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

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 15432

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Dr. Ilya G. Shenderovich

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Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
Interests: noncovalent interactions; H-bond; soft matter; surface; porous materials; NMR
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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

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Keywords

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

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Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions in Molecules (12 articles)

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13 pages, 1597 KiB

Open AccessArticle

Halogen Bonding and Rearrangements in Complexes of N-Chlorosuccinimide with Halides

by Maison Hardin, Matthias Zeller and Sergiy V. Rosokha

Molecules 2025, 30(3), 639; https://doi.org/10.3390/molecules30030639 - 31 Jan 2025

Viewed by 651

Abstract

The role of halogen bonding (HaB) in the reactions of N-chlorosuccinimide (SimCl), a versatile reagent in organic synthesis, was investigated through experimental and computational analyses of its interactions with halides. The reactions of SimCl with Br⁻ or I⁻ resulted in the crystallization of HaB complexes of chloride with N-iodosuccinimide (SimI) or N-bromosuccinimide (SimBr). Computational analysis revealed that halogen rearrangements, which occurred even at −73 °C, were facilitated by halogen bonding. The dissociation of SimCl∙Y⁻ (Y = I or Br) complexes into a Sim⁻ + ClY pair (followed by the rotation and re-binding of the interhalogen molecules) bypassed the formation of the high-energy Sim⁻ + Cl⁺ pair and drastically (about tenfold) reduced the dissociation energy of the N–Cl bond. Furthermore, while the dissociation energy of individual SimCl is higher (and its HaB is weaker) compared to that of SimI or SimBr, the dissociation of the N-Cl bond in SimCl∙Y⁻ requires less energy than in the complexes of SimBr or SimI. The facile cleavage of such bonds in HaB complexes explains the high reactivity of SimCl and its effectiveness as a halogenating agent. 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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21 pages, 4026 KiB

Open AccessArticle

Color Compounds Removal from Tequila Vinasses Using Silica Gel Adsorbents Functionalized with Thiol Moieties: Equilibrium and Kinetics Studies

by Carlos Gonzalez-Valerio, Alejandro A. Peregrina-Lucano, Ricardo Manríquez-González, Aida A. Pérez-Fonseca, Jorge R. Robledo-Ortíz, Ilya G. Shenderovich and Sergio Gómez-Salazar

Molecules 2024, 29(24), 5910; https://doi.org/10.3390/molecules29245910 - 15 Dec 2024

Viewed by 858

Abstract

Tequila vinasses are organic wastes generated during ethanol fermentation at elevated temperatures (≥90 °C) and pH ≤ 4.0, making them hazardous to the environment. This paper describes a new, simplified UV–vis spectroscopy-based procedure for monitoring the adsorption of color compounds in tequila vinasses onto silica-based adsorbents, along with an optimized synthesis method to produce the most efficient sol–gel synthesized thiol-functionalized adsorbent. Under optimized conditions, the uptake capacity of this adsorbent reaches 0.8 g g⁻¹ in 90 min. Experimental results demonstrate that the adsorbent has a specific affinity for melanoidin-type molecules. The adsorbent demonstrates excellent thermal stability (~316 °C). The results of this work indicate that the adsorbent possesses potential in the treatment of tequila vinasses from wastewater discharges. 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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15 pages, 1951 KiB

Open AccessArticle

Keep Your TEMPO Up: Nitroxide Radicals as Sensors of Intermolecular Interactions

by Ilya G. Shenderovich

Molecules 2024, 29(21), 5032; https://doi.org/10.3390/molecules29215032 - 24 Oct 2024

Viewed by 1299

Abstract

This study examines experimental data on the influence of the surrounding medium and non-covalent interactions on the isotropic hyperfine coupling constant, A_iso(¹⁴N), of the stable nitroxide radical 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl (TEMPO) in solution. The data were used to identify a density functional theory functional/basis set combination that accurately reproduces the experimental A_iso(¹⁴N) values. The variations in A_iso(¹⁴N) due to external factors are two orders of magnitude greater than the accuracy of its experimental measurements, making A_iso(¹⁴N) a highly sensitive experimental probe for quantifying these effects. Additionally, it was found that the proton-accepting ability of the N-O^• moiety in TEMPO resembles that of the P=O moiety, enabling the simultaneous formation of two equally strong hydrogen bonds. 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, 15492 KiB

Open AccessArticle

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 1054

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 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

Open AccessArticle

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

Cited by 2 | Viewed by 2372

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 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

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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

Cited by 2 | Viewed by 1498

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.

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

Open AccessArticle

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

Cited by 2 | Viewed by 900

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 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

Open AccessArticle

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

Cited by 2 | Viewed by 1120

Abstract

The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the

H_{2}

{NH}_{3}

, 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

H_{2}

{NH}_{3}

, 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

Open AccessArticle

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

Cited by 1 | Viewed by 1653

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 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

Open AccessReview

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 4 | Viewed by 1896

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 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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