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The authors would like to thank S. Aoki, S. Hartnoll, I. Kanamori,
H. Kawai, E. Poppitz, A. Schäfer, S. Shenker, L. Susskind,
M. Tezuka, A. Ueda, and M. Ünsal for discussions and comments.
M.H. is supported by the Hakubi Center for Advanced Research,
Kyoto University and by the National Science Foundation
under grant no. PHYS-1066293. M.H. and Y.H. are partially
supported by the Ministry of Education, Science, Sports and
Culture, Grant-in-Aid for Young Scientists (B), 25800163, 2013
(M.H.); 19740141, 2007 (Y.H.); and 24740140, 2012 (Y.H.).
The work of J.N. was supported in part by Grant-in-Aid for
Scientific Research (nos. 20540286 and 23244057) from the
Japan Society for the Promotion of Science. Computations
were carried out on PC cluster systems in KEK and the Osaka
University Cybermedia Center (the latter being provided by
the High Performance Computing Infrastructure System
Research Project, project ID: hp120162). All the data obtained
in the present work are presented in table S1 of the
Materials and Methods
23 December 2013; accepted 31 March 2014
Published online 17 April 2014;
Real-space imaging of molecular
structure and chemical bonding by
single-molecule inelastic tunneling probe
Chi-lun Chiang,1 Chen Xu,1 Zhumin Han,1 W. Ho1,2†
The arrangement of atoms and bonds in a molecule influences its physical and
chemical properties. The scanning tunneling microscope can provide electronic and
vibrational signatures of single molecules. However, these signatures do not relate
simply to the molecular structure and bonding. We constructed an inelastic
tunneling probe based on the scanning tunneling microscope to sense the local
potential energy landscape of an adsorbed molecule with a carbon monoxide
(CO)–terminated tip. The skeletal structure and bonding of the molecule are revealed
from imaging the spatial variations of a CO vibration as the CO-terminated tip
probes the core of the interactions between adjacent atoms. An application of the
inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers
in intramolecular and extramolecular bonding.
The achievement of a mechanistic under- standing of chemical and biological func- tions depends on knowing the geometric structure and the nature of the bonds in the molecules. Consequently, a number of
techniques have been extensively developed to
attain this knowledge, including x-ray diffrac-
tion, electron diffraction, and nuclear magnetic
resonance. These techniques, however, do not
provide a direct view of the molecules in real
space. Nonetheless, they have yielded three-
dimensional structures of many complex mol-
ecules that enabled the elucidation of their
chemical and biological properties. Only recently
has the atomic force microscope (AFM) been
used to obtain real-space images of the molecular
structures of mostly planar molecules (1, 2). The
AFM approach allows structural imaging that
can discriminate a reactant and its different pro-
ducts (3) or reveal hydrogen bonding between
The high spatial resolution of the AFM was
obtained by functionalizing the tip with a CO
molecule (5, 6) and measuring the shift in the
resonance frequency of the quartz tuning fork
above the adsorbed molecule (7). The spatial resolution arises from variations of the force gradient
sensed by the CO-tip as it scans over different
parts of the molecule. The observed contrast revealing the molecular structure implies that the
frequency shift is different over the atoms and
the bonds between them, relative to elsewhere.
The range of frequency shift is few Hz from the
resonance of 20 to 30 kHz.
In comparison, the scanning tunneling mi-
croscope (STM) has been shown to reveal the
electronic properties of the sample. Good agree-
ments have been obtained between theory and
experiment for the molecular orbitals in describ-
ing the spatial distributions for the electron den-
sity (8–10) and spin excitation (11). These images
reflect the electron wave functions that are re-
lated to (but do not directly display) the mo-
lecular structures. By trapping a hydrogen molecule
in the STM junction or transferring a Xe, CO,
or CH4 molecule to the tip, molecular structure
could be resolved from the topographic and dif-
ferential conductance images, and intermolec-
ular bonds were revealed (12–14).
Here, we demonstrate an approach based on
the STM to image the skeletal structure and
bonding in an adsorbed molecule by single-molecule inelastic tunneling probe (itProbe). A
CO molecule is transferred to the tip, and a vibrational mode of the tip CO senses the bonding
between two atoms in an adsorbed molecule.
As the CO-terminated tip is scanned over the
molecule during imaging, changes in the energy and intensity of the hindered translational vibration of CO are measured by inelastic
electron tunneling spectroscopy (IETS) with
the STM (15). This low-energy CO vibration
senses the spatially varying potential energy
landscape of the molecule and its surroundings.
The range of energy shift is on the order of the
vibrational energy of ~3 meV, or equivalently
All of the experiments were performed in
ultrahigh vacuum (5 × 10−11 torr); the spectra
reported were taken at a sample and STM temperature of 600 mK (16). A topographic image
taken with a bare Ag tip of cobalt phthalocyanine
(CoPc) coadsorbed with CO on Ag(110) is shown
in Fig. 1A. Adsorption configurations, labeled
CoPc(×) and CoPc(+), are possible on the surface.
Each CO molecule is identified by its hindered
translational (2.8 meV) and rotational (18.3 and
20.3 meV) modes in the vibrational spectra by
STM-IETS (Fig. 1B). The nondegenerate hindered rotation in the two orthogonal directions
parallel to the Ag(110) surface is resolved as a
peak splitting. The same area imaged after
1Department of Physics and Astronomy, University of
California, Irvine, CA 92697, USA. 2Department of Chemistry,
University of California, Irvine, CA 92697, USA.
*These authors contributed equally to this work. †Corresponding
author. E-mail: email@example.com