www.sciencemag.org/cgi/content/full/science.1242603/DC1
Supplementary Materials for
Real-Space Identification of Intermolecular Bonding with Atomic Force
Microscopy
Jun Zhang, Pengcheng Chen, Bingkai Yuan, Wei Ji,* Zhihai Cheng,* Xiaohui Qiu*
*Corresponding author. E-mail: [email protected] (X.Q.); [email protected] (Z.C.); [email protected]
(W.J.)
Published 26 September 2013 on Science Express
DOI: 10.1126/science.1242603
This PDF file includes:
Materials and Methods
Figs. S1 to S9
Full Reference List
Materials and Methods
SPM system and qPlus sensor
All of the experiments were carried out in an UHV LT scanning probe microscope
(Omicron) with a Nanonis control system. The instrument is located on an active vibration
isolation table to further reduce the environmental influence. The qPlus AFM sensors used in
the experiments were homemade. In order to reduce the electrical cross-talk between current
and force signal, the electrochemically etched tungsten tips were glued on the tuning forks
using non-conducting epoxy and made the tips ground through a separate gold wire to the
corresponding electrode on the tip holder.
Sample and tip preparation
Cu(111) single crystals were cleaned by repeated cycles of sputtering and annealing.
Low coverage of 8-hydroxyquinoline (8-hq) were evaporated onto the Cu(111) substrate at
the SPM stage of ~ 5 K except those indicated. CO molecules were in situ evaporated onto
the Cu(111) substrate at LHe temperature. Some of the tips were sharpen by focused ion
beam before being transferred into the SPM system. In experiments, the tips were further
cleaned and shaped by a combination of bias pulses and controlled indentation into the Cu
substrate. CO-functionalized tips were prepared by picking up CO from Cu(111), and
confirmed by the protrusion appearance of other CO molecules in the following STM
images.
STM and AFM measurements
STM and AFM images were acquired at LHe temperature. The bias voltages referred
to the sample in both STM and AFM images. The STM images were recorded in
constant-current mode. The AFM images were recorded in constant-height frequency
modulation mode with the CO-functionalized tip (resonance frequency f 0 2.7 104 Hz ,
oscillation amplitude A 100 pm , quality factor Q 104 ). The tip height Δz was set with
respect to a reference height given by the STM set point above the bare Cu(111) substrate in
the vicinity of the molecules. The plus (minus) sign means the increase (decrease) of tip
height.
DFT calculations
The calculations were carried out using the general gradient approximation (GGA) for
the exchange-correlation potential (28), the projector augmented wave method (29, 30), and
a plane wave basis set as implemented in the Vienna ab-initio simulation package (30, 31).
Dispersion forces were considered at the DFT-D2 level where the RPBE functional (28) was
used together with Grimme’s 06 version of dispersion correction (32).
Four layers of Cu atoms, separated by a 20Å vacuum region, were employed to model
the Cu(111) surface. Molecules were put on one side of the slab with a dipole correction
applied. A 6×5 supercell was adopted to model an isolated molecule adsorbed on the surface
2
and an 8×8 one for molecular dimers and trimers. A 3×3×1 and a 1×1×1 k-meshes were
adopted to sample the 2-D surface Brillouin zones of the 8×8 supercell for total energy
calculation and geometry optimization, respectively. The energy cutoff for plane-wave basis
was set to 400 eV for geometry optimization and increased to 600 eV in total energy
calculations. In geometry optimizations, all atoms except those for the bottom two Cu layers
were fully relaxed until the residual force per atom was less than 0.02 eV/Å.
Structural models for the molecules or charge densities shown in Figs. 1, 3, 4, S2, and
S7 were fully relaxed, and four layers of Cu substrate were considered in the calculation.
Models for the molecular clusters shown in Fig. 2 and Fig. S3 were relaxed without the
substrate and all atoms were constrained in a plane.
Simulation of AFM image using Moll’s model
In Moll’s model (27), the Pauli repulsion energy was evaluated by the increase of
kinetic energy in a power law form of ΔEkinetic(R) = Aρsample(R)B, where A and B are two
fitting parameters that are chemical element-dependent. We employed this model in our
calculation and found that it slightly improved the simulated results (Fig. S6) for the H-bond
dimers in Fig. 3.
For the dehydrogenated clusters (Fig. 4A and B), the species are composed of five
elements, i.e. Cu, C, H, O, and N, therefore the simulation should include five sets of
parameters. However, the aforementioned method only allows one set to be used in the
calculation. We used the parameter set of C suggested in the literature. The simulation
results (Fig. S9) were not as good as those shown in Fig. 4, and we ascribed it to the distinct
parameters for Cu and C. These results indicate that a modified approach is needed when
several chemical species are involved.
3
Fig. S1
Large-scale STM images of 8-hq assembled clusters for the samples of 8-hq molecules
deposited on Cu(111) at LHe (a) and room temperature (b). Imaging parameters: (a) V=
-100 mV, I= 10 pA; (b) V= -1.0 V, I= 30 pA. Image size: 20 nm × 20 nm. Different
assembled clusters can be observed for sample of 8-hq molecules deposited on Cu(111) at
LHe temperature, while identical trimers and dimers can be observed for the sample of 8-hq
molecules deposited on Cu(111) at room temperature. Metal tips and CO-terminated tips
were both used for imaging. In all cases, we did not observed significant difference in the
image resolution.
4
Fig. S2
AFM measurements and DFT calculations of single 8-hydroxyquinoline (8-hq) on
Cu(111). (a-f) Constant-height AFM frequency shift images (V=0V, A=100pm) at different
tip heights. (a): Δz= +40 pm; (b): Δz= +30 pm; (c): Δz= +20 pm; (d) Δz= +10 pm; (e): Δz= 0
pm; (f): Δz= -10 pm. he size of all AFM images is 1.3 nm×1.0 nm. (g,h) DFT-calculated
adsorption models in top and side view. 8-hq is slightly tilted along its long axis (the ring
with N is a little higher than the ring with C–OH).
5
Fig. S3
STM and AFM images of 8-hq assembled clusters on Cu(111). Constant-current STM
topography images (a-e) and constant-height frequency shift images (f-j) of typical clusters,
and their corresponding structure models (k-o). Imaging parameters: STM, V= -100 mV, I=
100 pA; AFM, V=0 V, A=100 pm, Δz= +10 pm. Image size: (a) 2.3 nm × 2.0 nm, (b) 2.5 nm
× 1.8 nm, (c) 1.7 nm × 2.2 nm, (d) 1.7 nm × 2.2 nm, (e) 2.0 nm × 2.4 nm.
6
Fig. S4
AFM image and
spectroscopy measurements on 8-hq molecular clusters on
Cu(111). The
spectra across and along the hydrogen bonds were obtained using force
mapping. The line profiles across the hydrogen bonds clearly show that
increased above
the bonds with respect to the metal substrate for constant height imaging. Along the
hydrogen bond directions, the
spectra indicated that the threshold heights for entering
Pauli repulsion regime are correlated with the chemical characteristics of the atoms.
7
Fig. S5
Measurements of frequency shifts and apparent bond lengths of hydrogen bonding
between the 8-hq molecules. (a,c) Constant-height AFM images after sharpening filtering
of Fig. 2A and B. The line profiles used for Δf determination and the lines used for the
determination of the apparent bond lengths are indicated in (b,d). The values of the
frequency shift Δf and the apparent bond length L for indicated hydrogen bonds in (b): Δf1 =
-10.6(1) Hz, Δf2 = -11.0(2) Hz, Δf3 = -11.3(4) Hz, Δf4 = -11.4(3) Hz, Δf5 = -11.5(1) Hz, Δf6 =
-11.4(3) Hz, Δf7 = -11.0(0) Hz; L1 = 2.56(7) Å, L2 = 2.87(2) Å, L3 = 2.00(2) Å, L4 = 2.00(2)
Å, L5 = 2.30(6) Å, L6 = 1.92(5) Å, L7 = 2.56(2) Å. The values of the frequency shift Δf and
the apparent bond length L for indicated hydrogen bonds in (d): Δf1 = -11.2(4) Hz, Δf2 =
-11.2(5) Hz, Δf3 = -11.4(4) Hz, Δf4 = -11.2(2) Hz, Δf5 = -11.4(1) Hz, Δf6 = -11.3(2) Hz, Δf7 =
-11.2(0) Hz; L1 = 2.02(0) Å, L2 = 2.02(0) Å, L3 = 2.82(8) Å, L4 = 1.85(9) Å, L5 = 2.42(4) Å,
L6 = 2.30(3) Å, L7 = 2.46(5) Å.
8
Fig. S6
Experimental and simulated AFM images of 8-hq dimers on Cu(111). (a,b) Experimental
AFM images, (c,d) computed electron densities, and (e,f) simulations using Moll’s model. A
parameter set of A=692 eV and B=0.78 were adopted. The vertical distance between the N
atom of the dehydrogenated 8-hq and the O atom of the CO molecule is 3.0 Å.
9
Fig. S7
STM and AFM measurements and DFT calculations of dehydrogenated 8-hq on
Cu(111). Constant-current STM topographic image (a) and constant-height AFM frequency
shift image (b) of dehydrogenated 8-hq, and DFT-calculated structure model in top (c) and
side (d) view, and electron density map (e). Imaging parameters: STM, V= -30mV, I=100pA;
AFM, V=0 V, A=100 pm, Δz= -20 pm. Image size: 1.4 nm × 1.4 nm. The tip height Δz was
set with respect to a reference height given by the STM set point (-100 mV, 100 pA) above
the bare Cu(111) substrate.
The dehydrogenation reaction takes place at room temperature due to the thermal
excitations. At LHe temperature, the -OH group of 8-hq can also be dehydrogenated by a
voltage pulse of ~ 3V in the vicinity of 8-hq molecule. The STM and AFM measurements on
this dehydrogenated 8-hq radical indicated a molecular species with stronger tilting
configuration.
10
Fig. S8
STM and AFM measurements and DFT calculations of coordination complexes with
copper adatoms on Cu(111). (a,b) Constant-current STM images of dimer (a) and trimer (b).
Imaging parameters: dimer, V= -1.0 V, I=100 pA, 2.0 nm × 2.0 nm; trimer, V= -30 mV,
I=100 pA, 2.4 nm × 2.4 nm. (c-f) Electron density map of dimer (c) and trimer (d), and their
DFT-calculated structure model (e,f) in side view. The coordinate complexes are stable
during our measurements, which is difficult to be moved by the tip due to the strong
coordinate bonding within the complexes.
11
Fig. S9
Simulated AFM images of dehydrogenated 8-hq molecular clusters on Cu(111).
Simulations of dehydrogenated 8-hq (a,b) dimer and (c,d) trimer using Moll’s model. The
color scale of (b,d) was adjusted to show the intermolecular feathers more clearly. A
parameter set of A=692 eV and B=0.78 were adopted. The vertical distance between the N
atom of the dehydrogenated 8-hq and the O atom of the CO molecule is 3.0 Å.
12
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