scholarly journals Noncovalent Interactions between 1,3,5-Trifluoro-2,4,6-triiodobenzene and a Series of 1,10-Phenanthroline Derivatives: A Combined Theoretical and Experimental Study

Crystals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 140 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Quantum Chemical ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Structural Competition

How many strong C−I⋯N halogen bonds can one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule form in a crystal structure? To answer this question, we investigated in detail the noncovalent interactions between 1,3,5-trifluoro-2,4,6-triiodobenzene and a series of 1,10-phenanthroline derivatives by employing a combined theoretical and experimental method. The results of the quantum chemical calculations and crystallographic experiments clearly show that there is a structural competition between a C−I⋯N halogen bond and π⋯π stacking interaction. For example, when there are much stronger π⋯π stacking interactions between two 1,10-phenanthroline derivative molecules or between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules in the crystal structures, then one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule forms only one C−I⋯N halogen bond with one 1,10-phenanthroline derivative molecule. Another example is when π⋯π stacking interactions in the crystal structures are not much stronger, one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule can form two C−I⋯N halogen bonds with two 1,10-phenanthroline derivative molecules.

scholarly journals The crystal structure of 1-(2-iodobenzoyl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by π–π stacking interactions and I...N halogen bonds

2019 ◽  
Vol 75 (2) ◽  
pp. 129-133 ◽  
Author(s):  
Ninganayaka Mahesha ◽  
Hemmige S. Yathirajan ◽  
Tetsundo Furuya ◽  
Takashiro Akitsu ◽  
Christopher Glidewell
Keyword(s):  
Phenyl Ring ◽  
Halogen Bond ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Π Stacking ◽  
Dimensional Network ◽  
Π Stacking Interaction ◽  
Related Compounds

In 1-(2-iodobenzoyl)-4-(pyrimidin-2-yl)piperazine, C15H15IN4O, the central piperazine ring adopts an almost perfect chair conformation with the pyrimidine substituent in an equatorial site. The planar amide unit makes a dihedral angle of 80.44 (7)° with the phenyl ring. A combination of C—H...O and C—H...π(arene) hydrogen bonds links the molecules into a complex three-dimensional network structure, augmented by a π–π stacking interaction and an I...N halogen bond, all involving different pairs of inversion-related molecules. Comparisons are made with the structures of a number of related compounds.

scholarly journals A Robust Supramolecular Heterosynthon Assembled by a Hydrogen Bond and a Chalcogen Bond

Crystals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1309
Author(s):  
Shaobin Miao ◽  
Yunfan Zhang ◽  
Linjie Shan ◽  
Mingyuan Xu ◽  
Jian-Ge Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Isophthalic Acid ◽  
Stacking Interactions ◽  
Chalcogen Bond ◽  
Good Agreement

The 1:1 and 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole have been successfully synthesized and resolved; the noncovalent interactions in the crystal structures have been studied in detail by quantum chemical calculations. In both of the crystal structures, isophthalic acid and 2,1,3-benzoselenadiazole are bound together by a cyclic supramolecular heterosynthon assembled by an O–H···N hydrogen bond and a N–Se···O chalcogen bond. The crystal structures of the 1:1 and 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole and the crystal structure of pure isophthalic acid are very similar, which indicates that the [COOH]···[Se−N] cyclic heterosynthon can be an effective alternative to the strong [COOH]2 cyclic homosynthon. The quantum theory of atoms in molecules further recognizes the existence of the hydrogen bond and chalcogen bond. The results of quantum chemical calculations show that the strengths of the π···π stacking interactions in the 1:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole are almost the same as those in the 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole, and the strengths of the [COOH]···[Se−N] cyclic heterosynthons (about 9.00 kcal/mol) are less than the strengths of the much stronger [COOH]2 cyclic homosynthons (14.00 kcal/mol). These calculated results are in good agreement with those experimentally observed, demonstrating that, although not as strong as the [COOH]2 cyclic homosynthon, the [COOH]···[Se−N] cyclic heterosynthon can also play a key role in the crystal growth and design.

scholarly journals The Face-to-Face σ-Hole···σ-Hole Stacking Interactions: Structures, Energies, and Nature

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 877
Author(s):  
Yu Zhang ◽  
Weizhou Wang
Keyword(s):  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Electrostatic Energy ◽  
Stacking Interactions ◽  
Energy Component ◽  
Stacking Interaction ◽  
Face To Face ◽  
The Face ◽  
Π Stacking Interaction ◽  
Induction Energy

The existence of the π···π stacking interaction is well-known. Similarly, it is reasonable to assume the existence of the σ-hole···σ-hole stacking interaction. In this work, the structures, energies, and nature of the face-to-face σ-hole···σ-hole stacking interactions in the crystal structures have been investigated in detail by the quantum chemical calculations. The calculated results clearly show that the face-to-face σ-hole···σ-hole stacking interactions exist and have unique properties, although their strengths are not very significant. The energy component analysis reveals that, unlike many other dispersion-dominated noncovalent interactions in which the induction energies always play minor roles for their stabilities, for the face-to-face σ-hole···σ-hole stacking interaction the contribution of the induction energy to the total attractive energy is close to or even larger than that of the electrostatic energy. The structures, energies, and nature of the face-to-face σ-hole···σ-hole stacking interactions confined in small spaces have also been theoretically simulated. One of the important findings is that encapsulation of the complex bound by the face-to-face σ-hole···σ-hole stacking interaction can tune the electronic properties of the container.

scholarly journals Structure of cis-dichlorobis(1,10-phenanthroline)manganese(II) and cis-dichlorobis(2,2´-bipyridine)manganese(II)

2014 ◽  
Vol 7 (1) ◽  
pp. 15-19 ◽  
Author(s):  
Danica Čechová ◽  
Alena Martišková ◽  
Jan Moncol
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Octahedral Geometry ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Pyridine Nitrogen

Abstract The crystal structures of the title compounds, [Mn(phen)2Cl2] (I) and [Mn(bipy)2Cl2] (II), have been determined at 150 K. The manganese atoms in both compounds are coordinated by four pyridine nitrogen atoms from two 1,10-phenanthroline or 4,4´-bipyridine ligands and two chloride anions, resulting in a distorted cis-MnN4Cl2 octahedral geometry. Both complexes are connected through C-H・・・Cl hydrogen bonds into frameworks. The π-π stacking interactions are observed in crystal structure of both ones.

A new method of syntheses of 18-membered macrocyclic diphenyltin(IV) compounds and crystal structures of {Ph2Sn[S(C6H3NO)O]}3·Y (Y = 2H2O or 4C6H6) and {Ph3Sn[S(C6H3NO)O]SnPh3(EtOH)}·[EtOH]

2004 ◽  
Vol 82 (5) ◽  
pp. 608-615 ◽  
Author(s):  
Chunlin Ma ◽  
Qin Jiang ◽  
Rufen Zhang
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
New Method ◽  
Macrocyclic Compounds ◽  
X Ray ◽  
Stacking Interaction ◽  
Π Stacking ◽  
Triphenyltin Chloride ◽  
Π Stacking Interaction ◽  
Solvent Molecules

Two diphenyltin(IV) compounds: {Ph2Sn[S(C6H3NO)O]}3·Y (Y = 2H2O, 1; 4C6H6, 2) have been unexpectedly obtained by the reactions of triphenyltin chloride with 2-mercaptonicotinic acid in the presence of Et3N. However, by the reaction of the same reactants in the presence of EtONa, only a new triphenyltin(IV) compound ({Ph3Sn[S(C6H3NO)O]SnPh3(EtOH)}·[EtOH], 3) was obtained. The X-ray analyses reveal that compounds 1 and 2 are trinuclear, 18-membered macrocyclic compounds while 3 is a dinuclear compound. Specially, π-π stacking interaction was recognized in crystals of compound 1, which makes it a dimer. Co-crystallization was found in the crystals of all the three compounds 1, 2, and 3, the co-crystallized solvent molecules are water, benzene, and ethanol molecules, respectively. A possible dephenylation mechanism of 1 and 2 was illustrated in detail.Key words: triphenyltin, 2-mercaptonicotinic acid, dephenylation, macrocyclic, π-π stacking interaction, co-crystallization, crystal structure.

Syntheses, characterization, and X-ray crystal structures of diorganotin(IV) derivatives of 2-pyridinethiolato-N-oxide

2003 ◽  
Vol 81 (10) ◽  
pp. 1070-1075 ◽  
Author(s):  
Chunlin Ma ◽  
Junhong Zhang ◽  
Rufen Zhang
Keyword(s):  
Crystal Structure ◽  
Stacking Interactions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Nmr Data ◽  
Π Stacking ◽  
Oxide Crystal ◽  
Distorted Trigonal Bipyramid ◽  
Π Stacking Interaction ◽  
Derivatives Of

The diorganotin(IV) dichloride reacts with sodium 2-pyridinethiolato-N-oxide in a 1:1 ratio to produce [Me2SnCl(2-SpyO)] (1), [Et2SnCl(2-SpyO)] (2), [Bu2SnCl(2-SpyO)] (3), [Ph2SnCl(2-SpyO)] (4), and [(PhCH2)2SnCl(2- SpyO)] (5). The new complexes have been characterized by elemental analysis and IR and NMR (1H, 119Sn, and 13C) spectroscopy. On the basis of 119Sn NMR data the effective coordination number in solution is five. The structures 1 and 4 have been confirmed by X-ray crystallography. Crystals of 1 are triclinic with space group P[Formula: see text] and those of 4 are monoclinic, P21/n. The tin environment is a distorted trigonal bipyramid with the Cl and oxygen atoms in apical positions. Both complexes exhibit strong π–π stacking interactions. Key words: diorganotin, π–π stacking interaction, 2-pyridinethiolato-N-oxide, crystal structure.

scholarly journals Crystal structures of 2,3,8,9,14,15-hexamethyl-5,6,11,12,17,18-hexaazatrinaphthylene and 2,3,8,9,14,15-hexaphenyl-5,6,11,12,17,18-hexazatrinaphthylene dichloromethane disolvate

2018 ◽  
Vol 74 (2) ◽  
pp. 167-171 ◽  
Author(s):  
Pia Fangmann ◽  
Marc Schmidtmann ◽  
Rüdiger Beckhaus
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Stacking Interactions ◽  
Bridging Ligands ◽  
Π Stacking ◽  
Solvent Molecules

The crystal structures of two substituted HATN (hexaazatrinaphthylene) derivatives, namely 2,3,8,9,14,15-hexamethyl- and 2,3,8,9,14,15-hexaphenyl-5,6,11,12,17,18- hexazatrinaphthylene (HATNMe6 and HATNPh6), are reported. Whereas the structure of the methyl-substituted derivative (HATNMe6) contains no solvent molecules (C30H24N6), the hexaphenyl-substituted structure (HATNPh6) contains two molecules of dichloromethane (C60H36N6·2CH2Cl2). This class of planar bridging ligands is known for its electron-deficient systems and its ability to form π–π stacking interactions. Indeed, in both crystal structures strong π–π stacking interactions are observed, but with different packing features. The dichloromethane molecules in the crystal structure of HATNPh6 are situated in the voids and are involved in C—H...N contacts to the nitrogen atoms of the pyrazine units.

scholarly journals Unexpected Sandwiched-Layer Structure of the Cocrystal Formed by Hexamethylbenzene with 1,3-Diiodotetrafluorobenzene: A Combined Theoretical and Crystallographic Study

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 379 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Layer Structure ◽  
Noncovalent Interactions ◽  
Density Functional Theory Calculations ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Functional Theory ◽  
Π Stacking ◽  
Cocrystal Structure

The cocrystal formed by hexamethylbenzene (HMB) with 1,3-diiodotetrafluorobenzene (1,3-DITFB) was first synthesized and found to have an unexpected sandwiched-layer structure with alternating HMB layers and 1,3-DITFB layers. To better understand the formation of this special structure, all the noncovalent interactions between these molecules in the gas phase and the cocrystal structure have been investigated in detail by using the dispersion-corrected density functional theory calculations. In the cocrystal structure, the theoretically predicted π···π stacking interactions between HMB and the 1,3-DITFB molecules in the gas phase can be clearly seen, whereas there are no π···π stacking interactions between HMB molecules or between 1,3-DITFB molecules. The attractive interactions between HMB molecules in the corrugated HMB layers originate mainly in the dispersion forces. The 1,3-DITFB molecules form a 2D sheet structure via relatively weak C–I···F halogen bonds. The theoretically predicted much stronger C–I···π halogen bonds between HMB and 1,3-DITFB molecules in the gas phase are not found in the cocrystal structure. We concluded that it is the special geometry of 1,3-DITFB that leads to the formation of the sandwiched-layer structure of the cocrystal.

scholarly journals Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

2016 ◽  
Vol 12 ◽  
pp. 1616-1623 ◽  
Author(s):  
Valeria Corne ◽  
Ariel M Sarotti ◽  
Carmen Ramirez de Arellano ◽  
Rolando A Spanevello ◽  
Alejandra G Suárez
Keyword(s):  
Electron Density ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Stacking Interactions ◽  
Nmr Studies ◽  
Stacking Interaction ◽  
Π Stacking ◽  
Acrylic Esters ◽  
Π Stacking Interaction

Chiral acrylic esters derived from biomass were developed as models to have a better insight in the aryl–vinyl π-stacking interactions. Quantum chemical calculations, NMR studies and experimental evidences demonstrated the presence of equilibriums of at least four different conformations: π-stacked and face-to-edge, each of them in an s-cis/s-trans conformation. The results show that the stabilization produced by the π–π interaction makes the π-stacked conformation predominant in solution and this stabilization is slightly affected by the electron density of the aromatic counterpart.

2,2′,2′′,2′′′-(3,6-Dioxaoctane-1,8-diyldinitrilo)tetrabenzimidazolium tetrakis(perchlorate) dihydrate

2007 ◽  
Vol 63 (11) ◽  
pp. o4334-o4335
Author(s):  
Chun-Shan Zhou ◽  
Ya-Mei Pei ◽  
Xiang-Gao Meng
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Noncovalent Interactions ◽  
Imidazole Ring ◽  
Stacking Interactions ◽  
Two Dimensional ◽  
Π Stacking

In the title crystal structure, C38H44N10O2 4+·4ClO4 −·2H2O, components are linked into a two-dimensional framework by a combination of N—H...O, C—H...O, O—H...O and N—H...N hydrogen bonds. In addition, weak π–π stacking interactions and anion–π noncovalent interactions between perchlorate anions and heteroaromatic imidazole rings [O...Cg = 3.328 (10) and 3.386 (11) Å; Cg is the centroid of an imidazole ring] consolidate the crystal structure.

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