Asymmetric bifurcated halogen bonds

2015 ◽  
Vol 17 (9) ◽  
pp. 6440-6450 ◽  
Author(s):  
Martin Novák ◽  
Cina Foroutan-Nejad ◽  
Radek Marek
Keyword(s):  
Halogen Bond ◽  
Lone Pair ◽  
Relative Orientation ◽  
Halogen Bonds ◽  
Donor And Acceptor

Depending on the relative orientation of the halogen-bond donor and acceptor, this bifurcated interaction may be classified as ‘σ-hole – lone pair’ or ‘σ-hole – π’ bonding.

scholarly journals Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4568
Author(s):  
Serigne Sarr ◽  
Julien Pilmé ◽  
Gilles Montavon ◽  
Jean-Yves Le Questel ◽  
Nicolas Galland
Keyword(s):  
Halogen Bond ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Unexpected Finding ◽  
Halogen Bonds ◽  
Chemical Topology ◽  
Donor And Acceptor ◽  
Pauli Repulsion ◽  
Quantum Chemical Topology ◽  
Charge Shift

The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin–orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C–At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.

scholarly journals Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3119
Author(s):  
Sergey V. Baykov ◽  
Artem V. Semenov ◽  
Eugene A. Katlenok ◽  
Anton A. Shetnev ◽  
Nadezhda A. Bokach
Keyword(s):  
Natural Bond Orbital ◽  
Halogen Bond ◽  
Lone Pair ◽  
Computational Studies ◽  
Halogen Bonds ◽  
Molecular Electrostatic Potentials ◽  
X Ray Diffraction ◽  
X Ray ◽  
Central Oxygen ◽  
Packing Effect

Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs.

Intermolecular binding preferences of haloethynyl halogen-bond donors as a function of molecular electrostatic potentials in a family of N-(pyridin-2-yl)amides

2021 ◽  
Author(s):  
Amila M. Abeysekera ◽  
Boris B. Averkiev ◽  
Pierre Le Magueres ◽  
Christer B. Aakeröy
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Halogen Bond ◽  
Electrostatic Potentials ◽  
Halogen Bonds ◽  
Molecular Electrostatic Potentials

The roles played by halogen bonds and hydrogen bonds in the crystal structures of N-(pyridin-2-yl)amides were evaluated and rationalised in the context of calculated molecular electrostatic potentials.

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

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 224 ◽  
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.

scholarly journals "ANTI-HALOGEN" BONDS AS A FACTOR DETERMINING THE TETRAHEDRAL STRUCTURE OF COPPER IN ITS COMPLEXES WITH (5Z, 5'Z)-2,2'- (ETHANE-1,2-DIYLDISULFANYLDIYL)BIS(5-(2-PYRIDYLMETHYLENE)-3-ALLYL-3,5-DIHYDRO- 4H-IMIDAZOLE-4-ONE)

2021 ◽  
Vol 2 (74) ◽  
pp. 38-41
Author(s):  
A. Al-Khazraji ◽  
I. Dudkin ◽  
E. Ofitserov ◽  
A. Finko ◽  
E. Beloglazkina
Keyword(s):  
Electron Density ◽  
Copper Atom ◽  
Halogen Bond ◽  
Halogen Bonds ◽  
Tetrahedral Structure ◽  
Angle Of Rotation

Analysis of the valence angles of the Si and carbon atoms of the C-S bond in the obtained complexes of CiVg2 c (5Z, 5'Z)-2,2’-(ethane-1,2-diyldisulfanyldiyl)bis(5-(2-pyridylmethylene)-3-allyl-3,5-dihydro-4Нimidazole-4-one) unambiguously indicates the determinant effect of the non-valent interactions of the electron density centroids of the NEP of bromine atoms and sulfur atoms, leading to a change in the plane structure of Cu(II) towards tetrahedral with a likely change in the magnetochemical properties of the copper atom, and the angle of rotation of the planes is almost 900. This interaction is the opposite of what is commonly called a halogen bond. In this case, it is an "anti-halogen" bond.

scholarly journals Using beryllium bonds to change halogen bonds from traditional to chlorine-shared to ion-pair bonds

2015 ◽  
Vol 17 (3) ◽  
pp. 2259-2267 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Otilia Mó ◽  
Manuel Yáñez ◽  
Janet E. Del Bene
Keyword(s):  
Halogen Bond ◽  
Ion Pair ◽  
Ternary Complexes ◽  
Halogen Bonds ◽  
Bond Type ◽  
Cooperative Effects ◽  
Pair Bonds

Dramatic synergistic cooperative effects between Be⋯F beryllium bonds and Cl⋯N halogen bonds in XYBe:FCl:N-base ternary complexes lead to changes in the halogen-bond type from traditional to chlorine-shared to ion-pair bonds.

scholarly journals Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik
Keyword(s):  
Base Pair ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Dna Bases ◽  
Halogen Bonds ◽  
Base Pairs ◽  
Rich Diversity ◽  
Different Types ◽  
Guanine Base ◽  
The Stability

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

scholarly journals Halogen bonds of halonium ions

2020 ◽  
Vol 49 (9) ◽  
pp. 2688-2700 ◽  
Author(s):  
Lotta Turunen ◽  
Máté Erdélyi
Keyword(s):  
Organic Chemistry ◽  
Halogen Bond ◽  
Halogen Bonds ◽  
Synthetic Organic Chemistry

Halonium ions are particularly strong halogen bond donors, and are accordingly valuable tools for a variety of fields, such as supramolecular and synthetic organic chemistry.

scholarly journals A systematic structural study of halogen bondingversushydrogen bonding within competitive supramolecular systems

IUCrJ ◽  
2015 ◽  
Vol 2 (5) ◽  
pp. 498-510 ◽  
Author(s):  
Christer B. Aakeröy ◽  
Christine L. Spartz ◽  
Sean Dembowski ◽  
Savannah Dwyre ◽  
John Desper
Keyword(s):  
Molecular Electrostatic Potential ◽  
Halogen Bond ◽  
Supramolecular System ◽  
Materials Chemistry ◽  
Halogen Bonds ◽  
X Ray Diffraction ◽  
Supramolecular Systems ◽  
X Ray ◽  
Practical Guidelines ◽  
Primary Interaction

As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

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