Local Chiral Inversion of Thymine Dimers by Manipulating Single Water Molecules

Conformational Selectivity and Chiral Self-Assembly Structures of Crown Ethers on Metal Surfaces

Crown ethers (CEs), macrocyclic polyethers, have attracted significant attention in supramolecular chemistry. It is known that they have many isomers due to their flexibility. It is challenging to select some exact conformation and tune the following self-assembly structure of CEs, and it has rarely been reported to date. Herein, by choosing 18-crown-6-ether and dibenzo-18-crown-6-ether for study, we report an effective stereoisomeric selectivity of CEs by a strategy of both chemical modification and CEs hosting Na/K ions. The conformational difference in CEs can further tune the molecular interactions, resulting in the chiral self-assembly structures of CEs. By the combination of scanning tunneling microscopy, density functional theory, and X-ray photoelectron spectroscopy, this study reveals the underlying mechanism of CEs in both conformational selectivity and the formation of chiral assembly structures.

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.

Directing Organometallic Ring-Chain Equilibrium by Electrostatic Interactions

Dynamic chemistry, which falls into the realm of both supramolecular and covalent chemistry, enables intriguing properties, such as structural diversity, self-healing, and adaptability. Due to robustness of covalent bonds compared to noncovalent ones, dynamic covalent chemistry has been exploited to synthesize complex molecular nanostructures at solid/liquid interfaces under ambient conditions, generally responsive to internal factors that directly regulate intermolecular covalent bonds. However, directing dynamics of covalent nanostructures, e.g., the typical ring-chain equilibria, on surface by extrinsic interactions remains elusive and challenging. Herein, we have controllably directed the ring-chain equilibrium of covalent organometallic structures by regulating intermolecular electrostatic interactions, thus achieving on-surface dynamic covalent chemistry under ultrahigh vacuum conditions. Our findings unravel the dynamic mechanism of covalent polymers governed by weak intermolecular interactions at the submolecular level, which not only bridges the gap between supramolecular and covalent chemistry but also offers great opportunities for the fabrication of adaptive polymeric nanostructures that respond to different conditions.

Constructing Molecular Networks on Metal Surfaces through Tellurium-Based Chalcogen-Organic Interaction

On-surface molecular self-assembly presents an important approach to the development of low-dimensional functional nanostructures and nanomaterials. Traditional strategies primarily exploit hydrogen bonding or metal coordination, yet the potential of chalcogen bonding (ChB) for on-surface self-assemblies remains underexplored. Here, we explore fabricating molecular networks via tellurium (Te)-directed chalcogen-organic interactions. Employing carbonitrile molecules as molecular building blocks, we have achieved extended 2D networks exhibiting a 4-fold binding motif on Au(111), marking a notable difference from the conventional coordinative interaction involving transition metals. Our findings, supported by density functional theory (DFT) and scanning tunneling spectroscopy (STS), show that the Te-carbonitrile interaction exhibits lower stability compared to the metal-organic coordination, and the construction of the Te-directed molecular networks does not alter the electronic properties of the involved molecules. Introducing chalcogen-directed interactions may expand the spectrum of strategies in supramolecular assembly, contributing to the design of advanced molecular architectures for nanotechnological applications.

Enantiopure molecules form apparently racemic monolayers of chiral cyclic pentamers

Ultra-high vacuum scanning tunneling microscopy (UHV-STM) was used to investigate two related molecules pulse-deposited onto Au(111) surfaces: indoline-2-carboxylic acid and proline (pyrrolidine-2-carboxylic acid). Indoline-2-carboxylic acid and proline form both dimers and C5-symmetric "pinwheel" pentamers. Enantiomerically pure S-(-)-indoline-2-carboxylic acid and S-proline were used, and the pentamer structures observed for both were chiral. However, the presence of apparently equal numbers of 'right-' and 'left-handed' pinwheels is contrary to the general understanding that the chirality of the molecule dictates supramolecular chirality. A variety of computational methods were used to elucidate pentamer geometry for S-proline. Straightforward geometry optimization proved difficult, as the size of the cluster and the number of possible intermolecular interactions produced an interaction potential with multiple local minima. Instead, the Amber force field was used to exhaustively search all of phase space for chemically reasonable pentamer structures, producing a limited number of candidate structures that were then optimized as gas-phase clusters using density functional theory (DFT). The binding energies of the two lowest-energy pentamers on the Au(111) surface were then calculated by plane-wave DFT using the VASP software, and STM images predicted. These calculations indicate that the right- and left-handed pentamers are instead two different polymorphs.

Recent advances in organic molecule reactions on metal surfaces

Chemical reactions of organic molecules on metal surfaces have been intensively investigated in the past decades, where metals play the role of catalysts in many cases. In this review, first, we summarize recent works on spatial molecules, small H2O, O2, CO, CO2 molecules, and the molecules carrying silicon groups as the new trends of molecular candidates for on-surface chemistry applications. Then, we introduce spectroscopy and DFT study advances in on-surface reactions. Especially, in situ spectroscopy technologies, such as electron spectroscopy, force spectroscopy, X-ray photoemission spectroscopy, STM-induced luminescence, tip-enhanced Raman spectroscopy, temperature-programmed desorption spectroscopy, and infrared reflection adsorption spectroscopy, are important to confirm the occurrence of organic reactions and analyze the products. To understand the underlying mechanism, the DFT study provides detailed information about reaction pathways, conformational evolution, and organometallic intermediates. Usually, STM/nc-AFM topological images, in situ spectroscopy data, and DFT studies are combined to describe the mechanism behind on-surface organic reactions.

Revealing the Influence of Molecular Chemisorption Direction on the Reaction Selectivity of Dehalogenative Coupling on Au(111): Polymerization versus Cyclization

The control of reaction selectivity is of great interest in chemistry and depends crucially on the revelation of key influencing factors. Based on well-defined molecule-substrate model systems, various influencing factors have been elucidated, focusing primarily on the molecular precursors and the underlying substrates themselves, while interfacial properties have recently been shown to be essential as well. However, the influence of molecular chemisorption direction on reaction selectivity, as a subtle interplay between molecules and underlying substrates, remains elusive. In this work, by a combination of scanning tunneling microscopy imaging and density functional theory calculations, we report the influence of molecular chemisorption direction on the reaction selectivity of two types of dehalogenative coupling on Au(111), i.e., polymerization and cyclization, at the atomic level. The diffusion step of a reactive dehalogenated intermediate in two different chemisorption directions was theoretically revealed to be the key to determining the corresponding reaction selectivity. Our results highlight the important role of molecular chemisorption directions in regulating the on-surface dehalogenative coupling reaction pathways and products, which provides fundamental insights into the control of reaction selectivity by exploiting some subtle interfacial parameters in on-surface reactions for the fabrication of target low-dimensional carbon nanostructures.

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.

Revealing the Orientation Selectivity of Tetrapyridyl-Substituted Porphyrins Constrained in Molecular "Klotski Puzzles"

Understanding and controlling molecular orientations in self-assembled organic nanostructures are crucial to the development of advanced functional nanodevices. Scanning tunneling microscopy (STM) provides a powerful toolbox to recognize molecular orientations and to induce orientation changes on surfaces at the single-molecule level. Enormous effort has been devoted to directly controlling the molecular orientations of isolated single molecules in free space. However, revealing and further controlling molecular orientation selectivity in constrained environments remain elusive. In this study, by a combination of STM imaging/manipulations and density functional theory calculations, we report the orientation selectivity of tetrapyridyl-substituted porphyrins in response to various local molecular environments in artificially constructed molecular "Klotski puzzles" on Au(111). With the assistance of STM lateral manipulations, "sliding-block" molecules were able to enter predefined positions, and specific molecular orientations were adopted to fit the local molecular environments, in which the intermolecular interaction was revealed to be the key to achieving the eventual molecular orientation selectivity. Our results demonstrate the essential role of local molecular environments in directing single-molecule orientations, which would shed light on the design of molecular structures to control preferred orientations for further applications in molecular nanodevices.

Insights into the Rearrangement of the Molecular Assembly Structure of 6-Aminonicotinic Acid in Its Hydrated Environment

Water, as a ubiquitous and essential component of life, is known to have a significant impact on the structure and function of organic molecules. In this study, we investigate the role of water in the phase transition of organic molecular assembly structures by scanning tunneling microscopy at room temperature. The results show that the -O-H···O hydrogen induced by water molecules can lead to a significant structural transition in the molecular assembly, specifically through selective weakening of -C-H···O between 6-aminonicotinic acid and the formation of new -O-H···O bonds between 6-aminonicotinic acid and water molecules. Subsequent thermal treatment of these molecular assembly structures reveals that the formation of -N-H···O hydrogen bonds induced by water molecules has created a different pathway for the phase transition of the molecular assembly structure. This knowledge has important implications for the design of organic molecules with specific nanostructures that can be controlled through hydration.

Concentration-modulated global organizational chirality at the liquid/solid interface

Understanding the origin of homochirality in macroscopic assemblies and manipulating organizational chirality still remain a challenge. Herein, homochirality is achieved by combination of the majority-rules principle and concentration-dependent molecular assembly at the liquid/solid interface. A lower molecular concentration in solution facilitates more efficient amplification of chirality, which is formulated by a cooperative equilibrium model based on the Langmuir adsorption isotherm. Our results contribute to gain a new insight into chiral amplification in supramolecular assemblies. Particularly, a homochiral monolayer can be obtained just through modulating the molecular concentration in mixed enantiomer systems.

Surface Diffusion Aided by a Chirality Change of Self-Assembled Oligomers under 2D Confinement

Chirality switching of self-assembled molecular structures is of potential interest for designing functional materials but is restricted by the strong interaction between the embedded molecules. Here, we report on an unusual approach based on reversible chirality changes of self-assembled oligomers using variable-temperature scanning tunneling microscopy supported by quantum mechanical calculations. Six functionalized diazomethanes each self-assemble into chiral wheel-shaped oligomers on Ag(111). At 130 K, a temperature far lower than expected, the oligomers change their chirality even though the molecules reside in an embedded self-assembled structure. Each chirality change is accompanied by a slight center-of-mass shift. We show how the identical activation energies of the two processes result from the interplay of the chirality change with surface diffusion, findings that open the possibility of implementing various functional materials from self-assembled supramolecular structures.

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.

Revealing intrinsic spin coupling in transition metal-doped graphene

Graphene materials offer attractive possibilities in spintronics due to their unique atomic and electronic structures, which is in contrast to their limited applications in the design of sophisticated spintronic devices. This should be attributed to the lack of knowledge about the intrinsic characteristics of graphene materials, especially the diverse correlations between sites within the materials and their roles in spin-signal generation and propagation. This work comprehensively studies the spin couplings between transition metal atoms doped on graphene and reveals their potential application in spintronic device design through the realization of various logic gates. In addition, the effects of the distance between doped metal atoms and the number of carbon layers on the logic gate implementation further verify that the spin-coupling effect can exhibit a certain distance dependence and space propagation. The achievements in this work uncover the potential value of graphene materials and are expected to open up new avenues for exploring their application in the design of sophisticated spintronic devices.