Exploration of relative π-electron localization in naphthalene aromatic rings by C–H⋯π interactions: experimental evidence, computational criteria, and database analysis

CrystEngComm ◽  
2019 ◽  
Vol 21 (42) ◽  
pp. 6432-6445 ◽  
Author(s):  
Ali Samie ◽  
Alireza Salimi ◽  
Jered C. Garrison
Keyword(s):  
Experimental Evidence ◽  
Aromatic Ring ◽  
Electron Localization ◽  
Aromatic Rings ◽  
Database Analysis ◽  
Π Interactions ◽  
Contact Position

In C–H⋯π interaction, the relative π-electron localization in aromatic ring led to the change of contact position from centre to edges of the ring (C–H⋯πe) which was confirmed by experimental evidences, computational criteria, and database analysis.

scholarly journals Crystal structure of 9,9′-{(1E,1′E)-[1,4-phenylenebis(azanylylidene)]bis(methanylylidene)}bis(2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-8-ol)

2016 ◽  
Vol 72 (10) ◽  
pp. 1366-1369 ◽  
Author(s):  
Md. Serajul Haque Faizi ◽  
Akram Ali ◽  
Vadim A. Potaskalov
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Aromatic Ring ◽  
Title Compound ◽  
Inversion Symmetry ◽  
Inversion Center ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Compound C

The whole molecule of the title compound, C32H34N2O2, is generated by inversion symmetry; the central benzene ring being situated about the crystallographic inversion center. The aromatic ring of the julolidine moiety is inclined to the central benzene ring by 33.70 (12)°. There are two intramolecular O—H...N hydrogen bonds in the molecule, generatingS(6) ring motifs. The conformation about the C=N bonds isE. The fused non-aromatic rings of the julolidine moiety adopt half-chair conformations. In the crystal, adjacent molecules are linked by pairs of C—H...π interactions, forming a ladder-like structure propagating along thea-axis direction.

scholarly journals Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1776
Author(s):  
Yan Zhu ◽  
Saad Alqahtani ◽  
Xiche Hu
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Protein Kinases ◽  
Aromatic Ring ◽  
Kinase Inhibitors ◽  
Binding Pocket ◽  
Atp Binding ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Molecular Determinants

Protein kinases are key enzymes in many signal transduction pathways, and play a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. However, aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Over the past three decades, thousands of protein kinase inhibitors (PKIs) with varying molecular frames have been developed. Large-scale data mining of the Protein Data Bank resulted in a database of 2139 non-redundant high-resolution X-ray crystal structures of PKIs bound to protein kinases. This provided us with a unique opportunity to study molecular determinants for the molecular recognition of PKIs. A chemoinformatic analysis of 2139 PKIs resulted in findings that PKIs are “flat” molecules with high aromatic ring counts and low fractions of sp3 carbon. All but one PKI possessed one or more aromatic rings. More importantly, it was found that the average weighted hydrogen bond count is inversely proportional to the number of aromatic rings. Based on this linear relationship, we put forward the exchange rule of hydrogen bonding interactions and non-bonded π-interactions. Specifically, a loss of binding affinity caused by a decrease in hydrogen bonding interactions is compensated by a gain in binding affinity acquired by an increase in aromatic ring-originated non-bonded interactions (i.e., π–π stacking interactions, CH–π interactions, cation–π interactions, etc.), and vice versa. The very existence of this inverse relationship strongly suggests that both hydrogen bonding and aromatic ring-originated non-bonded interactions are responsible for the molecular recognition of PKIs. As an illustration, two representative PKI–kinase complexes were employed to examine the relative importance of different modes of non-bonded interactions for the molecular recognition of PKIs. For this purpose, two FDA-approved PKI drugs, ibrutinib and lenvatinib, were chosen. The binding pockets of both PKIs were thoroughly examined to identify all non-bonded intermolecular interactions. Subsequently, the strengths of interaction energies between ibrutinib and its interacting residues in tyrosine kinase BTK were quantified by means of the double hybrid DFT method B2PLYP. The resulting energetics for the binding of ibrutinib in tyrosine kinase BTK showed that CH–π interactions and π–π stacking interactions between aromatic rings of the drug and hydrophobic residues in its binding pocket dominate the binding interactions. Thus, this work establishes that, in addition to hydrogen bonding, aromatic rings function as important molecular determinants for the molecular recognition of PKIs. In conclusion, our findings support the following pharmacophore model for ATP-competitive kinase inhibitors: a small molecule features a scaffold of one or more aromatic rings which is linked with one or more hydrophilic functional groups. The former has the structural role of acting as a scaffold and the functional role of participating in aromatic ring-originated non-bonded interactions with multiple hydrophobic regions in the ATP binding pocket of kinases. The latter ensure water solubility and form hydrogen bonds with the hinge region and other hydrophilic residues of the ATP binding pocket.

scholarly journals 5-Cyano-1,3-phenylene diacetate

2014 ◽  
Vol 70 (6) ◽  
pp. o712-o712
Author(s):  
Bahar Abbassi ◽  
Michela Brumfield ◽  
Lloyd M. Jones ◽  
Vladimir N. Nesterov ◽  
Andrew J. Carr
Keyword(s):  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Aromatic Ring ◽  
Crystal Packing ◽  
Carbonyl Groups ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Title Molecule

In the title molecule, C11H9NO4, the two acetoxy groups are twisted from the plane of the benzene ring by 67.89 (4) and 53.30 (5)°. Both carbonyl groups are on the same side of the aromatic ring. In the crystal, weak C—H...O hydrogen bonds link molecules into layers parallel to theacplane. The crystal packing exhibits π–π interactions between the aromatic rings, indicated by a short intercentroid distance of 3.767 (3) Å.

scholarly journals N′-(3-Hydroxybenzylidene)-4-methylbenzohydrazide

2012 ◽  
Vol 68 (6) ◽  
pp. o1816-o1816
Author(s):  
Ji-Lai Liu ◽  
Ming-Hui Sun ◽  
Jing-Jun Ma
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Compound C ◽  
Centroid Distance ◽  
Benzene Rings

The title compound, C15H14N2O2, was obtained from the reaction of 3-hydroxybenzaldhyde and 4-methylbenzohydrazide in methanol. In the molecule, the benzene rings form a dihedral angle of 2.9 (3)°. In the crystal, N—H...O and O—H...O hydrogen bonds link the molecules into layers parallel to (101). The crystal packing also exhibits π–π interactions between the aromatic rings [centroid–centroid distance = 3.686 (4) Å].

Dual role of silver in a fluorogenic N-squaraine probe based on Ag(I)-π interactions

2021 ◽  
Author(s):  
Manel Vega ◽  
Salvador Blasco ◽  
Enrique García-España ◽  
Bartolome Soberats ◽  
Antonio Frontera ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Experimental Evidence ◽  
Dual Role ◽  
Π Interactions ◽  
Turn On

In the presence of Ag(I), the monoanion of a cyano-N-squaraine (I) generates an intense fluorescent turn-on response. Experimental evidence and DFT calculations reveal a sequence of deprotonation-coordination events in which...

scholarly journals Crystal structures of 2-methylpyridinium hydrogen 2,3-bis(4-methylbenzoyloxy)succinate and bis-[4-methylpyridinium hydrogen 2,3-bis(4-methylbenzoyloxy)succinate] pentahydrate

2017 ◽  
Vol 73 (10) ◽  
pp. 1483-1487
Author(s):  
P. Sivakumar ◽  
S. Israel ◽  
G. Chakkaravarthi
Keyword(s):  
Hydrogen Bonds ◽  
Pyridine Ring ◽  
Crystal Packing ◽  
Water Molecules ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Dimensional Network ◽  
Anions And Cations

The title salt (I), C6H8N+·C20H17O8−, comprises a 2-methylpyridinium cation and a 2,3-bis(4-methylbenzoyloxy)succinate mono-anion while the salt (II), 2C6H8N+·2C20H17O8−·5H2O, consists of a pair of 4-methylpyridinium cations and 2,3-bis(4-methylbenzoyloxy)succinate mono-anions and five water molecules of solvation in the asymmetric unit. In (I), the dihedral angle between the aromatic rings of the anion is 40.41 (15)°, comparing with 43.0 (3) and 85.7 (2)° in the conformationally dissimilar anion molecules in (II). The pyridine ring of the cation in (I) is inclined at 23.64 (16) and 42.69 (17)° to the two benzene moieties of the anion. In (II), these comparative values are 4.7 (3), 43.5 (3)° and 43.5 (3), 73.1 (3)° for the two associated cation and anion pairs. The crystal packing of (I) is stabilized by inter-ionic N—H...O, O—H...O and C—H...O hydrogen bonds as well as weak C—H...π interactions, linking the ions into infinite chains along [100]. In the crystal packing of (II), the anions and cations are also linked by N—H...O and O—H...O hydrogen bonds involving also the water molecules, giving a two-dimensional network across (001). The crystal structure is also stabilized by weak C—H...O and C—H...π interactions.

Lariat Ether Receptor Systems Show Experimental Evidence for Alkali Metal Cation−π Interactions

2002 ◽  
Vol 35 (10) ◽  
pp. 878-886 ◽  
Author(s):  
George W. Gokel ◽  
Leonard J. Barbour ◽  
Riccardo Ferdani ◽  
Jiaxin Hu
Keyword(s):  
Alkali Metal ◽  
Experimental Evidence ◽  
Metal Cation ◽  
Alkali Metal Cation ◽  
Π Interactions ◽  
Lariat Ether

Pd−N−H···Cl−Pd Hydrogen Bonds and π−π Interactions between Fluorinated Aromatic Rings intrans-[PdCl2(NH2ArF)2]

2007 ◽  
Vol 7 (1) ◽  
pp. 117-123 ◽  
Author(s):  
Oscar Baldovino-Pantaleón ◽  
David Morales-Morales ◽  
Simón Hernández-Ortega ◽  
Rubén A. Toscano ◽  
Jesús Valdés-Martínez
Keyword(s):  
Hydrogen Bonds ◽  
Aromatic Rings ◽  
Π Interactions

scholarly journals Synthesis of Aromatic Rings Embedded in Polycyclic Scaffolds by Triyne Cycloaddition: Competition between Carbonylative and Non-Carbonylative Pathways

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 595
Author(s):  
Laura Salacz ◽  
Nicolas Girard ◽  
Jean Suffert ◽  
Gaëlle Blond
Keyword(s):  
Aromatic Ring ◽  
Aromatic Rings ◽  
One Pot ◽  
Polycyclic Compounds ◽  
One Pot Synthesis ◽  
The One

Cycloadditions have emerged as some of the most useful reactions for the formation of polycyclic compounds. The carbonylative cycloaddition of triynes can lead to carbonylative and non-carbonylative competitive pathways, each leading to the formation of an aromatic ring. We report herein the one-pot synthesis of fully- and unsymmetrically-substituted tetracyclic 6,5,7,5-troponic and 6,5,6,5-benzenoid scaffolds using pre-organized triynes showing the competition between these two pathways.

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