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Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd...
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Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition)

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: 20 July 2026 | Viewed by 7506

Special Issue Editor

Dr. Jane S. Murray

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Guest Editor
Department of Chemistry, The University of New Orleans, New Orleans, LA 70148, USA
Interests: energetic materials; noncovalent interactions; molecular and crystal properties; reaction force analyses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Crystals reflects the very significant role that crystallography has played in recognizing the existence of halogen bonding and arriving at an understanding of what has sometimes been described as an enigma. While halogen bonds were already observed in the 19th century, a major advance was the series of crystallographic studies by Hassel et al. in the 1960s. They characterized complexes between covalently bonded halogen atoms and oxygen/nitrogen Lewis bases, i.e., attractive interactions between two ostensibly negative sites.

Some years later, surveys of crystal structures by Murray-Rust et al. revealed close contacts and direction dependence between halogen atoms and both electrophiles and nucleophiles. The explanation came in 1992 with the surprising observation by Brinck et al. that covalently bonded halogen atoms can have regions of positive electrostatic potential along with extensions of these bonds and negative potentials on their lateral sides. These positive regions were labeled sigma holes by Clark et al. in 2007. Between 2007 and 2009, Murray et al. showed that covalently bonded atoms of Groups IV-VI can also have positive sigma holes. This accounts for Parthasarathy et al.’s finding, in surveys of divalent sulfide crystals, that the close contact of the sulfur follows patterns analogous to those of halogens.

The importance of halogen bonding and other sigma–hole interactions (which include hydrogen bonding) in biological systems and in areas such as the design of new materials is now well established and continues to increase.

This Special Issue intends to provide an overview of current activity. While emphasis is placed upon such interactions in crystals, related theoretical and computational analyses have also played a key part in the development of this field, which this Special Issue aims to reflect.

Dr. Jane S. Murray
Guest Editor

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Keywords

  • halogen bonding
  • sigma-hole bonding
  • electrostatic potentials
  • nature of noncovalent interactions

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Related Special Issue

Published Papers (6 papers)

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Research

18 pages, 6454 KB  
Article
Hydrogen Bond Triggers the Self-Assembly of Dihydrogen Arsenates into Supramolecular Anion⋯Anion Adducts
by Cristina Lo Iacono, Edem R. Chakalov, Roberta Beccaria, Araghni Bhattacharya, Andrea Pizzi, Peter M. Tolstoy and Giuseppe Resnati
Crystals 2026, 16(3), 162; https://doi.org/10.3390/cryst16030162 - 26 Feb 2026
Viewed by 686
Abstract
Eight H-bonded salts of arsenic acid and nitrogen bases (2,4,6-trimethylpyridine, pyridine-2,6-diamine, pyridin-4-ol, 4-methoxypyridine, 4-methoxyaniline, 1,3,5-triazine-2,4,6-triamine, diethylamine and N1,N1,N2,N2-tetraethylethane-1,2-diamine) were studied in the solid state by single crystal X-ray diffraction technique and DFT [...] Read more.
Eight H-bonded salts of arsenic acid and nitrogen bases (2,4,6-trimethylpyridine, pyridine-2,6-diamine, pyridin-4-ol, 4-methoxypyridine, 4-methoxyaniline, 1,3,5-triazine-2,4,6-triamine, diethylamine and N1,N1,N2,N2-tetraethylethane-1,2-diamine) were studied in the solid state by single crystal X-ray diffraction technique and DFT calculations. In all cases quite short (≤2.65 Å) OHO bonds were found in the self-assembled supramolecular ribbons or 2D networks of dihydrogen arsenates, constituting a repertoire of five different H-bonding patterns (motifs). The electron localization function maps revealed the spots of the nucleophilic sites on oxygen atoms that determine the preferable directions for H-bonding of H2AsO4− anions observed in the crystal packing. Analysis of the electrostatic potential maps for isolated species has demonstrated that upon H-bonding between H2AsO4− anions and protonated nitrogen bases, NH+⋯−OAsO(OH)2, the redistribution of electron density within the anion provides otherwise virtually non-existent electrophilic sites on hydrogen atoms, which balances the Coulomb repulsion and allows for the anion⋯anion pairing within the crystal. The topological analysis of the calculated crystalline electron density after relaxation of the hydrogen atoms’ positions was used to classify the OHO bonds as moderately strong ones (with an interaction energy up to 65 kJ/mol) and revealed a high degree of ionicity of molecular moieties within ion pairs (with an absolute charge up to 0.87 e). For the strongest OHO and NHO bonds, the noticeable covalent character was shown by using the crystal orbital Hamiltonian population analysis. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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17 pages, 1865 KB  
Article
Halogens On, H-Bonds Off—Insights into Structure Control of Dihalogenated Imidazole Derivatives
by Luca Mensing, Marcus Layh and Marian Hebenbrock
Crystals 2025, 15(11), 1000; https://doi.org/10.3390/cryst15111000 - 20 Nov 2025
Viewed by 889
Abstract
Halogen bonds play an important role in the targeted generation of solid-state structures, with polyhalogenated compounds enabling the simultaneous formation of various interactions. In this manuscript, we investigate the interactions of dihalogenated compounds in the solid state. Unlike investigated in previous studies, the [...] Read more.
Halogen bonds play an important role in the targeted generation of solid-state structures, with polyhalogenated compounds enabling the simultaneous formation of various interactions. In this manuscript, we investigate the interactions of dihalogenated compounds in the solid state. Unlike investigated in previous studies, the introduction of protective groups in these compounds prevents the formation of dominant hydrogen bonds. The structures of diiodo imidazole derivatives are compared with the analogous dibromo compounds. A total of four different protective groups (two benzylic and two oxycarbonyl protective groups) are introduced and the respective compounds are characterized by X-ray crystallography. The significance of the protective groups for the solid-state structure can be distinguished on the basis of the additional donor atoms and functional groups. It can be seen that the iodo compounds in particular are capable of forming halogen bonds and that additional structural motifs can be generated by suitable protective groups. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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16 pages, 3585 KB  
Article
Crystal Structure and Optical Behavior of Diamino-Substituted 1,4-Benzoquinones
by Anastasija Gaile, Sergey Belyakov, Svetlana Zhizhkun and Nelli Batenko
Crystals 2025, 15(11), 986; https://doi.org/10.3390/cryst15110986 - 15 Nov 2025
Viewed by 782
Abstract
Reactions of benzoquinone with amines can potentially lead to the formation of coupled merocyanine or merocyanine/polymethine systems. In this study, several diamino-substituted 1,4-benzoquinones were synthesized. The crystal structures for three derivatives bearing 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethyl)amino substituents were determined using single-crystal X-ray crystallographic analysis. [...] Read more.
Reactions of benzoquinone with amines can potentially lead to the formation of coupled merocyanine or merocyanine/polymethine systems. In this study, several diamino-substituted 1,4-benzoquinones were synthesized. The crystal structures for three derivatives bearing 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethyl)amino substituents were determined using single-crystal X-ray crystallographic analysis. A characteristic feature of all molecular structures is the presence of an extensive network of intermolecular interactions, significantly stabilized by hydrogen bonding. Additionally, changes in the optical behavior of the synthesized compounds were monitored by UV-Vis spectroscopy in the presence of Cu2+ and Zn2+ ions, followed by the addition of primary, secondary or biogenic (butane-1,4-diamine) amines. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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24 pages, 10390 KB  
Article
Electronic Structure and Binding Characteristics of Ionic Liquid Ions on Li-Metal Surfaces Through a DFT Approach
by Luis A. Selis, Dinau Velazco-Lorenzo, Juan Quillas and Diego E. Galvez-Aranda
Crystals 2025, 15(11), 928; https://doi.org/10.3390/cryst15110928 - 28 Oct 2025
Cited by 1 | Viewed by 1678
Abstract
Understanding the interactions between ionic liquid ions and lithium-metal surfaces is critical for designing safer and more efficient lithium metal batteries. In this work, we use density functional theory to investigate the electronic structure, binding energies, work-function shifts and interfacial charge redistribution of [...] Read more.
Understanding the interactions between ionic liquid ions and lithium-metal surfaces is critical for designing safer and more efficient lithium metal batteries. In this work, we use density functional theory to investigate the electronic structure, binding energies, work-function shifts and interfacial charge redistribution of several ionic liquid ions, including FSI−, TFSI−, PF6−, BF4−, DFOB−, Pyr14+, and EMIM+, on a Li-metal anode (Lim). Absorption orientation-dependent effects are examined for each molecule. Specifically, differences in charge density and electron localization function analyses revealed unique patterns of electron accumulation and delocalization that highlighted specific atomic roles in interfacial bonding. Interfacial charge transfer is analyzed through Bader charges, revealing a moderate charge redistribution for the cations (EMIM+, Pyr14+), and a more significant charge uptake for the reactive anions (FSI−, TFSI−, DFOB−). Among cations, EMIM+ was determined to have the most interfacial stability, while Pyr14+ displayed mid-level reactivity. For the anions, varying tendencies for bond formation with lithium metal and potential fragmentation could be determined. Overall, these discoveries detail an atomistic analysis of ionic liquid to Lim interactions providing additional pathways for molecular design techniques to stabilize electrolytes performing not high-cost computational calculations. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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14 pages, 1605 KB  
Article
Supramolecular Switching by Substituent Tuning: A Crystal Engineering Study of 2-Amino- and 2,3-Diamino-5-Halogenopyridines
by Irina S. Konovalova and Guido J. Reiss
Crystals 2025, 15(8), 700; https://doi.org/10.3390/cryst15080700 - 31 Jul 2025
Viewed by 1181
Abstract
The crystal structures of the 2-amino-5-halogenopyridines (halogen = Cl (1), Br (2)) and 2,3-diamino-5-halogenopyridines (halogen = Cl (3), Br (4)) were compared with respect to their intermolecular interactions. An ab-initio-based method for evaluating the interaction [...] Read more.
The crystal structures of the 2-amino-5-halogenopyridines (halogen = Cl (1), Br (2)) and 2,3-diamino-5-halogenopyridines (halogen = Cl (3), Br (4)) were compared with respect to their intermolecular interactions. An ab-initio-based method for evaluating the interaction energies between molecules was employed to estimate the driving forces of crystal formation. As a result, regularities in crystal structure organization were identified. For compounds 1 and 2, a dimeric building unit is formed by two N–H…Npyr hydrogen bonds. These dimers are further connected to neighboring units by C–H…π, C–H…N, N…X (X = Cl, Br), and non-specific interactions. The aforementioned intermolecular interactions give rise to layered structures that are similar but not isotypical. No significant contributions from π–π or N–H…N(H2) interactions are observed in 1 and 2. The structures of 3 and 4 are isotypical and crystallize in the non-centrosymmetric space group P212121. The most important intermolecular interactions are N–H…Npyr, N–H…N(H2), and stacking interactions. These interactions lead to identical columnar-layered structures in both 3 and 4. No significant contributions from halogen bonds of the type N…X (X = Cl, Br) are found in 3 and 4. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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12 pages, 5083 KB  
Article
α-Halogenated Curcumins
by Phuong-Truc T. Pham and Mamoun M. Bader
Crystals 2024, 14(12), 1041; https://doi.org/10.3390/cryst14121041 - 30 Nov 2024
Cited by 1 | Viewed by 1492
Abstract
α- or 4-Substituted curcumin analogues are scarce. We describe herein the syntheses and crystal structures of the first α-halogenated curcumin derivatives: (1E,6E)-1,7-bis (4-hydroxy-3-methoxyphenyl)-4-bromo-5-hydroxy-1,3,6-heptatriene-3-one or (4-bromocurcumin) (1) and (1E,6E)-1,7-bis (4-hydroxy-3-methoxyphenyl)-4-chloro-5-hydroxy-1,3,6-heptatriene-3-one or (4-chlorocurcumin) (2). We note that the key step in [...] Read more.
α- or 4-Substituted curcumin analogues are scarce. We describe herein the syntheses and crystal structures of the first α-halogenated curcumin derivatives: (1E,6E)-1,7-bis (4-hydroxy-3-methoxyphenyl)-4-bromo-5-hydroxy-1,3,6-heptatriene-3-one or (4-bromocurcumin) (1) and (1E,6E)-1,7-bis (4-hydroxy-3-methoxyphenyl)-4-chloro-5-hydroxy-1,3,6-heptatriene-3-one or (4-chlorocurcumin) (2). We note that the key step in the successful synthesis of the bromo-analog is the use of slightly acidic media to favor the diketo form of curcumin prior to carrying out the reaction. Both newly prepared compounds assume the keto–enol form in the solid state and crystallize in the monoclinic space group P21/c with four molecules in the unit cell each with slightly different dimensions. Inter- and intra- molecular hydrogen bonds were observed in the two structures. Most significant observed features were the inter-molecular O…O distances of 2.842 and 2.840 Å and intra-molecular O…O distances of 2.460 and 2.451 Å for bromo-or (1) and chloro- or (2) derivatives, respectively. No close halogen…halogen contacts were observed in either of the two structures. Both molecules are nearly planar with torsion angles of 0.54 and 1.16 °C between the planes of two terminal phenyl groups for (1) and (2), respectively. π-Stacks were observed in both structures with interplanar distances of 3.367 and 3.454 Å for the bromo- and chloro- compounds, respectively. Hirshfeld surface analysis confirms quantitively a picture of the inter- and intra-molecular interactions in both compounds compared with polymorph I (the most common form) of curcumin. UV–Vis absorption spectra are shifted to higher wavelengths with lmax of 475 and 477 nm for compounds 1 and 2, respectively, compared with 442 nm in dichloromethane solutions. The newly synthesized molecules will open the door for numerous possible synthetic modifications of the α-carbon to prepare valuable analogues of curcumin with more favorable solubility profiles. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals (2nd Edition))
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