Dataset Information

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 these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.

SUBMITTER: Song S

PROVIDER: S-EPMC8442717 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Song Shaotang S Wang Lulu L Su Jie J Xu Zhen Z Hsu Chia-Hsiu CH Hua Chenqiang C Lyu Pin P Li Jing J Peng Xinnan X Kojima Takahiro T Nobusue Shunpei S Telychko Mykola M Zheng Yi Y Chuang Feng-Chuan FC Sakaguchi Hiroshi H Wong Ming Wah MW Lu Jiong J

Chemical science 20210805 35

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 these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry cal ...[more]

PMID: 34667560

Similar Datasets

Project description:The future of materials chemistry will be defined by our ability to precisely arrange components that have considerably larger dimensions and more complex compositions than conventional molecular or macromolecular building blocks. However, exerting structural and constitutional control in the assembly of nanoscale entities presents a considerable challenge. Dynamic covalent nanoparticles are emerging as an attractive category of reaction-enabled solution-processable nanosized building block through which the rational principles of molecular synthetic chemistry can be extended into the nanoscale. From a mixture of two hydrazone-based dynamic covalent nanoparticles with complementary reactivity, specific molecular instructions trigger selective assembly of intimately mixed heteromaterial (Au-Pd) aggregates or materials highly enriched in either one of the two core materials. In much the same way as complementary reactivity is exploited in synthetic molecular chemistry, chemospecific nanoparticle-bound reactions dictate building block connectivity; meanwhile, kinetic regioselectivity on the nanoscale regulates the detailed composition of the materials produced. Selectivity, and hence aggregate composition, is sensitive to several system parameters. By characterizing the nanoparticle-bound reactions in isolation, kinetic models of the multiscale assembly network can be constructed. Despite ignoring heterogeneous physical processes such as aggregation and precipitation, these simple kinetic models successfully link the underlying molecular events with the nanoscale assembly outcome, guiding rational optimization to maximize selectivity for each of the three assembly pathways. With such predictive construction strategies, we can anticipate that reaction-enabled nanoparticles can become fully incorporated in the lexicon of synthetic chemistry, ultimately establishing a synthetic science that manipulates molecular and nanoscale components with equal proficiency.

Project description:The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe2 and 2-Y with Y = H, CN, NO2, OMe, NMe2) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional "back-of-the-envelope" open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe2 balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange-correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe2. REG-IQF also shows that exchange-correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets