Designation and Exploration of Halide–Anion Recognition Based on Cooperative Noncovalent Interactions Including Hydrogen Bonds and Anion−π

2015 ◽  
Vol 119 (22) ◽  
pp. 5842-5852 ◽  
Author(s):  
Yan-Zhi Liu ◽  
Kun Yuan ◽  
Ling-Ling Lv ◽  
Yuan-Cheng Zhu ◽  
Zhao Yuan
Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.


Author(s):  
Paul D. Beer ◽  
Nicholas C. Fletcher ◽  
Alan Grieve ◽  
John W. Wheeler ◽  
Christopher P. Moore ◽  
...  

2020 ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Adam I. Stash ◽  
Vladimir G. Tsirelson ◽  
Robert Fayzullin

A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of pi-stacking and intricate C=O...pi interactions and nonclassical hydrogen bonds. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with more well-known functions. Partitioning of crystal space into atomic-like potential basins led us to the definite description of the charge transfer. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.


Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1032
Author(s):  
Sonia Khemaissa ◽  
Sandrine Sagan ◽  
Astrid Walrant

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.


2020 ◽  
Vol 76 (8) ◽  
pp. 795-809
Author(s):  
Konstantin L'vovich Obydennov ◽  
Tatiana Andreevna Kalinina ◽  
Olga Alexandrovna Vysokova ◽  
Pavel Alexandrovich Slepukhin ◽  
Varvara Alexandrovna Pozdina ◽  
...  

The crystal structures of four new chiral [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines are described, namely, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C20H24N4O4S, ethyl 6,6-dimethyl-5-(4-methylbenzoyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C17H20N4O3S, and ethyl 5-benzoyl-6-(4-methoxyphenyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C21H20N4O4S. The crystallographic data and cell activities of these four compounds and of the structures of three previously reported similar compounds, namely, ethyl 5′-(4-methylbenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O4S, and ethyl 6-methyl-5-(4-methylbenzoyl)-6-phenyl-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C22H22N4O3S, are contrasted and compared. For both crystallization and an MTT assay, racemic mixtures of the corresponding [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines were used. The main manner of molecular packing in these compounds is the organization of either enantiomeric pairs or dimers. In both cases, the formation of two three-centre hydrogen bonds can be detected resulting from intramolecular N—H...O and intermolecular N—H...O or N—H...N interactions. Molecules of different enantiomeric forms can also form chains through N—H...O hydrogen bonds or form layers between which only weak hydrophobic contacts exist. Unlike other [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate contains molecules of only the (R)-enantiomer; moreover, the N—H group does not participate in any significant intermolecular interactions. Molecular mechanics methods (force field OPLS3e) and the DFT B3LYP/6-31G+(d,p) method show that the compound forming enantiomeric pairs via weak N—H...N hydrogen bonds is subject to greater distortion of the geometry under the influence of the intermolecular interactions in the crystal. For intramolecular N—H...O and S...O interactions, an analysis of the noncovalent interactions (NCIs) was carried out. The cellular activities of the compounds were tested by evaluating their antiproliferative effect against two normal human cell lines and two cancer cell lines in terms of half-maximum inhibitory concentration (IC50). Some derivatives have been found to be very effective in inhibiting the growth of Hela cells at nanomolar and submicromolar concentrations with minimal cytotoxicity in relation to normal cells.


2019 ◽  
Vol 55 (27) ◽  
pp. 3872-3875 ◽  
Author(s):  
Takashi Nakamura ◽  
Sota Yonemura ◽  
Tatsuya Nabeshima

An amide cyclodextrin with anion recognition ability exhibits unique binding mode in which unsymmetrically arranged functional groups play distinctive roles.


2019 ◽  
Author(s):  
Teresa Naranjo ◽  
Rubén Álvarez-Asencio ◽  
Patricia Pedraz ◽  
Belén Nieto-Ortega ◽  
Enrique Burzurí ◽  
...  

Hydrogen bonds are arguably the most important of noncovalent interactions. The physical properties of water and the information storage in DNA depend on H-bonding, for instance. To this day, the balance between the Coulombic and covalent contributions to H-bonds is still under debate. Here, we show that H-bonded host-guest systems associate in ionic liquids, pure salts with melting point below room temperature, in which dipole-dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (<i>K</i><sub>a</sub>) obtained from titrations of four H-bonded host-guest systems in two organic solvents and two ionic liquids yield smaller yet comparable <i>K</i><sub>a</sub>values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy. Our results indicate that strong H-bonds are only moderately affected by surroundings composed entirely of charges, suggesting that the balance of Coulombic to covalent forces is not tipped towards the former.


2019 ◽  
Author(s):  
Teresa Naranjo ◽  
Rubén Álvarez-Asencio ◽  
Patricia Pedraz ◽  
Belén Nieto-Ortega ◽  
Enrique Burzurí ◽  
...  

Hydrogen bonds are arguably the most important of noncovalent interactions. The physical properties of water and the information storage in DNA depend on H-bonding, for instance. To this day, the balance between the Coulombic and covalent contributions to H-bonds is still under debate. Here, we show that H-bonded host-guest systems associate in ionic liquids, pure salts with melting point below room temperature, in which dipole-dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (<i>K</i><sub>a</sub>) obtained from titrations of four H-bonded host-guest systems in two organic solvents and two ionic liquids yield smaller yet comparable <i>K</i><sub>a</sub>values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy. Our results indicate that strong H-bonds are only moderately affected by surroundings composed entirely of charges, suggesting that the balance of Coulombic to covalent forces is not tipped towards the former.


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