Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization

Song, Shaotang; Wang, Lulu; Su, Jie; Xu, Zhen; Hsu, Chia-Hsiu; Hua, Chenqiang; Lyu, Pin; Li, Jing; Peng, Xinnan; Kojima, Toshikatsu; Nobusue, Shunpei; Telychko, Mykola; Zheng, Yi; Chuang, Feng‐Chuan; Sakaguchi, Hiroshi; Wong, Ming Wah; Lu, Jiong

doi:10.1039/d1sc03733a

Cited by 13 publications

(14 citation statements)

References 49 publications

(58 reference statements)

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“…Thus, we propose that the self-assembled superstructure is mainly governed by the formation of triple I···I and I···H interactions (labeled by the blue and black dashed lines). Our finding is in line with previous observations in the formation of triple halogen bonds in supramolecular structures. − Apart from this structure, three other distinct self-assembled structures within a small domain are also observed (Figures S1–3), and their proposed molecular packing structures are summarized in Figure S4.…”

Section: Resultssupporting

confidence: 91%

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

Wang

Arramel

et al. 2022

ACS Nano

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Polycyclic hydrocarbons (PHs) share the same hexagonal structure of sp 2 carbons as graphene but possess an energy gap due to quantum confinement effect. PHs can be synthesized by a bottom-up strategy starting from small building blocks covalently bonded into large 2D organic sheets. Further investigation of the role of the covalent bonding/ coupling ways on their electronic properties is needed. Here, we demonstrate a surface-mediated synthesis of hexa-peri-hexabenzocoronene (HBC) and its extended HBC oligomers (dimers, trimers, and tetramers) via single-and triple-coupling ways and reveal the implication of different covalent bonding on their electronic properties. High-resolution low-temperature scanning tunneling microscopy and noncontact atomic force microscopy are employed to in situ determine the atomic structures of as-synthesized HBC oligomers. Scanning tunneling spectroscopy measurements show that the length extension of HBC oligomers narrows the energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Furthermore, the energy gaps of triple-coupling HBC oligomers are smaller and decrease more significantly than that of the single-coupling ones. We hypothesize that the triple coupling promotes a more effective delocalization of π-electrons than the single coupling, according to density functional theory calculations. We also demonstrate that the HBC oligomers can further extend across the substrate steps to achieve conjugated polymers and largearea porous carbon networks.

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Section: Resultssupporting

confidence: 91%

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

Wang

Arramel

et al. 2022

ACS Nano

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“…Furthermore, a similar technique was employed to study the self-assembly process of 3D molecular clusters driven by XB, HB, and lone pairÁ Á Áp interactions. 41 Overall, interaction study using surface science techniques has made a tremendous advance and offers realspace monitoring of intricate interactions and molecular assemblies at the atomic scale.…”

Section: Visualizing Ncis: a Formidable Taskmentioning

confidence: 99%

Non-covalent interactions (NCIs) in π-conjugated functional materials: advances and perspectives

et al. 2023

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“…The strength of the noncovalent interaction is indicated by the color of the isosurface: green represents attractive while blue denotes strongly attractive. The NCI analysis has been successfully used to shed light on the presence of halogen bonding in various chemical systems [ 48 , 49 , 50 , 51 ].…”

Section: Methodsmentioning

confidence: 99%

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Zhou

Wong

2022

Molecules

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Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future.

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Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization

Abstract: Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of...

Cited by 13 publications

References 49 publications

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

Non-covalent interactions (NCIs) in π-conjugated functional materials: advances and perspectives

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

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