Special Issue "Analysis of Halogen and Other σ-Hole Bonds in Crystals"

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

Deadline for manuscript submissions: closed (10 June 2017)

Special Issue Editors

Guest Editor
Prof. Dr. Peter Politzer

Department of Chemistry, The University of New Orleans, New Orleans, LA 70148, USA
E-Mail
Interests: energetic materials; noncovalent interactions; molecular and crystal properties; reaction force analyses
Guest Editor
Dr. Jane S. Murray

Department of Chemistry, The University of New Orleans, New Orleans, LA 70148, USA
E-Mail
Interests: energetic materials; noncovalent interactions; molecular and crystal properties; reaction force analyses

Special Issue Information

Dear Colleagues,

This Special Issue of Crystals reflects the very significant role that crystallography has played in the recognizing the existence of halogen bonding and in arriving at an understanding of what had sometimes been described as an enigma.  While halogen bonds had already been 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, direction-dependent, 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 the extensions of the bonds, and negative potentials on their lateral sides. These positive regions were labeled σ-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 σ- holes. This accounts for Parthasarathy et al. finding, in surveys of divalent sulfide crystals, that the close contacts of the sulfurs follow patterns analogous to those of halogens.

The importance of halogen bonding and other σ-hole interactions (which includes 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 is intended to present an overview of current activity.  While the emphasis is upon such interactions in crystals, related theoretical and computational analyses have played a key part in the development of the field, which this Special Issue should reflect.

Prof. Dr. Peter Politzer
Prof. Dr. Jane S. Murray
Guest Editors

Manuscript Submission Information

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Keywords

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

Published Papers (9 papers)

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Research

Open AccessArticle Strength and Character of R–X···π Interactions Involving Aromatic Amino Acid Sidechains in Protein-Ligand Complexes Derived from Crystal Structures in the Protein Data Bank
Crystals 2017, 7(9), 273; doi:10.3390/cryst7090273
Received: 1 July 2017 / Revised: 18 August 2017 / Accepted: 30 August 2017 / Published: 8 September 2017
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Abstract
Here, we investigate the strengths of R–X···π interactions, involving both chlorine and bromine, in model systems derived from protein-ligand complexes found in the PDB. We find that the strengths of these interactions can vary significantly, with binding energies ranging from −2.01 to −3.60
[...] Read more.
Here, we investigate the strengths of R–X···π interactions, involving both chlorine and bromine, in model systems derived from protein-ligand complexes found in the PDB. We find that the strengths of these interactions can vary significantly, with binding energies ranging from −2.01 to −3.60 kcal/mol. Symmetry adapted perturbation theory (SAPT) analysis shows that, as would be expected, dispersion plays the largest role in stabilizing these R–X···π interactions, generally accounting for about 50% to 80% of attraction. R–Br···π interactions are, for the most part, found to be stronger than R–Cl···π interactions, although the relative geometries of the interacting pair and the halogen’s chemical environment can also have a strong impact. The two factors that have the strongest impact on the strength of these R–X···π interactions is the distance between the halogen and the phenyl plane as well as the size of the halogen σ-hole. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle Electrostatic Potential and a Simple Extended Electric Dipole Model of Hydrogen Fluoride as Probes of Non-Bonding Electron Pairs in the Cyclic Ethers 2,5-Dihydrofuran, Oxetane and Oxirane
Crystals 2017, 7(9), 261; doi:10.3390/cryst7090261
Received: 7 July 2017 / Revised: 16 August 2017 / Accepted: 22 August 2017 / Published: 25 August 2017
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Abstract
The electrostatic potential near to the oxygen atom in each of the cyclic ethers 2,5-dihydrofuran, oxetane and oxirane has been calculated by using a distributed multipole analysis (DMA) of each molecule. The electrostatic potential energy V(φ) of a unit non-perturbing
[...] Read more.
The electrostatic potential near to the oxygen atom in each of the cyclic ethers 2,5-dihydrofuran, oxetane and oxirane has been calculated by using a distributed multipole analysis (DMA) of each molecule. The electrostatic potential energy V(φ) of a unit non-perturbing positive charge was calculated (via the DMA of the cyclic ether molecule) as a function of the angle φ between the C2 axis of the cyclic ether and a vector of length r from the O atom to the unit charge. The resulting potential energy functions each has two equivalent minima. The angles φmin at the minima are compared with the angles φ0 and φe made by the O⋯H bond with the C2 axes in the cyclic ether⋯HF complexes, as determined by rotational spectroscopy and ab initio calculations at the CCSD(T)-F12c/cc-pVTZ-F12 level of theory, respectively. An electrostatic model of cyclic ether⋯HF complexes in which the DMA of the cyclic ether interacts with a simple extended electric dipole representation of HF is also used to calculate the variation of the potential energy VHF(φ) of the HF molecule with φ. The angles φmin generated by this model are also compared with φ0 and φe. The extent to which the electrostatic potential and the extended electric dipole HF model can be used as probes for the directions of non-bonding electron pairs carried by O in these cyclic ethers is discussed. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle The Role of Halogen Bonding in Controlling Assembly and Organization of Cu(II)-Acac Based Coordination Complexes
Crystals 2017, 7(7), 226; doi:10.3390/cryst7070226
Received: 23 June 2017 / Revised: 15 July 2017 / Accepted: 17 July 2017 / Published: 20 July 2017
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Abstract
In order to explore the use of non-covalent interactions in the deliberate assembly of metal-supramolecular architectures, a series of β-diketone based ligands capable of simultaneously acting as halogen-bond donors and chelating ligands were synthesized. The three ligands, L1, L2, and L3
[...] Read more.
In order to explore the use of non-covalent interactions in the deliberate assembly of metal-supramolecular architectures, a series of β-diketone based ligands capable of simultaneously acting as halogen-bond donors and chelating ligands were synthesized. The three ligands, L1, L2, and L3, carry ethynyl-activated chlorine, bromine, and iodine atoms, respectively and copper(II) complexes of all three ligands were crystallized from different solvents, acetonitrile, ethyl acetate, and nitromethane in order to study specific ligand-solvent interaction. The free ligands L2 and L3, with more polarizable halogen atoms, display C-X⋯O halogen bonds in the solid state, whereas the chloro-analogue (L1) does not engage in halogen bonding. Both acetonitrile and ethyl acetate act as halogen-bond acceptors in Cu(II)-complexes of L2 and L3 whereas nitromethane is present as a ‘space-filling’ guest without participating in any significant intermolecular interactions in Cu(II)-complexes of L2. L3, which is decorated with an iodoethynyl moiety and consistently engages in halogen-bonds with suitable acceptors. This systematic structural analysis allows us to rank the relative importance of a variety of electron-pair donors in these metal complexes. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle The Interplay between Various σ- and π-Hole Interactions of Trigonal Boron and Trigonal Pyramidal Arsenic Triiodides
Crystals 2017, 7(7), 225; doi:10.3390/cryst7070225
Received: 26 June 2017 / Revised: 17 July 2017 / Accepted: 17 July 2017 / Published: 19 July 2017
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Abstract
Boron and arsenic triiodides (BI3 and AsI3, respectively) are similar molecules that differ mainly in their geometries. BI3 is a planar trigonal molecule with D3h symmetry, while AsI3 exhibits a trigonal pyramidal shape with C3v symmetry.
[...] Read more.
Boron and arsenic triiodides (BI3 and AsI3, respectively) are similar molecules that differ mainly in their geometries. BI3 is a planar trigonal molecule with D3h symmetry, while AsI3 exhibits a trigonal pyramidal shape with C3v symmetry. Consequently, the As atom of the AsI3 molecule has three σ-holes, whereas the B atom of the BI3 molecule has two symmetrical π-holes. Additionally, there are σ-holes on the iodine atoms in the molecules studied. In the first step, we have studied σ-hole and π-hole interactions in the known monocrystals of BI3 and AsI3. Quantum mechanical calculations have revealed that the crystal packing of BI3 is dominated by π-hole interactions. In the case of AsI3, the overall contribution of dihalogen bonding is comparable to that of pnictogen bonding. Additionally, we have prepared the [Na(THF)6]+[I(AsI3)6](AsI3)2 complex, which can be described as the inverse coordination compound where the iodine anion is the center of the aggregate surrounded by six AsI3 molecules in the close octahedral environment and adjacent two molecules in remote distances. This complex is, besides expected dihalogen and pnictogen bonds, also stabilized by systematically attractive dispersion interactions. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle σ-Holes on Transition Metal Nanoclusters and Their Influence on the Local Lewis Acidity
Crystals 2017, 7(7), 222; doi:10.3390/cryst7070222
Received: 10 June 2017 / Revised: 10 July 2017 / Accepted: 11 July 2017 / Published: 14 July 2017
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Abstract
Understanding the molecular interaction behavior of transition metal nanoclusters lies at the heart of their efficient use in, e.g., heterogeneous catalysis, medical therapy and solar energy harvesting. For this purpose, we have evaluated the applicability of the surface electrostatic potential [VS
[...] Read more.
Understanding the molecular interaction behavior of transition metal nanoclusters lies at the heart of their efficient use in, e.g., heterogeneous catalysis, medical therapy and solar energy harvesting. For this purpose, we have evaluated the applicability of the surface electrostatic potential [VS(r)] and the local surface electron attachment energy [ES(r)] properties for characterizing the local Lewis acidity of a series of low-energy TM13 transition metal nanoclusters (TM = Au, Cu, Ru, Rh, Pd, Ir, Pt, Co), including also Pt7Cu6. The clusters have been studied using hybrid Kohn–Sham density functional theory (DFT) calculations. The VS(r) and ES(r), evaluated at 0.001 a.u. isodensity contours, are used to analyze the interactions with H2O. We find that the maxima of VS(r), σ-holes, are either localized or diffuse. This is rationalized in terms of the nanocluster geometry and occupation of the clusters’s, p and d valence orbitals. Our findings motivate a new scheme for characterizing σ-holes as σs (diffuse), σp (localized) or σd (localized) depending on their electronic origin. The positions of the maxima in VS(r) (and minima in ES(r)) are found to coincide with O-down adsorption sites of H2O, whereas minima in VS(r) leads to H-down adsorption. Linear relationships between VS,max (and ES,min) and H2O interaction energies are further discussed. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle σ-Hole Interactions: Perspectives and Misconceptions
Crystals 2017, 7(7), 212; doi:10.3390/cryst7070212
Received: 4 June 2017 / Revised: 21 June 2017 / Accepted: 22 June 2017 / Published: 12 July 2017
Cited by 1 | PDF Full-text (6169 KB) | HTML Full-text | XML Full-text
Abstract
After a brief discussion of the σ-hole concept and the significance of molecular electrostatic potentials in noncovalent interactions, we draw attention to some common misconceptions that are encountered in that context: (1) Since the electrostatic potential reflects the contributions of both the nuclei
[...] Read more.
After a brief discussion of the σ-hole concept and the significance of molecular electrostatic potentials in noncovalent interactions, we draw attention to some common misconceptions that are encountered in that context: (1) Since the electrostatic potential reflects the contributions of both the nuclei and the electrons, it cannot be assumed that negative potentials correspond to “electron-rich” regions and positive potentials to “electron-poor” ones; (2) The electrostatic potential in a given region is determined not only by the electrons and nuclei in that region, but also by those in other portions of the molecule, especially neighboring ones; (3) A σ-hole is a region of lower electronic density on the extension of a covalent bond, not an electrostatic potential; (4) Noncovalent interactions are between positive and negative regions, which are not necessarily associated with specific atoms, so that “close contacts” between atoms do not always indicate the actual interactions. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle Halogen-Bonded Co-Crystals of Aromatic N-oxides: Polydentate Acceptors for Halogen and Hydrogen Bonds
Crystals 2017, 7(7), 214; doi:10.3390/cryst7070214
Received: 7 June 2017 / Revised: 6 July 2017 / Accepted: 7 July 2017 / Published: 11 July 2017
Cited by 1 | PDF Full-text (4591 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Seventeen new halogen-bonded co-crystals characterized by single crystal X-ray analysis are presented from 8 × 4 combinations using methyl-substituted pyridine N-oxides and 1,ω-diiodoperfluoroalkanes. The N−O group in six of 17 co-crystals is monodentate and 11 have μ-O,O bidentate halogen
[...] Read more.
Seventeen new halogen-bonded co-crystals characterized by single crystal X-ray analysis are presented from 8 × 4 combinations using methyl-substituted pyridine N-oxides and 1,ω-diiodoperfluoroalkanes. The N−O group in six of 17 co-crystals is monodentate and 11 have μ-O,O bidentate halogen bond acceptor modes. Remarkably, the N−O group in co-crystals of 3-methyl-, 4-methyl- and 3,4-dimethylpyridineN-oxides with octafluoro-1,4-diiodobutane acted as a μ-O,O,O,O halogen and hydrogen bond acceptor, while acting as a μ-O,O,O acceptor in the co-crystal of 2,5-dimethylpyridineN-oxide and tetrafluoro-1,2-diiodoethane. The C−H···O−N hydrogen bonds demonstrated the polydentate cooperativity of the N−O group as a mixed halogen-hydrogen bond acceptor. The co-crystal of 2,4,6-trimethylpyridineN-oxide and dodecafluoro-1,6-diiodohexane exhibited C−I···O−N+ halogen bonds with RXB value 0.76, the shortest of its kind compared to previously reported structures. The RXB values between 0.76 and 0.83 suggested that the C−I···O−N halogen bonds are moderately strong compared to our previously studied N−I···O−N system, with RXB in the order 0.66. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle On the Importance of Halogen–Halogen Interactions in the Solid State of Fullerene Halides: A Combined Theoretical and Crystallographic Study
Crystals 2017, 7(7), 191; doi:10.3390/cryst7070191
Received: 31 May 2017 / Revised: 17 June 2017 / Accepted: 22 June 2017 / Published: 26 June 2017
Cited by 1 | PDF Full-text (2987 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In this manuscript, we combined DFT (Density Functional Theory) calculations (BP86-D3/def2-TZVP level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the role of halogen–halogen interactions in the crystal structure of fullerene halides. We have used a theoretical model
[...] Read more.
In this manuscript, we combined DFT (Density Functional Theory) calculations (BP86-D3/def2-TZVP level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the role of halogen–halogen interactions in the crystal structure of fullerene halides. We have used a theoretical model of a halogenated C60 and evaluated the formation of halogen–halogen complexes between F, Cl, Br and I derivatives. In addition, we also carried out AIM (Atoms in Molecules) and NBO (Natural Bonding Orbital) analyses to further describe and characterize the interactions described herein. Finally, we have carried out a search in the CSD and found several X-ray structures where these interactions are present and important in governing the crystal packing of the fullerene halides, thus giving reliability to the results derived from the calculations. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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Open AccessArticle Lewis Acid Properties of Tetrel Tetrafluorides—The Coincidence of the σ-Hole Concept with the QTAIM Approach
Crystals 2017, 7(2), 43; doi:10.3390/cryst7020043
Received: 19 January 2017 / Revised: 2 February 2017 / Accepted: 3 February 2017 / Published: 8 February 2017
Cited by 1 | PDF Full-text (1924 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Tetrel bond is analysed for a series of ZF4 (Z = C, Si, Ge) complexes with one and two NH3 or AsH3 ligands. The MP2/aug-cc-pVTZ calculations were performed and supported by results of the Quantum Theory of “Atoms in Molecules”
[...] Read more.
Tetrel bond is analysed for a series of ZF4 (Z = C, Si, Ge) complexes with one and two NH3 or AsH3 ligands. The MP2/aug-cc-pVTZ calculations were performed and supported by results of the Quantum Theory of “Atoms in Molecules” (QTAIM) and the Natural Bond Orbitals (NBO) approaches. The Z-tetrel atoms of complexes analysed interact through their σ-holes with nitrogen or arsenic Lewis base centres; these interactions correspond to the Z…N/As bond paths according to the QTAIM approach. The QTAIM and NBO results show that these interactions are relatively strong and they possess numerous characteristics of covalent bonds. The theoretical analysis is supported by the discussion on crystal structures which are characterized by the same type interactions. Full article
(This article belongs to the Special Issue Analysis of Halogen and Other σ-Hole Bonds in Crystals)
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