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Electronic Supplementary Material
Steric and electronic selectivity in the synthesis of Fe–
1,2,4,5-tetracyanobenzene (TCNB) complexes on Au(111):
From topological confinement to bond formation
Shawulienu Kezilebieke1, Anis Amokrane1, Mauro Boero1, Sylvain Clair2, Mathieu Abel2, and
Jean-Pierre Bucher1 ()
1
2
Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS UMR 7504, Université de Strasbourg, F-67034 Strasbourg, France
Université Aix-Marseille, IM2NP, CNRS UMR 7334, Campus de Saint-Jérôme, Case 142, F-13397 Marseille Cedex 20, France
Supporting information to DOI 10.1007/s12274-014-0450-y
1
Gas phase calculation
Calculations were performed by first-principles molecular dynamics [S1, S2] within the density functional
theory (DFT) formulation of quantum mechanics [S3]. The Becke’s exchange functional [S4] and the Lee–
Yang–Parr functional [S5] for the correlation (BLYP) was complemented with Grimme’s empirical van der
Waals corrections [S6]. Valence electrons were treated explicitly and expanded in a plane-wave basis set with an
energy cut-off of 70 Ry. The valence–core interaction was described in terms of norm-conserving pseudopotentials [S7, S8] with a semi-core stated included in the case of transition metals (Fe). Single-molecule
calculations were performed in an isolated supercell [S9]. The initial structure of Fe(TCNB)4 was generated with
the ChemSketch software [S10] using a TCNB geometry, relaxed within our computational set-up, as a template.
The system was placed in an isolated orthorhombic simulation cell of 30 × 30 × 20 Å3. To equilibrate and relax
efficiently the Fe(TCNB)4, an initial heating to 100 K was done, controlling the temperature via a Nose–Hoover
thermostat [S11, S12], then the system was cooled down to 5 K. All the calculations were done for the gas phase
molecules.
2
Calculation for the neutral TCNB molecule
The calculation was performed for a neutral TCNB molecule since neutrality has been observed experimentally
on Au(111). In contrast to other noble metal substrates, neutrality has also been observed for other molecules
with similar cyano-containing ligands adsorbed on Au(111), such as TCNQ, TCNE and 11,11,12,12-tetracyano-2,
6-naphthoquinodimethane (TNAP) [S13, S15, S16]. Figures S1(a) and S1(b) show the highest occupied
molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) calculated for the optimized
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ground state geometry of TCNB. The analysis of the molecular density of states (DOS) as obtained upon
diagonalization of the Kohn–Sham Hamiltonian is shown in Fig. S1(c). The HOMO was set at the Fermi level
(0 eV), while the LUMO is close to 3 eV. The LUMO main feature corresponds to the shoulder at 1.8 eV in the
dI/dV spectra of the TCNB layer on Au(111) and the calculated HOMO–LUMO gap is in good agreement with
the 3.3 eV gap measured by STS.
Figure S1 (a) HOMO and (b) LUMO for ground state of TCNB with isovalue 0.03 e·Å–3. (c) Density of states of TCNB molecule
obtained by gas phase calculation with, Ef = –7.86 eV.
Figure S2 dI/dV spectra taken above the TCNB monolayer, on the pristine Au(111) surface and on an isolated Fe atom on the Au(111)
surface. A HOMO–LUMO gap of about 3.3 eV is found, in agreement with the calculation (see Fig. S1).
3
Fe and TCNB supramolecular models on Au (111)
The structural models are based on the unit cell distances and angles measured in the STM images for both
the confined phase and the final complex phase. The unit cell of the Fe-4(TCNB) confined superstructure is
indicated in Fig. S3(a), by the b1 and b2 vectors and the angle β. The unit cell parameter are |b1|  |b2| = 1.4 ±
0.1 nm and β = 85°; the azimuthal angle θ between vectors a1 and b1 is 20°.
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Figure S3 Model structures for (a) Fe–4(TCNB) confined and (b) Fe(TCNB)4 complex monomer on Au(111).
In the model, we assume that metal centers reside on energetically favorable hollow sites of the Au(111)
surface. Four molecules arrange around one Fe atom with their benzene rings adsorbed mainly on bridge sites
of the substrate. The Fe–N bond length is 2.1 Å and the Fe–N–C bond angle is close to 120°. The substrate and
overlayer lattice vectors for a given azimuthal orientation θ are related through a transformation matrix [S17].
The confined Fe–4(TCNB) superstructure can then be expressed by the commensurate matrix (4, 2 / –4, 6).
Similarly, Fig. S3(b) shows the Fe(TCNB)4 complex superstructure on Au(111) where the Fe atoms are still
assumed to reside on the hollow sites of the substrate. Unit cell parameters from STM data are: |b1|  |b2| =
1.55 ± 0.1 nm, β = 90°, and θ = 15°. The Fe–N bond length is estimated to be 1.9 Å and the Fe–N–C bond angle
is 180°. The commensurate superstructure for the Fe(TCNB)4 complex can then be expressed by the matrix
(4, 2 / –5, 6).
Figure S4 Low coverage of TCNB on Au(111) seeded with Fe atoms and annealed at T = 150 K. As expected, no confinement is
observed for small submonolayer islands. Circles show fully relaxed Fe(TCNB)4 complexes that form at the edge of TCNB islands
(image 16 nm × 7 nm, I = 0.2 nA, V = 0.7 V).
4
Calculation for the Fe(TCNB)4 complex
Although the interaction between the metal–organic complexes and the substrate is an important issue in the
self-assembly process, the effect of the substrate is not taken into account explicitly here owing to the very
demanding calculation this would necessitate. From Table S1 it can be seen that the valence is unchanged upon
complex formation except for Fe, where a remarkable change from 0 to 2 occurs. The origin of this change is the
newly formed coordination of Fe with the four TCNB ligands. From the valence change, we see that the Fe
donates 2 electrons and formally becomes Fe2+.
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Table S1 Mulliken charge distribution and valence of the main sites of TCNB and Fe(TCNB)4, respectively before and after the
formation of the coordination bond
Element
Before
After
Mulliken
Valence
Mulliken
Valence
Fe
1.958
0
3.063
2.094
N
–0.095
2.897
–0.379
2.938
C
0.158
3.838
0.171
3.79
C
0.064
3.904
0.044
3.858
The charge transfer occurring between the Fe and the four neighboring N atoms is found to be close to 1|e|.
Table S1 shows the Mulliken charge and valence analysis of the system before and after the formation of the
Fe(TCNB)4 complex. The charge becomes rather delocalized and redistributed among all the TCNB ligands.
This is confirmed by a comparative analysis of the difference in the Mulliken charges of the N atoms next
nearest neighbors of the Fe ion; about –0.28 |e| per N atom.
Table S2
Equilibrium geometry parameters, before (TCNB molecule only) and after the formation of the Fe(TCNB)4 complex
Before
After
Mayer bond
Distance
Mayer bond
Distance
C–N
2.72
1.16
2.42
1.17
Fe–N
—
—
0.32–0.38
1.86
N–H
—
—
0.014–0.054
2.2–2.5
Table S2 shows the equilibrium geometrical parameters of Fe(TCNB)4 complex. The Fe–N distance is 1.86 Å
which corresponds to a typical coordination bond length. Table S2 also shows evidence for a N–H hydrogen
bond between adjacent TCNB moieties inside the Fe(TCNB)4 complex. This interaction confers stability on the
structure in a way similar to that evidenced in biomolecular systems [S14].
Figure S5 Spin density of the Fe(TCNB)4 complex. The green color indicates spins are up, while the red color indicates spin down
3
contributions with isovalue 0.005 e·Å . The spin density is well localized on specific regions of the Fe(TCNB)4, in particular, the spin-up
amplitude is localized on the Fe ion, whereas the spin-down amplitude is spread over the four TCNB ligands. Moreover, we notice that
the repartition of the spin-down component on the four ligands is characterized by a well-defined pattern covering just half of the TCNB
moiety, adding spin chirality to the original geometrical chirality evidenced experimentally. The spin distribution on top of the Fe center
has dz2 character as confirmed by projecting the Kohn–Sham orbitals onto atomic wavefunctions. More specifically, we see that the
HOMO levels are the ones contributing mainly to this dz2 orbital and, as a consequence, they do not participate to the planar bonds
Fe–N–R and account for the spin sign of the metal.
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