Smeagol

• Developed in Trinity College Dublin in
collaboration with groups from
Oviedo in Spain and Lancaster in the UK
• Based on the DFT code SIESTA
• Smeagol: Rocha et. al., PRB 73,
085414 (2006);
Nature Materials 4, 335, (2005).
• SIESTA: Sanchez­Portal et. al.,
Int. J. Quant. Chem., 65, 453 (1997);
Soler et. al., Jour. Phys.: Condens. Matter,
14, 2745 (2002).
Non­Equilibrium Electronic Transport
gDFTB
• Developed in University of Rome
Tor Vergata
• Based on DFTB – DFT based tight­binding
• gDFTB: A. Pecchia and A. di Carlo, Rep.
Prog. Phys. 67, 1497, (2004).
• DFTB: D. Porezag, Th. Frauenheim,
Th. Kohler, G. Seifert, and R. Kaschner,
Phys. Rev. B 51, 12947, (1995).

DFT DOS Results for PTCDA
• DOS for PTCDA flat on Ag surface with periodic boundary conditions in each direction.
• Tip­surface distance is 5.0 Angstrom.
• Silver described by 4d5s basis set.

DFT DOS Results for PTCDA
• DOS for PTCDA peeled up from Ag surface (tip – surface separation is 12 Angstrom)
with periodic boundary conditions in each direction.

DFT DOS Results for PTCDA
• DOS showing change in molecular orbitals (carbon pi orbitals) as molecule is peeled
off silver surface.
• As the molecule is peeled up, the molecular orbitals increase in energy, shifting
upwards towards the Fermi level of the substrate.

Transmission Results for PTCDA from gDFTB
• Transmission coefficients for PTCDA on Ag surface from gDFTB.
• Resonance due to LUMO of molecule starts out 1eV below Fermi level, and then
moves up due to the reverse chemisorption effect.

Transmission Results for PTCDA from Smeagol
• Transmission coefficients for PTCDA on Ag surface from Smeagol.
• Similar to the gDFTB results, the resonance due to LUMO of molecule starts out
1eV below Fermi level, and then moves up due to the reverse chemisorption effect.

Local DOS at Transmission Resonances
HOMO
LUMO LUMO + 1
• Density of states isosurface for PTCDA flat on Ag surface in energy windows around
transmission resonances.
• Transmission resonances mostly correspond to pi orbitals on C and O atoms.

DOS on Oxygen atoms
• HOMO and LUMO of PTCDA includes pi orbitals on carboxylic atoms but not on
anhydride atoms – also apparent from local DOS on previous slide.

Comparison of gDFTB and Smeagol Results
• Transmission coefficients for PTCDA flat on Ag surface ­ comparison between gDFTB
and Smeagol results.
• Methods match well below Fermi level, not so well above Fermi level – may be due
to problems with DFT and unoccupied states. Also, sharp peak in transmission at Fermi
level does not appear to be present in the Smeagol results.

DOS of STM Tip from DFTB
5 Ang separation 12 Ang separation
• DOS for atoms in pyramid
representing STM tip.
• Spike in DOS in pyramid is
present for all tip positions.
• This may be responsible for spike
in transmission in gDFTB results.

DOS of STM Tip from SIESTA
• DOS for four silver atoms in pyramid representing STM tip.
• DOS due to d orbitals is far from Fermi level.
• Small peak near Fermi level due s orbital on atom at end of tip.

DOS of STM Tip
• Density of states isosurface for orbitals in energy region indicated by orange lines.
• Orbitals at this energy localized around tip and surface.
• Also some states present on molecule in this energy region.

Conductance as a Function of Tip Position
gDFTB Current
Smeagol Conductance
Experiment: Nanotechnology 19, 065401, (2008)
• Conductance at Fermi level for PTCDA on Ag surface from Smeagol.
• Large difference between experimental and computational results: in experiment,
conductance increases rapidly to a maximum and then falls off. In computational
results, conductance falls at first and then increases.

Conductance as a Function of Tip Position
• Comparison between low bias conductance for experimental results and results
from both Smeagol and gDFTB.
• Order of magnitude of maximum is similar for all results, however maximum for
experimental result is at minimum of theory results.

3 Layer
5 Layer PBC
• PRB 76, 115421, (2007)
DFT DOS Results for PTCDA
• DOS for carbon pz orbitals (z is direction perpendicular to surface) for PTCDA on 3
and 5 layers of silver. The STM tip and periodic boundary conditions in the z direction are
present for the 5 layer system.
• The calculations described in PRB 76, 115421 were done with 3 silver layers, and the
DOS for PTCDA on 3 layers most closely resembles the results present in that paper.

5 Layer PBC
• PRB 76, 115421, (2007)
DFT DOS Results for PTCDA
• DOS for carbon pz orbitals (z is direction perpendicular to surface) for PTCDA on 5 layers
of silver with periodic boundary conditions.
• LDA calculations predict a geometrical configuration where the molecule is 0.2 to 0.3
Angstroms closer to the surface than is seen in experiment.
• Altering the position of the molecule by this distance has a large effect on the DOS