Protocol for classical molecular dynamics simulations of nano-junctions in solution

Abstract

Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite gold electrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite gold surfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the gold electrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.

Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions

“…Previously, the Gao, Luedtke and Landman approach 14 has been employed for the study of conned liquids and it has been demonstrated that such a setup is useful for analyzing nanotube-electrode nanojunctions. 15 In particular, the efficiency of the procedure for estimating the number of molecules within the junction in the presence of a nanotube has been stressed. In the present study we employ the same approach to investigate the structure and the dynamics of non-aqueous solvents, namely acetone, cyclohexane and N,N-dimethylformamide (DMF) in Au/CNT/Au junctions.…”

“…This geometry is convenient for our device setup. 15 In fact the presence of the nanotube xes the distance between the two electrodes and therefore the size of the cell in the direction of the nanotube, so that a barostat-type optimization is impossible. We use electrodes with periodic boundary conditions in the x-direction only to reduce the complexity of adjusting the solvent's density for a given pressure by varying the volume.…”

“…We use electrodes with periodic boundary conditions in the x-direction only to reduce the complexity of adjusting the solvent's density for a given pressure by varying the volume. 15 We now investigate the structure and the dynamics of Au/CNT/Au nanojunctions immersed in different liquid solvents. In particular the properties of the nanoconned solvents are compared to those obtained under the simple connement provided by two Au electrodes only, i.e., in the absence of the nanotube.…”