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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 (15 December 2022) | Viewed by 21743

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Special Issue Editors

Prof. Dr. Qingzhong Li

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Guest Editor

School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
Interests: intermolecular interactions; theoretical calculations; tetrel bonds; triel bonds; molecular spectroscopy
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Prof. Dr. Steve Scheiner

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Guest Editor

Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
Interests: quantum chemistry; h-bonds; noncovalent bonds; tetrel bonds; pnicogen bonds; chalcogen bonds; halogen bonds; structure and function of biomolecules like proteins
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Prof. Dr. Zhiwu Yu

E-Mail Website
Guest Editor

Department of Chemistry, Tsinghua University, Beijing, China
Interests: molecular spectroscopy; hydrogen bonds; halogen bonds; molecular structures; phospholipids
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the geometrical and spectroscopic features as well as potential applications of halogen, chalcogen, pnictogen, tetrel, and triel bonds in chemical reactions, crystal engineering, molecular recognition, and biological systems. We aim to especially publish studies concerning the bonds formed between some novel important electron donors and acceptors, similarities and differences between these bonds, structures of the complexes composed of these bonds in solution and gas phases, spectroscopic methods for measuring these bonds in solution and gas phases, and applications of these bonds in chemical reactions, crystal engineering, molecular recognition, and biological systems.

Prof. Dr. Qingzhong Li
Prof. Dr. Steve Scheiner
Prof. Dr. Zhiwu Yu
Guest Editors

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Keywords

halogen bond
chalcogen bond
pnictogen bond
tetrel bond
triel bond

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Related Special Issue

Chemical Bond and Intermolecular Interactions, 2nd Edition in Molecules (4 articles)

Published Papers (10 papers)

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Research

14 pages, 5325 KiB

Open AccessArticle

Interaction of Vinyl-Type Carbocations, C₃H₅⁺ and C₄H₇⁺ with Molecules of Water, Alcohols, and Acetone

by Evgenii S. Stoyanov, Irina Yu. Bagryanskaya and Irina V. Stoyanova

Molecules 2023, 28(3), 1146; https://doi.org/10.3390/molecules28031146 - 23 Jan 2023

Cited by 2 | Viewed by 1609

Abstract

X-ray diffraction analysis and IR spectroscopy were used to study the products of the interaction of vinyl cations C₃H₅⁺ and C₄H₇⁺ (Cat⁺) (as salts of carborane anion CHB₁₁Cl₁₁⁻) with basic molecules of water, alcohols, and acetone that can crystallize from solutions in dichloromethane and C₆HF₅. Interaction with water, as content increased, proceeded via three-stages. (1) adduct Cat⁺·OH₂ forms in which H₂O binds (through the O atom) to the C=C⁺ bond of the cation with the same strength as seen in the binding to Na in Na(H₂O)₆⁺. (2) H⁺ is transferred from cation Cat⁺·OH₂ to a water molecule forming H₃O⁺ and alcohol molecules (L) having the CH=CHOH entity. The O- atom of alcohols is attached to the H atom of the C=C⁺-H moiety of Cat⁺ thereby forming a very strong asymmetric H–bond, (C=)C⁺-H⋅⋅⋅O. (3) Finally all vinyl cations are converted into alcohol molecule L and H₃O⁺ cations, yielding proton disolvates L-H⁺-L with a symmetric very strong H-bond. When an acetone molecule (Ac) interacts with Cat⁺, H⁺ is transferred to Ac giving rise to a reactive carbene and proton disolvate Ac-H⁺-Ac. Thus, the alleged high reactivity of vinyl cations seems to be an exaggeration. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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15 pages, 3451 KiB

Open AccessArticle

How the Position of Substitution Affects Intermolecular Bonding in Halogen Derivatives of Carboranes: Crystal Structures of 1,2,3- and 8,9,12-Triiodo- and 8,9,12-Tribromo ortho-Carboranes

by Kyrill Yu. Suponitsky, Sergey A. Anufriev and Igor B. Sivaev

Molecules 2023, 28(2), 875; https://doi.org/10.3390/molecules28020875 - 15 Jan 2023

Cited by 5 | Viewed by 1804

Abstract

The crystal structures of two isomeric triiodo derivatives of ortho-carborane containing substituents in the three most electron-withdrawing positions of the carborane cage, 1,2,3-I₃-1,2-C₂B₁₀H₉, and the three most electron-donating positions, 8,9,12-I₃-1,2-C₂B₁₀H₉, as well as the crystal structure of 8,9,12-Br₃-1,2-C₂B₁₀H₉, were determined by single-crystal X-ray diffraction. In the structure of 1,2,3-I₃-1,2-C₂B₁₀H₉, an iodine atom attached to the boron atom (position 3) donates its lone pairs simultaneously to the σ-holes of both iodine atoms attached to the carbon atoms (positions 1 and 2) with the I⋯I distance of 3.554(2) Å and the C-I⋯I and B-I⋯I angles of 169.2(2)° and 92.2(2)°, respectively. The structure is additionally stabilized by a few B-H⋯I-shortened contacts. In the structure of 8,9,12-I₃-1,2-C₂B₁₀H₉, the I⋯I contacts of type II are very weak (the I⋯I distance is 4.268(4) Å, the B8-I8⋯I12 and B12-I12⋯I8 angles are 130.2(3)° and 92.2(3)°) and can only be regarded as dihalogen bonds formally. In comparison with the latter, the structure of 8,9,12-Br₃-1,2-C₂B₁₀H₉ demonstrates both similarities and differences. No Br⋯Br contacts of type II are observed, while there are two Br⋯Br halogen bonds of type I. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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14 pages, 2195 KiB

Open AccessArticle

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

by Ana V. Cunha, Remco W. A. Havenith, Jari van Gog, Freija De Vleeschouwer, Frank De Proft and Wouter Herrebout

Molecules 2023, 28(2), 772; https://doi.org/10.3390/molecules28020772 - 12 Jan 2023

Cited by 15 | Viewed by 2729

Abstract

The halogen bond complexes CF

_{3}

X⋯Y and C

_{2}

_{3}

X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between [...] Read more.

The halogen bond complexes CF

_{3}

X⋯Y and C

_{2}

_{3}

X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the

π

-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C–X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the

π

-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet

π \to π^{*}

states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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23 pages, 3630 KiB

Open AccessArticle

Dihydrogen Bonding—Seen through the Eyes of Vibrational Spectroscopy

by Marek Freindorf, Margaret McCutcheon, Nassim Beiranvand and Elfi Kraka

Molecules 2023, 28(1), 263; https://doi.org/10.3390/molecules28010263 - 28 Dec 2022

Cited by 5 | Viewed by 1616

Abstract

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H

_{3}^{+}

kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms–in–Molecules analysis to assess the strength [...] Read more.

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H

_{3}^{+}

kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms–in–Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode–mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H

_{3}^{+}

_{2}

)

_{n}

systems, we conclude that the bond strength in these crystal–like structures makes them interesting for potential hydrogen storage applications. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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20 pages, 17581 KiB

Open AccessArticle

Dissecting Bonding Interactions in Cysteine Dimers

by Santiago Gómez, Sara Gómez, Jorge David, Doris Guerra, Chiara Cappelli and Albeiro Restrepo

Molecules 2022, 27(24), 8665; https://doi.org/10.3390/molecules27248665 - 7 Dec 2022

Cited by 4 | Viewed by 2182

Abstract

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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12 pages, 2327 KiB

Open AccessArticle

Abnormalities of the Halogen Bonds in the Complexes between Y₂CTe (Y = H, F, CH₃) and XF (X = F, Cl, Br, I)

by Ya-Qian Wang, Rui-Jing Wang, Qing-Zhong Li and Zhi-Wu Yu

Molecules 2022, 27(23), 8523; https://doi.org/10.3390/molecules27238523 - 3 Dec 2022

Cited by 2 | Viewed by 1631

Abstract

In this work, the hydrogen bonds and halogen bonds in the complexes between Y₂CTe (Y = H, F, CH₃) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F₂. Secondly, the halogen bonds formed by F₂ are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y₂CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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8 pages, 2638 KiB

Open AccessArticle

Stabilizing Halogen-Bonded Complex between Metallic Anion and Iodide

by Fei Ying, Xu Yuan, Xinxing Zhang and Jing Xie

Molecules 2022, 27(22), 8069; https://doi.org/10.3390/molecules27228069 - 21 Nov 2022

Cited by 3 | Viewed by 1887

Abstract

Halogen bonds (XBs) between metal anions and halides have seldom been reported because metal anions are reactive for XB donors. The pyramidal-shaped Mn(CO)₅⁻ anion is a candidate metallic XB acceptor with a ligand-protected metal core that maintains the negative charge and an open site to accept XB donors. Herein, Mn(CO)₅⁻ is prepared by electrospray ionization, and its reaction with CH₃I in gas phase is studied using mass spectrometry and density functional theory (DFT) calculation. The product observed experimentally at m/z = 337 is assigned as [IMn(CO)₄(OCCH₃)]⁻, which is formed by successive nucleophilic substitution and reductive elimination, instead of the halogen-bonded complex (XC) CH₃−I···Mn(CO)₅⁻, because the I···Mn interaction is weak within XC and it could be a transient species. Inspiringly, DFT calculations predict that replacing CH₃I with CF₃I can strengthen the halogen bonding within the XC due to the electro-withdrawing ability of F. More importantly, in so doing, the nucleophilic substitution barrier can be raised significantly, ~30 kcal/mol, thus leaving the system trapping within the XC region. In brief, the combination of a passivating metal core and the introduction of an electro-withdrawing group to the halide can enable strong halogen bonding between metallic anion and iodide. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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11 pages, 8052 KiB

Open AccessArticle

Three for the Price of One: Concomitant I⋯N, I⋯O, and I⋯π Halogen Bonds in the Same Crystal Structure

by Steven van Terwingen, Ruimin Wang and Ulli Englert

Molecules 2022, 27(21), 7550; https://doi.org/10.3390/molecules27217550 - 3 Nov 2022

Cited by 4 | Viewed by 3555

Abstract

The ditopic molecule 3-(1,3,5-trimethyl-1H-4-pyrazolyl)pentane-2,4-dione (HacacMePz) combines two different Lewis basic sites. It forms a crystalline adduct with the popular halogen bond (XB) donor 2,3,5,6-tetrafluoro-1,4-diiodobenzene (TFDIB) with a HacacMePz:TFDIB ratio of 2:3. In a simplified picture, the topology of the adduct corresponds to a hcb net. In addition to the expected acetylacetone keto O and pyrazole N acceptor sites, a third and less common short contact to a TFDIB iodine is observed: The acceptor site is again the most electron-rich site of the pyrazole π-system. This iminic N atom is thus engaged as the acceptor in two orthogonal halogen bonds. Evaluation of the geometric results and of a single-point calculation agree with respect to the strength of the intermolecular contacts: The conventional N⋯I XB is the shortest (2.909(4) Å) and associated with the highest electron density (0.150 eÅ

^{- 3}

) in the bond critical point (BCP), followed by the O⋯I contact (2.929(3) Å, 0.109 eÅ

^{- 3}

), and the π contact (3.2157(3) Å, 0.075 eÅ

^{- 3}

). If one accepts the idea of deducing interaction energies from energy densities at the BCP, the short contacts also follow this sequence. Two more criteria identify the short N⋯I contact as the most relevant: The associated C–I bond is significantly longer than the database average, and it is the only intermolecular interaction with a negative total energy density in the BCP. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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16 pages, 2743 KiB

Open AccessArticle

Thermodynamics and Spectroscopy of Halogen- and Hydrogen-Bonded Complexes of Haloforms with Aromatic and Aliphatic Amines

by Emmanuel Adeniyi, Olivia Grounds, Zachary Stephens, Matthias Zeller and Sergiy V. Rosokha

Molecules 2022, 27(18), 6124; https://doi.org/10.3390/molecules27186124 - 19 Sep 2022

Cited by 5 | Viewed by 2198

Abstract

Similarities and differences of halogen and hydrogen bonding were explored via UV–Vis and ¹H NMR measurements, X-ray crystallography and computational analysis of the associations of CHX₃ (X=I, Br, Cl) with aromatic (tetramethyl-p-phenylenediamine) and aliphatic (4-diazabicyclo[2,2,2]octane) amines. When the polarization of haloforms was taken into account, the strengths of these complexes followed the same correlation with the electrostatic potentials on the surfaces of the interacting atoms. However, their spectral properties were quite distinct. While the halogen-bonded complexes showed new intense absorption bands in the UV–Vis spectra, the absorptions of their hydrogen-bonded analogues were close to the superposition of the absorption of reactants. Additionally, halogen bonding led to a shift in the NMR signal of haloform protons to lower ppm values compared with the individual haloforms, whereas hydrogen bonding of CHX₃ with aliphatic amines resulted in a shift in the opposite direction. The effects of hydrogen bonding with aromatic amines on the NMR spectra of haloforms were ambivalent. Titration of all CHX₃ with these nucleophiles produced consistent shifts in their protons’ signals to lower ppm values, whereas calculations of these pairs produced multiple hydrogen-bonded minima with similar structures and energies, but opposite directions of the NMR signals’ shifts. Experimental and computational data were used for the evaluation of formation constants of some halogen- and hydrogen-bonded complexes between haloforms and amines co-existing in solutions. Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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16 pages, 2160 KiB

Open AccessArticle

Triel Bond Formed by Malondialdehyde and Its Influence on the Intramolecular H-Bond and Proton Transfer

by Qiaozhuo Wu, Shubin Yang and Qingzhong Li

Molecules 2022, 27(18), 6091; https://doi.org/10.3390/molecules27186091 - 18 Sep 2022

Cited by 3 | Viewed by 1377

Abstract

Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX₃ (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX₃ (X = Cl and Br) and MDA-AlX₃ (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH₂ substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH₃ (Tr = B and Al). Full article

(This article belongs to the Special Issue Chemical Bond and Intermolecular Interactions)

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