Bistable Molecular Switch Research Articles

Rational Design of Stimuli-Responsive Inorganic 2D Materials via Molecular Engineering: Toward Molecule-Programmable Nanoelectronics.

The ability of electronic devices to act as switches makes digital information processing possible. Succeeding graphene, emerging inorganic 2D materials (i2DMs) have been identified as alternative 2D materials to harbor a variety of active molecular components to move the current silicon-based semiconductor technology forward to a post-Moore era focused on molecule-based information processing components. In this regard, i2DMs benefits are not only for their prominent physiochemical properties (e.g., the existence of bandgap), but also for their high surface-to-volume ratio rich in reactive sites. Nonetheless, since this field is still in an early stage, having knowledge of both i) the different strategies for molecularly functionalizing the current library of i2DMs, and ii) the different types of active molecular components is a sine qua non condition for a rational design of stimuli-responsive i2DMs capable of performing logical operations at the molecular level. Consequently, this Review provides a comprehensive tutorial for covalently anchoring ad hoc molecular components-as active units triggered by different external inputs-onto pivotal i2DMs to assess their role in the expanding field of molecule-programmable nanoelectronics for electrically monitoring bistable molecular switches. Limitations, challenges, and future perspectives of this emerging field which crosses materials chemistry with computation are critically discussed.

Visible-light-driven bistable photoswitching with enhanced solid state NIR-fluorescence for multi-level optical storage

A visible-light driven solid-state NIR fluorescent bistable molecular switch was constructed by coupling bulky tetraphenylethylene, photochromic diarylethene and NIR emissive terrylene diimide. Multi-level optical storage was demonstrated based on its film.

Bistable H2Pc Molecular Conductance Switch on Ag(100)

Scanning tunneling microscopy (STM) and density functional theory (DFT) were used to study the tautomerization reaction of an H2Pc molecule adsorbed on a Ag(100) surface. The presence of two hydrogen atoms in the cavity of the H2Pc molecule enforces the existence of two molecular tautomers. It causes a reduction from 4- to 2-fold symmetry in STM images that can be recorded as two current states over the H2Pc molecule with a high-to-low current state ratio of ∼1.2. These findings are confirmed by the spatial distributions of the all-atom electron charge density calculated by using DFT and transmission maps together with tunneling current ratios (∼1.2) determined from the nonequilibrium Green’s function transport calculations. Therefore, we demonstrate that an H2Pc molecule adsorbed on a Ag(100) surface is a good candidate for a bistable molecular conductance switch since neither the presence of the Ag(100) surface nor that of the STM tip alters the tautomerization.

Bistable (Supra)molecular Switches on 3D-Printed Responsive Interfaces with Electrical Readout

Molecular switching memories have gained great importance in recent years because of the current sharp increase in the production of consumer electronics. Herein, 3D-printed nanocomposite carbon electrodes (3D-nCEs) have been explored as unconventional responsive interfaces to electrically readout bistable molecular switches via electrochemical impedance spectroscopy as the output system. As a proof-of-concept, two different 3D-printed responsive interfaces have been devised using surface engineering for covalently anchoring (supra)molecular components that well-define two electrical states (on/off) driven by either electrical or optical stimuli. Accordingly, this work paves the way for the functionalization of 3D-nCEs through fundamental chemistry, opening up new horizons in unprecedented tailored 3D-printed responsive interfaces which could be utilized as potential (bio)sensors, (opto)electronic devices, or molecular logic gates.

Greatwall-Endosulfine: A Molecular Switch that Regulates PP2A/B55 Protein Phosphatase Activity in Dividing and Quiescent Cells.

During the cell cycle, hundreds of proteins become phosphorylated and dephosphorylated, indicating that protein kinases and protein phosphatases play a central role in its regulation. It has been widely recognized that oscillation in cyclin-dependent kinase (CDK) activity promotes DNA replication, during S-phase, and chromosome segregation, during mitosis. Each CDK substrate phosphorylation status is defined by the balance between CDKs and CDK-counteracting phosphatases. In fission yeast and animal cells, PP2A/B55 is the main protein phosphatase that counteracts CDK activity. PP2A/B55 plays a key role in mitotic entry and mitotic exit, and it is regulated by the Greatwall-Endosulfine (ENSA) molecular switch that inactivates PP2A/B55 at the onset of mitosis, allowing maximal CDK activity at metaphase. The Greatwall-ENSA-PP2A/B55 pathway is highly conserved from yeast to animal cells. In yeasts, Greatwall is negatively regulated by nutrients through TORC1 and S6 kinase, and couples cell growth, regulated by TORC1, to cell cycle progression, driven by CDK activity. In animal cells, Greatwall is phosphorylated and activated by Cdk1 at G2/M, generating a bistable molecular switch that results in full activation of Cdk1/CyclinB. Here we review the current knowledge of the Greatwall-ENSA-PP2A/B55 pathway and discuss its role in cell cycle progression and as an integrator of nutritional cues.

An Octacationic [2]Catenane Formed by Oxime Condensation: A Bistable Molecular Switch

AbstractOxime condensation as well as template‐directed synthesis based on radical‐pairing interactions were used in the synthesis of an octacationic [2]catenane in 20 % yield. The [2]catenane consists of two identical mechanically interlocked tetracationic macrocyclic components. Each of the ring components contains two dicationic bipyridinium (BIPY2+) functions. The structure of the [2]catenane was fully characterized by NMR spectroscopy, mass spectrometry, as well as X‐ray crystallography. In the oxidized state, the [2]catenane exists in a co‐conformation where its four BIPY2+ units are located as far as possible from each other. Upon reduction of BIPY2+ into the radical state, namely BIPY+., we propose that the [2]catenane undergoes mechanical movement, driven by radical pairing interactions between these radical building blocks. The redox‐stimulated switching behavior of this [2]catenane was confirmed by electrochemistry, UV‐Vis‐NIR absorption spectroscopy, and 1H NMR spectroscopy.

Analog Signaling With the "Digital" Molecular Switch CaMKII.

Molecular switches, such as the protein kinase CaMKII, play a fundamental role in cell signaling by decoding inputs into either high or low states of activity; because the high activation state can be turned on and persist after the input ceases, these switches have earned a reputation as “digital.” Although this on/off, binary perspective has been valuable for understanding long timescale synaptic plasticity, accumulating experimental evidence suggests that the CaMKII switch can also control plasticity on short timescales. To investigate this idea further, a non-autonomous, nonlinear ordinary differential equation, representative of a general bistable molecular switch, is analyzed. The results suggest that switch activity in regions surrounding either the high- or low-stable states of activation could act as a reliable analog signal, whose short timescale fluctuations relative to equilibrium track instantaneous input frequency. The model makes intriguing predictions and is validated against previous work demonstrating its suitability as a minimal representation of switch dynamics; in combination with existing experimental evidence, the theory suggests a multiplexed encoding of instantaneous frequency information over short timescales, with integration of total activity over longer timescales.

MicroRNA Control of TGF-β Signaling.

Transcriptional and post-transcriptional regulation shapes the transcriptome and proteome changes induced by various cellular signaling cascades. MicroRNAs (miRNAs) are small regulatory RNAs that are approximately 22 nucleotides long, which direct the post-transcriptional regulation of diverse target genes and control cell states. Transforming growth factor (TGF)-β family is a multifunctional cytokine family, which plays many regulatory roles in the development and pathogenesis of diverse diseases, including fibrotic disease, cardiovascular disease and cancer. Previous studies have shown that the TGF-β pathway includes the miRNA pathway as an important component of its downstream signaling cascades. Multiple studies of epithelial–mesenchymal transition (EMT)-related miRNAs have highlighted that miRNAs constitute the intrinsic bistable molecular switches of cell states by forming double negative feedback loops with EMT-inducing transcription factors. This may be important for understanding the reversibility of EMT at the single-cell level, the presence of distinct EMT transition states and the intra- and inter-tumor heterogeneity of cancer cell phenotypes. In the present review, I summarize the connection between TGF-β signaling and the miRNA pathway, placing particular emphasis on the regulation of miRNA expression by TGF-β signaling, the modulation of TGF-β signaling by miRNAs, the miRNA-mediated modulation of EMT and endothelial–mesenchymal transition as well as the crosstalk between miRNA and TGF-β pathways in the tumor microenvironment.

Axon growth regulation by a bistable molecular switch

For the brain to function properly, its neurons must make the right connections during neural development. A key aspect of this process is the tight regulation of axon growth as axons navigate towards their targets. Neuronal growth cones at the tips of developing axons switch between growth and paused states during axonal pathfinding, and this switching behaviour determines the heterogeneous axon growth rates observed during brain development. The mechanisms controlling this switching behaviour, however, remain largely unknown. Here, using mathematical modelling, we predict that the molecular interaction network involved in axon growth can exhibit bistability, with one state representing a fast-growing growth cone state and the other a paused growth cone state. Owing to stochastic effects, even in an unchanging environment, model growth cones reversibly switch between growth and paused states. Our model further predicts that environmental signals could regulate axon growth rate by controlling the rates of switching between the two states. Our study presents a new conceptual understanding of growth cone switching behaviour, and suggests that axon guidance may be controlled by both cell-extrinsic factors and cell-intrinsic growth regulatory mechanisms.

The limiting dynamics of a bistable molecular switch with and without noise.

We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density.

Experimental testing of a new integrated model of the budding yeast Start transition.

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1-S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1-S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model's simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network.

Modeling CaMKII in cardiac physiology: from molecule to tissue

Post-translational modification of membrane proteins (e.g., ion channels, receptors) by protein kinases is an essential mechanism for control of excitable cell function. Importantly, loss of temporal and/or spatial control of ion channel post-translational modification is common in congenital and acquired forms of cardiac disease and arrhythmia. The multifunctional Ca2+/calmodulin-dependent protein kinase II (CaMKII) regulates a number of diverse cellular functions in heart, including excitation-contraction coupling, gene transcription, and apoptosis. Dysregulation of CaMKII signaling has been implicated in human and animal models of disease. Understanding of CaMKII function has been advanced by mathematical modeling approaches well-suited to the study of complex biological systems. Early kinetic models of CaMKII function in the brain characterized this holoenzyme as a bistable molecular switch capable of storing information over a long period of time. Models of CaMKII activity have been incorporated into models of the cell and tissue (particularly in the heart) to predict the role of CaMKII in regulating organ function. Disease models that incorporate CaMKII overexpression clearly demonstrate a link between its excessive activity and arrhythmias associated with congenital and acquired heart disease. This review aims at discussing systems biology approaches that have been applied to analyze CaMKII signaling from the single molecule to intact cardiac tissue. In particular, efforts to use computational biology to provide new insight into cardiac disease mechanisms are emphasized.

Electron transfer through coordination bond interaction between single molecules: conductance switching by a metal ion

Molecular tips were used to investigate electron transfer through metal-coordination bonds between single molecules. Coordination of a single metal ion to two carboxylate-terminated thiolate molecules formed a sandwich-type single molecular junction. It was found that a favorable charge transfer is induced through such molecular junctions. The electron transfer facilitated by metal coordination was utilized to implement conductance switching in a molecular junction of a head-to-head pyridine dimer. The present research offers a method to control electronic functions required in the construction of functional electronic molecular devices.

Preparing and regulating a bi-stable molecular switch by atomic manipulation

We present a scanning tunneling microscopy (STM) investigation into the influence of the STM tip on the adsorption site switching of polychlorinatedbiphenyl (PCB) molecules on the Si(111)-7 × 7 surface at room temperature. From an initially stable adsorption configuration, atomic manipulation by charge injection from the STM tip prepared a new bi-stable configuration that switched between two bonding arrangements. No switching rate bias dependence was found for + 1.0 to + 2.2 V. Assuming a thermally driven switching process we find that the measured energy barriers to switching are influenced by the exact location of the STM tip by more than 10%. We propose that this energy difference is due the dispersion interaction between the tip and the molecule.

Cell cycle commitment in budding yeast emerges from the cooperation of multiple bistable switches

The start-transition (START) in the G1 phase marks the point in the cell cycle at which a yeast cell initiates a new round of cell division. Once made, this decision is irreversible and the cell is committed to progressing through the entire cell cycle, irrespective of arrest signals such as pheromone. How commitment emerges from the underlying molecular interaction network is poorly understood. Here, we perform a dynamical systems analysis of an established cell cycle model, which has never been analysed from a commitment perspective. We show that the irreversibility of the START transition and subsequent commitment can be consistently explained in terms of the interplay of multiple bistable molecular switches. By applying an existing mathematical model to a novel problem and by expanding the model in a self-consistent manner, we achieve several goals: we bring together a large number of experimental findings into a coherent theoretical framework; we increase the scope and the applicability of the original model; we give a systems level explanation of how the START transition and the cell cycle commitment arise from the dynamical features of the underlying molecular interaction network; and we make clear, experimentally testable predictions.

Can a local, PKMξ dependent translational switch account for the maintenance of synaptic plasticity?

Memory can last a human lifetime, yet at the synaptic level it is encoded by proteins that turnover at rates that are much faster than the lifetime of memory. A critical open question in the neuroscience of learning and memory is how memory and its cellular basis synaptic plasticity can be maintained for longer than its molecular substrates. Recently it has been shown that the activity of a brain specific kinase, PKMξ, is necessary for the maintenance but not the induction of synaptic plasticity. It is also known that synthesis of new proteins is necessary for inducing long lasting synaptic plasticity and memory. We postulate that a molecular network that includes activation, translation and degradation of PKMξ can be a bi-stable molecular switch, that can account for the maintenance of long-term synaptic plasticity and memory. We formulate a mathematical model of such a molecular network, and show that it can be bi-stable and that it accounts for many of the experimental observations regarding the activation, synthesis and inhibition of PKMξ. Our model also makes testable experimental predictions.

A Bistable Molecular Switch Driven by Photoinduced Hydrogen‐Atom Transfer

The occurrence of photoinduced hydrogen atom transfer between two remote spots of a molecule is experimentally demonstrated. This photoprocess involves the intermediacy of an intramolecular "crane". In an experimental case study, 7-hydroxy-4-methylquinoline-8-carbaldehyde monomers isolated in low-temperature Ar matrices are investigated. On UV (lambda>295 nm) irradiation, a hydrogen atom is transferred from the O(7)H group to the N(1) atom of the quinoline ring. Subsequent irradiation with UV (lambda>360 nm) light reveals that the phototransformation is partially photoreversible. In the studied hydrogen-atom-transfer process, the exocyclic carbaldehyde group plays the role of an intramolecular crane. The possible application of systems analogous to 7-hydroxy-4-methylquinoline-8-carbaldehyde as optically driven molecular switches is discussed.

Pushing and Pulling a Sn Ion through an Adsorbed Phthalocyanine Molecule

Molecule-based functional devices on surfaces may take advantage of bistable molecular switches. The conformational dynamics and efficiency of switches are radically different on surfaces compared to the liquid phase. We present a design of molecular layers which enables bistable switching on a surface and, for the first time, demonstrate control of a single switch in a dense and ordered array at the spatial limit. Up and down motion of a central Sn ion through the frame of a phthalocyanine molecule is achieved via resonant electron or hole injection into molecular orbitals.

Bistable Molecular Switches Based on Linkage Isomerization in Ruthenium Polypyridyl Complexes with a Ligand‐Bound Ambidentate Motif

Electron-transfer-induced linkage isomerization was investigated in a series of bis-tridentate Ru polypyridyl complexes [Ru(L-X-OH)(Y-tpy)](2+) with ambidentate ligand L-X-OH=bpy-C(R)(OH)-py (bpy=2,2'-bipyridine; py=pyridine; R=H, Me, Ph, or tBu) and spectator ligand Y-tpy (tpy=2,2':6',2''-terpyridine; Y=p-tolyl, p-PhCO(2)Me, Cl, OEt, N-pyrrolidine). The ligand-bound ambidentate motif switches reversibly between N and O coordination in the Ru(II) and Ru(III) state, respectively. The potentials of the Ru(III/II) couple differ by about 0.5 V between the isomers, and this results in a bistable electrochemical response of the molecular switches. The effects of structural modifications in form of substituents on the linking carbon atom of the ambidentate ligand and on the central pyridine moiety of the spectator ligand were investigated by electrochemical and computational methods. Differences in isomerization behavior span six orders of magnitude in rate constants and two orders of magnitude in equilibrium constants. The results can be interpreted in terms of steric and electronic substituent effects and their influence on rotational barriers, ligation geometry, and electron deficiency of the metal center.

A surface-attached Ru complex operating as a rapid bistable molecular switch

An electrochemically bistable ruthenium polypyridyl complex was immobilised on platinum electrodes via amide condensation with an amine-terminated self-assembled thiol monolayer and underwent rapid electron transfer-induced linkage isomerism.