Controlling Dual Molecular Pumps Electrochemically

Artificial molecular machines can be operated using either physical or chemical inputs. Light‐powered motors display clean and autonomous operations, whereas chemically driven machines generate waste products and are intermittent in their motions. Herein, we show that controlled changes in applied electrochemical potentials can drive the operation of artificial molecular pumps in a semi‐autonomous manner—that is, without the need for consecutive additions of chemical fuel(s). The electroanalytical approach described in this Communication promotes the assembly of cyclobis(paraquat‐p‐phenylene) rings along a positively charged oligomeric chain, providing easy access to the formation of multiple mechanical bonds by means of a controlled supply of electricity.     

A Memristive Element Based on an Electrically Controlled Single‐Molecule Reaction

The exponential proliferation of data during the information age has required the continuous exploration of novel storage paradigms, materials, and devices with increasing data density. As a step toward the ultimate limits in data density, the development of an electrically controllable single‐molecule memristive element is reported. In this device, digital information is encoded through switching between two isomer states by applying a voltage signal to the molecular junction, and the information is read out by monitoring the electrical conductance of each isomer. The two states are cycled using an electrically controllable local‐heating mechanism for the forward reaction and catalyzed by a single charge‐transfer process for the reverse switching. This single‐molecule device can be modulated in situ, is fully reversible, and does not display stochastic switching. The I–V curves of this single‐molecule system also exhibit memristive character. These features suggest a new approach for the development of molecular switching systems and storage‐class memories.     

Motion Control of Polymeric Nanomotors Based on Host–Guest Interactions

Controlling the motion of artificial self‐propelled micro‐ and nanomotors independent of the fuel concentration is still a great challenge. Here we describe the first report of speed manipulation of supramolecular nanomotors via blue light‐responsive valves, which can regulate the access of hydrogen peroxide fuel into the motors. Light‐sensitive polymeric nanomotors are built up via the self‐assembly of functional block copolymers, followed by bowl‐shaped stomatocyte formation and incorporation of platinum nanoparticles. Subsequent addition of β‐cyclodextrin (β‐CD) leads to the formation of inclusion complexes with the trans‐isomers of the azobenzene derivatives grafted from the surfaces of the stomatocytes. β‐CDs attachment decreases the diffusion rate of hydrogen peroxide into the cavities of the motors because of partly blocking of the openings of the stomatocyte. This results in a lowering of the speed of the nanomotors. Upon blue light irradiation, the trans‐azobenzene moieties isomerize to the cis‐form, which lead to the detachment of the β‐CDs due to their inability to form complexes with the cis‐isomer. As a result, the speed of the nanomotors increases accordingly. Such a conformational change provides us with the unique possibility to control the speed of the supramolecular nanomotor via light‐responsive host–guest complexation. We envision that such artificial responsive nano‐systems with controlled motion could have potential applications in drug delivery.     

Reconstitution of Motor Proteins through Molecular Assembly

What is the most favorite and original chemistry developed in your research group?The most favorite and original chemistry developed in my research group is about the reconstitution of motor proteins in artificially designed and assembled units.It is based on the molecular assembly technique,but the method is different from the conventional approach.     

Are Two‐Station Biased Random Walkers Always Potential Molecular Motors?

The short answer to the title question is no. Despite their tremendous complexity, many nanomachines are simply one‐dimensional systems undergoing a biased, that is, unidirectional, walk on a two‐minima potential energy curve. The initially prepared state, or station, is higher in energy than the final equilibrium state that is reached after overcoming an energy barrier. All chemical reactions comply with this scheme, which does not necessarily imply that a generic chemical reaction is a potential molecular motor. If the barrier is low, the system may walk back and the motion will have a large purely Brownian component. Alternatively, a large distance from the barrier of either of the two stations may introduce a Brownian component. Starting from a general inequality that leverages on the idea that the amount of heat dissipated along the potential energy curve is a good indication of the effectiveness of the biased walk, we provide guidelines for the selection of the features of artificial molecular motors.     

Molecular Diffusion Measurement in Lipid Bilayers over Wide Concentration Ranges: A Comparative Study

Molecular diffusion in biological membranes is a determining factor in cell signaling and cell function. In the past few decades, three main fluorescence spectroscopy techniques have emerged that are capable of measuring molecular diffusion in artificial and biological membranes at very different concentration ranges and spatial resolutions. The widely used methods of fluorescence recovery after photobleaching (FRAP) and single‐particle tracking (SPT) can determine absolute diffusion coefficients at high (>100 μm^?2) and very low surface concentrations (single‐molecule level), respectively. Fluorescence correlation spectroscopy (FCS), on the other hand, is well‐suited for the intermediate concentration range of about 0.1–100 μm^?2. However, FCS in general requires calibration with a standard dye of known diffusion coefficient, and yields only relative measurements with respect to the calibration. A variant of FCS, z‐scan FCS, is calibration‐free for membrane measurements, but requires several experiments at different well‐controlled focusing positions. A recently established FCS method, electron‐multiplying charge‐coupled‐device‐based total internal reflection FCS (TIR‐FCS), referred to here as imaging TIR‐FCS (ITIR–FCS), is also independent of calibration standards, but to our knowledge no direct comparison between these different methods has been made. Herein, we seek to establish a comparison between FRAP, SPT, FCS, and ITIR–FCS by measuring the lateral diffusion coefficients in two model systems, namely, supported lipid bilayers and giant unilamellar vesicles.     

Fabrication of Self-Propelled Micro- and Nanomotors Based on Janus Structures

Delicate molecular and biological motors are tiny machines capable of achieving numerous vital tasks in biological processes. To gain a deeper understanding of their mechanism of motion, researchers from multiple backgrounds have designed and fabricated artificial micro- and nanomotors. These nano-/microscale motors can self-propel in solution by exploiting different sources of energy; thus showing tremendous potential in widespread applications. As one of the most common motor systems, Janus motors possess unique asymmetric structures and integrate different functional materials onto two sides. This review mainly focuses on the fabrication of different types of micro- and nanomotors based on Janus structures. Furthermore, some challenges still exist in the implementation of Janus motors in the biomedical field. With such common goals in mind, it is expected that the elaborate and multifunctional design of Janus motors will overcome their challenges in the near future.     

Protein folds recognized by an intelligent predictor based‐on evolutionary and structural information

Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks incorporated in an adaptive heterogeneous particle swarm optimizer. The main contribution of NiRecor is that it is a data‐driven and highly‐performing predictor without manually tuning control parameters for different data sets. In biological science, since evolutionary‐ and structure‐based information of amino acid sequences is greatly important in determination of tertiary structure of a protein, accordingly, in NiRecor we employ two different feature sets, which involve position specific scoring matrix and secondary structure prediction matrix, to predict the structural classes of protein folds. The experimental results demonstrate the proposed method is powerful in predicting protein folds with higher precisions by improvements of 1.1 ∼7.8 percentages on three benchmark datasets by comparing with several existing predictors. © 2015 Wiley Periodicals, Inc.     

Simulations of optically switchable molecular machines for particle transport

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first‐generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene‐derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on‐the‐fly photodynamics, excited‐state surface‐hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating‐occupation configuration interaction as the QM part and the OPLSAA‐L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi‐molecule arrangements. Our results provide valuable design guidelines for cilia‐driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium‐target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.     

Ultrafast Two‐Dimensional NMR Relaxometry for Investigating Molecular Processes in Real Time

Nuclear spin–lattice (T₁) and spin–spin (T₂) relaxation times provide versatile information about the dynamics and structure of substances, such as proteins, polymers, porous media, and so forth. Multidimensional experiments increase the information content and resolution of NMR relaxometry, but they also multiply the measurement time. To overcome this issue, we present an efficient strategy for a single‐scan measurement of a 2D T₁–T₂ correlation map. The method shortens the experimental time by one to three orders of magnitude as compared to the conventional method, offering an unprecedented opportunity to study molecular processes in real‐time. We demonstrate that, despite the tremendous speed‐up, the T₁–T₂ correlation maps determined by the single‐scan method are in good agreement with the maps measured by the conventional method. The concept of the single‐scan T₁–T₂ correlation experiment is applicable to a broad range of other multidimensional relaxation and diffusion experiments.     

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well‐organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light‐switching biosystems or light‐driven nanomachines. Here we review recent advances in azobenzene‐modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering.     

Designing light-driven rotary molecular motors

The ability to induce and amplify motion at the molecular scale has seen tremendous progress ranging from simple molecular rotors to responsive materials. In the two decades since the discovery of light-driven rotary molecular motors, the development of these molecules has been extensive; moving from the realm of molecular chemistry to integration into dynamic molecular systems. They have been identified as actuators holding great potential to precisely control the dynamics of nanoscale devices, but integrating molecular motors effectively into evermore complex artificial molecular machinery is not trivial. Maximising efficiency without compromising function requires conscious and judicious selection of the structures used. In this perspective, we focus on the key aspects of motor design and discuss how to manipulate these properties without impeding motor integrity. Herein, we describe these principles in the context of molecular rotary motors featuring a central double bond axle and emphasise the strengths and weaknesses of each design, providing a comprehensive evaluation of all artificial light-driven rotary motor scaffolds currently present in the literature. Based on this discussion, we will explore the trajectory of research into the field of molecular motors in the coming years, including challenges to be addressed, potential applications, and future prospects.

Various families of light-driven rotary molecular motors and the key aspects of motor design are discussed. Comparisons are made between the strengths and weaknesses of each motor. Challenges, applications, and future prospects are explored.     

Conformational studies of dammarane‐type triterpenoids using computational and NMR spectroscopic methods

Natural triterpenoids are of great interest to researchers of various fields as they possess diverse physicochemical and biological properties. In medicinal chemistry, detailed information about the chemical structures of bioactive triterpenoids often helps find new lead compounds. Herein, the low‐energy structures of (20S)‐protopanaxadiol and (20S)‐protopanaxatriol, the aglycones of various triterpenoid saponins found in Panax ginseng, and their (20R)‐epimers have been predicted by the geometry optimization of the conformers extracted from molecular dynamics simulations with the self‐consistent‐charge density functional tight‐binding method. By performing quantum mechanical calculations on the low‐energy conformers, we have estimated the NMR chemical shifts of the compounds, which display good agreement with the most recently reported experimental values within an expected range of errors. Our results indicate that theoretical estimation of the NMR parameters of a relatively large molecule with a molecular mass of 500 is feasible. Copyright © 2015 John Wiley & Sons, Ltd.     

Achieving Strong Positive Cooperativity through Activating Weak Non‐Covalent Interactions

Positive cooperativity achieved through activating weak non‐covalent interactions is common in biological assemblies but is rarely observed in synthetic complexes. Two new molecular tubes have been synthesized and the syn isomer binds DABCO‐based organic cations with high orientational selectivity. Surprisingly, the ternary complex with two hosts and one guest shows a high cooperativity factor (α=580), which is the highest reported for synthetic systems without involving ion‐pairing interactions. The X‐ray single‐crystal structure revealed that the strong positive cooperativity likely originates from eight C?H???O hydrogen bonds between the two head‐to‐head‐arranged syn tube molecules. These relatively weak hydrogen bonds were not observed in the free hosts and only emerged in the complex. Furthermore, this complex was used as a basic motif to construct a robust [2+2] cyclic assembly, thus demonstrating its potential in molecular self‐assembly.     

Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View

The relative structural location of a selected group of 27 sulfonamide‐like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para‐aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy‐like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three‐dimensional space (IT‐3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT‐3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para‐aminobenzoic acid than to the theoretically designed analogues.     

Photoisomerization of a Chiral Imine Molecular Switch Followed by Matrix‐Isolation VCD Spectroscopy

Characterizing the stereochemistry of transient photoisomerization products remains a big challenge for the design of molecular machines, such as unidirectional molecular motors. Often these states are not stable long enough to be characterized in detail using conventional spectroscopic tools. The structurally simple camphorquinone imine 1 serves to illustrate the advantage of combining the matrix‐isolation technique with vibrational circular dichroism (VCD) spectroscopy for the investigation of photoisomerizations of chiral molecules. In particular, it is shown that both (E )‐ and (Z )‐ 1 can be generated photochemically at cryogenic temperatures in an argon matrix, and more importantly, that the stereochemistry of both switching states can be characterized reliably.     

Atomic Force Microscopy Investigation of Poly[(R)‐3‐hydroxybutyrate] Lamellar Single Crystals: Relationship between Molecular Weight and Enzymatic Degradation Behavior

Enzymatic degradation behavior of a lamella of single crystals of poly(R)‐3‐hydroxybutyrate (P(3HB)) with an extracellular polyhydroxybutyrate (PHB) depolymerase purified from Alcaligenes faecalis T1 has been investigated by atomic force microscopy (AFM) in order to obtain further information for the chain packing state of P(3HB) in a lamellar single crystal. Two kinds of P(3HB) single crystals with different molecular weights, denoted respectively as H‐ and L‐P(3HB) for high and low molecular weights, respectively, were prepared. The enzymatic treatment was conducted for P(3HB) single crystals adsorbed on a surface of highly ordered pyrolytic graphite. The enzymatic degradation of both P(3HB) single crystals generates several crevices crosswise across the crystal at an early stage. Subsequently, the enzymatic degradation yields numbers of cracks lengthwise along the crystal. In addition to these common features, the interval between cracks crosswise across a lamella in H‐P(3HB) single crystal is longer than that in L‐P(3HB) single crystal, and each crack has V‐shaped and rectangular shaped morphology for H‐ and L‐P(3HB) single crystals, respectively. Based on these results, it is concluded that a lamella of P(3HB) single crystal has straight degradation pathways, that may correspond to a switchboard region, along the long axis of the crystal, independent of molecular weight of P(3HB) samples, and that a H‐P(3HB) single crystal has broader degradation pathways with longer intervals crosswise across the crystal than a L‐P(3HB) single crystal.