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Halogen Bonds: Combining Experiment and Theory
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Halogen Bonds: Combining Experiment and Theory

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

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 16907

Special Issue Editor

Prof. Dr. Gianluca Ciancaleoni

E-Mail Website
Guest Editor
Dipartimento di Chimica e Chimica Industriale (DCCI) Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
Interests: selenium chemistry; chemical bonding; weak interactions; DFT; organometallic chemistry; catalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last 20 years halogen bonding has passed from being considered just a scientific curiosity to being an established and widespread tool used in chemistry and material science. Even if many aspects of halogen bonding have already been revealed, some debates are still going on about its nature and its real and potential applications.

In order to constructively contribute to these debates, particularly helpful is the combination of experimental and theoretical data, which can offer a unified and multi-faceted view of halogen bonding interactions. In this way, it is possible to provide a solid framework to interpret the present results and to plan future works.

This Special Issue aims to present new interconnections between experimental and theoretical techniques, with the possibility to explore all fields of chemistry: halogen bond-catalyzed reactions, structure–property correlations, solution and solid-state spectroscopy, functional materials engineering. Therefore, original manuscripts (either full-length articles or short communications) reporting on the combination of experimental and theoretical data, and theoretical works strongly based on published experimental studies (and vice-versa), are welcome, together with perspective and review articles.

Dr. Gianluca Ciancaleoni
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
  • Halogen bonding
  • Computational studies
  • Catalysis
  • Spectroscopy
  • Crystal engineering
  • Bond analysis

Published Papers (5 papers)

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Research

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13 pages, 2417 KiB  
Article
Supramolecular Sandwiches: Halogen-Bonded Coformers Direct [2+2] Photoreactivity in Two-Component Cocrystals
by Jay Quentin, Dale C. Swenson and Leonard R. MacGillivray
Molecules 2020, 25(4), 907; https://doi.org/10.3390/molecules25040907 - 18 Feb 2020
Cited by 14 | Viewed by 2964
Abstract
The halogen-bond (X-bond) donors 1,3- and 1,4-diiodotetrafluorobenzene (1,3-di-I-tFb and 1,4-di-I-tFb, respectively) form cocrystals with trans-1,2-bis(2-pyridyl)ethylene (2,2′-bpe) assembled by N···I X-bonds. In each cocrystal, 2(1,3-di-I-tFb)·2(2,2′-bpe) and (1,4-di-I-tFb)·(2,2′-bpe), the donor molecules support [...] Read more.
The halogen-bond (X-bond) donors 1,3- and 1,4-diiodotetrafluorobenzene (1,3-di-I-tFb and 1,4-di-I-tFb, respectively) form cocrystals with trans-1,2-bis(2-pyridyl)ethylene (2,2′-bpe) assembled by N···I X-bonds. In each cocrystal, 2(1,3-di-I-tFb)·2(2,2′-bpe) and (1,4-di-I-tFb)·(2,2′-bpe), the donor molecules support the C=C bonds of 2,2′-bpe to undergo an intermolecular [2+2] photodimerization. UV irradiation of each cocrystal resulted in stereospecific and quantitative conversion of 2,2′-bpe to rctt-tetrakis(2-pyridyl)cyclobutane (2,2′-tpcb). In each case, the reactivity occurs via face-to-face π-stacked columns wherein nearest-neighbor pairs of 2,2′-bpe molecules lie sandwiched between X-bond donor molecules. Nearest-neighbor C=C bonds are stacked criss-crossed in both cocrystals. The reactivity was ascribed to the olefins undergoing pedal-like motion in the solid state. The stereochemistry of 2,2′-tpcb is confirmed in cocrystals 2(1,3-di-I-tFb)·(2,2′-tpcb) and (1,4-di-I-tFb)·(2,2′-tpcb). Full article
(This article belongs to the Special Issue Halogen Bonds: Combining Experiment and Theory)
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14 pages, 4369 KiB  
Article
The Significance of Halogen Bonding in Ligand–Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D4 Receptor
by Rafał Kurczab, Katarzyna Kucwaj-Brysz and Paweł Śliwa
Molecules 2020, 25(1), 91; https://doi.org/10.3390/molecules25010091 - 25 Dec 2019
Cited by 18 | Viewed by 3063
Abstract
Recently, a computational approach combining a structure–activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen [...] Read more.
Recently, a computational approach combining a structure–activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand–receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand–receptor complex by halogen bonding. Full article
(This article belongs to the Special Issue Halogen Bonds: Combining Experiment and Theory)
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15 pages, 907 KiB  
Article
Halogen-Bond Assisted Photoinduced Electron Transfer
by Bogdan Dereka, Ina Fureraj, Arnulf Rosspeintner and Eric Vauthey
Molecules 2019, 24(23), 4361; https://doi.org/10.3390/molecules24234361 - 29 Nov 2019
Cited by 5 | Viewed by 4286
Abstract
The formation of a halogen-bond (XB) complex in the excited state was recently reported with a quadrupolar acceptor–donor–acceptor dye in two iodine-based liquids (J. Phys. Chem. Lett. 2017, 8, 3927–3932). The ultrafast decay of this excited complex to the ground [...] Read more.
The formation of a halogen-bond (XB) complex in the excited state was recently reported with a quadrupolar acceptor–donor–acceptor dye in two iodine-based liquids (J. Phys. Chem. Lett. 2017, 8, 3927–3932). The ultrafast decay of this excited complex to the ground state was ascribed to an electron transfer quenching by the XB donors. We examined the mechanism of this process by investigating the quenching dynamics of the dye in the S1 state using the same two iodo-compounds diluted in inert solvents. The results were compared with those obtained with a non-halogenated electron acceptor, fumaronitrile. Whereas quenching by fumaronitrile was found to be diffusion controlled, that by the two XB compounds is slower, despite a larger driving force for electron transfer. A Smoluchowski–Collins–Kimball analysis of the excited-state population decays reveals that both the intrinsic quenching rate constant and the quenching radius are significantly smaller with the XB compounds. These results point to much stronger orientational constraint for quenching with the XB compounds, indicating that electron transfer occurs upon formation of the halogen bond. Full article
(This article belongs to the Special Issue Halogen Bonds: Combining Experiment and Theory)
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20 pages, 3447 KiB  
Article
The Halogen-Bond Nature in Noble Gas–Dihalogen Complexes from Scattering Experiments and Ab Initio Calculations
by Francesca Nunzi, Benedetta Di Erasmo, Francesco Tarantelli, David Cappelletti and Fernando Pirani
Molecules 2019, 24(23), 4274; https://doi.org/10.3390/molecules24234274 - 23 Nov 2019
Cited by 6 | Viewed by 2893
Abstract
In order to clarify the nature of the halogen bond (XB), we considered the prototype noble gas–dihalogen molecule (Ng–X2) systems, focusing on the nature, range, and strength of the interaction. We exploited data gained from molecular beam scattering experiments with the [...] Read more.
In order to clarify the nature of the halogen bond (XB), we considered the prototype noble gas–dihalogen molecule (Ng–X2) systems, focusing on the nature, range, and strength of the interaction. We exploited data gained from molecular beam scattering experiments with the measure of interference effects to obtain a suitable formulation of the interaction potential, with the support of high-level ab initio calculations, and charge displacement analysis. The essential interaction components involved in the Ng–X2 adducts were characterized, pointing at their critical balance in the definition of the XB. Particular emphasis is devoted to the energy stability of the orientational Ng–X2 isomers, the barrier for the X2 hindered rotation, and the influence of the X2 electronic state. The present integrated study returns reliable force fields for molecular dynamic simulations in Ng–X2 complexes that can be extended to systems with increasing complexity and whose properties depend on the selective formation of XB. Full article
(This article belongs to the Special Issue Halogen Bonds: Combining Experiment and Theory)
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Review

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17 pages, 3357 KiB  
Review
Charge Displacement Analysis—A Tool to Theoretically Characterize the Charge Transfer Contribution of Halogen Bonds
by Gianluca Ciancaleoni, Francesca Nunzi and Leonardo Belpassi
Molecules 2020, 25(2), 300; https://doi.org/10.3390/molecules25020300 - 11 Jan 2020
Cited by 17 | Viewed by 3149
Abstract
Theoretical bonding analysis is of prime importance for the deep understanding of the various chemical interactions, covalent or not. Among the various methods that have been developed in the last decades, the analysis of the Charge Displacement function (CD) demonstrated to be useful [...] Read more.
Theoretical bonding analysis is of prime importance for the deep understanding of the various chemical interactions, covalent or not. Among the various methods that have been developed in the last decades, the analysis of the Charge Displacement function (CD) demonstrated to be useful to reveal the charge transfer effects in many contexts, from weak hydrogen bonds, to the characterization of σ hole interactions, as halogen, chalcogen and pnictogen bonding or even in the decomposition of the metal-ligand bond. Quite often, the CD analysis has also been coupled with experimental techniques, in order to give a complete description of the system under study. In this review, we focus on the use of CD analysis on halogen bonded systems, describing the most relevant literature examples about gas phase and condensed phase systems. Chemical insights will be drawn about the nature of halogen bond, its cooperativity and its influence on metal-ligand bond components. Full article
(This article belongs to the Special Issue Halogen Bonds: Combining Experiment and Theory)
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