12/13/2022] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
We present a novel scheme to obtain robust, narrowband, and tunable THz emission using a nano-dimensional overdense plasma target, irradiated by two counter-propagating detuned laser pulses. So far, no narrowband THz sources with a field strength of GV/m-level have been reported from laser-solid interaction (mostly half-or single-cycle THz pulses with only broadband frequency spectrum). From two- and three-dimensional particle-in-cell simulations, we find that the strong plasma current generated by the beat ponderomotive force in the colliding region, produces beat-frequency radiation in the THz range. Here we report intense THz pulses [Formula: see text]THz) with an unprecedentedly high peak field strength of 11.9 GV/m and spectral width [Formula: see text], which leads to a regime of an extremely bright narrowband THz source of TW/cm[Formula: see text], suitable for various ambitious applications.
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Affiliation(s)
- Manoj Kumar
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyung Seon Song
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Jaeho Lee
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Dohyun Park
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyyong Suk
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Min Sup Hur
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
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3
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Bruckhuisen J, Dhont G, Roucou A, Jabri A, Bayoudh H, Tran TT, Goubet M, Martin-Drumel MA, Cuisset A. Intramolecular H-Bond Dynamics of Catechol Investigated by THz High-Resolution Spectroscopy of Its Low-Frequency Modes. Molecules 2021; 26:molecules26123645. [PMID: 34203730 PMCID: PMC8232127 DOI: 10.3390/molecules26123645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
Catechol is an oxygenated aromatic volatile organic compound and a biogenic precursor of secondary organic aerosols. Monitoring this compound in the gas phase is desirable due to its appreciable reactivity with tropospheric ozone. From a molecular point of view, this molecule is attractive since the two adjacent hydroxy groups can interchangeably act as donor and acceptor in an intramolecular hydrogen bonding due to the tunnelling between two symmetrically equivalent structures. Using synchrotron radiation, we recorded a rotationally-resolved Fourier Transform far-infrared (IR) spectrum of the torsional modes of the free and bonded -OH groups forming the intramolecular hydrogen bond. Additionally, the room temperature, pure rotational spectrum was measured in the 70–220 GHz frequency range using a millimeter-wave spectrometer. The assignment of these molecular transitions was assisted by anharmonic high-level quantum-chemical calculations. In particular, pure rotational lines belonging to the ground and the four lowest energy, vibrationally excited states were assigned. Splitting due to the tunnelling was resolved for the free -OH torsional state. A global fit combining the far-IR and millimeter-wave data provided the spectroscopic parameters of the low-energy far-IR modes, in particular those characterizing the intramolecular hydrogen bond dynamics.
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Affiliation(s)
- Jonas Bruckhuisen
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Guillaume Dhont
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Anthony Roucou
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Atef Jabri
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Hamdi Bayoudh
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Thi Thanh Tran
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
| | - Manuel Goubet
- UMR8523—PhLAM—Physique des Lasers Atomes et Molécules, Université de Lille, CNRS, F-59000 Lille, France;
| | | | - Arnaud Cuisset
- UR4493, LPCA, Laboratoire de Physico-Chimie de l’Atmosphère, Université du Littoral Côte d’Opale, F-59140 Dunkerque, France; (J.B.); (G.D.); (A.R.); (A.J.); (H.B.); (T.T.T.)
- Correspondence:
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4
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Lemmens A, Rap DB, Thunnissen JMM, Gruet S, Steber AL, Panchagnula S, Tielens AGGM, Schnell M, Buma WJ, Rijs AM. Far-IR Absorption of Neutral Polycyclic Aromatic Hydrocarbons (PAHs): Light on the Mechanism of IR-UV Ion Dip Spectroscopy. J Phys Chem Lett 2020; 11:8997-9002. [PMID: 33035060 PMCID: PMC7649846 DOI: 10.1021/acs.jpclett.0c02714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Gas-phase IR-UV double-resonance laser spectroscopy is an IR absorption technique that bridges the gap between experimental IR spectroscopy and theory. The IR experiments are used to directly evaluate predicted frequencies and potential energy surfaces as well as to probe the structure of isolated molecules. However, a detailed understanding of the underlying mechanisms is, especially in the far-IR regime, still far from complete, even though this is crucial for properly interpreting the recorded IR absorption spectra. Here, events occurring upon excitation to vibrational levels of polycyclic aromatic hydrocarbons by far-IR radiation from the FELIX free electron laser are followed using resonance-enhanced multiphoton ionization spectroscopy. These studies provide detailed insight into how ladder climbing and anharmonicity influence IR-UV spectroscopy and therefore the resulting IR signatures in the far-IR region. Moreover, the potential energy surfaces of these low-frequency delocalized modes are investigated and shown to have a strong harmonic character.
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Affiliation(s)
- Alexander
K. Lemmens
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Daniël B. Rap
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Johannes M. M. Thunnissen
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Sébastien Gruet
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Amanda L. Steber
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Sanjana Panchagnula
- Leiden
Observatory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | | | - Melanie Schnell
- Deutsches
Elektronen-Synchrotron, Notkestrasse 85, D-22607 Hamburg, Germany
- Institut
für Physikalische Chemie, Christian-Albrechts-Universität
zu Kiel, Max-Eyth-Strasse
1, D-24118 Kiel, Germany
| | - Wybren Jan Buma
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Anouk M. Rijs
- Radboud
University, Institute for Molecules
and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
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5
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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6
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches. J Phys Chem A 2019; 123:862-872. [DOI: 10.1021/acs.jpca.8b10881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Ranim Mallat
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Tim Gorn
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M. Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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Mihrin D, Wugt Larsen R. THz spectroscopy of weakly bound cluster molecules in solid para-hydrogen: a sensitive probe of van der Waals interactions. Phys Chem Chem Phys 2018; 21:349-358. [PMID: 30525164 DOI: 10.1039/c8cp05060k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work demonstrates that 99.9% enriched solid para-H2 below 3 K provides an excellent inert and transparent medium for the exploration of large-amplitude intermolecular vibrational motion of weakly bound van der Waals cluster molecules in the THz spectral region. THz absorption spectra have been generated for CO2/H2O and CS2/H2O mixtures embedded in enriched solid para-H2 and numerous observed transitions associated with large-amplitude librational motion of the weakly bound binary CO2H2O and CS2H2O van der Waals cluster molecules have been assigned together with tentative assignments for the ternary CS2(H2O)2 system. The interaction strength, directionality and anharmonicity of the weak van der Waals "bonds" between the molecules can be characterized via these THz spectral signatures and yield rigorous benchmarks for high-level ab initio methodologies. It is suggested that even a less stable linear conformation of the ternary CS2(H2O)2 system, where one H2O molecule is linked to each S atom of the CS2 subunit, may be formed due to the kinetics associated with the mobility of free H2O molecules in the soft para-H2 medium. In addition, the spectroscopic observations confirm a linear and planar global intermolecular potential energy minimum for the binary CS2H2O system with C2v symmetry, where the O atom on the H2O molecule is linked to one of the S atoms on the CS2 subunit. A semi-experimental value for the vibrational zero-point energy contribution of 1.93 ± 0.10 kJ mol-1 from the class of large-amplitude intermolecular vibrational modes is proposed. The combination with CCSD(T)/CBS electronic energy predictions provides a semi-experimental estimate of 5.08 ± 0.15 kJ mol-1 for the binding energy D0 of the CS2H2O van der Waals system.
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Affiliation(s)
- D Mihrin
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark.
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8
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High-Energy, Short-Duration Bursts of Coherent Terahertz Radiation from an Embedded Plasma Dipole. Sci Rep 2018; 8:145. [PMID: 29317689 PMCID: PMC5760715 DOI: 10.1038/s41598-017-18399-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/11/2017] [Indexed: 11/08/2022] Open
Abstract
Emission of radiation from electrons undergoing plasma oscillations (POs) at the plasma frequency has attracted interest because of the existence of intriguing and non-trivial coupling mechanism between the electrostatic PO and the emitted electromagnetic wave. While broadband emission from plasma waves in inhomogeneous plasma is well known, the underlying physics of narrowband emission at the plasma frequency observed in experiments and in solar radio-bursts is obscure. Here we show that a spatially-localized plasma dipole oscillation (PDO) can be generated when electrons are trapped in a moving train of potential wells produced by the ponderomotive force of two slightly detuned laser pulses that collide in plasma and give rise to a burst of quasi-monochromatic radiation. The energy radiated in the terahertz spectral region can reach an unprecedented several millijoules, which makes it suitable for applications requiring short pulses of high-intensity, narrowband terahertz radiation.
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9
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Hussain A, Huse N, Vendrell O. Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054102. [PMID: 28966931 PMCID: PMC5612798 DOI: 10.1063/1.5003404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/05/2017] [Indexed: 05/26/2023]
Abstract
Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN). Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.
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Affiliation(s)
- Abid Hussain
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, 22761 Hamburg, Germany
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10
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Yu Y, Fan W, Wang Y, Zhou X, Sun J, Liu S. C–H···O Interaction in Methanol–Water Solution Revealed from Raman Spectroscopy and Theoretical Calculations. J Phys Chem B 2017; 121:8179-8187. [DOI: 10.1021/acs.jpcb.7b06036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanqin Yu
- Department of Physics, Anhui University, Hefei, Anhui, 230601, China
| | - Wei Fan
- Hefei National Laboratory for Physical Sciences at the Microscale,
iChEM (Collaborative Innovation Center of Chemistry for Energy Materials),
Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Yuxi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale,
iChEM (Collaborative Innovation Center of Chemistry for Energy Materials),
Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale,
iChEM (Collaborative Innovation Center of Chemistry for Energy Materials),
Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jin Sun
- Department of Physics, Anhui University, Hefei, Anhui, 230601, China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale,
iChEM (Collaborative Innovation Center of Chemistry for Energy Materials),
Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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11
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Yatsyna V, Bakker DJ, Feifel R, Rijs AM, Zhaunerchyk V. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide. J Chem Phys 2017; 145:104309. [PMID: 27634262 DOI: 10.1063/1.4962360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.
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Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Daniël J Bakker
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M Rijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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Bakker DJ, Dey A, Tabor DP, Ong Q, Mahé J, Gaigeot MP, Sibert EL, Rijs AM. Fingerprints of inter- and intramolecular hydrogen bonding in saligenin–water clusters revealed by mid- and far-infrared spectroscopy. Phys Chem Chem Phys 2017; 19:20343-20356. [DOI: 10.1039/c7cp01951c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saligenin (2-(hydroxymethyl)phenol) exhibits both strong and weak intramolecular electrostatic interactions.
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Affiliation(s)
- Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Arghya Dey
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Daniel P. Tabor
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Qin Ong
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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13
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Mahé J, Bakker DJ, Jaeqx S, Rijs AM, Gaigeot MP. Mapping gas phase dipeptide motions in the far-infrared and terahertz domain. Phys Chem Chem Phys 2017; 19:13778-13787. [DOI: 10.1039/c7cp00369b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vibrational signatures of Ac-Phe-AA-NH2 dipeptides are recorded and analysed in the far IR/THz spectral domain (100–800 cm−1, 3–24 THz), with the ‘AA’ amino acid chosen within the series ‘AA’ = Gly, Ala, Pro, Cys, Ser, Val. Phe stands for phenylalanine.
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Affiliation(s)
- Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
| | - Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Sander Jaeqx
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- 91025 Evry
- France
- Université Paris-Saclay
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14
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Yatsyna V, Bakker DJ, Salén P, Feifel R, Rijs AM, Zhaunerchyk V. Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure. PHYSICAL REVIEW LETTERS 2016; 117:118101. [PMID: 27661721 DOI: 10.1103/physrevlett.117.118101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 06/06/2023]
Abstract
We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N-methylacetamide molecules in the mid-IR spectral range of 1000-1800 cm^{-1}, utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N-methylacetamide are measured in the full amide I-III range.
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Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Daniël J Bakker
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Peter Salén
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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