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TRANSpull computes the electronic transport properties of single molecules attached to gold electrodes as they are mechanically elongated 1. The code first determines a minimum energy trajectory for the elongation using molecular mechanics and then computes the transport properties of all conformations encountered during pulling in the Landauer limit 2 using the extended Huckel Hamiltonian.
The pulling is performed using TINKER 4.2 3 and the MM3 force field 4. For this, the distance between two user defined end atoms in the molecule is increased sequentially and the geometry optimized at each step of the extension. For the transport aspects, it is necessary that the end atoms from which the pulling occurs are sulfurs.
The transport properties are computed using HUSKY 0.1. The molecule is attached to a small gold cluster pyramid at each end through thiol-Au bonds on top of the terminal gold atom of the cluster. The extended Huckel Hamiltonian of this metal-molecule-metal system is obtained and used to compute the elastic transmission coefficient using Green’s function 5. The Fermi energy of the electrodes is an adjustable parameter whose default value is set to -10.5 eV and should be chosen to lie in the HOMO-LUMO gap of the molecule.
TRANSpull outputs the pulling trajectory, the MM3 energy, the transmission at the Fermi energy and the HOMO LUMO levels as a function of the end to end distance. For selected configurations it also outputs the full transmission spectrum, the molecular orbitals, the density of states, the current versus voltage and its derivative.
As input it requires the molecular geometry in xyz or TINKER xyz format and specification of pulling and transport parameters.
1 Mechanically Activated Molecular Switch through Single-Molecule Pulling, Franco, I.; George, C. B.; Solomon, G. C.; Schatz, G. C.; Ratner, M. A., Journal of the American Chemical Society 2011, 133 (7), 2242-2249.
2 Quantum Transport: Atom to transistor, Datta S., Cambridge University press (2005)
3 TINKER: Software tools for molecular design 4.2, Ponder, J. Washington University School of Medicine: Saint Louis, MO, 2004.
4 Molecular mechanics. The MM3 force field for hydrocarbons. 1, Allinger, N. L.; Yuh, Y. H.; Lii, J. H. J. Am. Chem. Soc. 1989, 111, 8551–8566
5 Ghost transmission: How large basis sets can make electron transport calculations worse, Herrmann, C.; Solomon, G. C.; Subotnik, J. E.; Mujica V.; Ratner, M. A.; J. Chem. Phys. 132, 024103 (2010)
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