Water Dimer-Driven DNA Base Superstructure with Mismatched Hydrogen Bonding

Water-mediated cytosine self-assembly in infrared perspective

Self-assembly plays a crucial role in the formation and allosteric processes of many biomolecules, water molecules can affect these processes. Cytosine (Cyt) has excellent self-assembly ability, forming a flat and ordered structure through hydrogen bonds (HBs) in the presence of water molecules. However, the vibration dynamics and interaction mechanism of water induced Cyt self-assembly are still unclear. In this work, infrared spectroscopy techniques, combined with density functional theory (DFT) theoretical calculations, were employed to investigate the vibrational characteristics and interactions of water molecule mediated self-assembly of Cyt and its reverse process. The results indicate that the induction of Cyt self-assembly by water molecules has differential effects on the various vibrational modes of the Cyt molecule. Multi-view infrared spectroscopy provides a powerful tool for the characterization of biomolecules in situ. This study will contribute to a deeper understanding and application of nucleic acid biological nanostructures.

Scanning Probe Microscopy Characterization of Biomolecules enabled by Mass-Selective, Soft-landing Electrospray Ion Beam Deposition

Scanning probe microscopy (SPM), in particular at low temperature (LT) under ultra-high vacuum (UHV) conditions, offers the possibility of real-space imaging with resolution reaching the atomic level. However, its potential for the analysis of complex biological molecules has been hampered by requirements imposed by sample preparation. Transferring molecules onto surfaces in UHV is typically accomplished by thermal sublimation in vacuum. This approach however is limited by the thermal stability of the molecules, i. e. not possible for biological molecules with low vapour pressure. Bypassing this limitation, electrospray ionisation offers an alternative method to transfer molecules from solution to the gas-phase as intact molecular ions. In soft-landing electrospray ion beam deposition (ESIBD), these molecular ions are subsequently mass-selected and gently landed on surfaces which permits large and thermally fragile molecules to be analyzed by LT-UHV SPM. In this concept, we discuss how ESIBD+SPM prepares samples of complex biological molecules at a surface, offering controls of the molecular structural integrity, three-dimensional shape, and purity. These achievements unlock the analytical potential of SPM which is showcased by imaging proteins, peptides, DNA, glycans, and conjugates of these molecules, revealing details of their connectivity, conformation, and interaction that could not be accessed by any other technique.

Dynamic Cleavage-Remodeling of Covalent Organic Networks into Multidimensional Superstructures

Superstructures with complex hierarchical spatial configurations exhibit broader structural depth than single hierarchical structures and the associated broader application prospects. However, current preparation methods are greatly constrained by cumbersome steps and harsh conditions. Here, for the first time, a concise and efficient thermally responsive dynamic synthesis strategy for the preparation of multidimensional complex superstructures within soluble covalent organic networks (SCONs) with tunable morphology from 0D hollow supraparticles to 2D films is presented. Mechanism study reveals the thermally responsive dynamic "cleavage-remodeling" characteristics of SCONs, synthesized based on the unique bilayer structure of (2.2)paracyclophane, and the temperature control facilitates the process from reversible solubility to reorganization and construction of superstructures. Specifically, during the process, the oil-water-emulsion two-phase interface can be generated through droplet jetting, leading to the preparation of 0D hollow supraparticles and other bowl-like complex superstructures with high yield. Additionally, by modulating the volatility and solubility of exogenous solvents, defect-free 2D films are prepared relying on an air-liquid interface. Expanded experiments further confirm the generalizability and scalability of the proposed dynamic "cleavage-remodeling" strategy. Research on the enrichment mechanism of guest iodine highlights the superior kinetic mass transfer performance of superstructural products compared to single-hierarchical materials.

From Short- to Long-Range Chiral Recognition on Surfaces: Chiral Assembly and Synthesis

Research on chiral behaviors of small organic molecules at solid surfaces, including chiral assembly and synthesis, can not only help unravel the origin of the chiral phenomenon in biological/chemical systems but also provide promising strategies to build up unprecedented chiral surfaces or nanoarchitectures with advanced applications in novel nanomaterials/nanodevices. Understanding how molecular chirality is recognized is considered to be a mandatory basis for such studies. In this review, a series of recent studies in chiral assembly and synthesis at well-defined metal surfaces under ultra-high vacuum conditions are outlined. More importantly, the intrinsic mechanisms of chiral recognition are highlighted, including short/long-range chiral recognition in chiral assembly and two main strategies to steer the reaction pathways and modulate selective synthesis of specific chiral products on surfaces.

Visualizing the Promoting Role of Interfacial Water in the Deprotonation of Formic Acid on Cu(111)

Water plays a crucial role in various heterogeneous catalytic reactions, but the atomic-scale characterization of how water participates in these chemical processes remains a significant challenge. Here we directly visualize the promoting role of interfacial water in the deprotonation of formic acid (FA) on a metal surface, using combined scanning tunneling microscopy and qPlus-based noncontact atomic force microscopy. We find the dissociation of FA when coadsorbed with water on the Cu(111) surface, resulting in the formation of hydronium and formate ions. Interestingly, most of the hydrated proton and formate ions exhibit a phase-separated behavior on Cu(111), in which Eigen and Zundel cations assemble into a monolayer hexagonal hydrogen-bonding (H-bonding) network, and bidentate formate ions are solvated with water and aggregate into one-dimensional chains or two-dimensional H-bonding networks. This phase-separated behavior is essential for preventing the proton transfer back from hydronium to formate and the reformation of FA. Density functional theory calculations reveal that the participation of water significantly reduces the deprotonation barrier of FA on Cu(111), in which water catalyzes the decomposition of FA through the Grotthuss proton transfer mechanism. In addition, the separate solvation of hydronium and bidentate formate ions is energetically preferred due to the enhanced interaction with the copper substrate. The promoting role of water in the deprotonation of FA is further confirmed by the temperature-programmed desorption experiment, which shows that the intensity of the H2 desorption peak significantly increases and the desorption of FA declines when water and FA coadsorbed on the Cu(111) surface.