Towards reality in modeling of molecule-electrode contacts
Graduate School of Energy, Environment, Water, and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
Molecule-electrode contacts are the critical factor that determines the characteristics of molecular electronic devices, but their atomic-scale understanding and controlling still remains elusive. In this talk, I will present several recent works within our group that are concerned with the molecule-electrode contacts. First, focusing on the ubiquitous S-Au contacts in molecular electronics, I will discuss how the single-molecule conductance is correlated with the S-Au linkage coordination number (CN). Ab initio molecular dynamics (MD) simulations show that CN three that is stable in vacuum becomes destabilized upon solvation and spontaneously converts into CN two, which will reduce the number of multiple conductance peaks robustly observed across different experimental platforms. It will be shown that our popular force fields (FFs) optimized for self-assembled monolayers  fail to give the correct CN-dependent conductance ordering for single-molecule junctions, and an improved FF parameterization will be presented.
In the second part, I will consider the DNA sequencing based on low-dimensional carbon nanoelectrodes. Controlling the dynamics of DNA translocation is again a central issue in the emerging solid-state DNA sequencing approach . Performing large-scale FF molecular dynamics simulations, I will show that the N doping of carbon nanoelectrdoes not only increases the sensitivity and selectivity for tunneling-current nucleobase reading  but also benefits the control of DNA conformations by slowing down the translocation speed and reducing structural fluctuations of nucleobases.
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