Xing Yin

Length-Dependent Conductance of Molecular Wires and Contact Resistance in Metal-Molecule-Metal Junctions

Molecular wires are covalently bonded to gold electrodes--to form metal-molecule-metal junctions--by functionalizing each end with a -SH group. The conductance of a wide variety of molecular junctions is studied theoretically by using first-principles density functional theory (DFT) combined with the nonequilibrium Greens function (NEGF) formalism. Based on the chain-length-dependent conductance of the series of molecular wires, the attenuation factor beta is obtained and compared with the experimental data. The beta value is quantitatively correlated to the molecular HOMO-LUMO gap. Coupling between the metallic electrode and the molecular bridge plays an important role in electron transport. A contact resistance of 6.0+/-2.0 Kohms is obtained by extrapolating the molecular-bridge length to zero. This value is of the same magnitude as the quantum resistance.

Electronic transportation through asymmetrically substituted oligo(phenylene ethynylene)s: Studied by first principles nonequilibrium Green’s function formalism

Theoretical investigations of a series of asymmetrically substituted conducting molecular wires [oligo(phenylene ethynylene)s] have been carried out using density functional theory and nonequilibrium Greens function formalism. To get the molecular rectification, the electron-donating group (-NH2) and the electron-withdrawing group (-NO2) are placed on the different positions of the molecular wire. The dependences of spatial distribution and lowest unoccupied molecular orbital (LUMO) energy level on the applied voltage have been found playing dominating but opposite roles in controlling the rectification behavior. In the tested bias range, since the shift LUMO energy level is more important, the electrons transfer more easily from donor to acceptor through the molecular junction in general.

Theoretical investigation on molecular rectification on the basis of asymmetric substitution and proton transfer reaction.

A series of linear conjugated molecular wires (diphenylacetylene connected by double or triple bonds) asymmetrically substituted by various functional groups was investigated by using density functional theory combined with nonequilibrium Greens function method. The transportation behaviors of these models did not show obvious rectification, inferring that the simple asymmetric substitution of the conjugation chain was insufficient to improve the molecular rectification. We proposed that the molecular transportation can be modulated by proton transfer between the adjacent dissociable groups on the molecular wire. The theoretical calculations showed that the rectification ratio increased about six times at 1.0 V after proton transfer. This behavior was interpreted by means of transmission spectra and spatial distribution of molecular orbitals; the alignment of molecular orbitals to the Fermi level promoted by proton transfer is also responsible for the rectification.

Conformational analysis of diphenylacetylene under the influence of an external electric field

Theoretical investigation of the torsional potentials of a molecular wire, diphenylacetylene, was carried out at the B3LYP/6-311+G** level by considering the influence of the external electric field (EF). It demonstrates that many molecular features are sensitive to the EF applied. In particular, the torsional barrier increases and the LUMO-HOMO gap decreases with the increase of EF. Quantitative correlations between these features and the external EF were revealed. The current-voltage behavior corresponding to different conformers was studied as well by non-equilibrium Greens function method combined with the density functional theory. Further, the evolution of the LUMO-HOMO gap and the spatial distribution of molecular orbital were used to analyze these structure-property relationships.

Ultra-large Scale Molecular Dynamics Simulation for Nano-engineering

In light of the special need of nano-engineering, an ultra-large scale and high-performance molecular dynamics(MD) simulation program was implemented. In many nano-engineering processes, the free boundary condition should be adopted. To meet this particular requirement, a pointer link and dynamic array data structures were employed so that both reliability and accuracy of simulation could be ensured. Using this method, one could realize the MD simulation of the nano-engineering system consisting of several million atoms per single CPU.

Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.

The interface and surface effects of the bicrystal nanowires on their mechanical behaviors under uniaxial stretching

Using molecular dynamics simulations, we have investigated systematically the mechanical deformation of bicrystalline metallic nanowires with [110]∥[100], [111]∥[100], and [111]∥[110] interfaces. When the size of the nanowire is larger than 20×20×60 (units: cell), the effect from the grain boundary is dominant in breaking as compared with the nanowire surface effect. For [110]∥[100] bicrystal, breaking occurred easily at the interface with no clear structural deformation of the grain interior. When the [111] direction was addressed, the sliding most likely took place in [100] region for [111]∥[100] but in both regions for [111]∥[110], causing obvious elongation of the nanowire. By exploring the stress-strain property and the stress concentration along the tensile direction, we elucidated how the interfacial microstructure affected the mechanical behavior. Reducing the wire size, the effect from the nanowire surface gradually becomes more pronounced, showing a new breaking position from the grain boundary ...

The effect of oxygen heteroatoms on the single molecule conductance of saturated chains.

Single molecule conductance measurements on alkanedithiols and alkoxydithiols (dithiolated oligoethers) were performed using the STM-controlled break junction method in order to ascertain how the oxygen heteroatoms in saturated linear chains impact the molecular conductance. The experimental results show that the difference in conductance increases with chain length, over the range studied. Comparisons with electronic structure calculations and previous work on alkanes indicate that the conductance of the oligoethers is lower than that of alkane chains with the same length. Electronic structure calculations allow the difference in the conductance of these two families of molecules to be traced to differences in the spatial distribution of the molecular orbitals that contribute most to the conductance. A pathway analysis of the electronic coupling through the chain is used to explain how the difference in conductance between the alkane and oligoether molecules depends on the chain length.

Luminescence Quenching by Photoinduced Charge Transfer between Metal Complexes in Peptide Nucleic Acids

A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.

Theoretical analysis of the potential distribution and transportation behavior of the ordered alkyl monolayer-silicon junction.

A theoretical approach to the determination of the potential distribution within an organic monolayer sandwiched metal-insulator-semiconductor junction has been proposed with two simplified models, e.g. static (capacitance) model and dynamic (resistance) model. Compared with the resistance model, the capacitance model has been confirmed to be more valid for determining the potential distribution of the system. Further, the transportation behavior of the system has been simulated with a modified electron-tunneling model.