Japanese Journal of Applied Physics
Vol. 47, No. 7, 2008, pp. 6153–6155#2008 The Japan Society of Applied Physics

Scanning Tunneling Microscopy and Spectroscopy Studies of Glycine on Cuð100Þ:
Inelastic-Tunneling Manipulation of Single Glycine Molecule
Ken K ANAZAWA, Shoji YOSHIDA, Atsushi T ANINAKA, Keisuke N AKAMURA,
Osamu T AKEUCHI, and Hidemi S HIGEKAWA
Institute of Applied Physics, CREST-JST, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan(Received February 21, 2008; accepted April 17, 2008; published online July 18, 2008)

The chemical reaction of a glycine molecule on a Cuð100Þ surface from the neutral (NH2 CH2 COOH) to the glycinate(NH2 CH2 COO ) form via deprotonation, which had been analyzed on the basis of the results obtained by, for example,
vibrational spectroscopy and diﬀraction methods, was studied at the single-molecule level by scanning tunneling microscopy(STM) and spectroscopy. The chemical reaction was successfully reproduced by the inelastic tunneling process thoroughdeprotonation. The threshold bias voltage for the reaction process could be attributed to the energy of the O–H stretch
vibrational mode, and the asymmetric STM image after the reaction was in good agreement with the structure based on thepredicted model. [DOI: 10.1143/JJAP.47.6153]
KEYWORDS: scanning tunneling microscopy, glycine, single molecule, manipulation, Cu, amino-acid, inelastic electron tunneling

1.

Introduction(a)

The development of novel devices based on ultrasmall
molecular structures, which consist of functional molecules
such as biological molecules, is one of the most attractive
goals of current research. The glycine molecule is thesimplest amino acid with carboxyl and amino groups, which
are both common to all amino acids, and is one of thefundamental components of biological molecules such asproteins and peptides. Owing to the basic and practicalinterest in this material, self-assembled molecular structuresof glycine adsorbed on a Cu surface have been widelystudied.1–7) Recently, an anisotropic two-dimensional freeelectron-like electronic structure was realized for glycine ona Cuð100Þ surface, which has made this system furtherattractive.6)
Glycine molecules are evaporated in a neutral form
(NH2 CH2 COOH). When the substrate is maintained at room
temperature (RT), the hydrogen atom in the carboxyl groupis removed from the surface and glycine molecules areadsorbed in a glycinate form (NH2 CH2 COO ). Among theamino acids, glycine is the only molecule that does not havechirality, but enantiomeric isomers are observed on the Cu
surface depending on the directional relationship of the twogroups in the adsorbed form, as schematically shown in
Fig. 1. The adsorption properties of this system have been
expected to provide us with the basis for the understandingof, and a method of applying, the mechanism of the selfassembly of a polarized molecule with chirality. For furtheradvance, the control and analysis of individual single
molecules is of great importance.
Scanning tunneling microscopy (STM) is not only for
microscopic observation, but also a novel technique of
inducing chemical reactions on the atomic scale using
tunneling current, which may not be achieved in an ordinaryway, for example, the irradiation of light or electrons,
because of the diﬀraction limit. Although various processes
are included in chemical reactions, pinpoint manipulations
are realized through inelastic tunneling. Therefore, for thepurpose described above, STM has been extensively used
these last few decades.8–11)
In this study, we analyzed the inelastic-tunneling induced
chemical reaction of isolated glycine molecules adsorbed on(b)Fig. 1. (a) Molecular structure of glycine molecule. (b) Two conformations of adsorbed glycine molecule on a Cuð100Þ.

a Cuð100Þ surface by STM at 5 K. The structural transformation of the glycine molecule from its neutral form,
NH2 CH2 COOH, to a glycinate form, NH2 CH2 COO , wassuccessfully observed.
2.

Experimental

Sample preparation and STM measurements were performed under ultrahigh-vacuum conditions (base pressure <1  108 Pa). A clean Cuð100Þ surface was obtained after
several cycles of Arþ ion bombardment and annealing at820 K. After the glycine source was outgassed by heating theAl2 O3 crucible at 330 K for 5 hours, glycine molecules wereadsorbed on the substrate, where the source and Cu sample
temperatures were maintained at 370 and 5 K, respectively.
Then STM measurements were performed at 5 K using anelectrochemically sharpened tungsten tip ( ¼ 0:3 mm).
3.

Results and Discussion

Figure 2(a) shows a typical STM image of the isolated
glycine molecules adsorbed on a Cuð100Þ surface at 5 K.
Although molecules form the cð24Þ or pð24Þ periodic
structure on the Cu surface when they are adsorbed at room
temperature,7) molecules are individually observed in thiscase. Most of the molecules were imaged as an egglike
shape as shown by A and B, while a small number ofmolecules exhibited a bright round shape, as shown by C inFig. 2(a). The egglike spots had their long axis along oneof the four crystal axes, ½010, ½01 0, ½001, and ½001 ,6153

Jpn. J. Appl. Phys., Vol. 47, No. 7 (2008)(a)K. KANAZAWA et al.

(a)

(b)

(b)

(d)

(c)

YX

YA

Fig. 3. Schematic illustrations of a glycine molecule adsorbed on aCuð100Þ surface (a) before and (b) after the excitation treatment by STM.

AX

YA’X

A’(e)

B’B”

C’C’

Fig. 2. (a) STM topographic image obtained at 5 K. (b) STM image after
excitation of molecules A, B, and C in (a) by applying bias voltage(500 mV, 10 s). (c) Magniﬁed images of a glycine molecule before(upside) and after (downside) excitation. (d) Cross-sections along X–Y in(c). (e) Hopping and sliding of molecule B0 (to B00 ) due to excitation.
White dashed line is a mirror plane.

indicating the existence of a speciﬁc interaction of themolecules with the Cuð100Þ surface.
According to a vibrational spectroscopy study, when theCu substrate is kept a low temperature (<77 K), adsorbed
glycine molecules retain the structure of NH2 CH2 COOH,
while, with increasing substrate temperature, deprotonationfrom the carboxylic group is induced, resulting in theformation of the glycinate form, NH2 CH2 COO .1) Thischemical reaction is expected to have occurred in theprevious experiments on the formation of self-assembled
structures, where molecules were adsorbed at RT.7)
To study the transformation mechanism of the moleculeson the Cu surface, we performed the STM-induced manipulation of single glycine molecules. The STM tip was held
over the top of three molecules, A, B, and C, and they wereexcited by the tunneling current under the condition of asample bias voltage of þ500 mV applied for 10 s for eachmolecule. After this treatment, the three molecules changed
to the same shape, as shown by images A0 , B0 , and C0 in
Fig. 2(b), respectively. A slight positional change caused byhopping of the molecule induced by the application ofvoltage was observed in the procedure, as shown by B and B0in Figs. 2(a) and 2(b), respectively. Repetitions of thisprocedure induced changes in the molecular position or thedirection of it axis, namely, hopping or sliding, but nevercaused an opposite directional change in the shape, forexample, B0 to B. Figure 2(e) shows an example of thisexperiment. A second excitation was applied to B0 in
Fig. 2(b), resulting in the rotation and hopping of molecule
B0 to B00 , as shown by its positional and directional
relationship to C0 .
Two marked changes were observed in the molecular
images from Fig. 2(a) to Fig. 2(b). One is the change inthe shape of the molecule. An internal structure with anasymmetric shape is imaged after the treatment, as clearlyshown by the magniﬁed images in Fig. 2(c). This change inthe molecule generates chirality, as shown in the schematic
model in Fig. 1. The other characteristic is the lowering of
the topographic geometry. Cross sections obtained for theSTM images along the lines X–Y on molecules A and A0 inFig. 2(c) are shown in Fig. 2(d), where, the dotted line
represents the height obtained for a molecule in the cð24Þstructure.7)
Figure 3 shows schematic illustrations of a glycine
molecule adsorbed on the Cuð100Þ surface before andafter the excitation treatment by STM. Since the unreacted
molecule with hydrogen in the carboxylic group wasobserved as the achiral egglike shape directed along theh100i axis of the Cuð100Þ substrate, its possible structuralmodel is the bidentate structure produced by the binding of anitrogen atom of the amino group and an oxygen atom of thecarbonyl group (–C=O) with the substrate Cu atoms, as
shown in Fig. 3(a), where the hydroxyl group (–OH) is awayfrom the substrate. If the structural change of the molecule
induced by the treatment is deprotonation, the glycine
molecule has a ﬂat tridentate structure with the one nitrogenand two oxygen atoms in the molecule bonded to the top of
the Cu substrate atoms [Fig. 3(b)], then the height becomes
lower than the structure before the treatment, as wasobserved.
Here, the height of the glycine molecule in the cð24Þ
arrangement is between the heights observed for those
before and after the treatment. This result may indicate thatmolecules have a slightly standing conformation in thecð24Þ arrangement owing to the interaction between
molecules in the structure. For molecule C in Fig. 2(a), apossible adsorbed structure that produces the observed highgeometry is either a carboxylic or an amino group bound to a6154

Jpn. J. Appl. Phys., Vol. 47, No. 7 (2008)(a)Vs =+100 mV, It =1 nA

(c)

(b)

K. KANAZAWA et al.

deﬁned as the threshold, 427  4 mV. It is well known
that chemical reactions are induced by the excitation of
speciﬁc internal molecular vibrations in inelastic tunnelingprocesses. The threshold energy observed seems closer tothe value of the NH2 symmetric stretch vibrational mode
(3414 cm1 ¼ 423 meV) than the O–H stretch vibrationalmode (3566 cm1 ¼ 442 meV) of the glycine molecule.
However, since the chemical reaction process of a glycine
molecule on a Cuð100Þ surface is the transformation from theneutral (NH2 CH2 COOH) to the glycinate (NH2 CH2 COO )form due to deprotonation,1) the excitation of O–H vibrational mode is more probable. In fact, the energies of thevibrational modes are those calculated for a free moleculeand it was reported that the energy of the NH2 vibrationalmode decreased to 402 meV by the formation of a NH2 –Cubonding.1) Therefore a similar change of the O–H stretch
vibrational mode, 20 meV decrease in the energy due toadsorption on a Cu surface, may have an energy close to theobserved value.

Vs =+100 mV, It =2 nA

Vs =-100 mV, It =1 nAFig. 4. Typical I–V curves measured for a bare Cuð100Þ surface andisolated glycine molecules. Rapid change in the tunneling current
presents the chemical reaction due to protonation.

substrate Cu atom, with the other groups being away fromthe substrate.
To conﬁrm the mechanism of deprotonation in greater
detail, we analyzed the threshold for the reaction process bychanging the set point of the measurement. We placed theSTM tip just above the target molecules under various set
point conditions and measured current–voltage (I–V) curves
by changing the bias voltage from 0 to 0:8 V. Since such as
hopping and rotation of the molecule were excited by theapplied bias voltage lower than that for the deprotonation, it
was diﬃcult to determine the vibrational mode in ordinaryway. To achieve the chemical reaction, we swept the voltage
100 times faster (500 mV/s) than that for the ordinary IETS
measurement (5 mV/s).
Due to hopping and rotation of the molecule excited by
the applied bias voltage, the molecular position, therefore,
I–V curve measurement was not stable. However, when thechemical reaction was induced, the I–V curve showed asudden increase or decrease from the linear I–V line. In sucha case, we could conﬁrm the occurrence of deprotonation bySTM observation. Figure 4 shows typical I–V curves withsuch changes obtained under diﬀerent measurement conditions: (a) Vs ¼ þ100 mV, It ¼ 1 nA, (b) Vs ¼ þ100 mV,
It ¼ 2 nA, (c) Vs ¼ 100 mV, It ¼ 1 nA. The bias voltage
was increased at from 0 to þ0:8 V in (a) and (b), anddecreased from 0 to 0:8 V in (c). The voltage of thereaction for each set point was (a) 451  4, (b) 431  4,and (c) 427  4 mV, respectively, where the uncertainty of4 mV is the sweep step of the bias voltage. The values areclose to each other independent of the tunneling current andpolarity of the sample bias voltage, suggesting that thereaction is caused by an inelastic tunneling process.
Since it was diﬃcult to determine the exact value of thethreshold, measurements were performed several times at
each condition, and the lowest bias voltage among thosewhich produced sudden change as shown in Fig. 4 was4.

Conclusions

We observed adsorbed isolated glycine molecules on aCuð100Þ surface. The chemical reaction process of a glycine
molecule from the neutral (NH2 CH2 COOH) to the glycinate(NH2 CH2 COO ) form via deprotonation, which had been
analyzed on the basis of the results obtained by, for example,
vibrational spectroscopy and diﬀraction methods, wassuccessfully reproduced at a single-molecule level by theinelastic tunneling process induced by STM. The thresholdbias voltage for the reaction process could be attributed tothe O–H stretch vibrational mode, and the asymmetric STM
image after the reaction was in good agreement with thestructure based on the predicted model.
Acknowledgements
This work was supported in part by a Grant-in-Aid for
Scientiﬁc Research from the Ministry of Education, Culture,Sports, Science, and Technology of Japan. We thank Ms. Rie
Yamashita, in our group at the University of Tsukuba, for
her help in preparing this paper.

1) S. M. Barlow, K. J. Kitching, S. Haq, and N. V. Richardson: Surf. Sci.
401 (1998) 322.
2) V. Efstathiou and D. P. Woodruﬀ: Surf. Sci. 531 (2003) 304.
3) X. Zhao, H. Wang, R. G. Zhao, and W. S. Yang: Mater. Sci. Eng. C 16
(2001) 41.
4) K. Mae and Y. Morikawa: Surf. Sci. 553 (2004) L63.
5) R. B. Rankin and D. S. Sholl: J. Phys. Chem. B 109 (2005) 16764.
6) K. Kanazawa, Y. Sainoo, Y. Konishi, S. Yoshida, A. Taninaka,A. Okada, M. Berthe, N. Kobayashi, O. Takeuchi, and H. Shigekawa:J. Am. Chem. Soc. 129 (2007) 740.
7) K. Kanazawa, A. Taninaka, O. Takeuchi, and H. Shigekawa: Phys.
Rev. Lett. 99 (2007) 216102.
8) S.-W. Hla, L. Bartels, G. Meyer, and K.-H. Rieder: Phys. Rev. Lett. 85(2000) 2777.
9) W. Ho: J. Chem. Phys. 117 (2002) 11033, and references therein.
10) J. I. Pascual, N. Lorente, Z. Song, H. Conrad, and H.-P. Rust: Nature423 (2003) 525.
11) Y. Sainoo, Y. Kim, T. Okawa, T. Komeda, H. Shigekawa, andM. Kawai: Phys. Rev. Lett. 95 (2005) 246102.

6155