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Molecules
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Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions
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Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions

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

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 22674

Special Issue Editors

Dr. Gang Feng

E-Mail Website1 Website2
Guest Editor
School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
Interests: high-resolution spectroscopy; supersonic expansion; molecular clusters; non-covalent interactions; large amplitude motions
Dr. Weixing Li

E-Mail Website
Guest Editor
Department of Chemistry, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
Interests: structures and noncovalent bonds of molecular clusters; nuclear quantum tunneling; microwave spectroscopy

Special Issue Information

Dear Colleagues,

Molecular clusters, a direct link between single molecules and macroscopic condensed matter, are important for understanding the nature of many chemical and physical processes such as solvation, molecular recognition and nucleation. These clusters are unified together through intermolecular non-covalent interactions (also known as weak intermolecular interactions) such as hydrogen bonding and van der Waals. The properties of the concerned clusters are highly dominated by the NCIs and their binding topologies. Molecular structure is the key information for revealing the mechanism upon the formation of critical clusters. A molecular level of characterization and interpretation of molecular clusters will advance our understanding on the above mentioned chemical and physical processes. One feature of these weakly bound clusters is their strong internal dynamic effect dominated by large-amplitude motions, i.e., proton transfer, internal rotation.

The Special Issue on "Spectroscopic characterization of molecular clusters and large amplitude motions" is announced to provide a common platform for researchers to share their investigations and findings in this promising field and increase their visibility thanks to the open access platform. Contributions to this issue, both in the form of original research or review articles, are warm welcome. Potential topics suitable for this Special Issue include, but are not limited to:

  • the state-of-the-art spectroscopic technology to characterize molecular structures and internal dynamics;
  • molecular aggregation and clusters;
  • hydrogen bonds;
  • van der Waals complexes;
  • non-covalent interactions;
  • large amplitude motions

Dr. Gang Feng
Dr. Weixing Li
Guest Editors

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Keywords

  • High resolution spectroscopy
  • molecular cluster
  • molecular structure
  • non-covalent interactions
  • tunneling splitting
  • internal motion

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Published Papers (8 papers)

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Research

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15 pages, 2624 KiB  
Article
Skeletal Torsion Tunneling and Methyl Internal Rotation: The Coupled Large Amplitude Motions in Phenyl Acetate
by Lynn Ferres, Luca Evangelisti, Assimo Maris, Sonia Melandri, Walther Caminati, Wolfgang Stahl and Ha Vinh Lam Nguyen
Molecules 2022, 27(9), 2730; https://doi.org/10.3390/molecules27092730 - 23 Apr 2022
Cited by 6 | Viewed by 2244
Abstract
The rotational spectrum of phenyl acetate, CH3COOC6H5, is measured using a free jet absorption millimeter-wave spectrometer in the range from 60 to 78 GHz and two pulsed jet Fourier transform microwave spectrometers covering a total frequency range [...] Read more.
The rotational spectrum of phenyl acetate, CH3COOC6H5, is measured using a free jet absorption millimeter-wave spectrometer in the range from 60 to 78 GHz and two pulsed jet Fourier transform microwave spectrometers covering a total frequency range from 2 to 26.5 GHz. The features of two large amplitude motions, the methyl group internal rotation and the skeletal torsion of the CH3COO group with respect to the phenyl ring C6H5 (tilted at about 70°), characterize the spectrum. The vibrational ground state is split into four widely spaced sublevels, labeled as A0, E0, A1, and E1, each of them with its set of rotational transitions and with additional interstate transitions. A global fit of the line frequencies of the four sublevels leads to the determination of 51 spectroscopic parameters, including the ΔEA0/A1 and ΔEE0/E1 vibrational splittings of ~36.4 and ~33.5 GHz, respectively. The V3 barrier to methyl internal rotation (~136 cm−1) and the skeletal torsion B2 barrier to the orthogonality of the two planes (~68 cm−1) are deduced. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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17 pages, 2483 KiB  
Article
Hydrogen Bonding in the Dimer and Monohydrate of 2-Adamantanol: A Test Case for Dispersion-Corrected Density Functional Methods
by Marcos Juanes, Rizalina Tama Saragi, Cristóbal Pérez, Luca Evangelisti, Lourdes Enríquez, Martín Jaraíz and Alberto Lesarri
Molecules 2022, 27(8), 2584; https://doi.org/10.3390/molecules27082584 - 17 Apr 2022
Cited by 3 | Viewed by 2711
Abstract
Weakly-bound intermolecular clusters constitute reductionist physical models for non-covalent interactions. Here we report the observation of the monomer, the dimer and the monohydrate of 2-adamantanol, a secondary alcohol with a bulky ten-carbon aliphatic skeleton. The molecular species were generated in a supersonic jet [...] Read more.
Weakly-bound intermolecular clusters constitute reductionist physical models for non-covalent interactions. Here we report the observation of the monomer, the dimer and the monohydrate of 2-adamantanol, a secondary alcohol with a bulky ten-carbon aliphatic skeleton. The molecular species were generated in a supersonic jet expansion and characterized using broadband chirped-pulse microwave spectroscopy in the 2–8 GHz frequency region. Two different gauche-gauche O-H···O hydrogen-bonded isomers were observed for the dimer of 2-adamantanol, while a single isomer was observed for the monomer and the monohydrate. The experimental rotational parameters were compared with molecular orbital calculations using density functional theory (B3LYP-D3(BJ), B2PLYP-D3(BJ), CAM-B3LYP-D3(BJ), ωB97XD), additionally providing energetic and electron density characterization. The shallow potential energy surface makes the dimer an interesting case study to benchmark dispersion-corrected computational methods and conformational search procedures. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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9 pages, 1805 KiB  
Article
Stabilizing the Exotic Carbonic Acid by Bisulfate Ion
by Huili Lu, Shi-Wei Liu, Mengyang Li, Baocai Xu, Li Zhao, Tao Yang and Gao-Lei Hou
Molecules 2022, 27(1), 8; https://doi.org/10.3390/molecules27010008 - 21 Dec 2021
Cited by 3 | Viewed by 2998
Abstract
Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic [...] Read more.
Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic complex [H2CO3·HSO4]− using density functional theory calculations, molecular dynamics simulations, and topological analysis to investigate if the exotic H2CO3 molecule could be stabilized by bisulfate ion, which is a ubiquitous ion in various environments. We found that bisulfate ion could efficiently stabilize all the three conformers of H2CO3 and reduce the energy differences of isomers with H2CO3 in three different conformations compared to the isolated H2CO3 molecule. Calculated isomerization pathways and ab initio molecular dynamics simulations suggest that all the optimized isomers of the complex have good thermal stability and could exist at finite temperatures. We also explored the hydrogen bonding properties in this interesting complex and simulated their harmonic infrared spectra to aid future infrared spectroscopic experiments. This work could be potentially important to understand the fate of carbonic acid in certain complex environments, such as in environments where both sulfuric acid (or rather bisulfate ion) and carbonic acid (or rather carbonic dioxide and water) exist. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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13 pages, 1491 KiB  
Article
Perfluorination of Aromatic Compounds Reinforce Their van der Waals Interactions with Rare Gases: The Rotational Spectrum of Pentafluoropyridine-Ne
by Alberto Macario, Susana Blanco, Ibon Alkorta and Juan Carlos López
Molecules 2022, 27(1), 17; https://doi.org/10.3390/molecules27010017 - 21 Dec 2021
Cited by 3 | Viewed by 2751
Abstract
The rotational spectrum of the pentafluoropyridine-Ne complex, generated in a supersonic jet, has been investigated using chirped-pulse microwave Fourier transform spectroscopy in the 2–8 GHz range. The spectra of the 20Ne and 22Ne species have been observed, and the rotational constants [...] Read more.
The rotational spectrum of the pentafluoropyridine-Ne complex, generated in a supersonic jet, has been investigated using chirped-pulse microwave Fourier transform spectroscopy in the 2–8 GHz range. The spectra of the 20Ne and 22Ne species have been observed, and the rotational constants have been used to determine the structure of the complex. This structure, and those of the previously experimentally studied complexes benzene-Ne and pyridine-Ne, are an excellent benchmark for the theoretical calculations on these adducts. These complexes and hexafluorobenzene-Ne have been investigated at the CCSD/6-311++G(2d,p) level. The calculations reproduce the experimental structures well and show how the van der Waals complexes are stronger for the perfluorinated compound. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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14 pages, 2096 KiB  
Article
From Molecular to Cluster Properties: Rotational Spectroscopy of 2-Aminopyridine and of Its Biomimetic Cluster with Water
by Adam Kraśnicki, Zbigniew Kisiel and Jean-Claude Guillemin
Molecules 2021, 26(22), 6870; https://doi.org/10.3390/molecules26226870 - 15 Nov 2021
Cited by 2 | Viewed by 2264
Abstract
We report the observation and analysis of the rotational spectrum of a 1:1 cluster between 2-aminopyridine and water (AMW) carried out with supersonic expansion Fourier transform microwave spectroscopy at 4.7–16.5 GHz. Measurements of the 2-aminopyridine monomer (AMP) were also extended up to 333 [...] Read more.
We report the observation and analysis of the rotational spectrum of a 1:1 cluster between 2-aminopyridine and water (AMW) carried out with supersonic expansion Fourier transform microwave spectroscopy at 4.7–16.5 GHz. Measurements of the 2-aminopyridine monomer (AMP) were also extended up to 333 GHz for the room-temperature rotational spectrum and to resolved hyperfine splitting resulting from the presence of two 14N quadrupolar nuclei. Supersonic expansion measurements for both AMP and AMW were also carried out for two synthesized isotopic species with single deuteration on the phenyl ring. Nuclear quadrupole hyperfine structure has also been resolved for AMW and the derived splitting constants were used as an aid in structural analysis. The structure of the AMW cluster was determined from the three sets of available rotational constants and the hydrogen bonding configuration is compared with those for clusters with water of similarly sized single-ring molecules. Experimental results aided by quantum chemistry computations allow the conclusion that the water molecule is unusually strongly bound by two hydrogen bonds, OH...N and O...HN, to the NCNH atomic chain of AMP with the potential to replace hydrogen bonds to the identical structural segment in cytosine and adenine in CT and AT nucleic acid base pairs. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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7 pages, 1586 KiB  
Article
The Reactive Sites of Methane Activation: A Comparison of IrC3+ with PtC3+
by Zizhuang Liu, Hechen Wu, Wei Li and Xiaonan Wu
Molecules 2021, 26(19), 6028; https://doi.org/10.3390/molecules26196028 - 4 Oct 2021
Cited by 3 | Viewed by 1760
Abstract
The activation reactions of methane mediated by metal carbide ions MC3+ (M = Ir and Pt) were comparatively studied at room temperature using the techniques of mass spectrometry in conjunction with theoretical calculations. MC3+ (M [...] Read more.
The activation reactions of methane mediated by metal carbide ions MC3+ (M = Ir and Pt) were comparatively studied at room temperature using the techniques of mass spectrometry in conjunction with theoretical calculations. MC3+ (M = Ir and Pt) ions reacted with CH4 at room temperature forming MC2H2+/C2H2 and MC4H2+/H2 as the major products for both systems. Besides that, PtC3+ could abstract a hydrogen atom from CH4 to generate PtC3H+/CH3, while IrC3+ could not. Quantum chemical calculations showed that the MC3+ (M = Ir and Pt) ions have a linear M-C-C-C structure. The first C–H activation took place on the Ir atom for IrC3+. The terminal carbon atom was the reactive site for the first C–H bond activation of PtC3+, which was beneficial to generate PtC3H+/CH3. The orbitals of the different metal influence the selection of the reactive sites for methane activation, which results in the different reaction channels. This study investigates the molecular-level mechanisms of the reactive sites of methane activation. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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28 pages, 5416 KiB  
Article
Quantifying Conformational Isomerism in Chain Molecules by Linear Raman Spectroscopy: The Case of Methyl Esters
by Maxim Gawrilow and Martin A. Suhm
Molecules 2021, 26(15), 4523; https://doi.org/10.3390/molecules26154523 - 27 Jul 2021
Cited by 6 | Viewed by 2662
Abstract
The conformational preferences of the ester group have the potential to facilitate the large amplitude folding of long alkyl chains in the gas phase. They are monitored by Raman spectroscopy in supersonic jet expansions for the model system methyl butanoate, after establishing a [...] Read more.
The conformational preferences of the ester group have the potential to facilitate the large amplitude folding of long alkyl chains in the gas phase. They are monitored by Raman spectroscopy in supersonic jet expansions for the model system methyl butanoate, after establishing a quantitative relationship with quantum–chemical predictions for methyl methanoate. This requires a careful analysis of experimental details, and a simulation of the rovibrational contours for near-symmetric top molecules. The technique is shown to be complementary to microwave spectroscopy in quantifying coexisting conformations. It confirms that a C−O−C(=O)–C–C chain segment can be collapsed into a single all-trans conformation by collisional cooling, whereas alkyl chain isomerism beyond this five-membered chain largely survives the jet expansion. This sets the stage for the investigation of linear alkyl alkanoates in terms of dispersion-induced stretched-chain to hairpin transitions by Raman spectroscopy. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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Review

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37 pages, 7855 KiB  
Review
The LAM of the Rings: Large Amplitude Motions in Aromatic Molecules Studied by Microwave Spectroscopy
by Ha Vinh Lam Nguyen, Walther Caminati and Jens-Uwe Grabow
Molecules 2022, 27(12), 3948; https://doi.org/10.3390/molecules27123948 - 20 Jun 2022
Cited by 12 | Viewed by 3830
Abstract
Large amplitude motions (LAMs) form a fundamental phenomenon that demands the development of specific theoretical and Hamiltonian models. In recent years, along with the strong progress in instrumental techniques on high-resolution microwave spectroscopy and computational capacity in quantum chemistry, studies on LAMs have [...] Read more.
Large amplitude motions (LAMs) form a fundamental phenomenon that demands the development of specific theoretical and Hamiltonian models. In recent years, along with the strong progress in instrumental techniques on high-resolution microwave spectroscopy and computational capacity in quantum chemistry, studies on LAMs have become very diverse. Larger and more complex molecular systems have been taken under investigation, ranging from series of heteroaromatic molecules from five- and six-membered rings to polycyclic-aromatic-hydrocarbon derivatives. Such systems are ideally suited to create families of molecules in which the positions and the number of LAMs can be varied, while the heteroatoms often provide a sufficient dipole moment to the systems to warrant the observation of their rotational spectra. This review will summarize three types of LAMs: internal rotation, inversion tunneling, and ring puckering, which are frequently observed in aromatic five-membered rings such as furan, thiophene, pyrrole, thiazole, and oxazole derivatives, in aromatic six-membered rings such as benzene, pyridine, and pyrimidine derivatives, and larger combined rings such as naphthalene, indole, and indan derivatives. For each molecular class, we will present the representatives and summarize the recent insights on the molecular structure and internal dynamics and how they help to advance the field of quantum mechanics. Full article
(This article belongs to the Special Issue Spectroscopic Characterization of Molecular Clusters and Large Amplitude Motions)
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