Molecular Electronics

One of the main trend in to date research and development is the miniaturization of electronic devices. In this perspective, integrated nanodevices based on proteins or biomolecules are attracting a major interest. In fact, it has been shown that proteins like bacteriorhodopsin and azurin, manifest electrical properties which are promising for the development of active components in the field of molecular electronics. Here we focus on two relevant kinds of proteins: The bovine rhodopsin, prototype of GPCR protein, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer disease. Both these proteins exert their functioning starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different electrical response associated with the different configurations. The model resolution of the electrical response is found able to monitor the structure and the conformational change of the given protein. In this respect, rhodopsin exhibits a better differential response than AChE. This result gives room to different interpretations of the degree of conformational change and in particular supports a recent hypothesis on the existence of a mixed state already in the native configuration of the protein.

We theoretically analyzed inelastic effects in the electron transport through molecular junctions originating from electron-vibron interactions. The molecular bridge was simulated by a periodical chain of identical hydrogenlike atoms with the nearest neighbors interaction thus providing a set of energy states for the electron tunneling. To avoid difficulties inevitably arising when advanced computational techniques are employed to study inelastic electron transport through multilevel bridges, we propose and develop a semiphenomenological approach. The latter is based on Buttiker’s dephasing model within the scattering matrix formalism. We apply the proposed approach to describe features associated with electron energy transfer to vibrational phonons that appear in the second derivative of the current in the junction with respect to the bias voltage. In the particular case of a single level bridge our results agree with those obtained by proper calculations carried out within the non...

Given a set of flexible branched junction DNA molecules with sticky-ends (building blocks), called here tiles, we consider the problem of determining the proper stoichiometry such that all sticky-ends could end up connected. In general, the stoichiometry is not uniform, and the goal is to determine the proper proportion (spectrum) of each type of molecules present to allow for complete assembly. We partition multisets of tiles, called here pots, into three classes: weakly satisfiable, satisfiable and strongly satisfiable according to possible components that assemble in complete complexes. This classification is characterized through the spectrum of the pot, which can be computed in PTIME using the standard Gauss-Jordan elimination method. 1 Other than the assumption of uniform mixing, the thermodynamic properties of the molecules in the test tube (pot) are not included in the description of the assembly process. Also, a relatively uniform melting temperature for the sticky-ends is assumed.

a) Pd(dba) 2 , CuI, PPh 3 , Et 3 N, 89%; (b) nBu 4 NF, THF, MeOH, 96%; (c) CuI, Et 2 NH, 85%; (d) Pd(dba) 2 , CuI, PPh 3 , Et 3 N, 82%; (e) nBu 4 NF, THF, MeOH, 94%; (f) CuI, Et 2 NH, 81%; (g) Pd(PPh 3 ) 4 , CuI, iPr 2 NH, THF, 68%; (h) Pd(PPh 3 ) 4 , CuI, iPr 2 NH, DMF, 65 o C, 75%; (i) KF, MeOH, THF, 80%; (j) CuI, Et 2 NH, THF, 85%; (k) CuI, Et 2 NH, THF, 65% 2. Synthetic Schemes N

We describe a simple analog electronic circuit that mimics the behavior of a well-known synthetic gene oscillator, the repressilator, which represents a set of three genes repressing one another. Synchronization of a population of such units is thoroughly studied, with the aim to comparing the role of global coupling with that of global forcing on the population. Our results show that coupling is much more efficient than forcing in leading the gene population to synchronized oscillations. Furthermore a modification of the proposed analog circuit leads to a simple electronic version of a genetic toggle switch, which is a simple network of two mutually repressor genes, where control by external forcing is also analyzed.

The ability to control the placement of molecules is essential for the patterning and fabrication of nanoscale electronic devices. We apply selective chemistry and self-assembly in combination with conventional nanolithographic techniques to reach higher resolution, greater precision, and chemical versatility in the nanostructures that we create. We illustrate three successful approaches: (1) phase separation of self-assembled monolayers (SAMs) by terminal and internal functionalization, (2) phase separation of SAMs induced by post-adsorption processing and (3) control of molecular placement by insertion into a self-assembled monolayer. These methods demonstrate the possibilities of patterning films by exploiting the intrinsic properties of the molecules. We then employ these self-assembled monolayers as a means to isolate molecules with electronic function to determine the mechanisms of function, and the relationships between molecular structure, environment, connection, coupling, and function. Using self-assembly techniques in combination with scanning tunneling microscopy (STM) we are able to study candidate molecular switches individually and in small bundles. Alkanethiolate SAMs on gold are used as a host two-dimensional matrix to isolate and to insulate electrically the molecular switches. We then individually address and electronically probe each molecule using STM. The conjugated molecules exhibit reversible conductance switching, manifested as a change in the topographic height in the STM images. The origins of switching and the relevant aspects of the molecular structure and environment required will be discussed.

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive but they can also interfere with each other leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

After evaporation of the organic solvents, benzene, toluene, and cyclohexane on gold substrates, Scanning Tunneling Microscope (STM) shows the presence of a remaining adsorbed layer. The different solvent molecules were individually observed at ambient conditions, and their electronic transport properties characterized through the STM in the Break Junction approach. The combination of both techniques reveals, on one hand, that solvents are not fully evaporated over the gold electrode and, secondly, determines the role of the electronic transport of the solvents in molecular electronics.

The oxidative electrochemistry of 1-di-tert-butylphosphino-1 ,2 ,3 ,4 ,5 -pentaphenylferrocene (Q-phos), 1-di-tert-butylphosphino-1 ,2 ,3 ,4 ,5 -penta(4-trifluoromethylphenyl)ferrocene (Q-phos-CF 3 ), 1-di-tert-butylphosphino-1 ,2 ,3 ,4 ,5 -penta(4-methoxyphenyl)ferrocene (Q-phos-OMe) and 1-di-tert-butylphosphino-1 ,2 ,3 ,4 ,5 -penta(4-methylphenyl)ferrocene (Q-phos-Me) was explored. All of the compounds undergo a reversible oxidation, and the formal potentials are sensitive to the R groups on the phenyl rings.

We describe two methods to fabricate metal-molecule-metal junctions. The first method starts with a pair of electrodes separated with a molecular scale gap on an oxidized silicon substrate. These electrodes are fabricated by combining electron beam lithography and electrochemical deposition/etching. A molecular junction is formed when a molecule bridges the gap. This method can fabricate rather stable molecular junctions, however, the yield is low and the exact number of molecules in the junctions is uncertain. The second method forms a molecular junction by separating a scanning tunneling microscope tip from contact with a metal substrate in a solution containing sample molecules. This method, although is not device compatible, can create a large number of molecular junctions over a short period of time, which is ideal for statistical analysis.

for an Invited Paper for the SES09 Meeting of the American Physical Society Controlling, modulating, and monitoring the electronic and mechanical properties of molecular junction devices at single-molecule level BINGQIAN XU, University of Georgia Molecular electronics, where single molecules are used as devices-molecular wires, rectifiers and transistors -is a topic of considerable interest at present. Although substantial efforts are being made to bring the ideas of molecular devices into reality, this field is still somewhat futuristic and need further experimental and theoretical investigation. Future experimental techniques that can fabricate molecular junction devices with molecule electrode contacts that are well defined on the atomic scale and that can characterize the atomic-scale structures of the molecule-electrode contacts with more efficient and more precise control of electron transport will contribute enormously to the field of molecular electronics. We will describe highly integrated and effective methods to simultaneously fabricate, control and modulate, and monitor the electronic and mechanical properties of molecular junction devices at the single-molecule level. The simultaneity will minimize variations normally occur in individualized approaches and thus offer more detailed information and greater understanding of molecular junctions and of processes. Various molecule systems will be discussed.

The electronic structure and ground-state geometry of cyclopentene monolayers on Si(001) are studied using ab initio pseudopotential density-functional theory (DFT). Quasiparticle excitation spectra are calculated within the GW approximation. Both cis and trans cyclopentene monolayers are considered. In both geometries, a strong electronic coupling between the monolayer and Si substrate is found; substantial inter-molecular interactions are present, as indicated by broadening in molecular levels that are decoupled from the substrate. It is argued that the cis structure is kinetically favored, and we evaluate self-energy corrections to the eigenstates of this configuration near the band edges within the GW approximation. The calculated self-energy corrections are large, exceeding those of bulk Si, and increase the energy gap between occupied and unoccupied frontier adsorbate states by 1.3 eV.

Molecular electronics offers the potential to control device functions through the fundamental electronic properties of individual molecules, but realization of such possibilities is typically frustrated when such specialized molecules are integrated into a larger area device. Here we utilize highly conjugated (porphinato)metal-based oligomers (PMn structures) as molecular wire components of nanotransfer printed (nTP) molecular junc-tions; electrical characterization of these 'bulk' nTP devices high-lights device resistances that depend on PMn wire length. This length dependence parallels that evaluated previously in single molecule break junction measurements of identical molecules, underscoring that nanotransfer printing is a viable and reliable method for designing 'bulk' molecular electronics junctions with these molecular wires. Device resistance measurements, deter-mined as a function of PMn molecular length, were utilized to evaluate the magnitude of a phenome...

Single molecule break junction experiments and nonequilibrium Green's function calculations using density functional theory (NEGF-DFT) of carbodithioate-and thiol-terminated [5,15bis(phenylethynyl)-10,20-diarylporphinato]zinc(II) complexes reveal the impact of the electrode-linker coordination mode on charge transport at the single-molecule level. Replacement of thiolate (-S -) by the carbodithioate (-CS 2 - ) anchoring motif leads to an order of magnitude increase of single molecule conductance. In contrast to thiolate-terminated structures, metal-molecule-metal junctions that exploit the carbodithioate linker manifest three distinct conductance values. We hypothesize that the magnitudes of these conductances depend upon carbodithoate linker hapticity with measured conductances across Au-[5,15-bis(4′-(dithiocarboxylate)phenylethynyl)-10,20-diarylporphinato]zinc(II)-Au junctions the greatest when both anchoring groups attach to the metal surface in a bidentate fashion. We support this hypothesis with NEGF-DFT calculations, which consider the electron transport properties for specific binding geometries. These results provide new insights into the origin of molecule-to-molecule conductance heterogeneity in molecular charge transport measurements and the factors that optimize electrode-molecule-electrode electronic coupling and maximize the conductance for charge transport.

All solvents were SLR or analytical grade and were used as supplied unless specified as dry solvents. Dichloromethane was dried over calcium hydride, MEK over K 2 CO 3 , diethyl ether and DME from sodium. THF was dried over sodium and benzophenone. Petroleum ether used for column chromatography was of boiling range 40-60 o C. Pyrrole was distilled over anhydrous K 2 CO 3 and used immediately. Water refers to distilled water and brine refers to a saturated solution of sodium chloride in water. Commercially available materials were used without further purification unless stated otherwise. Evaporation of solvent was carried out on a Buchi rotary evaporator at reduced pressure. Column chromatography was performed on Fluka silica gel 60 (Metrex 70-230 mesh). Thin layer chromatography (TLC) was performed on Merck aluminium backed silica gel 60 F 254 coated plates and were viewed under UV light at 254 nm or 366 nm. Preparative TLC used Analtech uniplate silica gel G F plates. Infrared spectra were recorded on a Perkin-Elmer 1720X FT-IR spectrophotometer using nujol mulls and sodium chloride plates. 1 H NMR ( δ H ) spectra were recorded at either 270 MHz on a Jeol EX270 FT spectrometer, at 300 MHz using a Varian

The clock speed of topological quantum computers based on Majorana zero mode (MZM) - supporting nanoscale devices is limited by the time taken for electrons to traverse the device. We employ the time-dependent Landauer-Büttiker transport theory for current cross-lead correlations in a superconducting nanowire junction hosting MZMs. From the time-dependent quantum noise, we are able to extract traversal times for electrons crossing the system. After demonstrating a linear scaling of traversal times with nanowire length, we present a heuristic formula for the traversal times which accurately captures their behaviour. We then connect our framework to a proposed experimental verification of this discriminant between spurious and genuine MZMs utilizing time-resolved transport measurements.

The charge-energy transport mechanism in molecules is of fundamental importance and practical interest in the design of highly efficient molecular electronic devices. Importantly, the production of entropy due to charge dynamics-associated energy flux variation in the molecular solids causes nonequilibrium transport, and it leads to physics of deviation in Einstein's diffusion-mobility relation of = D k T q B (Hurowitz, D.; Cohen, D.,

Conjugated polymers, of which polyacetylene is the simplest example, combine good mechanical and electronic properties that may be exploited in future technological applications. To this end, a proper description of photo-generation of charged and neutral excitations is crucial. In particular, if quantum vibrational modes (phonons) can be excited, the adiabatic approximation is no longer applicable and this will affect the transfer of energy from the electronic excitations. I show here that neglecting quantum fluctuations of atoms can lead to a qualitatively wrong account of the relaxation dynamics of photoexcited short polyacetylene chains. Indeed, even at zero temperature, quantum fluctuations of the molecular degrees of freedom can trigger the decay of an excited electronic state, through spontaneous emission of phonons: within a mean-field approach, such a process cannot be described at all. A proper study of this quantum phenomenon is given here by an improved version of Correl...

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We propose a new theoretical framework-the Resonant Consciousness Field Theory (RCFT)-which postulates the existence of a fundamental, pervasive energy field responsible for both the stability of observable reality and the emergence of consciousness in living systems. Drawing structural analogy to the Higgs field, which uniformly permeates spacetime and confers mass upon particles through interaction, we hypothesize that this consciousness field is similarly distributed throughout the universe and interacts with biological and quantum systems to produce the phenomenon of subjective awareness. We further propose that this field is structured as a frequency spectrum, where each frequency band corresponds to a distinct mode of stable reality and consciousness, and that our observable universe represents one resonant node within this broader spectrum. We argue that this field operates at or below the threshold imposed by the Heisenberg Uncertainty Principle, rendering it inaccessible to direct measurement with current technology, but potentially detectable through indirect observational signatures. Connections to pilot wave theory, Bohm's implicate order, Integrated Information Theory, and the quantum measurement problem are explored. We outline a framework for future theoretical formalization and indirect experimental investigation.

The Breit-Wigner resonance formula is used to model a class of molecular electronic devices, in order to establish an abstract model for exploration of their applicability in future nanoelectronic systems. The model is used to characterize molecular device I-V curves in terms of the coupling between the molecule and the leads, and demonstrate digital circuit functionality. Circuit metrics such as noise margin, speed and power are investigated.

We have used the Breit-Wigner resonance formula to model a class of molecular electronics devices with the aim to establish an abstract model for a molecular electronic device that can be used in a general cross bar architecture of future nanoelectronic systems. We show that the molecular I-V curves can be characterized by a very small number of variables including the couplings between the contact and leads.

The ability to manipulate electron spin in organic molecular materials offers a new and extremely tantalizing route towards spin electronics, both from fundamental and technological points of view. This is mainly due to the unquestionable advantage of weak spin-orbit and hyperfine interactions in organic molecules, which leads to the possibility of preserving spin-coherence over times and distances much longer than in conventional metals or semiconductors. Here we demonstrate theoretically that organic spin valves, obtained by sandwiching an organic molecule between magnetic contacts, can show a large bias-dependent magnetoresistance and that this can be engineered by an appropriate choice of molecules and anchoring groups. Our results, obtained through a combination of state-of-the-art non-equilibrium transport methods and density functional theory, show that although the magnitude of the effect varies with the details of the molecule, large magnetoresistance can be found both in t...

TRINITY COLLEGE DUBLIN COLLABORATION, LANCASTER UNIVERSITY COLLABORATION -We report a detailed theoretical study of the atomic arrangement and conduction channels of an H 2 molecule joining either Platinum or Palladium electrodes. We find that the bonding state of the molecule does not hybridize with the leads if the molecule forms a bridge, thereby providing a single conductance channel. On the contrary, both channels hybridize heavily, leading to high conductances, if the molecule lies perpendicular to the electrodes,. We propose that the occurrence of additional transitory peaks in conductance histograms of Pd electrodes are due to the dissolution of Hydrogen atoms in the neighborhood of the bridge, which form metastable states.

Using a scattering technique combined with density-functional theory, a computational study of electron transport through two recently synthesized molecules is presented. The effect of connecting the molecules to gold electrodes is studied by iteratively increasing the number of gold layers, treated self -consistently as part of the molecule.