A graph-theoretical model for ballistic conduction in single-molecule conductors

2011 ◽  
Vol 83 (8) ◽  
pp. 1515-1528 ◽  
Author(s):  
Patrick W. Fowler ◽  
Barry T. Pickup ◽  
Tsanka Z. Todorova
Keyword(s):  
Single Molecule ◽  
Molecular Graph ◽  
Tight Binding ◽  
Transmission Function ◽  
Kekulé Structure ◽  
Qualitative Description ◽  
Frontier Orbital ◽  
Conduction Behavior ◽  
Ballistic Conduction ◽  
Source And Sink

The tight-binding version of the source-and-sink potential (SSP) model of ballistic conduction can be cast in a graph-theoretical form where the transmission through a molecular wire depends on four characteristic polynomials: those of the molecular graph and the vertex-deleted subgraphs with one or both of the molecular vertices contacting the electrodes removed. This gives an explicit function for the dependence of transmission on energy, one that is well adapted for qualitative description of general classes of conductors and conduction behavior. It also leads directly to a selection-rule criterion for conduction in terms of counting zero roots of the polynomials, which for benzenoids and graphenes is shown to subsume literature approaches based on Kekulé structure counting, bond order, and frontier-orbital matching. As explicitly demonstrated here, the SSP transmission function agrees with that derived by the Green’s function (GF) method.

Charge Transfer Complexation Boosts Molecular Conductance Through Fermi Level Pinning

2018 ◽  
Author(s):  
Kun Wang ◽  
Andrea Vezzoli ◽  
Iain Grace ◽  
Maeve McLaughlin ◽  
Richard Nichols ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Single Molecule ◽  
Quantum Interference ◽  
Transmission Function ◽  
Scanning Tunneling ◽  
Charge Transfer Complexes ◽  
Tunneling Microscopy ◽  
Quantum Interference Effect ◽  
Single Molecule Junctions ◽  
Charge Transfer Complexation

We have used scanning tunneling microscopy to create and study single molecule junctions with thioether-terminated oligothiophene molecules. We find that the conductance of these junctions increases upon formation of charge transfer complexes of the molecules with tetracyanoethene, and that the extent of the conductance increase is greater the longer is the oligothiophene, i.e. the lower is the conductance of the uncomplexed molecule in the junction. We use non-equilibrium Green's function transport calculations to explore the reasons for this theoretically, and find that new resonances appear in the transmission function, pinned close to the Fermi energy of the contacts, as a consequence of the charge transfer interaction. This is an example of a room temperature quantum interference effect, which in this case boosts junction conductance in contrast to earlier observations of QI that result in diminished conductance.<br>

Electrical Transport Properties of Carbon Nanotube Metal-Semiconductor Heterojunction

2016 ◽  
Vol 15 (05n06) ◽  
pp. 1660009 ◽  
Author(s):  
Keka Talukdar ◽  
Anil Shantappa
Keyword(s):  
Electrical Transport ◽  
Nearest Neighbor ◽  
Electronic Devices ◽  
Tight Binding ◽  
Transmission Function ◽  
Topological Defects ◽  
Dynamics Simulation ◽  
Internal Stresses ◽  
Electrical Transport Properties ◽  
Tight Binding Approximation

Carbon nanotubes (CNTs) have been proved to have promising applicability in various fields of science and technology. Their fascinating mechanical, electrical, thermal, optical properties have caught the attention of today’s world. We have discussed here the great possibility of using CNTs in electronic devices. CNTs can be both metallic and semiconducting depending on their chirality. When two CNTs of different chirality are joined together via topological defects, they may acquire rectifying diode property. We have joined two tubes of different chiralities through circumferential Stone–Wales defects and calculated their density of states by nearest neighbor tight binding approximation. Transmission function is also calculated to analyze whether the junctions can be used as electronic devices. Different heterojunctions are modeled and analyzed in this study. Internal stresses in the heterojunctions are also calculated by molecular dynamics simulation.

Mechanism of Force Generation in Kinesin Motility

2007 ◽  
Author(s):  
Wonmuk Hwang ◽  
Matthew J. Lang
Keyword(s):  
Single Molecule ◽  
Forward Bias ◽  
Tight Binding ◽  
Basic Mechanism ◽  
Binding Pocket ◽  
Force Generation ◽  
Power Stroke ◽  
Additional Element ◽  
Dynamics Simulations ◽  
Motor Head

Conventional kinesin is a dimeric motor protein that uses adenosine triphosphate (ATP) to walk processively along the microtubule. Although its nucleotide dependent conformational switching and binding of the neck linker (NL) on the motor head are known to be key events in kinesin motility, the basic mechanism by which it amplifies a small conformational change upon ATP binding to generate the force of the walking stroke has not been known. We combined structural analysis with a set of molecular dynamics simulations to identify the 9-residue long N-terminal region, which we named the ‘cover strand’ (CS), as an additional element essential for kinesin’s power stroke. It operates by differentially forming a β-sheet with NL when ATP binds, whereby the ‘cover-neck bundle’ (CNB) has an inherent conformational bias that drives NL into its binding pocket on the motor head. After the initial stroke, the later half of NL, starting with the ‘asparagine latch’ in the middle, forms specific bonds with the motor head to ensure tight binding. We constructed the force map generated by CNB, which showed a forward bias in agreement with single molecule motility measurements. Our result is consistent with other experimental observations, including the estimated stall force and the transverse anisotropy. The novel mechanism of force generation by the dynamic folding of CNB appears to hold in various kinesin families, and elucidates the economy in the design principle of the smallest known processive motor.

Single Molecule Rectification Induced by the Asymmetry of a Single Frontier Orbital

2014 ◽  
Vol 10 (8) ◽  
pp. 3393-3400 ◽  
Author(s):  
Wendu Ding ◽  
Christian F. A. Negre ◽  
Leslie Vogt ◽  
Victor S. Batista
Keyword(s):  
Single Molecule ◽  
Frontier Orbital ◽  
The Asymmetry

Understanding Single-Molecule Parallel Circuits on the Basis of Frontier Orbital Theory

2020 ◽  
Vol 124 (5) ◽  
pp. 3322-3331 ◽  
Author(s):  
Kazuki Okazawa ◽  
Yuta Tsuji ◽  
Kazunari Yoshizawa
Keyword(s):  
Single Molecule ◽  
Frontier Orbital ◽  
Orbital Theory ◽  
Parallel Circuits

Different molecular enumeration influences in deep learning: an example using aqueous solubility

2020 ◽  
Author(s):  
Jen-Hao Chen ◽  
Yufeng Jane Tseng
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Single Molecule ◽  
Chemical Structure ◽  
Molecular Graph ◽  
Aqueous Solubility ◽  
Solubility Prediction ◽  
Input Line ◽  
Biological Phenomena ◽  
Feature Based

Abstract Aqueous solubility is the key property driving many chemical and biological phenomena and impacts experimental and computational attempts to assess those phenomena. Accurate prediction of solubility is essential and challenging, even with modern computational algorithms. Fingerprint-based, feature-based and molecular graph-based representations have all been used with different deep learning methods for aqueous solubility prediction. It has been clearly demonstrated that different molecular representations impact the model prediction and explainability. In this work, we reviewed different representations and also focused on using graph and line notations for modeling. In general, one canonical chemical structure is used to represent one molecule when computing its properties. We carefully examined the commonly used simplified molecular-input line-entry specification (SMILES) notation representing a single molecule and proposed to use the full enumerations in SMILES to achieve better accuracy. A convolutional neural network (CNN) was used. The full enumeration of SMILES can improve the presentation of a molecule and describe the molecule with all possible angles. This CNN model can be very robust when dealing with large datasets since no additional explicit chemistry knowledge is necessary to predict the solubility. Also, traditionally it is hard to use a neural network to explain the contribution of chemical substructures to a single property. We demonstrated the use of attention in the decoding network to detect the part of a molecule that is relevant to solubility, which can be used to explain the contribution from the CNN.

scholarly journals The role of quantum interference in determining transport properties of molecular bridges

2004 ◽  
Vol 2 (3) ◽  
pp. 524-533 ◽  
Author(s):  
Kamil Walczak
Keyword(s):  
Quantum Interference ◽  
Molecular System ◽  
Tight Binding ◽  
Transmission Function ◽  
Molecular Devices ◽  
Binding Model ◽  
Quantum Interference Effect ◽  
Current Voltage ◽  
Essential Question

AbstractAn analytical approach to the electron transport phenomena in molecular devices is presented. The analyzed devices are composed of various molecular bridges attached to two semi-infinite electrodes. Molecular system is described within the tight-binding model, while the coupling to the electrodes is analyzed through the use of Newns-Anderson chemisorption theory. The current-voltage (I-V) characteristics are calculated through the integration of transmission function in the standard Landauer formulation. The essential question of quantum interference effect of electron waves is diseussed in three aspects: (i) the geometry of a molecular bridge, (ii) the presence of an external magnetic field and (iii) the location of chemical substituent.

A tight-binding study of a 1-bit half-adder based on diode logic integrated inside a single molecule

2003 ◽  
Vol 14 (7) ◽  
pp. 722-732 ◽  
Author(s):  
R Stadler ◽  
S Ami ◽  
M Forshaw ◽  
C Joachim
Keyword(s):  
Single Molecule ◽  
Tight Binding ◽  
Binding Study ◽  
Half Adder

scholarly journals Predicting Finite-Bias Tunneling Current Properties from Zero-Bias Features: The Frontier Orbital Bias Dependence at an Exemplar Case of DNA Nucleotides in a Nanogap

Nanomaterials ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3021
Author(s):  
Ivana Djurišić ◽  
Vladimir P. Jovanović ◽  
Miloš S. Dražić ◽  
Aleksandar Ž. Tomović ◽  
Radomir Zikic
Keyword(s):  
Transport Properties ◽  
Single Molecule ◽  
Density Functional ◽  
Tunneling Current ◽  
High Sensitivity ◽  
Orbital Energy ◽  
Frontier Orbital ◽  
Zero Bias ◽  
Electronic Tunneling ◽  
Tunneling Transport

The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green’s functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.

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