Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Rings ◽  
Structural Database

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings have been studied by analyzing crystal structures in the Cambridge Structural Database and performing quantum chemical calculations.

scholarly journals Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

2019 ◽  
Vol 75 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Ivana S. Antonijević ◽  
Dušan P. Malenov ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Energy Surface ◽  
Organic Conductors ◽  
Electron Donors ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Structural Database ◽  
Calculated Potential Energy

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.

scholarly journals Geometrical and energetic characteristics of Se…Se interactions in crystal structures of organoselenium molecules

CrystEngComm ◽  
2021 ◽  
Author(s):  
Ivana S Veljković ◽  
Danijela S. Kretić ◽  
Dušan Ž Veljković
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
Cambridge Structural Database ◽  
Structural Database ◽  
High Level

Non-covalent selenium-selenium interactions between selenium-containing organic molecules were studied in crystal structures from the Cambridge Structural Database and by high-level quantum chemical calculations. Se…Se contacts in crystal structures were analyzed...

scholarly journals What’s in an Atom? a Comparison of Carbon and Silicon-Centered Amidinium···carboxylate Frameworks

2020 ◽  
Author(s):  
Stephanie Boer ◽  
Li-Juan Yu ◽  
Tobias Genet ◽  
Kaycee Low ◽  
Duncan Cullen ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Building Blocks ◽  
Cambridge Structural Database ◽  
Bond Angles ◽  
Framework Materials ◽  
Carboxylate Anions ◽  
Tetrahedral Bond ◽  
Structural Database ◽  
Apparent Similarity

<div><div><div><p>Despite their apparent similarity, framework materials based on tetraphenylmethane and tetraphenylsilane building blocks often have quite different structures and topologies. Herein, we describe a new silicon tetraamidinium compound and use it to prepare crystalline hydrogen bonded frameworks with carboxylate anions in water. The silicon-containing frameworks are compared with those prepared from the analogous carbon tetraamidinium: when biphenyldicarboxylate or tetrakis(4-carboxyphenyl)methane anions were used similar channel-containing networks are observed for both the silicon and carbon tetraamidinium. When terephthalate or bicarbonate anions were used, different products form. Insights into possible reasons for the different products are provided by a survey of the Cambridge Structural Database and quantum chemical calculations, both of which indicate that, contrary to expectations, tetraphenylsilane derivatives have less geometrical flexibility than tetraphenylmethane derivatives, i.e. they are less able to distort away from ideal tetrahedral bond angles.</p></div></div></div>

scholarly journals Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

2020 ◽  
Vol 76 (1) ◽  
pp. 122-136 ◽  
Author(s):  
Ivana S. Đorđević ◽  
Marko Popadić ◽  
Mirjana Sarvan ◽  
Marija Petković-Benazzouz ◽  
Goran V. Janjić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Binding Sites ◽  
Quantum Chemical ◽  
Electrostatic Interactions ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Structural Database ◽  
Insight Into ◽  
Influence Of Substituents

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C—H...Se and C—H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C—H...Se (∼−0.8 kcal mol−1) and C—H...S interactions are weaker than the most stable parallel interaction (∼−3.3 kcal mol−1) and electrostatic interactions of σ/π type (∼−2.6 kcal mol−1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O—H...Se (∼−4.4 kcal mol−1) and N—H...Se interactions (∼−2.2 kcal mol−1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

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 Aliphatic–aromatic stacking interactions in cyclohexane–benzene are stronger than aromatic–aromatic interaction in the benzene dimer

2016 ◽  
Vol 18 (37) ◽  
pp. 25791-25795 ◽  
Author(s):  
D. B. Ninković ◽  
D. Z. Vojislavljević-Vasilev ◽  
V. B. Medaković ◽  
M. B. Hall ◽  
E. N. Brothers ◽  
...  
Keyword(s):  
Ab Initio ◽  
Crystal Structures ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Stacking ◽  
Benzene Dimer ◽  
Structural Database ◽  
Aromatic Interaction

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.

scholarly journals Parallel interactions of aromatic and heteroaromatic molecules

2016 ◽  
Vol 70 (6) ◽  
pp. 649-659 ◽  
Author(s):  
Dusan Malenov ◽  
Snezana Zaric
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Supramolecular Structures ◽  
Cambridge Structural Database ◽  
Model Systems ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Structural Database ◽  
Horizontal Displacements

Parallel interactions of aromatic and heteroaromatic molecules are very important in chemistry and biology. In this review, recent findings on preferred geometries and interaction energies of these molecules are presented. Benzene and pyridine were used as model systems for studying aromatic and heteroaromatic molecules, respectively. Searches of Cambridge Structural Database show that both aromatic and heteroaromatic molecules prefer interacting at large horizontal displacements, even though previous calculations showed that stacking interactions (with offsets of about 1.5 ?) are the strongest. Calculations of interaction energies at large horizontal displacements revealed that the large portion of interaction energy is preserved even when two molecules do not overlap. These substantial energies, as well as the possibility of forming larger supramolecular structures, make parallel interactions at large horizontal displacements more frequent in crystal structures than stacking interactions.

Sign in / Sign up

Export Citation Format

Share Document