C-halogen…pi interactions in nucleic acids: a database study

Mitra, Debarghya; Bankoti, Namrata; Michael, Daliah; Sekar, K.; Row, Tayur N. Guru

doi:10.1007/s12039-020-01794-1

Cited by 17 publications

(15 citation statements)

References 11 publications

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“…This interaction has been described as key for the ligand binding and recognition to the enzyme representing a similar relevance to halogen bond interactions [44,45]. A common halogen-π bond describes the aromatic rings as donors and the C-X bonds (with X = F, Cl, Br, I) as acceptors [46]. This characteristic is perfectly in line with the conformations adopted by compounds 8p, 8k and 8l with residue Tyr228 of S1.…”

Section: Molecular Dockingmentioning

confidence: 63%

“…Compounds 8k and 8l also engage in halogen-π interactions with residue Tyr228 at distances of 3.91 Å and 3.88 Å, respectively. The differences in length of the halogen-π interaction and the Tyr228 residue are not only related to the structural conformations adopted by each compound, but also to the exact type of halogen atom present, since distances and bonding forces increase with their molecular weight (F < Cl < Br < I) [46]. The performed docking studies showed that the lactam ring of all compounds exhibited a Van der Waals interaction with Thr98 and Phe174, while the heteroatom is solvent-exposed.…”

Section: Molecular Dockingmentioning

confidence: 99%

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Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units

et al. 2021

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Green chemistry implementation has led to promising results in waste reduction in the pharmaceutical industry. However, the early sustainable development of pharmaceutically active compounds and ingredients remains a considerable challenge. Herein, we wish to report a green synthesis of new pharmaceutically active peptide triazoles as potent factor Xa inhibitors, an important drug target associated with the treatment of diverse cardiovascular diseases. The new inhibitors were synthesized in three steps, featuring cycloaddition reactions (high atom economy), microwave-assisted organic synthesis (energy efficiency), and copper nanoparticle catalysis, thus featuring Earth-abundant metals. The molecules obtained showed FXa inhibition, with IC50-values as low as 17.2 μM and no associated cytotoxicity in HEK293 and HeLa cells. These results showcase the environmental potential and chemical implications of the applied methodologies for the development of new molecules with pharmacological potential.

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Section: Molecular Dockingmentioning

confidence: 63%

Section: Molecular Dockingmentioning

confidence: 99%

Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units

et al. 2021

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“…. π could be considered since the shortest distance between the centroid of the ring and chloride atom is 3.504 Å [29,30]. On the other hand, the organic part of (C6H8Cl2N2)2[Cd3Cl10]•6H2O is made by two crystallographic independent [C6H8Cl2N2] 2+ dictations.…”

Section: Crystal Structure Descriptionmentioning

confidence: 99%

“…The cations containing C17, C18 and C19 carbon atoms (molecule A) are located at (0,0,0), while those formed by C15, C16 and C20 (molecule B) carbon atoms are located over the inversion center at (1/2,1/2,0) and are linked to the water molecules via N-H…O and O-H…O hydrogen bonds to form ribbons extending along the c-axis and located at y = ½ (Figure 6). It is worth mentioning that all organic molecules are parallel to each other and are stacked in an offset manner, but there is nevertheless a degree of π-π overlap between adjacent rings since the distance between two organic cations corresponds to a unit cell, equal to 6.784(4), while the interaction C-Cl…π could be considered since the shortest distance between the centroid of the ring and chloride atom is 3.504Å [29,30].…”

Section: Crystal Structure Descriptionmentioning

confidence: 99%

Synthesis, Crystal Structure, DFT Theoretical Calculationand Physico-Chemical Characterization of a New Complex Material (C6H8Cl2N2)2[Cd3Cl10]·6H2O

et al. 2021

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The chemical preparation, crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the novel cadmium (II) 2,5-dichloro-p-phenylendiaminium decachlorotricadmate(II) hexahydrate complex, (C6H8Cl2N2)2[Cd3Cl10]·6H2O, has been reported. The atomic arrangement can be described as built up by an anionic framework, formed by edge-sharing [CdCl6]2− octahedra in linear polymeric chains spreading along the a-axis, while the organic cations surround these latters. The inspection of the Hirshfeld surface analysis helps to discuss the strength of hydrogen bonds and to quantify the inter-contacts, which reveal that H…Cl/Cl…H (38.9%), H…H (13.9%), and Cd…Cl/Cl…Cd (12.4%) are the main interactions that govern the crystal packing of the studied structure. SEM/EDXwas carried out and the powder XRD confirmed the good crystallinity of the material. FT-IR and the DFT calculation reveal the good correlation between the experimental and the theoretical wavenumbers. The HOMO-LUMO energy gap was used to predict the electric conductivity of the compound. Finally, the thermal TGA/DTA analysis shows stability until 380 K.

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“…Among the essential noncovalent interactions are π-system-based interactions. The importance of such interactions is clearly manifested in a multitude of chemical and biological phenomena. − An aromatic π-system can be electron-rich or electron-deficient, as in benzene and hexafluorobenzene, respectively. However, no matter a π-system is electron-rich or electron-deficient, it can be noncovalently bonded to a σ-hole-containing molecule as in the case of halogen-containing molecule···π-system interactions .…”

Section: Introductionmentioning

confidence: 99%

Cospatial σ-Hole and Lone Pair Interactions of Square-Pyramidal Pentavalent Halogen Compounds with π-Systems: A Quantum Mechanical Study

et al. 2021

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In the spirit of the mounting interest in noncovalent interactions, the present study was conducted to scrutinize a special type that simultaneously involved both σ-hole and lone pair (lp) interactions with aromatic π-systems. Square-pyramidal pentavalent halogen-containing molecules, including X-Cl-F4, F-Y-F4, and F-I-X4 compounds (where X = F, Cl, Br, and I and Y = Cl, Br, and I) were employed as σ-hole/lp donors. On the other hand, benzene (BZN) and hexafluorobenzene (HFB) were chosen as electron-rich and electron-deficient aromatic π-systems, respectively. The investigation relied upon a variety of quantum chemical calculations that complement each other. The results showed that (i) the binding energy of the X-Y-F4···BZN complexes increased (i.e., more negative) as the Y atom had a larger magnitude of σ-hole, contrary to the pattern of X-Y-F4···HFB complexes; (ii) the interaction energies of X-Y-F4···BZN complexes were dominated by both dispersion and electrostatic contributions, while dispersive interactions dominated X-Y-F4···HFB complexes; and (iii) the X4 atoms in F-I-X4···π-system complexes governed the interaction energy pattern: the larger the X4 atoms were, the greater the interaction energies were, for the same π-system. The results had illuminating facets in regard to the rarely addressed cases of the σ-hole/lp contradictory scene.

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C-halogen…pi interactions in nucleic acids: a database study

Cited by 17 publications

References 11 publications

Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units

Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units

Synthesis, Crystal Structure, DFT Theoretical Calculationand Physico-Chemical Characterization of a New Complex Material (C6H8Cl2N2)2[Cd3Cl10]·6H2O

Cospatial σ-Hole and Lone Pair Interactions of Square-Pyramidal Pentavalent Halogen Compounds with π-Systems: A Quantum Mechanical Study

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