Theoretical studies on the nature of bonding in σ-hole complexes

Mohajeri, Afshan; Pakiari, A.H.; Bagheri, N.

doi:10.1016/j.cplett.2008.11.017

Cited by 79 publications

(90 citation statements)

References 40 publications

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“…The directionality of halogen bonding further confirms that the origin of the r-hole is electrostatic in nature [14]. The value of V S,MAX at the r-hole correlates to the calculated interaction energy (hydrogen or halogen bonding) between these relatively positive sites and a selected Lewis base [14,15]. The direct correlation between BrÁ Á ÁO halogen bond strength and the V S,MAX value [9] shows that the electrostatic properties of a molecule are vitally important to its ability to form a halogen bond.…”

Section: Introductionsupporting

confidence: 65%

“…The presence of a positive r-hole explains how halogens can interact favorably with negative sites on neighboring molecules, thus forming halogen bonds. The directionality of halogen bonding further confirms that the origin of the r-hole is electrostatic in nature [14]. The value of V S,MAX at the r-hole correlates to the calculated interaction energy (hydrogen or halogen bonding) between these relatively positive sites and a selected Lewis base [14,15].…”

Section: Introductionsupporting

confidence: 61%

See 1 more Smart Citation

Electrostatic surface potential analysis of the I3- ion in the gas phase, the condensed phase and a novel extrapolation to the solid state

Groenewald

Esterhuysen

Dillen

2016

Computational and Theoretical Chemistry

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Section: Introductionsupporting

confidence: 65%

Section: Introductionsupporting

confidence: 61%

Electrostatic surface potential analysis of the I3- ion in the gas phase, the condensed phase and a novel extrapolation to the solid state

Groenewald

Esterhuysen

Dillen

2016

Computational and Theoretical Chemistry

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“…S5, suggesting that the halogen bond plays a significant role in the formation of the OPV3-CHO/bromides composite structure. Theoretical calculation finds that there is a positive charge, called a σ-hole, on halogen atoms' surfaces (35,36). Therefore, the halogen atoms will interact with electronegative groups such as oxygen, nitrogen, hydroxyl, or carbonyl groups (26).…”

Section: Resultsmentioning

confidence: 99%

Structure and structural transition of chiral domains in oligo(p-phenylenevinylene) assembly investigated by scanning tunneling microscopy

Chen

Wang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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OPV3-CHO molecules are employed to prepare assembly on highly oriented pyrolytic graphite, and the so-prepared assembly is investigated by scanning tunneling microscopy. In the assembly chiral domains are observed with various structures such as linear and windmill. The chiral structural formation, stability, transition, and possible unification are intensively studied. After thermal annealing, linear structure was the only structure. To achieve a unified assembly with a single structure, an efficient method is proposed by coadsorption of OPV3-CHO with selected molecules. For example, an assembly with side-by-side helix structure is formed by a simple coadsorption of OPV3-CHO with alkyl bromide (C n H 2nþ1 Br, n ¼ 15-18). The experiments by cocrystallization of OPV3-CHO∕ C n H 2nþ1 X (X ¼ Cl, Br, and I) show the important role of halogen bonding in formation of the uniform structure. The results are significant in understanding the intermolecular noncovalent interactions that dominate the surface structure and chirality.coadsorption | halogen bonding | surface chirality U nderstanding the formation and structural transition of molecular nanostructure is an important issue in chemistry, molecular science, and nanodevice fabrication. Among various molecular nanostructures, two-dimensional surface chirality is a property of asymmetry and of great interest in fundamental research and industrial application such as life genesis, nonlinear optics, enantioselective heterogeneous catalysis, and surface modification (1-3). With atomic resolution, scanning tunneling microscopy (STM) is powerful in surface chirality study (4-7). From absolute chirality determination to chiral structure fabrication with chiral molecules or achiral molecules on a solid surface, a few results have been reported (8-13). Xu et al. directly observed the chirality of (R)-and (S)-2-phenylpropionamide molecules on Cu(111) in solution by using electrochemical STM (14). De Feyter et al. studied solvent-induced homochirality in selfassembled monolayers of achiral molecules. The chirality of the solvent directs the macroscopic chirality of the monolayer (15). After these results, we focus on the current challenge in surface chirality, which includes understanding the underlying driving force for the chiral formation, amplification, transition, and controlling the chiral structure.Recently, oligo(p-phenylenevinylene) (OPV) and its derivatives have attracted a lot of attention because of their advanced optical and electronic properties and possible application in organic electronic devices (16)(17)(18). In the present report, an aldehyde-substituted OPV molecule (OPV3-CHO, Scheme 1) is used as a model compound to study its structure on a solid surface. It is found that achiral OPV3-CHO can form chiral domains on highly oriented pyrolytic graphite (HOPG). The OPV3-CHO adlayer is investigated by STM including structural formation, stability, transition, and possible unification of the chiral domains. The OPV3-CHO chiral domains appear in linear and windmil...

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“…However, a few articles have been devoted in the literature to the study of intramolecular YBs. The nature of the YB has been rationalized by Politzer et al based on the σ-hole concept [423,424,425]. The term σ -hole refers to the electron-deficient outer lobe of a p orbital involved in forming a covalent bond.…”

Section: The Importance In Drug Design Of Similar To Hb Bondsmentioning

confidence: 99%

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

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The effect of weak intermolecular interactions on the binding affinity between ligand-protein complexes plays an important role in stabilizing a ligand at the interface of a protein structure. In this review article, we will explore the different ways of taking into account these interactions, mainly intramolecular hydrogen bonds, in docking calculations. Their possible limitations and their suitable application domains are highlighted. Inspection of the outliers of this study probed very stimulating, as it provides opportunities and inspiration to medicinal chemists, being a reminder of the impact that minimal chemical modifications can have on biological activities.

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Theoretical studies on the nature of bonding in σ-hole complexes

Cited by 79 publications

References 40 publications

Electrostatic surface potential analysis of the I3- ion in the gas phase, the condensed phase and a novel extrapolation to the solid state

Electrostatic surface potential analysis of the I3- ion in the gas phase, the condensed phase and a novel extrapolation to the solid state

Structure and structural transition of chiral domains in oligo(p-phenylenevinylene) assembly investigated by scanning tunneling microscopy

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

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