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 Tailoring Long-Range Superlattice Chirality in the Molecular Selfassemblies via Weak Fluorine-Mediated Interactions

2021 ◽  
Author(s):  
Mykola Telychko ◽  
Lulu Wang ◽  
Chia-Hsiu Hsu ◽  
Guangwu Li ◽  
Xinnan Peng ◽  
...  
Keyword(s):  
Long Range ◽  
Density Functional ◽  
Chiral Recognition ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Controllable Fabrication

Controllable fabrication of the enantiospecific molecular superlattices is a matter of imminent scientific and technological interest. Herein, we demonstrate that long-range superlattice chirality in molecular self-assemblies can be tailored by tuning the interplay of weak intermolecular non-covalent interactions. Different chiral recognition patterns are achieved in the two molecular self-assemblies comprised by two molecular enantiomers with identical steric conformations, derived from the hexaphenylbenzene – the smallest star-shaped polyphenylene. By means of high-resolution scanning tunneling microscopy measurements, we demonstrate that functionalization of star-shaped polyphenylene with fluorine (F) atoms leads to the formation of molecular self-assemblies with the distinct long-range chiral recognition patterns. We employed the density functional theory calculations to quantify F-mediated lone pair F ···π, C-H··· F, F···F interactions attributed to the tunable enantiospecific molecular self-organizations. Our findings underpin a viable route to tailor long-range chiral recognition patterns in supramolecular assemblies by engineering the weak non-covalent intermolecular interactions.

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 Halogen Bonding in New Dichloride-Cobalt(II) Complex with Iodo Substituted Chalcone Ligands

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 354 ◽  
Author(s):  
Lukáš Masaryk ◽  
Ján Moncol ◽  
Radovan Herchel ◽  
Ivan Nemec
Keyword(s):  
Density Functional ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Noncovalent Interaction ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
The Density Functional Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The synthesis and properties of new chalcone ligand 4I-L ((2E)-1-[4-(1H-imidazol-1-yl)phenyl]-3-(4-iodophenyl)prop-2-en-1-one) and tetracoordinate Co(II) complex [Co(4I-L)2Cl2], (1a), are reported in this article. Upon recrystallization of 1a, the single crystals of [Co(4I-L)4Cl2]·2DMF·3Et2O (1b) were obtained and crystal structure was determined using X-ray diffraction. The non-covalent interactions in 1b were thoroughly analyzed and special attention was dedicated to interactions formed by the peripheral iodine substituents. The density functional theory (DFT), atoms in molecule (AIM) and noncovalent interaction (NCI) methods and electronic localization function (ELF) calculations were used to investigate halogen bond formed between the iodine functional groups and co-crystallized molecules of diethyl ether.

scholarly journals High-Pressure Phases of SnO and PbO: A Density Functional Theory Combined with an Evolutionary Algorithm Approach

Materials ◽  
2021 ◽  
Vol 14 (21) ◽  
pp. 6552
Author(s):  
Long Truong Nguyen ◽  
Guy Makov
Keyword(s):  
Density Functional Theory ◽  
High Pressure ◽  
Evolutionary Algorithm ◽  
Density Functional ◽  
Experimental Studies ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Lead Monoxide ◽  
Tin Monoxide

Tin monoxide, SnO, and its analog, lead monoxide, PbO, have the same tetragonal P4/nmm structure, shaped by nonbonding dispersion forces and lone pairs. The high-pressure phases of SnO and PbO have been explored in several experimental and theoretical studies, with conflicting results. In this study, the high-pressure structures of SnO and PbO are investigated using density functional theory calculations combined with an evolutionary algorithm to identify novel high-pressure phases. We propose that the monoclinic P21/m SnO and orthorhombic Pmmn PbO phases, which are metastable at 0 GPa, are a slight rearrangement of the tetragonal P4/nmm-layered structure. These orthorhombic (and their closely related monoclinic) phases become more favored than the tetragonal phase upon compression. In particular, the transition pressures to the orthorhombic γ-phase Pmn21of SnO/PbO and the monoclinic phase P21/m of SnO are found to be consistent with experimental studies. Two new high-pressure SnO/PbO polymorphs are predicted: the orthorhombic Pbcm phase of SnO and the monoclinic C2/m of PbO. These phases are stabilized in our calculations when P > 65 GPa and P > 50 GPa, respectively. The weakening of the lone pair localization and elastic instability are the main drivers of pressure-induced phase transitions. Modulations of the SnO/PbO electronic structure due to structural transitions upon compression are also discussed.

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

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.

scholarly journals Tailoring Long-Range Superlattice Chirality in the Molecular Selfassemblies via Weak Fluorine-Mediated Interactions

2021 ◽  
Author(s):  
Mykola Telychko ◽  
Lulu Wang ◽  
Chia-Hsiu Hsu ◽  
Guangwu Li ◽  
Xinnan Peng ◽  
...  
Keyword(s):  
Long Range ◽  
Density Functional ◽  
Chiral Recognition ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Controllable Fabrication

Controllable fabrication of the enantiospecific molecular superlattices is a matter of imminent scientific and technological interest. Herein, we demonstrate that long-range superlattice chirality in molecular self-assemblies can be tailored by tuning the interplay of weak intermolecular non-covalent interactions. Different chiral recognition patterns are achieved in the two molecular self-assemblies comprised by two molecular enantiomers with identical steric conformations, derived from the hexaphenylbenzene – the smallest star-shaped polyphenylene. By means of high-resolution scanning tunneling microscopy measurements, we demonstrate that functionalization of star-shaped polyphenylene with fluorine (F) atoms leads to the formation of molecular self-assemblies with the distinct long-range chiral recognition patterns. We employed the density functional theory calculations to quantify F-mediated lone pair F ···π, C-H··· F, F···F interactions attributed to the tunable enantiospecific molecular self-organizations. Our findings underpin a viable route to tailor long-range chiral recognition patterns in supramolecular assemblies by engineering the weak non-covalent intermolecular interactions.

scholarly journals Halogen bonding stabilizes acis-azobenzene derivative in the solid state: a crystallographic study

2017 ◽  
Vol 73 (2) ◽  
pp. 227-233 ◽  
Author(s):  
Marco Saccone ◽  
Antti Siiskonen ◽  
Franisco Fernandez-Palacio ◽  
Arri Priimagi ◽  
Giancarlo Terraneo ◽  
...  
Keyword(s):  
Solid State ◽  
Density Functional ◽  
Rational Design ◽  
Halogen Bond ◽  
Phase Segregation ◽  
Halogen Bonding ◽  
Density Functional Theory Calculations ◽  
Aliphatic Chain ◽  
Molecular Arrangement

Crystals oftrans- andcis-isomers of a fluorinated azobenzene derivative have been prepared and characterized by single-crystal X-ray diffraction. The presence of F atoms on the aromatic core of the azobenzene increases the lifetime of the metastablecis-isomer, allowing single crystals of thecis-azobenzene to be grown. Structural analysis on thecis-azobenzene, complemented with density functional theory calculations, highlights the active role of the halogen-bond contact (N...I synthon) in promoting the stabilization of thecis-isomer. The presence of a long aliphatic chain on the azobenzene unit induces a phase segregation that stabilizes the molecular arrangement for both thetrans- andcis-isomers. Due to the rarity ofcis-azobenzene crystal structures in the literature, our paper makes a step towards understanding the role of non-covalent interactions in driving the packing of metastable azobenzene isomers. This is expected to be important in the future rational design of solid-state, photoresponsive materials based on halogen bonding.

The Molecular Structures and Conformational Preferences of Bis(dimethylstibyl)- Oxane, -Sulfane and -Selane, E(SbMe2)2, E = O, S or Se, Me = CH3, by Density Functional Theory Calculations and Gas Electron Diffraction

1997 ◽  
Vol 52 (2) ◽  
pp. 296-300 ◽  
Author(s):  
Arne Haaland ◽  
Vasili Ivanovitch Sokolov ◽  
Hans Vidar Volden ◽  
Hans Joachim Breunig ◽  
Michael Denker ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electron Diffraction ◽  
Density Functional ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Molecular Structures ◽  
Gas Electron Diffraction ◽  
Electron Diffraction Data ◽  
Functional Theory ◽  
Anti Conformer

Abstract Density Functional Theory calculations on E(SbMe2)2, E = O, S or Se, Me = CH3, indicate that the equilibrium structures are syn-syn or near syn-syn conformers with over-all C2 symmetry. The barriers restricting rotation about E-Sb bonds are very low, the equilibrium values for the dihedral angles ϕ(Sb-E-Sb-lp) where lp denotes the direction of the electron lone pair on one of the Sb atoms are probably less than 45°. The calculations further indicate the existence of syn-anti conformers some 4 kJ mol-1 above the more stable syn-syn. Gas electron diffraction data show that both conformers are present in gaseous O(SbMe2)2, while the presence of the syn-anti conformer in gaseous Se(SbMe2)2 is uncertain; least-squares refinements yielded the mole fraction χ = 0.27(18). The Sb-O and Sb-Se bond distances are 197.6(14) and 255.1(5) pm respectively, the valence angles of the syn-syn conformers are <SbOSb = 122.3(16)° and <SbSeSb = 96.3(11)°. It is suggested that the wide <SbOSb angle is due to across-angle repulsion between the Sb atoms.

scholarly journals Tetrabromoethane as σ-Hole Donor toward Bromide Ligands: Halogen Bonding between C2H2Br4 and Bromide Dialkylcyanamide Platinum(II) Complexes

Crystals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 835
Author(s):  
Anna M. Cheranyova ◽  
Daniil M. Ivanov
Keyword(s):  
Density Functional ◽  
Halogen Bonding ◽  
Density Functional Theory Calculations ◽  
Electron Localization ◽  
Potential Surfaces ◽  
Functional Theory ◽  
Topology Analysis ◽  
X Ray ◽  
Homo Lumo ◽  
Isolated Molecules

The complexes trans-[PtBr2(NCNR2)2] (R2 = Me21, (CH2)52) were cocrystallized with 1,1,2,2-tetrabromoethane (tbe) in CH2Cl2 forming solvates 1·tbe and 2·tbe, respectively. In both solvates, tbe involved halogen bonding, viz. the C–Br···Br–Pt interactions, were detected by single-crystal X-ray diffractions experiments. Appropriate density functional theory calculations (M06/def2-TZVP) performed for isolated molecules and complex-tbe clusters, where the existence of the interactions and their noncovalent nature were confirmed by electrostatic potential surfaces (ρ = 0.001 a.u.) for isolated molecules, topology analysis of electron density, electron localization function and HOMO-LUMO overlap projections for clusters.

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