Supporting Information
Theoretical investigation on the chemical sensing of
metalloporphyrin-based molecular junction
Hongmei Liu,1 Zhong Xu,2 Nan Wang,1 Cui Yu,1 Nengyue Gao1, Jianwei Zhao, 1,a) and Ning Li2,b)
1Key
laboratory of Analytical Chemistry for Life Science (Ministry of Education), School of
Chemistry and Chemical Engineering, Nanjing University, Nanjing 210008, P. R. China
2School
of Chemical Engineering and Technology, Harbin Institute of Technology,
Harbin 150001, P. R. China
*Author
to whom correspondence should be addressed: a) zhaojw@nju.edu.cn, b)
lininghit@263.net
Content:
1. Schematic presentation of models
2. Potential energy surface of the complexes
3. The energy of different spin coupling and geometric features of the
complexes
4. The spatial distribution of some important orbitals obtained by HF
method.
5. The relaxed I-V curve of P-FeP-CO.
1
1. Schematic presentation of models
Figure S1. (a) Schematic illustration of the theoretical models for P-FeP-NO and
D-FeP-NO used in geometric optimization and current calculation by ATK program.
All the model molecules connect to two Au (111) surfaces via sulfur-linkers. (b) Top
view of the junction structure in periodic boundary condition and the red contour
indicates a unit cell.
2.
Potential energy surface of the complexes
2.1 The PES of FeP-XO
The potential energy surface (PES) scanning was performed as well for
comparing the flexibility of the adsorbed molecules around the stable position. The
calculations were performed using Gaussian 03 program, B3LYP functional and
6-31G* basis set.
2
The PES of FeP-XO is shown in Figure S2. As the Fe-X bond is scanned,
Fe-X-O is fixed to be 180. For different spin multiplicities of FeP-CO (Figure S2a),
the singlet state S=1 of FeP-CO is the most stable state with Fe-C bond of 1.7 Å. Then,
the Fe-X distance in FeP-XO was scanned for the lowest spin multiplicity, which is 1
(FeP-CO), 2(FeP-NO), and 1 (FeP-O2) as shown in Figure S2b. For FeP-NO and
FeP-O2, the Fe-N bond and Fe-O bond are 1.75 Å and 1.80 Å, respectively. Based on
the Fe-X bond, the PES of Fe-X-O is performed (Figure S2c). The Fe-C-O=180
in FeP-CO, Fe-N-O=140 in FeP-NO, and Fe-O-O=130 in FeP-O2. Finally, the
orientation of the N-O bond in FeP-NO was confirmed by the dihedral of O-O-Fe-O,
which is 45 as plotted in Figure S2d. Based on the structural information, further
Figure SI-1
structural optimization was performed.
200
a
FeP-CO
160
Relative energy/ kJ mol-1
Relative energy/ kJ mol -1
200
S=1
S=3
S=5
120
80
40
160
120
80
40
Fe-X distance/ angstrom
300
12
c
Relative energy/ kJ mol-1
Relative energy / kJ mol
-1
Fe-C distance/ angstrom
FeP-CO S=1
FeP-NO S=2
FeP-O2 S=1
200
100
0
80
120
140
160
Fe-X-O / degree
180
FeP-O2
10
d
S=1
8
6
4
2
0
100
b
0
1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0
0
1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0
400
FeP-CO S=1
FeP-NO S=2
FeP-O2 S=1
0
10 20 30 40 50 60 70 80 90
O-O-Fe-N dihedral/ degree
Figure S2. (a) The PES of Fe-C distance for FeP-CO complex with S=1, 3, and 5. (b) The PES of
Fe-C distance for FeP-XO complexes. (c) The PES of angle Fe-X-O for FeP-XO complexes. (d)
The PES of dihedral O-O-Fe-N for FeP-O2.
3
2.2 The PES of MnP-XO
The PES of MnP-XO that calculated by the same method for FeP-XO is shown
in Figure S3. For different spin multiplicities of MnP-CO as shown in Figure S3a, the
most stable state for MnP-CO is S=2 with Mn-C bond of 1.8 Å. Then, the Mn-X
distance in MnP-XO was scanned for the lowest spin multiplicity (Figure S3b). For
MnP-NO and MnP-O2, the Mn-N bond and Mn-O bond are 1.6 Å and 1.7 Å,
respectively. Based on the Mn-X bond, the PES of Mn-X-O is performed (Figure
S3c). The Mn-C-O=180 in MnP-CO, Mn-N-O=180 in MnP-NO, and
Mn-O-O=130 in MnP-O2. Based on the structural information, further structural
optimization was performed.
1.6
1.8
2.0
2.2
2.4
240
a
MnP-CO
S=2
S=4
S=6
2.6
-1
360
320
280
240
200
160
120
80
40
0
Relative energy / kJ mol
Relative energy / kJ mol
-1
Figure SI-2
200
Mn-C distance/ angstrom
MnP-CO S=2
MnP-NO S=1
MnP-O2 S=2
160
120
80
40
0
1.4
2.8
b
1.6
1.8
2.0
2.2
2.4
2.6
2.8
Mn-X distance/ angstrom
160
Relative energy / kJ mol
-1
MnP-CO S=2
MnP-NO S=1
MnP-O2 S=2
120
c
80
40
0
120
130
140
150
160
170
180
Mn-X-O / degree
Figure S3. (a) The PES of Mn-C distance for MnP-CO complex with S=2, 4, and 6. (b) The PES
of Mn-C distance for MnP-XO complexes. (c) The PES of angle Mn-X-O for MnP-XO
complexes.
4
3. Different spin coupling and geometric structures of the complexes
The molecular geometries of the FeP and MnP have been well-characterized.1
The FeP (S=3) and MnP (S=4) exhibit a perfect planar D4h symmetry. However, the
adsorption of diatomic atoms reduces the symmetry of FeP-XO and MnP-XO. The Fe
and Mn atoms deviate from the mean porphyrin plane for 0.2-0.3 Å. Table 1 and Table
2 present key optimized geometry parameters of model molecules. We obtained
end-on configurations for all the structures. As opposed to the high-spin ground state
of FeP and MnP, the complexes with CO, NO and O2 ligands exist a low-spin ground
state.2 For FeP-CO, MnP-CO and MnP-NO, the M-X (M=Fe, Mn) axis is
perpendicular to the mean porphyrin plane and the M-X-O=180.0. However, the
FeP-NO, FeP-O2 and MnP-O2 form bent structures, in which the projections of N-O
or O-O bonds lie along the bisector of Np-Fe-Np angle or Np-Mn-Np angle respectively.
The mechanism of forming the bent structure as the diatomic molecules bind to the
FeP and MnP has been studied in detail by Rovira et al.3 and Nguyen et al.4,5
Due to the bent structure, the NO and O2 molecules induce asymmetrical
distribution of the equatorial M-Np bond distances in FeP-NO, FeP-O2 and MnP-O2
(where Np denotes the porphyrin nitrogen). The shorter bonds always are on the same
side as the NO and O2 ligands, which are in agreement with the DFT study of FeP-NO
by Ghosh et al.6 The asymmetry is caused by the special bond of Fe-N, Fe-O, and
Mn-O. The Fe-N and Fe-O are titled by 0.27 in FeP-NO and 0.27 in FeP-O2, in
which Fe-N-O=124.0 and Fe-O-O=121.9. In the case of MnP-XO, only Mn-O is
titled by 1.12 to porphyrin plane with Mn-O-O=118.5. The calculated structural
5
parameters are in good agreement with experimental results.
Table 1：The energy of different spin multiplicities of FeP-XO and MnP-XO
complexes
Molecule
Fe(II)P
FeP-CO
FeP-NO
FeP-O2
Spin
multiplicity
Energy / hartree
Spin
multiplicity
Energy / hartree
S=1
-2251.48382534
S=2
-2138.80738505
S=3
S=5
-2251.52168561
-2251.47727339
S=4
S=6
-2138.85881961
-2138.83834360
S=1
S=3
S=5
-2364.83225570
-2364.81717144 MnP-CO
-2364.75814879
S=2
S=4
S=6
-2252.13572907
-2252.13503054
S=2
-2381.42259630
S=1
-2268.72953833
S=4
-2381.39125593 MnP-NO
S=3
-2268.68959055
S=6
-2831.39129640
S=5
-2268.61447189
S=1
S=3
S=5
-2401.79450792
-2401.79438409

S=2
S=4
S=6
-2289.12252710
Molecule
Mn(II)P
MnP-O2



*All calculations were performed with UX3LYP/6-31G (d) basis set. Some
configurations without stable chemical adsorptions are noted as ().
6
Table 2：Comparison of the optimized geometry structures of present work with
literature results for FeP-XO complexes.
molecule
Fe-Np/Å
Fe-X/Å
X-O/Å
Fe-X-O
d/Å
This work
FeP-CO
2.00
1.72
1.15
180.0
0.197
FeP-NO
2.00 / 2.01
1.89
1.18
124.0
0.184
FeP-O2
1.99 / 2.01
1.69
1.27
121.9
0.234
Theoretical result in literature3,7
FeP-CO
1.99
1.69
1.17
180.0
FeP-NO
2.01 / 2.03
1.69
1.19
150.0
FeP-O2
1.99 / 2.02
1.74
1.28
123.0
Experimental result in literature
FeP-CO8
2.02(3)
1.77 (2)
1.12 (2)
179 (2)
FeP-NO9
2.001(3)
1.717 (7)
1.122
(12)
149.2 (6)
FeP-O210
1.99(1)/1.9
7(1)
1.75 (2)
1.17 (4)
129 (2)
Table 3：The geometry structures of MnP-XO obtained in this work.
molecule
Mn-Np/Å
Mn-X/Å
X-O/Å
Mn-X-O/
d/Å
MnP-CO
2.02
1.74
1.16
180.0
0.213
MnP-NO
2.02
1.59
1.18
180.0
0.319
MnP-O2
2.01/ 2.02
1.90
1.27
118.5
0.189
a) X=C, N, and O.
b) Np denotes the porphyrin nitrogen.
c) d is the metal atom displacement from mean porphyrin plane.
7
4. The spatial distribution of some important orbitals obtained by
HF method.
To compare with the rusults of ab inio method and DFT method, we performed the
geometry optimizations for all the models HF method with basis set of 6-311+G(d,p)
basis set. Some important molecular orbitals obtained by the HF method with basis set
of 6-311+G(d,p) are shown in Figure S4. Both the DFT and HF methods give similar
spatial distributions of frontier molecular orbitals.
Figure S4. The spatial distribution of FeP-XO and MnP-XO complexes calculated by
HF method with 6-311+G (d,p) basis set.
8
5. The relaxed I-V curve of P-FeP-CO.
We optimized the geometry structures of the molecular junctions under zero bias,
but used a rigid model under bias. This is because the bias effect on the geometry and
electronic structures is minor in the bias region less than 1.0 V as demonstrated in our
previous work.11 In order to clarify the bias effect, we optimized the P-FeP-CO
molecular junction under the bias region of 0.0-0.5 V and recalculated the current. A
comparison of relaxed and frozen P-FeP-CO is shown in Figure S5. The results reveal
that the current of the relaxed system is similar with the frozen one, especially in the
low bias region. As the bias reaches to 0.5 V, the current only changes 5.6%.
Comparing with the current decrease induced by adsorption, and bias effect is weak.
Therefore, the electron transport results in the present study are reliable.
8
Current /A
P-FeP-CO
6
relax
frozen
4
2
0
0.0
0.1
0.2
0.3
0.4
0.5
Bias / V
Figure S5. The I-V curves of relaxed and frozen P-FeP-CO junction under applied
bias.
9
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