scholarly journals On the Importance of Halogen Bonding Interactions in Two X-ray Structures Containing All Four (F, Cl, Br, I) Halogen Atoms

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1406
Author(s):  
Dmitriy F. Mertsalov ◽  
Rosa M. Gomila ◽  
Vladimir P. Zaytsev ◽  
Mikhail S. Grigoriev ◽  
Eugeniya V. Nikitina ◽  
...  
Keyword(s):  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Halogen Bonding ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Halogen Atoms ◽  
Interaction Plot

This manuscript reports the synthesis and X-ray characterization of two octahydro-1H-4,6-epoxycyclopenta[c]pyridin-1-one derivatives that contain the four most abundant halogen atoms (Ha) in the structure with the aim of studying the formation of Ha···Ha halogen bonding interactions. The anisotropy of electron density at the heavier halogen atoms provokes the formation of multiple Ha···Ha contacts in the solid state. That is, the heavier Ha-atoms exhibit a region of positive electrostatic potential (σ-hole) along the C–Ha bond and a belt of negative electrostatic potential (σ-lumps) around the atoms. The halogen bonding assemblies in both compounds were analyzed using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of “atom-in-molecules” (QTAIM), the noncovalent interaction plot (NCIplot), and the electron localization function (ELF).

scholarly journals Sildenafil–Resorcinol Cocrystal: XRPD Structure and DFT Calculations

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1126
Author(s):  
Rafael Barbas ◽  
Vineet Kumar ◽  
Oriol Vallcorba ◽  
Rafel Prohens ◽  
Antonio Frontera
Keyword(s):  
Crystal Structure ◽  
Dft Calculations ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Interaction Plot

Herein, the X-ray powder diffraction (XRPD) crystal structure of a new Sildenafil cocrystal is reported, where resorcinol has been used as the coformer. The crystal structure has been solved by means of direct space methods used in combination with density functional theory (DFT) calculations. In the structure, the Sildenafil and resorcinol molecules form cooperative hydrogen bond (HB) and π-stacking interactions that have been analyzed using DFT calculations, the molecular electrostatic potential (MEP) surface, and noncovalent interaction plot (NCI plot). The formation of O–H⋯N H-bonds between resorcinol and Sildenafil increases the dipole moment and enhances the antiparallel π-stacking interaction.

scholarly journals Synthesis, X-ray Characterization and Density Functional Theory (DFT) Studies of Two Polymorphs of the α,α,α,α, Isomer of Tetra-p-Iodophenyl Tetramethyl Calix[4]pyrrole: On the Importance of Halogen Bonds

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 285
Author(s):  
Dragoș Dăbuleanu ◽  
Antonio Bauzá ◽  
Joaquín Ortega-Castro ◽  
Eduardo C. Escudero-Adán ◽  
Pablo Ballester ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Single Crystals ◽  
Density Functional ◽  
Halogen Bonding ◽  
Acetonitrile Solution ◽  
Functional Theory ◽  
Crystal Lattices ◽  
Cone Conformation ◽  
X Ray

This manuscript reports the improved synthesis of the α,α,α,α isomer of tetra-p-iodophenyl tetra-methyl calix[4]pyrrole and the X-ray characterization of two solvate polymorphs. In the solid state, the calix[4]pyrrole receptor adopts the cone conformation, including one acetonitrile molecule in its aromatic cavity by establishing four convergent hydrogen bonds between its nitrogen atom and the four pyrrole NHs of the former. The inclusion complexes pack into rods, displaying a unidirectional orientation. In turn, the rods form flat 2D-layers by alternating the orientation of their p-iodo substituents. The 2D layers stack on top of another, resulting in a head-to-head and tail-to-tail orientation of the complexes or their exclusive arrangement in a head-to-tail geometry. The dissimilar stacking of the layers yields two solvate polymorphs that are simultaneously present in the structures of the single crystals. The ratio of the two polymorph phases is regulated by the amount of acetonitrile added to the chloroform solutions from which the crystals grow. Halogen bonding interactions are highly relevant in the crystal lattices of the two polymorphs. We analyzed and characterized these interactions by means of density functional theory (DFT) calculations and several computational tools. Remarkably, single crystals of a solvate containing two acetonitrile molecules per calix[4]pyrrole were obtained from pure acetonitrile solution.

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 Intramolecular Spodium Bonds in Zn(II) Complexes: Insights from Theory and Experiment

2020 ◽  
Vol 21 (19) ◽  
pp. 7091 ◽  
Author(s):  
Mainak Karmakar ◽  
Antonio Frontera ◽  
Shouvik Chattopadhyay ◽  
Tiddo J. Mooibroek ◽  
Antonio Bauzá
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Noncovalent Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Structure Database ◽  
Interaction Plot ◽  
Solid State Structures ◽  
Theory And Experiment

Two new dinuclear zinc(II) complexes, [Zn2(µ1,3-OAc)(L1)2]I·MeOH (1) and [Zn2(µ1,3-OAc)(L2)(NCS)] (2), (where HL1 = 2-(((3-(dimethylamino)propyl)amino)methyl)-6-methoxy-phenol and H2L2 = 2,2′-[(1-Methyl-1,2-ethanediyl)bis(iminomethylene)]bis[6-ethoxyphenol]) have been synthesized and characterized by elemental and spectral analysis. Their X-ray solid state structures have been determined, revealing the existence of intramolecular Zn···O spodium bonds in both complexes due to the presence of methoxy (1) or ethoxy (2) substituents adjacent to the coordinated phenolic O-atom. These noncovalent interactions have been studied using density functional theory (DFT) calculations, the quantum theory of “atoms-in-molecules” and the noncovalent interaction plot. Moreover, a search in the Cambridge structure database (CSD) has been conducted in order to investigate the prevalence of intramolecular spodium bonds in Zn complexes. To our knowledge this is the first investigation dealing with intramolecular spodium bonds.

scholarly journals Oxalic Acid, a Versatile Coformer for Multicomponent Forms with 9-Ethyladenine

Crystals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 89
Author(s):  
Mónica Benito ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera ◽  
Elies Molins
Keyword(s):  
Oxalic Acid ◽  
Density Functional ◽  
Noncovalent Interaction ◽  
Supramolecular Interactions ◽  
Molar Ratio ◽  
Functional Theory ◽  
X Ray ◽  
Solution Crystallization ◽  
Interaction Plot ◽  
Salt Screening

Six new multicomponent solids of 9-ethyladenine and oxalic acid have been detected and characterized. The salt screening has been performed by mechanochemical and solvent crystallization processes. Single crystals of the anhydrous salts in 1:1 and 2:1 nucleobase:coformer molar ratio were obtained by solution crystallization and elucidated by single-crystal X-ray analysis. The supramolecular interactions observed in these solids have been studied using density functional theory (DFT) calculations and characterized by the quantum theory of “atoms in molecules” (QTAIM) and the noncovalent interaction plot (NCIPlot) index methods. The energies of the H-bonding networks observed in the solid state of the anhydrous salts in 1:1 and 2:1 nucleobase:coformer are reported, disclosing the strong nature of the charge assisted NH···O hydrogen bonds and also the relative importance of ancillary C–H··O H-bonds.

scholarly journals Metal-Rich Metallaboranes: Synthesis, Structures and Bonding of Bi- and Trimetallic Open-Faced Cobaltaboranes

Inorganics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 28
Author(s):  
Kriti Pathak ◽  
Chandan Nandi ◽  
Jean-François Halet ◽  
Sundargopal Ghosh
Keyword(s):  
Electronic Structures ◽  
Density Functional ◽  
Room Temperature ◽  
Electron Pair ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Cluster 2 ◽  
Cobalt Center

Synthesis, isolation, and structural characterization of unique metal rich diamagnetic cobaltaborane clusters are reported. They were obtained from reactions of monoborane as well as modified borohydride reagents with cobalt sources. For example, the reaction of [Cp*CoCl]2 with [LiBH4·THF] and subsequent photolysis with excess [BH3·THF] (THF = tetrahydrofuran) at room temperature afforded the 11-vertex tricobaltaborane nido-[(Cp*Co)3B8H10] (1, Cp* = η5-C5Me5). The reaction of Li[BH2S3] with the dicobaltaoctaborane(12) [(Cp*Co)2B6H10] yielded the 10-vertex nido-2,4-[(Cp*Co)2B8H12] cluster (2), extending the library of dicobaltadecaborane(14) analogues. Although cluster 1 adopts a classical 11-vertex-nido-geometry with one cobalt center and four boron atoms forming the open pentagonal face, it disobeys the Polyhedral Skeletal Electron Pair Theory (PSEPT). Compound 2 adopts a perfectly symmetrical 10-vertex-nido framework with a plane of symmetry bisecting the basal boron plane resulting in two {CoB3} units bridged at the base by two boron atoms and possesses the expected electron count. Both compounds were characterized in solution by multinuclear NMR and IR spectroscopies and by mass spectrometry. Single-crystal X-ray diffraction analyses confirmed the structures of the compounds. Additionally, density functional theory (DFT) calculations were performed in order to study and interpret the nature of bonding and electronic structures of these complexes.

scholarly journals Novel Cd (II) Coordination Polymers Afforded with EDTA or Trans-1,2-Cdta Chelators and Imidazole, Adenine, or 9-(2-Hydroxyethyl) Adenine Coligands

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 391
Author(s):  
Jeannette Carolina Belmont-Sánchez ◽  
María Eugenia García-Rubiño ◽  
Antonio Frontera ◽  
Antonio Matilla-Hernández ◽  
Alfonso Castiñeiras ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Coordination Polymers ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Aqua Ligand ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Mixed Ligands

Three mixed-ligands of Cd(II) coordination polymers were unintentionally obtained: {[Cd(µ3-EDTA)(Him)·Cd(Him)(H2O)2]·H2O}n (1), {[Cd(µ4-CDTA)(Hade)·Cd(Hade)2]}n (2), and {[Cd(µ3-EDTA)(H2O)·Cd(H9heade)(H2O)]·2H2O}n (3), having imidazole (Him), adenine (Hade) or 9-(2-hydroxyethyl)adenine (9heade) as the N-heterocyclic coligands. Compounds 2 and 3 were obtained by working with an excess of corresponding N-heterocyclic coligands. The single-crystal X-ray diffraction structures and thermogravimetric analyses are reported. The chelate moieties in all three compounds exhibit hepta-coordinated Cd centers, whereas the non-chelated Cd center is five-coordinated in 1 and six-coordinated in 2 and 3. Him and Hade take part in the seven-coordinated chelate moieties in 1 and 2, respectively. In contrast, 9heade is unable to replace the aqua ligand of the chelate [Cd (EDTA) (H2O)] moiety in 3. The thermogravimetric analysis (TGA) behavior of [Cd (H2EDTA) (H2O)]·2H2O in 1 and 3 leads to a residue of CdO, whereas the N-rich compound 2 yields CdO·Cd(NO3)2 as a residue. Density functional theory (DFT) calculations along with molecular electrostatic potential (MEP) and quantum theory of atoms-in-molecules computations were performed in adenine (compound 2) and (2-hydroxyethyl)adenine (compound 3) to analyze how the strength of the H-bonding and π-stacking interactions, respectively, are affected by their coordination to the Cd-metal center.

scholarly journals Crystal structure and DFT study of a zinc xanthate complex

2019 ◽  
Vol 75 (11) ◽  
pp. 1582-1585 ◽  
Author(s):  
Adnan M. Qadir ◽  
Sevgi Kansiz ◽  
Necmi Dege ◽  
Georgina M. Rosair ◽  
Igor O. Fritsky
Keyword(s):  
Molecular Structure ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Energy Gap ◽  
Three Dimensional ◽  
Intramolecular Interactions ◽  
Lumo Energy ◽  
Functional Theory ◽  
Homo Lumo

In the title compound, bis(2-methoxyethyl xanthato-κS)(N,N,N′,N′-tetramethylethylenediamine-κ2 N,N′)zinc(II) acetone hemisolvate, [Zn(C4H7O2S2)2(C6H16N2)]·0.5C3H6O, the ZnII ion is coordinated by two N atoms of the N,N,N′,N′-tetramethylethylenediamine ligand and two S atoms from two 2-methoxyethyl xanthate ligands. The amine ligand is disordered over two orientations and was modelled with refined occupancies of 0.538 (6) and 0.462 (6). The molecular structure features two C—H...O and two C—H...S intramolecular interactions. In the crystal, molecules are linked by weak C—H...O and C—H...S hydrogen bonds, forming a three-dimensional supramolecular architecture. The molecular structure was optimized using density functional theory (DFT) at the B3LYP/6–311 G(d,p) level. The smallest HOMO–LUMO energy gap (3.19 eV) indicates the suitability of this crystal for optoelectronic applications. The molecular electrostatic potential (MEP) further identifies the positive, negative and neutral electrostatic potential regions of the molecules. Half a molecule of disordered acetone was removed with the solvent-mask procedure in OLEX2 [Dolomanov et al. (2009). J. Appl. Cryst. 42, 339–341] and this contribition is included in the formula.

scholarly journals Theoretical Evaluation on The Interaction Between Triglycerides and Methylxanthines Using Density Functional Theory B3LYP/6-31G(d,p) and Molecular Electrostatic Potential

2020 ◽  
Vol 33 (1) ◽  
pp. 171-178
Author(s):  
N.F.M. Azmi ◽  
R. Ali ◽  
A.A. Azmi ◽  
M.Z.H. Rozaini ◽  
K.H.K. Bulat ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Basis Set ◽  
Individual Species ◽  
Interaction Energies ◽  
Binding Interaction ◽  
Functional Theory

The binding, interaction and distortion energies between the main triglycerides, palmitic-oleic-stearic (POS) in cocoa butter versus palmitic-oleic-palmitic (POP) in refined, bleached and deodorized (RBD) palm oil with cocoa′s methylxanthines (caffeine, theobromine, and theophylline) during the production of chocolate were theoretically studied and reported. The quantum mechanical software package of Gaussian09 at the theoretical level of density functional theory B3LYP/6-31G(d,p) was employed for all calculations, optimization, and basis set superposition errors (BSSE). Geometry optimizations were carried out to the minimum potential energy of individual species and binary complexes formed between the triglycerides, methylxanthines and polyphenols. The interaction energies for the optimized complexes were then corrected for the BSSE using the counterpoise method of Boys and Bernardi. The results revealed that the binding energy and interaction energy between methylxanthine components in cocoa powder with triglycerides were almost of the same magnitude (13.6-14.5 and 3.4-3.7 kJ/mol, respectively), except for the binary complex of POS-caffeine (25.1 and 10.7 kJ/mol, respectively). Based on the molecular geometry results, the hydrogen bond length and angle correlated well with the interaction energies. Meanwhile, the POS-caffeine complex with two higher and almost linear bond angles showed higher binding and interaction energies as compared to the other methylxanthines. Therefore, a donor-acceptor analysis showed that the hydrogen bond strength was proven using the molecular electrostatic potential (MEP), which resulted in parallel outcomes. The research results were believed to be one of the factors that contributed to the rheological behaviour and sensory perception of cocoa products, especially chocolate.

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