Methods
The electronic structure calculations of heterostructures designed by
deposition of porphyrin and iron-porphyrin atop of AGNR-11 (Figure 1),
the angle-dependent orientation of the porphyrin and the potential
energy surface of Fe-porphyrin migration atop AGNR-11 were performed
using Long-Corrected Generalized Gradient Approximation HSE
functional20 along with Gaussian-type basis
set21 (6-21G on hydrogen and 6-31G⁄ on carbon) and
Periodic Boundary Conditions (PBC LC GGA/HSE DFT) implemented in
Gaussian 09.22 To optimize AGNR-11 and calculate
energy profiles, 128 points in k-space for the Brillouin zone
integration scheme was used. The self-consistency threshold of
10-6 Hartree for the total energy was used during SCF
iterations. All geometries were optimized without symmetry restrictions
to avoid converging to higher energy solution wave functions imposed by
preliminarily determined symmetry restrictions.
In perpendicular to the main nanoribonn axis, the AGNR-11 contains 9
hexagonal carbon rings, which perfectly matches the dimension of
porphyrin molecule (Figure 1). To satisfy the dimension of the porphyrin
molecule and avoid any physical and chemical interactions between the
porphyrin molecules in neighbouring PBC images, the length of the
AGNR-11 supercell was chosen equal to 6 hexagonal carbon rings (Figure
1). In order to avoid dangling bonds and keep puresp 2 nature of all carbon-carbon connections,
the edge carbon atoms are passivated by hydrogen atoms.
To localize global and local minima, several initial configurations of
porphyrin and Fe-porphyrin were considered. In particular, four
different coordinations of porphyrin atop AGNR-11 (P/AGNR) were
considered: carbon atoms of AGNR are located under N-H bond of porphyrin
(O1), C-C bond of AGNR is located under N-H bond of porphyrin (O2),
carbon atom of AGNR is located under N atom of porphyrin (O3), and
carbon atoms of AGNR are located under N-H bond of porphyrin like (O1)
but turned at 450 around the normal to plane (O4)
(Figure S1). For FeP/AGNR heterostructures 3 different types of
rotational coordinations were considered: For the first coordination,
two Fe-N bonds were located above C-C bond of ARNG, another two were
located above C atoms (C1); In second coordination all Fe-N bonds were
located above C atoms(C2); And finally, the third coordination is
characterized geometrically like (C1) turned at 300around the normal direction (C2).
The standard notations for hexagon orientation were used
(ηx)23 to distinguish different mutual
coordination of Fe ion of FeP complex to the AGNR-11 substrate at the
migration pathway determination. In particular, 3 positions of FeP
relatively to AGNR-11 were set, namely η1,η2, η6, which correspond to coordination
of Fe ion atop of single carbon atom of AGNR, the centre of C-C bond and
centre of carbon hexagon, respectively.
Following reasonable assumption, the migration has no impact on details
of atomic structure of FeP complex, but do have the impact on the
distance between complex and AGNR in normal direction. The procedure of
the PES determination was consisted on restrained optimization of
constituting fragments (Fe-porphyrine and AGNR-11) only along z
direction on η1, η2, and
η6 pathways.