Molecular transport junction

Section 4 is entitled Ideas (for mechanisms and models). It deals with how we can interpret/calculate the behavior of molecular transport junctions utilizing particular model approaches and chemical mechanisms. It also discusses time parameters, and coherence/decoherence as well as pathways and structure/function relationships. 

Section 5 is on one particular molecule, p-benzene dithiol. This is one of the most commonly studied molecules in molecular electronic transport junctions [7] (although it is also one of the most problematic). Section 6 discusses a separate measurement, inelastic electron tunneling spectroscopy [8, 9] (IETS). This can be quite accurate because it can be done on single molecules at low temperatures. It occurs because of small perturbations on the coherent transport, but it can be very indicative of such issues as the geometrical arrangement in the molecular transport junction, and pathways for electron transport through the molecular structure. 

By definition, a molecular transport junction consists of a molecule extended between two macroscopic electrodes. The nature of the molecule, the environment (whether it is solvated or not), the electrode s shape and composition, the temperature, the binding of the molecule to the electrodes, and the applied field are all variables that are relevant to the measurement, which is usually one of differential conductance, defined as the derivative of the current with respect to voltage. 

Figure 1 shows two things a number of sketches of possible geometries for solid-state molecular transport junctions, and some electron microscopy images of actual functional transport junctions. There are two striking features to note first, the... 

Mesoscopic physics has defined many of the issues (Landauer limit transport [10, 11], Coulomb blockade regime [12], Kondo resonance regime [13-15]...) that will occur later in this chapter describing molecular transport junctions. These concepts are relevant, but must be reinterpreted to understand the molecular case. 

The categories just described compromise the majority of the measurements on molecular transport junctions. 

In general, however, many relevant geometric parameters are unknown in molecular transport junctions, and therefore it is necessary to make assumptions, and calculations, to help in understanding the geometry. One interesting approach is... 

Several categories of models appear as the basis for the study of molecular electronics in general, and molecular transport junctions in particular. These are the geometrical (or molecular), Hamiltonian, and transport analysis models. 

Then, there are model Hamiltonians. Effectively a model Hamiltonian includes only some effects, in order to focus on those effects. It is generally simpler than the true full Coulomb Hamiltonian, but is made that way to focus on a particular aspect, be it magnetization, Coulomb interaction, diffusion, phase transitions, etc. A good example is the set of model Hamiltonians used to describe the IETS experiment and (more generally) vibronic and vibrational effects in transport junctions. Special models are also used to deal with chirality in molecular transport junctions [42, 43], as well as optical excitation, Raman excitation [44], spin dynamics, and other aspects that go well beyond the simple transport phenomena associated with these systems. 

In molecular transport junctions, the Hamiltonian models are usually based on Kohn-Sham density functional theory [46—48]. They use relatively small basis sets because the calculations are sufficiently complicated, they take a number of empirical steps for dealing with the basis sets and their potential integrals, and they... 

Models are also required for analysis of the transport. For calculations of current/ voltage curves, current density, inelastic electron scattering, response to external electromagnetic fields, and control of transport by changes in geometry, one builds transport models. These are generally conceptual - more will be said below on the current density models and IETS models that are used to interpret those experiments within molecular transport junctions. 

In mesoscopic physics, because the geometries can be controlled so well, and because the measurements are very accurate, current under different conditions can be appropriately measured and calculated. The models used for mesoscopic transport are the so-called Landauer/Imry/Buttiker elastic scattering model for current, correlated electronic structure schemes to deal with Coulomb blockade limit and Kondo regime transport, and charging algorithms to characterize the effects of electron populations on the quantum dots. These are often based on capacitance analyses (this is a matter of thinking style - most chemists do not consider capacitances when discussing molecular transport junctions). 

The third set of models is for understanding the actual currents, and the pathways that the currents follow through molecular transport junctions. This is to some... 

Given the understanding that our description of molecular transport junctions is based on a description of the model that we build, we can proceed to some of the concepts that characterize the mechanistic behaviors. 

Molecular transport junctions differ from traditional chemical kinetics in that they are fundamentally electronic rather than nuclear - in chemical kinetics one talks about nucleophilic substitution reactions, isomerization processes, catalytic insertions, crystal forming, lattice changes - nearly always these are describing nuclear motion (although the electronic behavior underlies it). In general the areas of both electron transfer and electron transport focus directly on the charge motion arising from electrons, and are therefore intrinsically quantum mechanical. 

The simplest and most significant new idea in trying to understand molecular transport junctions comes from mesoscopic physics, and in particular from the... 

Lindsay SM, Ratner MA (2007) Molecular transport junctions clearing mists. Adv Mater 19(1) 23—31... 

Galperin M, Ratner MA, Nitzan A (2007) Molecular transport junctions vibrational effects. J Phys Condens Matter 19(10) 103201... 

Troisi A, Ratner MA (2006) Molecular transport junctions propensity rules for inelastic electron tunneling spectra. Nano Lett 6(8) 1784-1788... 

Maassen J, Zahid F, Guo H (2009) Effects of dephasing in molecular transport junctions using atomistic first principles. Phys Rev B 80(12) 125423... 

Reuter MG, Hansen T, Seideman T, Ratner MA (2009) Molecular transport junction with semiconductor electrodes analytical forms for one-dimensional self-energies J. Phys Chem A 113 4665... 

Galperin M, Nitzan A, Ratner MA (2007) Heat conduction in molecular transport junction. Phys Rev B 75 155312... 

Density of States and Transmission in Molecular Transport Junctions... 

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