Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

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.

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Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study

Crystals ◽

10.3390/cryst9040224 ◽

2019 ◽

Vol 9 (4) ◽

pp. 224 ◽

Cited By ~ 7

Author(s):

Yannick Roselló ◽

Mónica Benito ◽

Elies Molins ◽

Miquel Barceló-Oliver ◽

Antonio Frontera

Keyword(s):

Density Functional ◽

Halogen Bond ◽

Lone Pair ◽

Halogen Bonding ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Adenine Ring ◽

Bonding Interaction ◽

Donor Ability ◽

Adenine Derivative

In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.

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

Inorganics ◽

10.3390/inorganics7100119 ◽

2019 ◽

Vol 7 (10) ◽

pp. 119 ◽

Cited By ~ 2

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.

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Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Frontiers in Chemistry ◽

10.3389/fchem.2021.623595 ◽

2021 ◽

Vol 9 ◽

Author(s):

Goulielmina Anyfanti ◽

Antonio Bauzá ◽

Lorenzo Gentiluomo ◽

João Rodrigues ◽

Gustavo Portalone ◽

...

Keyword(s):

Density Functional ◽

Halogen Bond ◽

Interaction Strength ◽

Covalent Bond ◽

Halogen Bonding ◽

Molar Ratio ◽

Halogen Bonds ◽

Functional Theory ◽

Ligand Exchange Reaction ◽

Density Values

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X–X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X–X···N with the chloride of N-chlorosuccinimide lead to Cl–X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (−11.2 to −12.5 kcal/mol) are smaller than the values for (imide)I···N (−8.4 to −29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N–I covalent bond and I···N non-covalent bond of a (saccharin)N–I···N motif signify the covalent character for I···N halogen bonding.

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Computational study on the mechanism of metal-free photochemical borylation of aryl halides

10.22541/au.162550161.13972740/v1 ◽

2021 ◽

Author(s):

Chenhao Tu ◽

Nana Ma ◽

Qingli Xu ◽

Wenyue Guo ◽

Lanxin Zhou ◽

...

Keyword(s):

Density Functional ◽

Uv Light ◽

Computational Study ◽

Halogen Bond ◽

Bond Cleavage ◽

Aryl Halides ◽

Homolytic Cleavage ◽

Functional Theory ◽

Aryl Radicals

C-radical borylation is an significant approach for the construction of carbon−boron bond. Photochemical borylation of aryl halides successfully applied this strategy. However, precise mechanisms, such as the generation of aryl radicals and the role of base additive(TMDAM) and water, remain controversy in these reactions. In this study, photochemical borylation of aryl halides has been researched by density functional theory (DFT) calculations. Indeed, the homolytic cleavage of the C−X bond under irradiation with UV-light is a key step for generation of aryl radicals. Nevertheless, the generation of aryl radicals may also undergo the process of single electron transfer and the heterolytic carbon-halogen bond cleavage sequence, and the latter is favorable during the reaction.

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

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520617002335 ◽

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.

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Halogen Bonding Organocatalysis Enhanced through Intramolecular Hydrogen Bonds

Chemical Communications ◽

10.1039/d1cc05475a ◽

2022 ◽

Author(s):

Asia Marie S Riel ◽

Daniel Adam Decato ◽

Jiyu Sun ◽

Orion Berryman

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Halogen Bond ◽

Direct Interaction ◽

Halogen Bonding ◽

Intramolecular Hydrogen Bonds ◽

Intramolecular Hydrogen

Recent results indicate a halogen bond donor is strengthened through direct interaction with a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond enhanced Halogen Bond...

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Computational study of Mg insertion into amorphous silicon: advantageous energetics over crystalline silicon for Mg storage

MRS Proceedings ◽

10.1557/opl.2013.1036 ◽

2013 ◽

Vol 1540 ◽

Cited By ~ 1

Author(s):

Fleur Legrain ◽

Oleksandr I. Malyi ◽

Teck L. Tan ◽

Sergei Manzhos

Keyword(s):

Density Functional ◽

Nearest Neighbor ◽

Defect Formation ◽

Crystalline Silicon ◽

Computational Study ◽

Binding Energies ◽

Functional Theory ◽

Wide Range ◽

Insertion Sites ◽

Formation Energies

ABSTRACTWe show in a theoretical density functional theory study that amorphous Si (a-Si) has more favorable energetics for Mg storage compared to crystalline Si (c-Si). Specifically, Mg and Li insertion is compared in a model a-Si simulation cell. Multiple sites for Mg insertion with a wide range of binding energies are identified. For many sites, Mg defect formation energies are negative, whereas they are positive in c-Si. Moreover, while clustering in c-Si destabilizes the insertion sites (by about 0.1/0.2 eV per atom for nearest-neighbor Li/Mg), it is found to stabilize some of the insertion sites for both Li (by up to 0.27 eV) and Mg (by up to 0.35 eV) in a-Si. This could have significant implications on the performance of Si anodes in Mg batteries.

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A Halogen Bonding Perspective on Iodothyronine Deiodinase Activity

Molecules ◽

10.3390/molecules25061328 ◽

2020 ◽

Vol 25 (6) ◽

pp. 1328 ◽

Cited By ~ 1

Author(s):

Eric S. Marsan ◽

Craig A. Bayse

Keyword(s):

Active Site ◽

Polybrominated Diphenyl Ethers ◽

Density Functional ◽

Endocrine System ◽

Halogen Bonding ◽

Binding Energies ◽

Active Site Residues ◽

Iodothyronine Deiodinase ◽

Donor Acceptor ◽

Small Models

Iodothyronine deiodinases (Dios) are involved in the regioselective removal of iodine from thyroid hormones (THs). Deiodination is essential to maintain TH homeostasis, and disruption can have detrimental effects. Halogen bonding (XB) to the selenium of the selenocysteine (Sec) residue in the Dio active site has been proposed to contribute to the mechanism for iodine removal. Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are known disruptors of various pathways of the endocrine system. Experimental evidence shows PBDEs and their hydroxylated metabolites (OH-BDEs) can inhibit Dio, while data regarding PCB inhibition are limited. These xenobiotics could inhibit Dio activity by competitively binding to the active site Sec through XB to prevent deiodination. XB interactions calculated using density functional theory (DFT) of THs, PBDEs, and PCBs to a methyl selenolate (MeSe−) arrange XB strengths in the order THs > PBDEs > PCBs in agreement with known XB trends. THs have the lowest energy C–X*-type unoccupied orbitals and overlap with the Se lp donor leads to high donor-acceptor energies and the greatest activation of the C–X bond. The higher energy C–Br* and C–Cl* orbitals similarly result in weaker donor-acceptor complexes and less activation of the C–X bond. Comparison of the I···Se interactions for the TH group suggest that a threshold XB strength may be required for dehalogenation. Only highly brominated PBDEs have binding energies in the same range as THs, suggesting that these compounds may inhibit Dio and undergo debromination. While these small models provide insight on the I···Se XB interaction itself, interactions with other active site residues are governed by regioselective preferences observed in Dios.

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Superior anion induced shuttling behaviour exhibited by a halogen bonding two station rotaxane

Chemical Science ◽

10.1039/c6sc00783j ◽

2016 ◽

Vol 7 (8) ◽

pp. 5171-5180 ◽

Cited By ~ 32

Author(s):

Timothy A. Barendt ◽

Sean W. Robinson ◽

Paul D. Beer

Keyword(s):

Hydrogen Bonding ◽

Halogen Bond ◽

Translational Motion ◽

Anion Recognition ◽

Halogen Bonding ◽

Recognition Site ◽

Naphthalene Diimide

Two bistable halogen and hydrogen bonding-naphthalene diimide [2]rotaxanes have been prepared and the system incorporating a halogen bond donor anion recognition site is demonstrated to exhibit superior anion induced translational motion of the macrocyclic wheel component relative to the hydrogen bonding analogue.

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

Materials ◽

10.3390/ma13092163 ◽

2020 ◽

Vol 13 (9) ◽

pp. 2163 ◽

Cited By ~ 3

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.

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