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Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 9015

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Prof. Dr. Arnaud Cuisset

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Laboratory of Physical Chemistry of the Atmosphere, University of Littoral, 189A Ave. M. Schumann, 59140 Dunkerque, France
Interests: terahertz; rovibrational spectroscopy; conformational analysis; trace gas monitoring; atmospheric compounds

Special Issue Information

Dear Colleagues,

In a large variety of scientific fields, there is a strong interest in probing the low-frequency modes (LFM) of molecules involving large amplitude motions. For example, it has been widely accepted that delocalized large amplitude vibrations throughout the entire protein molecule can be well described with a few LFM. From a physical chemistry point of view, it is now well established than the LFM are very sensitive to the conformational landscape of highly flexible molecules and drive the intramolecular and intermolecular dynamics of hydrogen bonds. The vibrational frequencies of LFM lay in the Terahertz (THz) domain, considered as a spectral gap between the electronic and the photonic parts of the electromagnetic spectrum. Technological progresses in THz sources and detectors allow us today to probe molecular transitions associated with LFM. In particular, numerous diluted and condensed phase studies have been performed in the far-infrared domain with synchrotron-based sources and in the submillimeter domain with electronic and optoelectronic sources.

To highlight and celebrate current developments in this field, our journal Molecules will launch a Special Issue on “Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions”, to be published in 2021. We encourage the contribution of high-quality papers and review articles in all areas of physical chemistry involved in the THz probe of LFM large amplitude dynamics by spectroscopic tools, at the molecular level. We hope that submissions will show the diversity and potential of this field.

We look forward to receiving your contributions.

Prof. Dr. Arnaud Cuisset
Guest Editor

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Keywords

low frequency modes
terahertz
large amplitude motion
conformational flexibility
intra and intermolecular vibrations

Published Papers (4 papers)

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Research

17 pages, 1128 KiB

Open AccessArticle

Millimeter-Wave Spectroscopy of Methylfuran Isomers: Local vs. Global Treatments of the Internal Rotation

by Jonas Bruckhuisen, Sathapana Chawananon, Isabelle Kleiner, Anthony Roucou, Guillaume Dhont, Colwyn Bracquart, Pierre Asselin and Arnaud Cuisset

Molecules 2022, 27(11), 3591; https://doi.org/10.3390/molecules27113591 - 2 Jun 2022

Cited by 1 | Viewed by 1828

Abstract

Methylfurans are methylated aromatic heterocyclic volatile organic compounds and primary or secondary pollutants in the atmosphere due to their capability to form secondary organic aerosols in presence of atmospheric oxidants. There is therefore a significant interest to monitor these molecules in the gas phase. High resolution spectroscopic studies of methylated furan compounds are generally limited to pure rotational spectroscopy in the vibrational ground state. This lack of results might be explained by the difficulties arisen from the internal rotation of the methyl group inducing non-trivial patterns in the rotational spectra. In this study, we discuss the benefits to assign the mm-wave rotational-torsional spectra of methylfuran with the global approach of the BELGI-C

_{s}

code compared to local approaches such as XIAM and ERHAM. The global approach reproduces the observed rotational lines of 2-methylfuran and 3-methylfuran in the mm-wave region at the experimental accuracy for the ground v

_{t} = 0

and the first torsional v

_{t} = 1

states with a unique set of molecular parameters. In addition, the

V_{3}

and

V_{6}

parameters describing the internal rotation potential barrier may be determined with a high degree of accuracy with the global approach. Finally, a discussion with other heterocyclic compounds enables the study of the influence of the electronic environment on the hindered rotation of the methyl group. Full article

(This article belongs to the Special Issue Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions)

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16 pages, 2622 KiB

Open AccessArticle

Epithelial Sodium Channel Inhibition by Amiloride Addressed with THz Spectroscopy and Molecular Modeling

by Maria Mernea, Roxana Ștefania Ulăreanu, Dana Cucu, Jasim Hafedh Al-Saedi, Cristian-Emilian Pop, Sergiu Fendrihan, Giorgiana Diana Carmen Anghelescu and Dan Florin Mihăilescu

Molecules 2022, 27(10), 3271; https://doi.org/10.3390/molecules27103271 - 19 May 2022

Cited by 4 | Viewed by 1876

Abstract

THz spectroscopy is important for the study of ion channels because it directly addresses the low frequency collective motions relevant for their function. Here we used THz spectroscopy to investigate the inhibition of the epithelial sodium channel (ENaC) by its specific blocker, amiloride. Experiments were performed on A6 cells’ suspensions, which are cells overexpressing ENaC derived from Xenopus laevis kidney. THz spectra were investigated with or without amiloride. When ENaC was inhibited by amiloride, a substantial increase in THz absorption was noticed. Molecular modeling methods were used to explain the observed spectroscopic differences. THz spectra were simulated using the structural models of ENaC and ENaC—amiloride complexes built here. The agreement between the experiment and the simulations allowed us to validate the structural models and to describe the amiloride dynamics inside the channel pore. The amiloride binding site validated using THz spectroscopy agrees with previous mutagenesis studies. Altogether, our results show that THz spectroscopy can be successfully used to discriminate between native and inhibited ENaC channels and to characterize the dynamics of channels in the presence of their specific antagonist. Full article

(This article belongs to the Special Issue Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions)

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14 pages, 2902 KiB

Open AccessArticle

Large Amplitude Motions of Pyruvic Acid (CH₃-CO-COOH)

by María Luisa Senent and Samira Dalbouha

Molecules 2021, 26(14), 4269; https://doi.org/10.3390/molecules26144269 - 14 Jul 2021

Cited by 5 | Viewed by 1972

Abstract

Torsional and rotational spectroscopic properties of pyruvic acid are determined using highly correlated ab initio methods and combining two different theoretical approaches: Second order perturbation theory and a variational procedure in three-dimensions. Four equilibrium geometries of pyruvic acid, Tc, Tt, Ct, and CC, outcome from a search with CCSD(T)-F12. All of them can be classified in the C_s point group. The variational calculations are performed considering the three internal rotation modes responsible for the non-rigidity as independent coordinates. More than 50 torsional energy levels (including torsional subcomponents) are localized in the 406–986 cm⁻¹ region and represent excitations of the ν₂₄ (skeletal torsion) and the ν₂₃ (methyl torsion) modes. The third independent variable, the OH torsion, interacts strongly with ν₂₃. The A₁/E splitting of the ground vibrational state has been evaluated to be 0.024 cm⁻¹ as it was expected given the high of the methyl torsional barrier (338 cm⁻¹). A very good agreement with respect to previous experimental data concerning fundamental frequencies (ν^CAL − ν^EXP ~ 1 cm⁻¹), and rotational parameters (B₀^CAL − B₀^EXP < 5 MHz), is obtained. Full article

(This article belongs to the Special Issue Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions)

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20 pages, 3193 KiB

Open AccessArticle

Intramolecular H-Bond Dynamics of Catechol Investigated by THz High-Resolution Spectroscopy of Its Low-Frequency Modes

by Jonas Bruckhuisen, Guillaume Dhont, Anthony Roucou, Atef Jabri, Hamdi Bayoudh, Thi Thanh Tran, Manuel Goubet, Marie-Aline Martin-Drumel and Arnaud Cuisset

Molecules 2021, 26(12), 3645; https://doi.org/10.3390/molecules26123645 - 15 Jun 2021

Cited by 10 | Viewed by 2480

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. Full article

(This article belongs to the Special Issue Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions)

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Terahertz Spectroscopy and Dynamics of Low-Frequency Modes Involving Large Amplitude Molecular Motions

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