Topological dynamics in supramolecular rotors

Self-Accommodating Honeycomb Networks from Supramolecular Self-Assembly of s-Indacene-tetrone on Silver Surfaces

We describe the self-assembly of s-indacene-tetrone on Ag(111), Ag(100), and Ag(110) surfaces and the formation of three hydrogen-bonded supramolecular phases representing a complex self-accommodating honeycomb network. The differences in terms of relative host-guest stability and molecular density are analyzed and discussed. Different epitaxial behaviors of the two-dimensional self-assembly are found as a response to the variations in the crystallographic orientation of the surface.

Rotation in an Enantiospecific Self-Assembled Array of Molecular Raffle Wheels

Tailored nano-spaces can control enantioselective adsorption and molecular motion. We report on the spontaneous assembly of a dynamic system-a rigid kagome network with each pore occupied by a guest molecule-employing solely 2,6-bis(1H-pyrazol-1-yl)pyridine-4-carboxylic acid on Ag(111). The network cavity snugly hosts the chemically modified guest, bestows enantiomorphic adsorption and allows selective rotational motions. Temperature-dependent scanning tunnelling microscopy studies revealed distinct anchoring orientations of the guest unit switching with a 0.95 eV thermal barrier. H-bonding between the guest and the host transiently stabilises the rotating guest, as the flapper on a raffle wheel. Density functional theory investigations unravel the detailed molecular pirouette of the guest and how the energy landscape is determined by H-bond formation and breakage. The origin of the guest's enantiodirected, dynamic anchoring lies in the specific interplay of the kagome network and the silver surface.

Topological Dynamic Matter

The principles of topology in condensed matter physics have expanded to areas such as photonics, acoustics, electronics, and mechanics. Their extension to dynamic (soft) matter could enable the control and design of topological thermodynamic (micro)states and nonreciprocal dynamics, potentially leading to paradigmatic applications in molecular and thermal waveguiding, logics, and energy management. This Perspective explores distinct topological concepts for dynamic matter and prospective function. Topological tools are exemplified and discussed for the study of nonlocal order parameters or invariants in dynamic molecular matter, toward the engineering of assemblies, reactions, and system chemistry with unconventional global properties-a scope which has the potential to push the frontiers of physical chemistry and transform chemical topology from form to function.

Rotation of Ethoxy and Ethyl Moieties on a Molecular Platform on Au(111)

Molecular rotors have attracted considerable interest for their prospects in nanotechnology. However, their adsorption on supporting substrates, where they may be addressed individually, usually modifies their properties. Here, we investigate the switching of two closely related three-state rotors mounted on platforms on Au(111) using low-temperature scanning tunneling microscopy and density functional theory calculations. Being physisorbed, the platforms retain important gas-phase properties of the rotor. This simplifies a detailed analysis and permits, for instance, the identification of the vibrational modes involved in the rotation process. The symmetry provided by the platform enables active control of the rotation direction through electrostatic interactions with the tip and charged neighboring adsorbates. The present investigation of two model systems may turn out useful for designing platforms that provide directional rotation and for transferring more sophisticated molecular machines from the gas phase to surfaces.

Theoretical Modeling of the Surface-Guided Self-Assembly of Functional Molecules

Directing the self-assembly of organic building blocks with 2D templates has been a promising method to create molecular superstructures having unique physicochemical properties. In this work the on-surface self-assembly of simple ditopic functional molecules confined inside periodic nanotemplates was modeled by means of the lattice Monte Carlo simulation method. Two types of confinement, that is honeycomb porous networks and parallel grooves of controlled diameter and width were used in the calculations. Additionally, the effect of (pro)chirality of the adsorbing molecules on the outcome of the templated self-assembly was examined. To that end, enantiopure and racemic assemblies were studied and the resulting structures were identified and classified. The obtained findings demonstrated that suitable tuning of the structural parameters of the templates enables directing the self-assembly towards linear and cyclic aggregates with controlled size. Moreover, chiral resolution of the molecular conformers using honeycomb networks with adjusted pore size was found possible. Our theoretical predictions can be helpful in designing structured surfaces to direct self-assembly and polymerization of organic functional building blocks.

Modification of the Potential Landscape of Molecular Rotors on Au(111) by the Presence of an STM Tip

Molecular rotors on solid surfaces are fundamental components of molecular machines. No matter whether the rotation is activated by heat, electric field or light, it is determined by the intrinsic rotational potential landscape. Therefore, tuning the potential landscape is of great importance for future applications of controlled molecular rotors. Here, using scanning tunneling microscopy (STM), we demonstrate that both tip-molecule distance and sample bias can modify the rotational potential of molecular rotors. We achieve the potential energy difference variations of ∼0.3 meV/pm and ∼18 meV/V between two configurations of a molecular rotor, a tetra- tert-butyl nickel phthalocyanine molecule on Au(111) substrate. Further analysis indicates that the mechanism of modifying the rotational potential is a combination of the van der Waals interaction and the interaction between the molecular dipole and an electric field. This work provides insight into the methods used to modify the effective rotational potential energy of molecular rotors.

Electronic effects and fundamental physics studied in molecular interfaces

Scanning probe instruments in conjunction with a very low temperature environment have revolutionized the ability of building, functionalizing, and analysing two dimensional interfaces in the last twenty years. In addition, the availability of fast, reliable, and increasingly sophisticated methods to simulate the structure and dynamics of these interfaces allow us to capture even very small effects at the atomic and molecular level. In this review we shall focus largely on metal surfaces and organic molecular compounds and show that building systems from the bottom up and controlling the physical properties of such systems is no longer within the realm of the desirable, but has become day to day reality in our best laboratories.

Interlocking Molecular Gear Chains Built on Surfaces

Periodic chains of molecular gears in which molecules couple with each other and rotate on surfaces have been previously explored by us theoretically using ab initio simulation tools. On the basis of the knowledge and experience gained about the interactions between neighboring molecular gears, we here explore the transmission of rotational motion and energy over larger distances, namely, through a longer chain of gear-like passive "slave" molecules. Such microscopic gears exhibit quite different behaviors compared to rigid cogwheels in the macroscopic world due to their structural flexibility affecting intermolecular interaction. Here, we investigate the capabilities of such gear chains and reveal the mechanisms of the transmission process in terms of both quantum-level density functional theory (DFT) and simple classical mechanics. We find that the transmission of rotation along gear chains depends strongly on the gear-gear distance: short distances can cause tilting of gears and even irregular "creep-then-jump" (or "stick-slip") motion or expulsion of gears; long gear-gear distances cause weak coupling between gears, slipping and skipping. More importantly, for transmission of rotation at intermediate gear-gear distances, our modeling clearly exhibits the relative roles of several important factors: flexibility of gear arms, axles, and supports, as well as resulting rotational delays, slippages, and thermal and other effects. These studies therefore allow better informed design of future molecular machine components involving motors, gears, axles, etc.

Interlocking Mechanism between Molecular Gears Attached to Surfaces

While molecular machines play an increasingly significant role in nanoscience research and applications, there remains a shortage of investigations and understanding of the molecular gear (cogwheel), which is an indispensable and fundamental component to drive a larger correlated molecular machine system. Employing ab initio calculations, we investigate model systems consisting of molecules adsorbed on metal or graphene surfaces, ranging from very simple triple-arm gears such as PF₃ and NH₃ to larger multiarm gears based on carbon rings. We explore in detail the transmission of slow rotational motion from one gear to the next by these relatively simple molecules, so as to isolate and reveal the mechanisms of the relevant intermolecular interactions. Several characteristics of molecular gears are discussed, in particular the flexibility of the arms and the slipping and skipping between interlocking arms of adjacent gears, which differ from familiar macroscopic rigid gears. The underlying theoretical concepts suggest strongly that other analogous structures may also exhibit similar behavior which may inspire future exploration in designing large correlated molecular machines.

Acid-active supramolecular anticancer nanoparticles based on cyclodextrin polyrotaxanes damaging both mitochondria and nuclei of tumor cells

Acid-active supramolecular theranostics based on cyclodextrin polyrotaxanes for enhanced cancer therapy.

Sequential nested assembly at the liquid/solid interface

Studying the stepwise assembly of a four component hybrid structure on Au(111)/mica, the pores of a hydrogen bonded bimolecular network of 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) and 1,3,5-triazine-2,4,6-triamine (melamine) were partitioned by three and four-armed molecules based on oligo([biphenyl]-4-ylethynyl)benzene, followed by the templated adsorption of either C₆₀ fullerene or adamantane thiol molecules. The characterisation by ambient scanning tunneling microscopy (STM) reveals that the pore modifiers exhibit dynamics which pronouncedly depend on the molecular structure. The three-armed molecule 1,3,5-tris([1,1'-biphenyl]-4-ylethynyl)benzene (3BPEB) switches between two symmetry equivalent configurations on a time scale fast compared to the temporal resolution of the STM. Derivatisation of 3BPEB by hydroxyl groups substantially reduces the switching rate. For the four-armed molecule configurational changes are observed only occasionally. The observation of isolated fullerenes and small clusters of adamantane thiol molecules, which are arranged in a characteristic fashion, reveals the templating effect of the trimolecular supramolecular network. However, the fraction of compartments filled by guest molecules is significantly below one for both the thermodynamically controlled adsorption of C₆₀ and the kinetically controlled adsorption of the thiol with the latter causing partial removal of the pore modifier. The experiments, on the one hand, demonstrate the feasibility of templating by nested assembly but, on the other hand, also pinpoint the requirement for the energy landscape to be tolerant to variations in the assembly process.

Supramolecular Motors on Graphite Surface Stabilized by Charge States and Hydrogen Bonds

Molecular motors are nanoscale machines that convert external energies into controlled mechanical movements. In supramolecular motors, the rotator and stator are held together mechanically, and thus the rotation can be essentially barrier free when molecular conformation is negligible. However, nearly all the supramolecular motors appeared in solutions or host-guest complexes. Surface-mounted supramolecular motors have rarely been addressed, even though they are easily manipulated by external fields. Here we report a surface-mounted supramolecular motor assembled by charge states and hydrogen bonds. On a graphite surface, individual ethanol clusters can be charged with a scanning tunneling microscopy tip and then trap the ethanol chains with a permanent dipole moment. Serving as a rotator, the trapped ethanol chains rotate around a charged cluster driven by the inelastic tunneling electrons. Random rotation in clockwise or anticlockwise direction occurs in the chiral molecular chains through chiral flipping. Directional rotation with clockwise chirality can be realized by introducing a chiral branch to the near end of ethanol chains to suppress the chiral flipping with steric hindrance.

Chiral Kagome Lattices from On-Surface Synthesized Molecules

Kagome lattices have attracted much attention owing to their potential applications in spin-frustrated magnetism and host-guest chemistry. Examples toward the fabrication of 2D Kagome lattices reported previously have in common that the precursor molecules were typically deposited on the surface structurally intact with no chemical reactions accompanied. Herein, by using a combination of synchrotron radiation photoelectron spectroscopy (SRPES) and scanning tunneling microscopy (STM), we demonstrated the fabrication of two types of chiral Kagome lattices from on-surface synthesized organometallic compounds, which are known as intermediates of Glaser coupling on silver single crystal surfaces. These Kagome lattices are stabilized by the interplay of various intermolecular interactions, including Br⋅⋅⋅Br bonds, C-Br⋅⋅⋅π bonds and π-π stacking. The chiral transference and host-guest supramolecular structure in the novel Kagome lattices were also studied. Our studies may pave a new way to engineer complex supramolecular networks through on-surface reactions.

A universal mechanism of the planar boron rotors B11-, B13+, B15+, and B19-: inner wheels rotating in pseudo-rotating outer bearings

Planar boron clusters B₁₁^-, B₁₃⁺, B₁₅⁺, and B₁₉^- have been introduced recently as molecular Wankel motors or tank treads. Here we present a universal mechanism for these dynamically fluxional clusters; that is, they are molecular rotors with inner wheels that rotate almost freely in pseudo-rotating outer bearings, analogous to rotating molecules trapped in pseudo-rotating cages. This mechanism has significant quantum mechanical consequences: the global-minimum structures of the clusters have C_2v symmetry, whereas the wheels rotating in pseudo-rotating bearings generate rosette-type shapes with D_9h, D_10h, D_11h, and D_13h symmetries. The related rotational/pseudo-rotational energies appear with characteristic band structures, effecting the dynamics.

Dynamics of Spatially Confined Bisphenol A Trimers in a Unimolecular Network on Ag(111)

Bisphenol A (BPA) aggregates on Ag(111) shows a polymorphism between two supramolecular motifs leading to formation of distinct networks depending on thermal energy. With rising temperature a dimeric pairing scheme reversibly converts into a trimeric motif, which forms a hexagonal superstructure with complex dynamic characteristics. The trimeric arrangements notably organize spontaneously into a self-assembled one-component array with supramolecular BPA rotors embedded in a two-dimensional stator sublattice. By varying the temperature, the speed of the rotors can be controlled as monitored by direct visualization. A combination of scanning tunneling microscopy and dispersion-corrected density-functional tight-binding (DFTB-vdW(surf)) based molecular modeling reveals the exact atomistic position of each molecule within the assembly as well as the driving force for the formation of the supramolecular rotors.

Nanoarchitectonics for Dynamic Functional Materials from Atomic-/Molecular-Level Manipulation to Macroscopic Action

Objects in all dimensions are subject to translational dynamism and dynamic mutual interactions, and the ability to exert control over these events is one of the keys to the synthesis of functional materials. For the development of materials with truly dynamic functionalities, a paradigm shift from "nanotechnology" to "nanoarchitectonics" is proposed, with the aim of design and preparation of functional materials through dynamic harmonization of atomic-/molecular-level manipulation and control, chemical nanofabrication, self-organization, and field-controlled organization. Here, various examples of dynamic functional materials are presented from the atom/molecular-level to macroscopic dimensions. These systems, including atomic switches, molecular machines, molecular shuttles, motional crystals, metal-organic frameworks, layered assemblies, gels, supramolecular assemblies of biomaterials, DNA origami, hollow silica capsules, and mesoporous materials, are described according to their various dynamic functions, which include short-term plasticity, long-term potentiation, molecular manipulation, switchable catalysis, self-healing properties, supramolecular chirality, morphological control, drug storage and release, light-harvesting, mechanochemical transduction, molecular tuning molecular recognition, hand-operated nanotechnology.

Theoretical Modeling of Surface Confined Chiral Nanoporous Networks: Cruciform Molecules as Versatile Building Blocks

Patterning of solid surfaces with functional organic molecules has been a convenient route to fabricate two-dimensional materials with programmed architecture and activities. One example is the chiral nanoporous networks that can be created via controlled self-assembly of star-shaped molecules under 2D confinement. In this contribution we use computer modeling to predict the formation of molecular networks in adsorbed overlayers comprising cruciform molecular building blocks equipped with discrete interaction centers. To that end, we employ the Monte Carlo simulation method combined with a coarse-grained representation of the adsorbed molecules which are treated as collections of interconnected segments. The interaction centers within the molecules are represented by active segments whose number and distribution are adjusted. Our particular focus is on those distributions that produce prochiral molecules able to occur in adsorbed configurations being mirror images of each other (surface enantiomers). We demonstrate that, depending on size, aspect ratio, and intramolecular distribution of active sites, the surface enantiomers can co-crystallize or segregate into extended homochiral domains with largely diversified nanosized cavities. The insights from our theoretical studies can be helpful in designing 2D chiral porous networks with potential applications in enantioselective adsorption and asymmetric heterogeneous catalysis.

Visualization and thermodynamic encoding of single-molecule partition function projections

Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and enthalpy at finite temperatures are challenging to determine with ensemble averaging alone. Here we report a method to directly record time-averaged equilibrium probability distributions by confining an individual molecule to a nanoscopic pore of a two-dimensional metal-organic nanomesh, using temperature-controlled scanning tunnelling microscopy. We associate these distributions with partition function projections to assess real-space-projected thermodynamic quantities, aided by computational modelling. The presented molecular dynamics-based analysis is able to reproduce experimentally observed projected microstates with high accuracy. By an in silico customized energy landscape, we demonstrate that distinct probability distributions can be encrypted at different temperatures. Such modulation provides means to encode and decode information into position-temperature space.

Two-dimensional soft supramolecular networks

Soft networks are self-assembled at the solid/liquid interface and characterized by local disorder arising from multivalent flexible intermolecular interactions.