A predicted new type of directional noncovalent interaction

Murray, Jane S.; Lane, Pat; Politzer, Peter

doi:10.1002/qua.21352

Cited by 355 publications

(291 citation statements)

References 31 publications

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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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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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“…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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“…Similiar to halogens, the pnictogen atoms possess a sigma-hole: a region of positive electrostatic potential in the direction of the bond, which is attracted to a lone pair on a nucleophile with an outer negative electrostatic potential. [82,83] Pnictogen bonding is present in the complex between NH 3 and PH 3 ( Figure 10a) [77] where the N atom is the donor of electron density. The sigma-hole gives rise to the equilibrium geometries: the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom.…”

Section: Pnictogen Bondingmentioning

confidence: 99%

A Complete NCI Perspective: From New Bonds to Reactivity

Narth¹,

Maroun²,

Boto³

et al. 2016

Challenges and Advances in Computational Chemistry and Physics

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The Non-Covalent Interaction (NCI) index is a new topological tool that has recently been added to the theoretical chemist's arsenal. NCI fills a gap that existed within topological methods for the visualization of non-covalent interactions. Based on the electron density and its derivatives, it is able to reveal both attractive and repulsive interactions in the shape of isosurfaces, whose color code reveals the nature of the interaction. It is interesting to note that NCI can even be calculated at the promolecular level, making it a suitable tool for big systems, such as proteins or DNA. Within this chapter we will review the main characteristics of NCI, its similarities with and differences from previous approaches. Special attention will be paid to the visualization of new interaction types. Being based on the electron density, NCI is not only very stable with respect to the calculation method, but it is also a suitable tool for detecting new bonding mechanisms, since all such mechanisms should have a detectable effect on the electron density. This type of approach overcomes the limitations of bond definition, revealing all interaction types, irrespective of whether they have a name or have previously been identified. Finally, we will show how this tool can be used to understand chemical change along a chemical reaction. We will show several examples of torquoselectivity and put forward an explanation of selectivity based on secondary interactions which is complementary to the historical orbital approach.A complete NCI perspective: from new bonds to reactivity 3

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A predicted new type of directional noncovalent interaction

Cited by 355 publications

References 31 publications

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

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?

A Complete NCI Perspective: From New Bonds to Reactivity

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