Collective Molecular Machines: Multidimensionality and Reconfigurability

Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical work.During the last 60 years,designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense research.Effective progress has been made,attributed to advances in various fields such as supramolecular chemistry,biology and nanotechnology,and informatics.However,individual molecular machines are only capable of producing nanometer work and generally have only a single functionality.In order to address these problems,collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new paradigm.In this review,we comprehensively discuss recent developments in the collective behaviors of molecular machines.In particular,collective behavior is divided into two paradigms.One is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional materials.The other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale operations.We discuss design strategies for both modes and focus on the modulation of features and properties.Subsequently,in order to address existing challenges,the idea of transferring experience gained in the field of micro/nano robotics is presented,offering prospects for future developments in the collective behavior of molecular machines.

Molecular insight into the GaP(110)-water interface using machine learning accelerated molecular dynamics

GaP has been shown to be a promising photoelectrocatalyst for selective CO_(2)reduction to methanol.Due to the relevance of the interface structure to important processes such as electron/proton transfer,a detailed understanding of the GaP(110)-water interfacial structure is of great importance.Ab initio molecular dynamics(AIMD)can be used for obtaining the microscopic information of the interfacial structure.However,the GaP(110)-water interface cannot converge to an equilibrated structure at the time scale of the AIMD simulation.In this work,we perform the machine learning accelerated molecular dynamics(MLMD)to overcome the difficulty of insufficient sampling by AIMD.With the help of MLMD,we unravel the microscopic information of the structure of the GaP(110)-water interface,and obtain a deeper understanding of the mechanisms of proton transfer at the GaP(110)-water interface,which will pave the way for gaining valuable insights into photoelectrocatalytic mechanisms and improving the performance of photoelectrochemical cells.

Artificial molecular machines that can perform work

An artificial molecular machine consists of molecule or substituent components jointed together in a specific way so that their mutual displacements could be initiated using appropriate outside stimuli. Such an ability of performing mechanical motions by consuming external energy has endowed these tiny machines with vast fascinating potential applications in areas such as actuators, manipulating atoms/molecules, drug delivery, molecular electronic devices, etc. To date, although vast kinds of molecular machine archetypes have been synthesized in facile ways, they are inclined to be defined as switches but not true machines in most cases because no useful work has been done during a working cycle. More efforts need to be devoted on the utilization and amplification of the nanoscale mechanical motions among synthetic molecular machines to accomplish useful tasks. Here we highlight some of the recent advances relating to molecular machines that can perform work on different length scales, ranging from microscopic levels to macroscopic ones.

Artificial muscles driven by the cooperative actuation of electrochemical molecular machines.Persistent discrepancies and challenges

Here we review the persisting conceptual discrepancies between different research groups working on artificial muscles based on conducting polymers and other electroactive material.The basic question is if they can be treated as traditional electro-mechanical(physical)actuators driven by electric fields and described by some adaptation of their physical models or if,replicating natural muscles,they are electro-chemo-mechanical actuators driven by electrochemical reaction of the constitutive molecular machines:the polymeric chains.In that case the charge consumed by the reaction will control the volume variation of the muscular material and the motor displacement,following the basic and single Faraday’s laws:the charge consumed by the reaction determines the number of exchanged ions and solvent,the film volume variation to lodge/expel them and the amplitude of the movement.Deviations from the linear relationships are due to the osmotic exchange of solvent and to the presence of parallel reactions from the electrolyte,which originate creeping effects.Challenges and limitations are underlined.

Recent advances in molecular machines based on toehold-mediated strand displacement reaction

Background： The DNA strand displacement reaction, which uses flexible and programmable DNA molecules as reaction components, is the basis of dynamic DNA nanotechnology, and has been widely used in the design of complex autonomous behaviors. Results： In this review, we first briefly introduce the concept of toehold-mediated strand displacement reaction and its kinetics regulation in pure solution. Thereafter, we review the recent progresses in DNA complex circuit, the assembly of AuNPs driven by DNA molecular machines, and the detection of single nucleotide polymorphism （SNP） using DNA toehold exchange probes in pure solution and in interface state. Lastly, the applications of toehold-mediated strand displacement in the genetic regulation and silencing through combining gene circuit with RNA interference systems are reviewed. Conclusions： The toehold-mediated strand displacement reaction makes DNA an excellent material for the fabrication of molecular machines and complex circuit, and may potentially be used in the disease diagnosis and the regulation of gene silencing in the near future.

Parallel Molecular Dynamics on the Connection Machines

Abstract Abstract:We have demonstrated using vectorized parallel Lennard-Jones fluid program that vectorizing general-purpose parallel molecular package for simulating biomolecules which currently runs on the Connection Machine CM-5 using CMMD message passing would offer a significant improvement over 4 non-vectorized version. Our results indicate that the Lennard-Jones fluid program written in C*/CMNID is five times faster than the same program written in C/CMMD.

Water structures and anisotropic dynamics at Pt(211)/water interface revealed by machine learning molecular dynamics

Water molecules at solid–liquid interfaces play a pivotal role in governing interfacial phenomena that underpin electrochemical and catalytic processes.The organization and behavior of these interfacial water molecules can significantly influence the solvation of ions,the adsorption of reactants,and the kinetics of electrochemical reactions.The stepped structure of Pt surfaces can alter the properties of the interfacial water,thereby modulating the interfacial environment and the resulting surface reactivity.Revealing the in situ details of water structures at these stepped Pt/water interfaces is crucial for understanding the fundamental mechanisms that drive diverse applications in energy conversion and material science.In this work,we have developed a machine learning potential for the Pt(211)/water interface and performed machine learning molecular dynamics simulations.Our findings reveal distinct types of chemisorbed and physisorbed water molecules within the adsorbed layer.Importantly,we identified three unique water pairs that were not observed in the basal plane/water interfaces,which may serve as key precursors for water dissociation.These interfacial water structures contribute to the anisotropic dynamics of the adsorbed water layer.Our study provides molecular-level insights into the anisotropic nature of water behavior at stepped Pt/water interfaces,which can influence the reorientation and distribution of intermediates,molecules,and ions—crucial aspects for understanding electrochemical and catalytic processes.

Thermomechanical Energy Converters for Harvesting Thermal Energy:A Review

Thermal energy,i.e.,the electromagnetic energy in the infrared range that originates from the direct solar radiation,outgoing terrestrial radiation,waste heat from combustion of fuels,heat-emitting electrical devices,decay of radioactive isotopes,organic putrefaction and fermentation,human body heat,and so on,constitutes a huge energy flux circulating on the earth surface.However,most energy converters designed for the conversion of electromagnetic energy into electricity,such as photovoltaic cells,are mainly focused on using a narrow part of the solar energy lying in the visible spectrum,while thermomechanical engines that are fueled by heat in the broad energy range and then convert it into mechanical work or store it as mechanical deformation,are paid less attention.Although the efficiency of thermomechanical devices is relatively low,they can be applied to collect waste heat which otherwise contributes to negative climate changes.In this review,operational principles of thermomechanical energy converters and a description of basic devices and materials that utilize thermal energy are given.In addition to conventional macroscopic engines,based on thermoacoustic,thermomagnetic,thermoelastic,hydride heat converters,and shape memory alloys,the emergent devices are described which are classified as smart actuators,breathing frameworks,thermoacoustic micro-transducers,nanomechanical resonators,plasmomechanical systems,and optothermal walkers.The performance of the different types of thermomechanical energy converters is described and compared.

Seeing Is Believing:Directly Imaging Contractions of Artificial Molecular Muscles with Platinum Atom Markers

Artificial molecular muscles undergo well-controlled contractile and extensile motions upon external stimulation,leading to remarkable length changes.Evaluating such length changes at the molecular level is essential to the design of integrated artificial molecular muscles that mimic biological muscles.Taking advantage of the strong contrast of platinum(Pt)atoms in high-angle annular dark-field scanning transmission electron microscopy images,we imaged Pt-containing molecular[c2]daisy chains directly by employing metal atom markers.The length changes and associated conformational transformations of these newly developed artificial molecular muscles have been measured experimentally in combination with theoretical calculations.The contraction ratios of these two molecular muscles with the TEMPO or pyrene anchoring group were calculated to be 21.0%or 15.7%respectively,suggesting a substantial anchoring effect.This study demonstrates the experimental measurement of the length changes of artificial molecular muscles and provides a new avenue for investigating the motion of artificial molecular machines.

Single-Molecule Studies on Artificial Small-Molecule Machines

Molecular machines transduce energy from one form to another through controlled motion in response to stimuli.Despite the ubiquitous use of molecular machines in biology,understanding the detailed mechanisms of such complex structures remains challenging.Recent progress in studying the modes of operation of synthetic small-molecule machines at the single-molecule level has shed new light on the mechanisms of nano-machinery.In this mini-review,we focus on the study of artificial small-molecule machines using single-molecule techniques,including single-molecule force spectroscopy,single-molecule electrical spectroscopy,and single-molecule optical spectroscopy.We survey the techniques used to monitor single-molecule behavior to date and describe the latest studies on small-molecule machines,highlighting their common features and challenges that need to be overcome to realize the potential of these techniques in unraveling the behavior of small molecule systems.

Mono-functionalized pillar[n]arenes: Syntheses, host–guest properties and applications

Pillar[n]arenes are a novel class of macrocyclic hosts reported by Ogoshi and co-workers in 2008. Because of their rigid pillar structures, interesting host-guest properties and ease of modifications, pillar[n]arenes have been developed rapidly in the field of functional materials and biomedicine. The modifications of pillar[n]arenes at different positions can give them varied characteristics. Functional groups can be introduced into one position of pillar[n]arenes without changing host-guest properties of pillar[n]arenes. A series of pillar[n]arene dimers, trimers, tetramers and metallacycles can be constructed by mono-functionalized pillar[n]arenes. In this review, two synthetic methods of mono-functionalized pillar[n]arenes are summarized and structures containing mono-functionalized pillar[n]arenes are described. Furthermore, the applications of mono-functionalized pillar[n]arenes in different fields (e.g., supramolecular polymers, sensors, molecular machines, catalysis, biological applications and light-harvesting systems) are also introduced. Hopefully, this article will be useful for researchers studying pillar[n]arenes, especially the mono-functionalized pillar[n]arenes.

Thermal Energy-Driven Solid-State Molecular Rotation Monitored by Real-Time Emissive Color Switching

Inspired by nature’s molecular machines,the scientific research on solid-state molecular rotors is of great interest yet remains largely unexplored.Herein,we report a unique example of a thermal energydriven stimuli-responsive solid-state molecular rotor,which features an o-carborane moiety as a rotor that directly transduces the surrounding thermal energy into molecular rotations in the crystalline state.Its rotation is confirmed by X-ray diffraction.

Fluorescent Linear Supramolecular Polymer Based on Host-Guest Interactions

Construction of supramolecular polymers, in which functional monomer components are held together by non- covalent interactions, is considered as a promising design principle for functional materials. Linear fluorescent su- pramolecular polymer assembled on account of electrostatic attractions based host-guest interaction is synthesized and illustrated here. 1H NMR was involved to ensure the structure of guest and polymer, UV-vis and fluorescent spectra were recorded to be a readout signal to investigate the assemble process of polymer. TEM and AFM meas- urements were carried out to confirm the homogeneous nanometer-sized molecular assembly. It shows the way to be used as remote readout fluorescent functional material in the future.

[c2]Daisy Chain Rotaxanes as Molecular Muscles

Bistable[c2]daisy chain rotaxanes represent a par-ticularly intriguing class of interlocked molecules that can produce internal sliding movements with a net contraction or extension at the single-molecule level.

The supramolecular redox functions of metallomacromolecules

Metallomacromolecules are frequently encountered in redox proteins including metal-tanned hide collagen and play crucial roles involving supramolecular properties in biological electron-transfer processes.They are also currently found in non-natural families,such as:metallopolymers,metallodendrimers and metallodendronic polymers.This mini-review discusses the supramolecular redox functions of such nanomaterials developed in our research group.Electron-transfer processes are first examined in mono-,bis-and hexa-nuclear ferrocenes and other electron-reservoir organoiron systems showing the influence of supramolecular and reorganization aspects on their mechanism.Then applications of electron-transfer processes using these same organoiron redox systems in metallomacromolecules and their supramolecular functions are discussed including redox recognition/sensing,catalysis templates,electrocatalysis,redox catalysis,molecular machines,electrochromes,drug delivery device and nanobatteries.

Molecular rotors as a class of generally highly active ion transporters

We describe here a class of unconventional ion transporters,molecular rotors that transport ions through a rotating function rather than via traditional carrier or channel mechanisms.Mimicking macroscopic rotors,these molecular rotors consist of three modularly tunable components,i.e.,a membrane-anchoring stator,a crown ether-containing rotator for ion binding and transport,and a triple bond-based axle that allows the rotator to freely rotate around the stator in the lipid membrane.Lipid bilayer experiments reveal the generally high ability of all molecular rotors in promoting the highly efficient transmembrane K^(+)flux(EC50 values=0.49-1.37 mol%relative to lipid).While molecular rotors differing only in the ion-binding unit exhibit similar ion transport activities,those differing in the rotator’s length display activity differences by up to 174%.

Research on the nanometric machining of a single crystal nickel via molecular dynamics simulation

Molecular dynamics simulations are employed to study the nanometric machining process of single crystal nickel. Atoms from different machining zones had different atomic crystal structures owing to the differences in the actions of the cutting tool. The stacking fault tetrahedral was formed by a series of dislocation reactions, and it maintained the stable structure after the dislocation reactions. In addition, evidence of crystal transition and recovery was found by analyzing the number variations in different types of atoms in the primary shear zone, amorphous region, and crystalline region. The effects of machining speed on the cutting force, chip and subsurface defects, and temperature of the contact zone between the tool and workpiece were investigated. The results suggest that higher the machining speed, larger is the cutting force. The degree of amorphousness of chip atoms and the depth and extent of subsurface defects increase with the machining speed. The average friction coefficient first decreases and then increases with the machining speed because of the temperature difference between the chip and machining surface.

Pillar[5]arene-based [3]rotaxanes: Convenient construction via multicomponent reaction and pH responsive self-assembly in water

Four pillar[5]arene based[3]rotaxanes(1-4)involving two 1,4-diethoxypillar[5]arene(DEP5)rings and a dumbbell-shaped component were successfully synthesized.The dumbbell-shape molecules contain one longer bridge,two triazole sites and two multicomponent stoppers.After threading DEP5 rings with linear guests(G1-G4)which contain two benzaldehyde units,the base catalyzed three-component reaction of dimedone,malononitrile and benzaldehyde was performed to construct the stoppers and connected the pseudorotaxanes with stoppers to generate 1-4.The structures of[3]rotaxanes and their self-assembly behaviors were characterized by 1 H NMR,13C NMR,NOESY,HR-ESI-MS,DLS and TEM technologies.We hope that pillar[5]arene based[3]rotaxanes may have potential applications in drug delivery systems and molecular devices.

Unveiling the Hidden Movements in the Shuttling of Rotaxanes

Movements in molecular machines are usually diverse and coupled,but some of them are often implicit and hard to be observed in experiments.In the present work,the two-or three-dimensional free-energy landscapes characterizing the coupled shutthng and other movements of a series of pH-triggered rotaxanes composed of a crown ether and an H-shaped axle with distinct number of phenyl rings(n=1-3)have been explored.The results show that although the calculated free-energy barriers against shutthng in the rotaxanes(n=2 and 3)change slightly,the move-ments coupled with the shutthng vary significantly with the axle length.At high pH,the shutthng in the rotaxane of n=2 is coupled with the isomerization of the wheel,while the shutthng in the one of n=3 is accompanied by both the isomerization and the rotation of the macrocycle.In addition,the crown ether imdenvent greater conlomiational change during shutthng at low pH compared to that at high pH.These results indicate that disentangling the coupled movements is important to reveal the underlying molecular mechanism of the shutthng.