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Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II)

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: 30 September 2024 | Viewed by 7863

Special Issue Editor

Dr. Ilya G. Shenderovich

E-Mail Website
Guest Editor
Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
Interests: noncovalent interactions; H-bond; soft matter; surface; porous materials; NMR
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Noncovalent interactions are the bridge between the ideal gas abstraction and the real world. In the past, most studies were limited to the analysis of the single strongest interaction in a molecular system under consideration, which was held responsible for the most important structural properties of the system. The current challenge is to go beyond this limitation.

The first edition of the Special Issue “Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions” (2020) was very successful:

https://www.mdpi.com/1420-3049/26/1/158

It was published as a standalone book: https://www.mdpi.com/books/book/3554 .

The second edition of this Special Issue will collect ideas on how to study the interplay of noncovalent interactions in complex molecular systems, including the effects of cooperation and anti-cooperation, solvation, reaction fields, steric hindrance, intermolecular dynamics, and other weak but numerous impacts on molecular conformation, chemical reactivity, and condensed matter structure. Publications about the experimental manifestations of these effects or their theoretical analysis are cordially invited.

The following five leading contributions initiate this flow of ideas:

Prof. Dr. Martin Suhm (Georg-August-Universität Göttingen, Germany): "Vibrational spectroscopy of flavors: Microsolvation preferences of piperonal".

Prof. Dr. Jan Lundell (University of Jyväskylä, Finland): "Revisiting vibrational spectroscopy of the H2O...CO complex".

Prof. Dr. Chiara Cappelli (Scuola Normale Superiore Pisa, Italy): "Modeling H-bond in solvation".

Prof. Dr. Constantinos C. Stoumpo (University of Crete, Greece).

Prof. Dr. Rene Wugt Larsen and Dr. Dmytro Mihrin (Technical University of Denmark).

Dr. Ilya G. Shenderovich
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • noncovalent interactions
  • H-bond
  • halogen bonds
  • molecular recognition
  • IR and Raman spectroscopy
  • NMR
  • X-ray diffraction

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Related Special Issue

Published Papers (7 papers)

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Research

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16 pages, 15492 KiB  
Article
Intermolecular Interactions between Aldehydes and Alcohols: Conformational Equilibrium and Rotational Spectra of Acrolein-Methanol Complex
by Dingding Lv, David Sundelin, Assimo Maris, Luca Evangelisti, Wolf Dietrich Geppert and Sonia Melandri
Molecules 2024, 29(15), 3444; https://doi.org/10.3390/molecules29153444 - 23 Jul 2024
Viewed by 562
Abstract
The rotational spectra of the 1:1 complex formed by acrolein and methanol and its deuterated isotopologues have been analyzed. Two stable conformations in which two hydrogen bonds between the two moieties are formed were detected. The rotational lines show a hyperfine structure due [...] Read more.
The rotational spectra of the 1:1 complex formed by acrolein and methanol and its deuterated isotopologues have been analyzed. Two stable conformations in which two hydrogen bonds between the two moieties are formed were detected. The rotational lines show a hyperfine structure due to the methyl group internal rotation in the complex and the V3 barriers hindering the motion were determined as 2.629(5) kJ mol−1 and 2.722(5) kJ mol−1 for the two conformations, respectively. Quantum mechanical calculations at the MP2/aug-cc-pVTZ level and comprehensive analysis of the intermolecular interactions, utilizing NCI and SAPT approaches, highlight the driving forces of the interactions and allow the determination of the binding energies of complex formation. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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18 pages, 2481 KiB  
Article
The Role of Hydrogen Bonding in the Raman Spectral Signals of Caffeine in Aqueous Solution
by Sara Gómez and Chiara Cappelli
Molecules 2024, 29(13), 3035; https://doi.org/10.3390/molecules29133035 - 26 Jun 2024
Viewed by 1146
Abstract
The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra [...] Read more.
The identification and quantification of caffeine is a common need in the food and pharmaceutical industries and lately also in the field of environmental science. For that purpose, Raman spectroscopy has been used as an analytical technique, but the interpretation of the spectra requires reliable and accurate computational protocols, especially as regards the Resonance Raman (RR) variant. Herein, caffeine solutions are sampled using Molecular Dynamics simulations. Upon quantification of the strength of the non-covalent intermolecular interactions such as hydrogen bonding between caffeine and water, UV-Vis, Raman, and RR spectra are computed. The results provide general insights into the hydrogen bonding role in mediating the Raman spectral signals of caffeine in aqueous solution. Also, by analyzing the dependence of RR enhancement on the absorption spectrum of caffeine, it is proposed that the sensitivity of the RR technique could be exploited at excitation wavelengths moderately far from 266 nm, yet achieving very low detection limits in the quantification caffeine content. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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16 pages, 2850 KiB  
Article
Self-Association and Microhydration of Phenol: Identification of Large-Amplitude Hydrogen Bond Librational Modes
by Dmytro Mihrin, Karen Louise Feilberg and René Wugt Larsen
Molecules 2024, 29(13), 3012; https://doi.org/10.3390/molecules29133012 - 25 Jun 2024
Viewed by 887
Abstract
The self-association mechanisms of phenol have represented long-standing challenges to quantum chemical methodologies owing to the competition between strongly directional intermolecular hydrogen bonding, weaker non-directional London dispersion forces and C–H⋯π interactions between the aromatic rings. The present work explores these subtle self-association [...] Read more.
The self-association mechanisms of phenol have represented long-standing challenges to quantum chemical methodologies owing to the competition between strongly directional intermolecular hydrogen bonding, weaker non-directional London dispersion forces and C–H⋯π interactions between the aromatic rings. The present work explores these subtle self-association mechanisms of relevance for biological molecular recognition processes via spectroscopic observations of large-amplitude hydrogen bond librational modes of phenol cluster molecules embedded in inert neon “quantum” matrices complemented by domain-based local pair natural orbital-coupled cluster DLPNO-CCSD(T) theory. The spectral signatures confirm a primarily intermolecular O-H⋯H hydrogen-bonded structure of the phenol dimer strengthened further by cooperative contributions from inter-ring London dispersion forces as supported by DLPNO-based local energy decomposition (LED) predictions. In the same way, the hydrogen bond librational bands observed for the trimeric cluster molecule confirm a pseudo-C3 symmetric cyclic cooperative hydrogen-bonded barrel-like potential energy minimum structure. This structure is vastly different from the sterically favored “chair” conformations observed for aliphatic alcohol cluster molecules of the same size owing to the additional stabilizing London dispersion forces and C–H⋯π interactions between the aromatic rings. The hydrogen bond librational transition observed for the phenol monohydrate finally confirms that phenol acts as a hydrogen bond donor to water in contrast to the hydrogen bond acceptor role observed for aliphatic alcohols. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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11 pages, 5576 KiB  
Article
Chalcogen-Bond-Assisted Formation of the N→C Dative Bonds in the Complexes between Chalcogenadiazoles/Chalcogenatriazoles and Fullerene C60
by Yu Zhang and Weizhou Wang
Molecules 2024, 29(11), 2685; https://doi.org/10.3390/molecules29112685 - 6 Jun 2024
Viewed by 497
Abstract
The existence of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative [...] Read more.
The existence of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative bonds in the complexes formed by fullerene C60 with 1,2,5-chalcogenadiazoles, 2,1,3-benzochalcogenadiazoles, and 1,2,4,5-chalcogenatriazoles, respectively. It was found that the N→C dative bonds are formed along with the formation of the N–Ch···C (Ch = S, Se, Te) chalcogen bonds. In the gas phase, from S-containing complexes through Se-containing complexes to Te-containing complexes, the intrinsic interaction energies become more and more negative, which indicates that the N–Ch···C chalcogen bonds can facilitate the formation of the N→C dative bonds. The intrinsic interaction energies are compensated by the large deformation energy of fullerene C60. The total interaction energies of Te-containing complexes are negative, while both total interaction energies of the S-containing complexes and Se-containing complexes are positive. This means that the N→C dative bonds in the Te-containing complexes are more easily observed in experiments in comparison with those in the S-containing complexes and Se-containing complexes. This study provides a new theoretical perspective on the experimental observation of the N→C dative bonds in complexes involving fullerenes. Further, the formation of stable N→C dative bonds in the complexes involving fullerenes can significantly change the properties of fullerenes, which will greatly simulate and expand the application range of fullerenes. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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14 pages, 8297 KiB  
Article
Characteristics of Intermolecular Interactions between Encapsulated Molecules and the Lantern-Like Carcerand Superphanes
by Mirosław Jabłoński
Molecules 2024, 29(3), 601; https://doi.org/10.3390/molecules29030601 - 26 Jan 2024
Viewed by 801
Abstract
The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the H2O, NH3, HF, HCN, and MeOH molecules trapped inside them. Despite the large cavity, the freedom of [...] Read more.
The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the H2O, NH3, HF, HCN, and MeOH molecules trapped inside them. Despite the large cavity, the freedom of the trapped molecules is significantly limited by the presence of numerous interaction sites on the side chains of the superphane molecule. It is shown that the molecule trapped inside the superphane is stabilized mainly by only one or, less often, two strong hydrogen bonds involving the imino nitrogen atom, but QTAIM calculations also suggest the presence of many other intermolecular interactions, mainly hydrogen bonds involving imino or central hydrogen atoms from the side chains of the superphane molecule. Moreover, it is also shown that the structural simplification of the side chains does not significantly affect both the size of the superphane molecule and the obtained encapsulation energies, which is important in modeling this type of carceplexes. Noticeably, the parent superphane considered here was previously synthesized by the group of Qing He, so the results obtained will help in understanding this type and similar systems. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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16 pages, 3877 KiB  
Article
Internal Vibrations of Pyridinium Cation in One-Dimensional Halide Perovskites and the Corresponding Halide Salts
by Anna Yu. Samsonova, Alena Yu. Mikheleva, Kirill M. Bulanin, Nikita I. Selivanov, Anton S. Mazur, Peter M. Tolstoy, Constantinos C. Stoumpos and Yury V. Kapitonov
Molecules 2024, 29(1), 78; https://doi.org/10.3390/molecules29010078 - 22 Dec 2023
Viewed by 1186
Abstract
We investigate vibrations of the pyridinium cation PyH+ = C5H5NH+ in one-dimensional lead halide perovskites PyPbX3 and pyridinium halide salts PyHX (X− = I−, Br−), combining infrared absorption and Raman scattering [...] Read more.
We investigate vibrations of the pyridinium cation PyH+ = C5H5NH+ in one-dimensional lead halide perovskites PyPbX3 and pyridinium halide salts PyHX (X− = I−, Br−), combining infrared absorption and Raman scattering methods at room temperature. Internal vibrations of the cation were assigned based on density functional theory modeling. Some of the vibrational bands are sensitive to perovskite or the salt environment in the solid state, while halide substitution has only a minor effect on them. These findings have been confirmed by 1H, 13C and 207Pb solid-state nuclear magnetic resonance (NMR) experiments. Narrower vibrational bands in perovskites indicate less disorder in these materials. The splitting of NH-group vibrational bands in perovskites can be rationalized the presence of nonequivalent crystal sites for cations or by more exotic phenomena such as quantum tunneling transition between two molecular orientations. We have shown how organic cations in hybrid organic–inorganic crystals could be used as spectators of the crystalline environment that affects their internal vibrations. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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Review

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26 pages, 6802 KiB  
Review
Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry
by Nadia B. Haro Mares, Sonja C. Döller, Till Wissel, Markus Hoffmann, Michael Vogel and Gerd Buntkowsky
Molecules 2024, 29(7), 1669; https://doi.org/10.3390/molecules29071669 - 8 Apr 2024
Cited by 2 | Viewed by 1092
Abstract
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica [...] Read more.
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores. Full article
(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))
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