Molecular Nanodevices Research Articles

Design and Electronic Characterization of Bio-Molecular QCA: A First Principle Approach

Molecular Quantum-dot Cellular Automata is the most promising and challenging technology nowadays for its high operating frequency, extremely high device density and non-cryogenic working temperature. In this paper, we report a First Principle approach based on analytical model of 3-dot Bio Molecular Quantum-dot Cellular Automata. The device is 19.62Å long and this bio molecular Quantum dot Cell has been made with two Adenine Nucleotide bio-molecules along with one Carbazole and one Thiol group. This whole molecular structure is supported onto Gold substrate. In this paper, two Adenine Nucleotides act as two quantum dots and Carbazole acts as another dot. These 3-Quantum-dots are mounted in a tree like structure supported with Thiol group. This model has been demonstrated with Extended Hückel Theory based semi-empirical method. The quantum ballistic transmission and HOMO-LUMO plot support the polarization state change. This state changing ability has been observed for this molecular device. Therefore, this property has been investigated and reported in this paper. HOMO-LUMO plot shows the two logic states along with null state for this 3-dots system. This phenomenon illustrates how the charge transfers take place. Two polarization states along with one additional null state have been obtained for this bio molecular nano device. This molecular device has been operated with 1000THz frequency. This nanoscale design approach will initiate one step towards the modeling of high frequency bio molecular Quantum dot Cell at room temperature.

Electric-field-controlled phase transition in a 2D molecular layer

Self-assembly of organic molecules is a mechanism crucial for design of molecular nanodevices. We demonstrate unprecedented control over the self-assembly, which could allow switching and patterning at scales accessible by lithography techniques. We use the scanning tunneling microscope (STM) to induce a reversible 2D-gas-solid phase transition of copper phthalocyanine molecules on technologically important silicon surface functionalized by a metal monolayer. By means of ab-initio calculations we show that the charge transfer in the system results in a dipole moment carried by the molecules. The dipole moment interacts with a non-uniform electric field of the STM tip and the interaction changes the local density of molecules. To model the transition, we perform kinetic Monte Carlo simulations which reveal that the ordered molecular structures can form even without any attractive intermolecular interaction.

A DNA Nanodevice That Loads and Releases a Cargo with Hemoglobin-Like Allosteric Control and Cooperativity.

Here we report the rational design of a synthetic molecular nanodevice that is directly inspired from hemoglobin, a highly evolved protein whose oxygen-carrying activity is finely regulated by a sophisticated network of control mechanisms. Inspired by the impressive performance of hemoglobin we have designed and engineered in vitro a synthetic DNA-based nanodevice containing up to four interacting binding sites that, like hemoglobin, can load and release a cargo over narrow concentration ranges, and whose affinity can be finely controlled via both allosteric effectors and environmental cues like pH and temperature. As the first example of a synthetic DNA nanodevice that undergoes a complex network of nature-inspired control mechanisms, this represents an important step toward the use of similar nanodevices for diagnostic and drug-delivery applications.

A reusable aptasensor of thrombin based on DNA machine employing resonance light scattering technique

The design of molecular nanodevices attracted great interest in these years. Herein, a reusable, sensitive and specific aptasensor was constructed based on an extension-contraction movement of DNA interconversion for the application of human thrombin detection. The present biosensor was based on resonance light scattering (RLS) using magnetic nanoparticles (MNPs) as the RLS probe. MNPs coated with streptavidin can combine with biotin labeled thrombin aptamers. The combined nanoparticles composite is monodispersed in aqueous medium. When thrombin was added a sandwich structure can form on the surface of MNPs, which induced MNPs aggregation. RLS signal was therefore enhanced, and there is a linear relationship between RLS increment and thrombin concentration in the range of 60pM–6.0nM with a limit of detection at 3.5pM (3.29SB/m, according to the recent recommendation of IUPAC). The present aptasensor can be repeatedly used for at least 6 cycling times by heat to transfer G-quadruplex conformation to single strand of DNA sequence and release thrombin. MNPs can be captured by applying the external magnetic field. Furthermore, the proposed biosensor was successfully applied to detect thrombin in human plasma.

Molecular Tools and Nanodevices Built from DNA

Over the last decades, DNA has proven to be an excellent choice for the designed self-assembly of functional two- and three-dimensional nanostructures and materials [1,2]. By offering attachment sites for active nano-components on DNA-based objects, our group has realized complex and nanometer-precise assemblies of fluorophores, plasmonic nanoparticles and biomolecules [3].

Biophysics of Microtubule End Coupling at the Kinetochore.

The main physiological function of mitotic kinetochores is to provide durable attachment to spindle microtubules, which segregate chromosomes in order to partition them equally between the two daughter cells. Numerous kinetochore components that can bind directly to microtubules have been identified, including ATP-dependent motors and various microtubule-associated proteins with no motor activity. A major challenge facing the field is to explain chromosome motions based on the biochemical and structural properties of these individual kinetochore components and their assemblies. This chapter reviews the molecular mechanisms responsible for the motions associated with dynamic microtubule tips at the single-molecule level, as well as the activities of multimolecular ensembles called couplers. These couplers enable persistent kinetochore motion even under load, but their exact composition and structure remain unknown. Because no natural or artificial macro-machines function in an analogous manner to these molecular nano-devices, understanding their underlying biophysical mechanisms will require conceptual advances.

Spin-dependent transport properties of a Co-Salophene molecule between graphene nanoribbon electrodes

Molecular spintronics has attracted much attention because of many novel functionalities at the single molecule level over the past decades.Recently,much research has focused on organic molecules containing transition metals in the field of molecular spintronics,which possesses desired spin-dependent transport properties for spintronic device applications. In this paper,based on non-equilibrium Green's function formalism combined with the first-principles density functional theory,the spin-dependent transport properties of an organic Co-Salophen molecule sandwiched between two zigzag graphene nanoribbon (ZGNR) electrodes are investigated.By applying an external magnetic field,the spin directions of the left and right ZGNR electrodes may be switched to two different configurations:the parallel (P) and antiparallel (AP) spin configurations.It is found that for the P spin configuration,the spin-up current is significantly larger than the spin-down one which is nearly zero in a bias range from -1.0 V to 1.0 V,exhibiting a nearly perfect spin filtering effect (up to 100%).Moreover,the spin-up current shows negative differential resistance behavior at 0.3 V.For the AP spin configuration,the spin-down current is much larger than the spin-up one at the positive bias.On the contrary,the spinup current is much larger than the spin-down one at the positive bias.Therefore,the device exhibits bipolar spin filtering effect.It is also found that the spin-up current at the negative bias is much larger than that at the corresponding positive bias,while the spin-down current at the negative bias is much smaller than that at the corresponding positive bias,which shows the outstanding spin rectifying effect.Besides,a significant giant magnetoresistance effect is also obtained in the device when the spin directions of the left and right ZGNR electrodes switch between P and AP spin configurations. The spin transport properties of the device under P and AP spin configurations are attributed to the different orbital symmetries of spin subbands (* and ) of the electrodes and the spatial distribution of molecular orbitals within the bias window.By analyzing the spin-polarization transmission spectrum,the local density of states,the band structures and symmetries of the ZGNR electrodes and the projected self-consistent Hamiltonian states of molecular orbitals,the internal mechanism for multiple functional characteristics of the device is explained in detail.Our results indicate the Co-Salophen molecule can be a promising candidate for future applications in molecular spintronics device,and also provide a theoretical reference for designing the next-generation molecular nano-devices.

A Fully Charge-Delocalized Two-Dimensional Porphyrin System with Two Different Class III States.

Understanding of charge-delocalization over two-dimensional (2D) frameworks is a further step in the path towards the development of molecular nanodevices and nanomaterials. Here, we report a porphyrin-nickel complex with four peripheral redox-active ruthenium pendants (1). A cyclic voltammogram of compound 1 displays reversible five-electron, four redox waves with large potential separations, suggesting that one-electron- (1+ ) and two-electron-oxidized species (12+ ) are thermodynamically stable with respect to disproportionation. The paramagnetic one-electron-oxidized species 1+ prepared by a comproportionation reaction of compounds 1 and 12+ , turns out to be a highly charge-delocalized two-dimensional class III compound as clearly indicated by its characteristic intervalence charge-transfer (IVCT) band as is further supported by IR and ESR spectroscopy as well as DFT and time-dependent (TD) DFT calculations. Furthermore, the diamagnetic dicationic species 12+ has a spin-paired electronic structure with a fully charge-averaged class III character. The substantial contribution of the cumulenic structures to compound 12+ is confirmed by 13 C NMR and IR spectroscopy as well as X-ray structure analyses. Such unique electronic features of the 2D systems provide a clue to development of nanoscale molecular devices.

Polymer surface properties control the function of heavy meromyosin in dynamic nanodevices

The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro- and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

Formation of single carbon chain bridging two SWCNTs via tensile deformation of nanobud junction

Molecular junctions formed by a single carbon chain (SCC) bridging two SWCNTs are highly desirable for molecular electronic nanodevices; however, the fabrication is still quite challenging. In this study, we present a novel method to produce a SCC bridging the outer wall of two SWNTs. By separating the carbon nanotube embedding nanobuds junction, carbon atom chain including a few tens of atoms or even up to 100 carbon atoms bridging two SWNTs can be formed. Moreover, we find that embedding nanobuds junction shows extraordinary room temperature superplasticity. The laddering effect, in which the atom chain can be continuously pulled out from the fullerene molecule in the nanobuds junction under tensile loading, is exhibited in this work.

A molecular nanodevice for targeted degradation of mRNA during protein synthesis.

RNase H is an endonuclease that catalyzes the cleavage of RNA. Because it only acts on RNA in RNA:DNA hybrids, RNase H can be used for targeted degradation of RNA when used in combination with antisense oligodeoxyribonucleotides (ASODNs) designed against a specific sequence of the target RNA. In this study, ASODN and RNase H were co-conjugated on magnetic nanoparticles. The resulting nanoparticles, having integrated functions of probing and processing target RNA, were able to remove target mRNA sequences more effectively than free ASODNs. The paramagnetic property of the nanoparticles also enabled timed engagement and disengagement of the RNA-degrading components in a given system, and these nanoparticles were able to be used for ON/OFF control of gene expression during cell-free protein synthesis reactions.

Molecular design driving tetraporphyrin self-assembly on graphite: a joint STM, electrochemical and computational study.

Tuning the intermolecular interactions among suitably designed molecules forming highly ordered self-assembled monolayers is a viable approach to control their organization at the supramolecular level. Such a tuning is particularly important when applied to sophisticated molecules combining functional units which possess specific electronic properties, such as electron/energy transfer, in order to develop multifunctional systems. Here we have synthesized two tetraferrocene-porphyrin derivatives that by design can selectively self-assemble at the graphite/liquid interface into either face-on or edge-on monolayer-thick architectures. The former supramolecular arrangement consists of two-dimensional planar networks based on hydrogen bonding among adjacent molecules whereas the latter relies on columnar assembly generated through intermolecular van der Waals interactions. Scanning Tunneling Microscopy (STM) at the solid-liquid interface has been corroborated by cyclic voltammetry measurements and assessed by theoretical calculations to gain multiscale insight into the arrangement of the molecule with respect to the basal plane of the surface. The STM analysis allowed the visualization of these assemblies with a sub-nanometer resolution, and cyclic voltammetry measurements provided direct evidence of the interactions of porphyrin and ferrocene with the graphite surface and offered also insight into the dynamics within the face-on and edge-on assemblies. The experimental findings were supported by theoretical calculations to shed light on the electronic and other physical properties of both assemblies. The capability to engineer the functional nanopatterns through self-assembly of porphyrins containing ferrocene units is a key step toward the bottom-up construction of multifunctional molecular nanostructures and nanodevices.

Enzyme-Operated DNA-Based Nanodevices.

Functional molecular nanodevices and nanomachines have attracted a growing interest for their potential use in life science and nanomedicine. In particular, due to their versatility and modularity DNA-based nanodevices appear extremely promising. However, a limitation of such devices is represented by the limited number of molecular stimuli and cues that can be used to control and regulate their function. Here we demonstrate the possibility to rationally control and regulate DNA-based nanodevices using biocatalytic reactions catalyzed by different enzymes. To demonstrate the versatility of our approach, we have employed three model DNA-based systems and three different enzymes (belonging to several classes, i.e., transferases and hydrolases). The possibility to use enzymes and enzymatic substrates as possible cues to operate DNA-based molecular nanodevices will expand the available toolbox of molecular stimuli to be used in the field of DNA nanotechnology and could open the door to many applications including enzyme-induced drug delivery and enzyme-triggered nanostructures assembly.

A First Principle Approach to Design Gated p-i-n Nanodiode

Thanks to the world of nanotechnology; it is possible to build molecular nanodevices. In this paper, GaAs single nanowire molecular p-i-n diode is designed and its electronic transmission properties, Local Device Density of States, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital plot and Negative Differential Resistance property are investigated from the atomic perspective using first principle Density Functional Theory-Non Equilibrium Green Function approach. This molecular structure is built and simulated in Virtual nanoLab atmosphere. The Negative Differential Resistance of the device is revealed through the current-voltage characteristics of the nanowire. The band-to-band tunneling current is observed for this p-i-n junction nanodiode. Thermal coefficient, Peltier co-efficient, and Seebeck coefficients at different gate bias are obtained. This nanowire GaAs molecular diode is attractive for the next generation low power nanodevice design. Electrical doping effect has been introduced in the wire without adding unambiguous dopants to the molecular wire.

Nanopatterning of Surfaces with Monometallic and Heterobimetallic 1D Coordination Polymers: A Molecular Tectonics Approach at the Solid/Liquid Interface.

The self-assembly of multiple molecular components into complex supramolecular architectures is ubiquitous in nature and constitutes one of the most powerful strategies to fabricate multifunctional nanomaterials making use of the bottom-up approach. When spatial confinement in two dimensions on a solid substrate is employed, this approach can be exploited to generate periodically ordered structures from suitably designed molecular tectons. In this study we demonstrate that physisorbed directional periodic arrays of monometallic or heterobimetallic coordination polymers can be generated on a highly oriented pyrolitic graphite surface by combinations of a suitably designed directional organic tecton or metallatecton based on a porphyrin or nickel(II) metalloporphyrin backbone bearing both a pyridyl unit and a terpyridyl unit acting as coordinating sites for CoCl2. The periodic architectures were visualized at the solid/liquid interface with a submolecular resolution by scanning tunneling microscopy and corroborated by combined density functional and time-dependent density functional theory calculations. The capacity to nanopattern the surface for the first time with two distinct metallic centers exhibiting different electronic and optical properties is a key step toward the bottom-up construction of robust multicomponent and, thus, multifunctional molecular nanostructures and nanodevices.

Surface strain mediated dipole alignment of ClAlPc on Au(111)

In this letter, we demonstrate the control of dipole alignment of monolayer chloroaluminum phthalocyanine (ClAlPc) molecules via the strain in Au(111) substrates. Local ordering of ClAlPc dipole comprising alternate Cl-up and Cl-down configurations is found on the tensile-strained Au(111)/mica as a result of strain-enhanced absorption of Cl-down ClAlPc's and the dipole-dipole interaction. In contrast, the strain-released single crystal Au(111) substrate shows negligible coupling to Cl-down ClAlPc, therefore, facilitating the formation of unidirectionally aligned Cl-up ClAlPc dipole array. The dipole-dipole interaction becomes less prominent at low ClAlPc coverage where ClAlPc molecules can find their favorable absorption sites more easily according to their inherent dipole orientation. Our results emphasize the superior role of molecule-substrate interaction in functional molecular engineering on metal surface hence provide fundamental insight into the potential applications in molecular nanodevices with tunable and controllable properties.

Electronic properties of doped hexagonal graphene

Zigzag- and armchair-edged hexagonal graphenes are sandwiched between two Au electrodes to construct molecular nanodevices, and the effects of the orderly and locally doped with B, N, and BN for such graphene nanoflakes are considered, respectively. Based on the first-principles method, the electronic transport properties of these devices are investigated systematically. Our calculated results show that the using of B and BN to dope armchair-edged hexagonal graphenes can modulate the electronic transport properties significantly. Intrinsic and doped zigzag-hexagonal graphenes presents a semiconductoring behavior, and when it is doped with N and BN, there appears a negative differential resistance (NDR) phenomenon, especially for N-doping, and a very obvious NDR can be observed in zigzag-edged hexagonal grapheme: this might be important for developing molecular switches. The underlying causes for these findings are clearly elucidated by the transmission features and the doping-induced changes in electronic properties of a hexagonal graphene.

Rational design of two-dimensional molecular donor-acceptor nanostructure arrays.

The construction of long-range ordered organic donor-acceptor nanostructure arrays over microscopic areas supported on solid substrates is one of the most challenging tasks towards the realization of molecular nanodevices. They can also be used as ideal model systems to understand light induced charge transfer, charge separation and energy conversion processes and mechanisms at the nanometer scale. The aim of this paper is to highlight recent advances and progress in this topic. Special attention is given to two different strategies for the construction of organic donor-acceptor nanostructure arrays, namely (i) molecular self-assembly on artificially patterned or pre-defined molecular surface nanotemplates and (ii) molecular nanostructure formation steered via directional and selective intermolecular interactions. The interfacial charge transfer and the energy level alignment of these donor-acceptor nanostructures are also discussed.

Stability optimisation of molecular electronic devices based on nanoelectrode–nanoparticle bridge platform in air and different storage liquids

The long-term stability of metal nanoparticle–molecule junctions in molecular electronic devices based on nanoelectrodes (NEL) is a major challenge in the effort to bring related molecular electronic devices to application. To optimize the reproducibility of molecular electronic nanodevices, the time-dependent modification of such junctions as exposed to different media needs to be known. Here, we have studied (1) the stability of Au-NEL and (2) the electrical stability of molecule–Au nanoparticle (AuNP) junctions themselves with the molecule being 1,8-octanedithiol (ODT). Both the NELs only and the junctions were exposed to air and liquids such as deionized water, tetrahydrofuran, toluene and tetramethylethylenediamine (TMEDA) over a period of 1 month. The nanogaps remained stable in width when stored in either deionized water or toluene, whereas the current through 1,8-octanedithiol–NP junctions remained most stable when stored in TMEDA as compared to other solvents. Although it is difficult to follow the chemical processes in such devices in the 10-nm range with analytical methods, the behavior can be interpreted from known interactions of solvent molecules with electrodes and ODT.

Nanoscale Optical and Mechanical Manipulation of Molecular Alignment in Metal–Molecule–Metal Structures

Equilibrium molecular orientations, monitored using surface enhanced Raman scattering, are controlled by both optical and mechanical means in metal–molecule–metal nanogap structures, formed on an atomically planar Au(111) surface. The spatially confined optical near-fields exert a torque on the molecules in the nanogaps and align the molecular orientations along the field vector. The mechanical compression from the metal nanogaps not only disturbs the molecular alignments but also perturbs the electronic structures at metal–molecule interfaces. The implications of such interactions are discussed with respect to control and detection of local electronic properties in molecular nanodevices.