Cyclic networks of halogen-bonding interactions in molecular self-assemblies: a theoretical N—X...NversusC—X...N investigation

2017 ◽  
Vol 73 (2) ◽  
pp. 179-187
Author(s):  
Ruben D. Parra ◽  
Álvaro Castillo
Keyword(s):  
Electron Density ◽  
Self Assembly ◽  
Metal Ion ◽  
Halogen Atom ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Nbo Analysis ◽  
Binding Energies ◽  
Cyclic Network ◽  
Ability To Drive

The geometries and energetics of molecular self-assembly structures that contain a sequential network of cyclic halogen-bonding interactions are investigated theoretically. The strength of the halogen-bonding interactions is assessed by examining binding energies, electron charge transfer (NBO analysis) and electron density at halogen-bond critical points (AIM theory). Specifically, structural motifs having intramolecular N—X...N (X= Cl, Br, or I) interactions and the ability to drive molecular self-assemblyviathe same type of interactions are used to construct larger self-assemblies of up to three unit motifs. N—X...N halogen-bond cooperativity as a function of the self-assembly size, and the nature of the halogen atom is also examined. The cyclic network of the halogen-bonding interactions provides a suitable cavity rich in electron density (from the halogen atom lone pairs not involved in the halogen bonds) that can potentially bind an electron-deficient species such as a metal ion. This possibility is explored by examining the ability of the N—X...N network to bind Na+. Likewise, molecular self-assembly structures driven by the weaker C—X...N halogen-bonding interactions are investigated and the results compared with those of their N—X...N counterparts.

Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective

2010 ◽  
Vol 88 (8) ◽  
pp. 759-768 ◽  
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Potential Energy Surfaces ◽  
Metal Ion ◽  
Theoretical Perspective ◽  
Binding Energies ◽  
Interacting Systems ◽  
Intramolecular Hydrogen ◽  
Energy Surfaces ◽  
Doubly Charged

The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.

scholarly journals Functional properties ensue from cooperation of different interactions

2014 ◽  
Vol 70 (a1) ◽  
pp. C630-C630
Author(s):  
Giuseppe Resnati ◽  
Pierangelo Metrangolo ◽  
Giancarlo Terraneo ◽  
Gabriella Cavallo
Keyword(s):  
Hydrogen Bond ◽  
Self Assembly ◽  
Halogen Atom ◽  
Crystal Packing ◽  
Halogen Bond ◽  
Decisive Role ◽  
Solid Materials ◽  
Two Component ◽  
Confined Environment ◽  
Specific Profile

According to the definition recommended by IUPAC [1], a halogen bond (XB) occurs when there is evidence of a net attractive interaction between an electrophilic region in a halogen atom and a nucleophilic region in another atom. The halogen bond has many similarities with the hydrogen bond (HB) and here we discuss the specific profile of the two interactions. We also show how the cooperation between the two interactions afford crystalline systems possessing unique and useful properties. For instance, the diiodide, dibromide, and dichloride salts of the 1,6-bis(trimethylammonium)hexane cation (hexamethonium, HMET2+, cation) react with two equivalents of diiodine in a solid-gas reaction and the corresponding bis-trihalides (halogen bonded adducts) are formed [2]. No cavities are present in the starting dihalides and the observed behavior reveals the dynamically porous character of bis(trimethylammonium)alkane dihalides. In the obtained bis-trihalides a net of X-···H-C HBs (X=Cl, Br, I) plays a decisive role in controlling the crystal packing: Four cationic columns embrace an anionic twin column formed by stacking of trihalide dimers. When heated, these bis-trihalides lose one diiodine molecule and the virtually unknown tetrahalide dianions [I4]2-, [I2Br2] 2-, and [I2Cl2]2-are formed. These dianions are the product of the double pinning of a diiodine molecule by two halide anions via strong XBs. The last two tetrahalides were never obtained in solution. The confined environment of dynamically porous materials clearly confers useful synthetic opportunities relative to solution-state processes. Other cases are described wherein XB and HB cooperate in driving self-assembly processes which afford solid materials endowed with useful properties. For instance, we will discuss the formation of two-component supramolecular gels [3] wherein a bis-urea and a diiodoarene self-assemble via cooperative XB and HB.

scholarly journals Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes

Materials ◽  
2020 ◽  
Vol 13 (9) ◽  
pp. 2163 ◽  
Author(s):  
Ibon Alkorta ◽  
Jose Elguero ◽  
Josep M. Oliva-Enrich
Keyword(s):  
Electron Density ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Bond Critical Point ◽  
Total Energy Density ◽  
Comparison Of The Results ◽  
Intermolecular Distances

A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.

scholarly journals Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 798
Author(s):  
Iñigo Iribarren ◽  
Goar Sánchez-Sanz ◽  
Cristina Trujillo
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Anion Recognition ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Binding Energies ◽  
Bond Critical Point ◽  
Density Values ◽  
Intramolecular Hydrogen

A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X⋯I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

scholarly journals A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Inorganics ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 119 ◽  
Author(s):  
Hardin ◽  
Ellington ◽  
Nguyen ◽  
Rheingold ◽  
Tschumper ◽  
...  
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Normal Modes ◽  
Halogen Bonding ◽  
Building Blocks ◽  
Molecular Assembly ◽  
X Ray ◽  
X Ray Crystallography

Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

Applications of halogen bonding in solution

2015 ◽  
Vol 87 (1) ◽  
pp. 15-41 ◽  
Author(s):  
Andreas Vargas Jentzsch
Keyword(s):  
Halogen Atom ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Solvent System ◽  
Noncovalent Interaction ◽  
Solution Phase ◽  
Anion Binding ◽  
Lewis Bases ◽  
The Past ◽  
Catalytic Applications

AbstractHalogen bonding is the noncovalent interaction where the halogen atom acts as an electrophile towards Lewis bases. Known for more than 200 years, only recently it has attracted interest in the context of solution-phase applications, especially during the last decade which was marked by the introduction of multitopic systems. In addition, the small yet rich collection of halogen-bond donor moieties that appeared in this period is shown to be versatile enough as to be applied in virtually any solvent system. This review covers the applications of halogen bonding in solution during the past ten years in a semi-comprehensive way. Emphasis is made on molecular recognition, catalytic applications and anion binding and transport. Medicinal applications are addressed as well with key examples. Focussing on the major differences observed for halogen bonding, as compared to the ubiquitous hydrogen bonding, it aims to contribute to the design of future solution-phase applications.

scholarly journals Porphyrin’s Ring Current as a Driving Force for Halogen Bond Interactions: A Computational Study

2019 ◽  
Author(s):  
Jyoti Rani ◽  
Hatem M. Titi ◽  
Ranjan Patra
Keyword(s):  
Self Assembly ◽  
Driving Force ◽  
Ring Current ◽  
Computational Study ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Porphyrin Ring

<p>We demonstrate herein a computational study probing the influence of metalloporphyrin ring current directionality on intermolecular halogen bonding (XB) during supramolecular self-assembly. The results demonstrate that porphyrin ring current can activate or deactivate halogen bonding interactions, an essential superamolecular driving force.</p>

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

Synthesis of Chiral Triazole-Based Halogen Bond Donors

Synthesis ◽  
2019 ◽  
Vol 51 (10) ◽  
pp. 2128-2135 ◽  
Author(s):  
Mikk Kaasik ◽  
Sandra Kaabel ◽  
Kadri Kriis ◽  
Ivar Järving ◽  
Tõnis Kanger
Keyword(s):  
Click Chemistry ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Easy Access ◽  
Enantiomerically Pure ◽  
Wide Variability ◽  
Supramolecular Aggregation

The number of applications that use halogen bonding in the fields of self-assembly, supramolecular aggregation, and catalysis is growing. However, the accessibility of chiral halotriazoles shows that there is still a lot more to explore. The simple click-chemistry is applied for the straightforward synthesis of enantiomerically pure mono- and bidentate as well as multifunctional iodotriazole-based XB donors. The methodology is characterized by a wide variability due to easy access of chiral azides.

Sign in / Sign up

Export Citation Format

Share Document