Conformational Switching of Verdazyl Radicals on Au(111)

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Received: July 15, 2019; Revised: August 19, 2019; Accepted: August 22, 2019; Published online: August 30, 2019. *Corresponding authors. Emails: [email protected] (K.W.); [email protected] (J.P.). Tel.: +86-10-62754005 (K.W.).
The project was supported by the National Natural Science Foundation of China (21821004) and the Ministry of Science and Technology of China
(2017YFA0204702).
(21821004)(2017YFA0204702)

Conformational Switching of Verdazyl Radicals on Au(111)
Zhichao Huang, Yazhong Dai, Xiaojie Wen, Dan Liu, Yuxuan Lin, Zhen Xu, Jian Pei *, Kai Wu *
Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry and Molecular Engineering, Peking University,
Beijing 100871, P. R. China.
Abstract: Pure organic radical molecules on metal surfaces are of
great significance in exploration of the electron spin behavior.
However, only a few of them are investigated in surface studies due to
their poor thermal stability. The adsorption and conformational
switching of two verdazyl radical molecules, namely, 1,5-biisopropyl-3-
(benzo[b]benzo[4,5]thieno[2,3-d]thiophen-2-yl)-6-oxoverdazyl (B2P)
and 1,5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2,3-d]thiophen-4-yl)-
6-oxoverdazyl (B4P), are studied by scanning tunneling microscopy
(STM) and density functional theory (DFT). The adsorbed B2P
molecules on Au(111) form dimers, trimers and tetramers without any
ordered assembly structure in which two distinct appearances of B2P
in STM images are observed and assigned to be its “P” and “T” conformations. The “P” conformation molecules appear in
the STM image with a large elliptical protrusion and two small ones of equal size, while the “T” ones appear with a large
protrusion and two small ones of different size. Likewise, the B4P molecules on Au(111) form dimers at low coverage, strip
structure at medium coverage and assembled structure at high coverage which also consists of above-mentioned two
conformations. Both B2P molecules and B4P molecules are held together by weak intermolecular interaction rather than
chemical bond. STM tip induced conformational switching of both verdayzl radicals is observed at the bias voltage of +2.0
V. The “T” conformation of B2P can be switched to the “P” while the “P” conformation of B4P can be switched to the “T”
one. For both molecules, such a conformational switching is irreversible. The DFT calculations with Perdew-Burke-
Ernzerhof version exchange-correlation functional are used to optimize the model structure and simulate the STM images.
STM images of several possible molecular conformations with different isopropyl orientation and different tilt angle between
verdazyl radical and Au(111) surface are simulated. For conformations with different isopropyl orientation, the STM
simulated images are similar, while different tilt angles of verdazyl radical lead to significantly different STM simulated
images. Combined STM experiments and DFT simulations reveal that the conformational switching originates from the
change of tilting angle between the verdazyl radical and Au(111) surface. The tilt angles in “P” and “T” conformations are
0° and 50°, respectively. In this study, two different adsorption conformations of verdazyl radicals on the Au(111) surface
are presented and their exact adsorption structures are identified. This study provides a possible way to study the
relationship between the electron spin and configuration conversion of pure organic radical molecules and a reference for
designing more conformational switchable radical molecules that can be employed as interesting molecular switches.
Key Words: Verdazyl radical; Scanning tunneling microscopy; Density functional theory; Electron spin
Acta Phys. -Chim. Sin. 2020, 36 (1), 1907043 (2 of 6)
Au(111) Verdazyl
** 100871
(STM)(DFT)1,5--3-([b][4,5][2,3-
d] -2- )-6-oxoverdazyl (B2P )1,5- -3-( [b] [4,5] [2,3-d] -4- )-6-
oxoverdazyl(B4P)Au(111)B2PAu(111)
Au(111)B4PSTM
“P”“T”+2.0 VB2PB4P
STMDFTverdazylAu(111)
O647
1 Introduction Exploration of magnetic molecules on metal surfaces is of
great importance in understanding the molecular spin properties
including spin interaction. Scanning tunneling microscopy
(STM) is one of the most popular and powerful tools in surface
spin research due to its capability of measuring the Kondo effect 1
and its ultrahigh spatial resolution in real-space. The magnetic
molecules employed in STM measurements are abundant 2,
including single molecule magnets containing transition metals 3,4,
phthalocyanines 5–8, porphyrins 9, and pure organic radical
molecules 10. Pure organic radical molecules have been
extensively studied in organic chemistry. However, owing to
their poor thermal stability, only a few of them are practically
applied in surface studies. The first observation of the Kondo
resonance for a stable neutral pure organic radical is 1,3,5-
Triphenyl-6-oxoverdazyl adsorbed on Au(111) 11. Moreover,
organic molecules containing the radical nitronyl-nitroxide side
group also exhibit the Kondo resonance on metal surfaces 10,12,13.
In recent years, people have adopted in situ pulse-induced
method to create free radical molecules on surface 14. These
created new organic radical molecules on surface well serve as
the models for systematical studies to understand the spin-spin
interactions.
using STM and density functional theory (DFT). The molecular
structures of these two molecules, namely, 1,5-biisopropyl-3-
(benzo[b]benzo[4,5]thieno[2,3-d]thiophen-2-yl)-6-oxoverdazyl
(B2P) and 1,5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2,3-
d]thiophen-4-yl)-6-oxoverdazyl (B4P), are showed in Fig. 1a, b,
respectively. The thiophene protecting group (termed BTBT)
and eight-electron-conjugated six-membered ring 15 in B2P or
B4P lead to high thermal stability of the radicals which are
suitable for surface study. Both B2P and B4P remained intact
when evaporated on Au(111). More interestingly, they formed
two similar conformations named as “P” and “T”. In the “P”
conformation, the angle between the BTBT and verdazyl radical
ring is near 0°. In the “T” conformation, however, the angle is
about 50°. The “T” conformation of B2P could be switched to
“P” by tip induction at the bias of +2.0 V, while the “P”
conformation of B4P could be switched to “T” under similar
condition. Conformational switching of neutral pure organic
radicals has hardly been reported in surface science, which offers
the opportunity to explore the switching properties of spin
carriers.
2 Experimental and calculation methods Sample preparation and data acquisition were performed on
commercial STM (Unisoku USM-1300, Japan) working under
ultrahigh vacuum (UHV) conditions. The Au(111) single crystal
was purchased (MaTeck, 99.999% in purity, Germany), and
cleaned and ordered by several cycles of Ar+ bombardment (1.5
keV, 10 A, 10 min) followed by annealing(~750 K, 15 min).
The B2P and B4P molecules were synthesized in one of our
laboratories (JP group), and evaporated onto the single crystal
from a home-made Ta boat. The evaporation rate was monitored
by an SQM-160 quartz balance. The Au (111) substrate was kept
at room temperature (about 298 K) during the evaporation
process. All STM images were acquired at 4.2 K with a
Fig. 1 Molecular structures of (a) B2P and (b) B4P.
background pressure below 2 × 10−10 mbar (1 mbar =100 Pa).
The tip was simply prepared by cutting of a commercial Pt-Ir
wire.
The STM image simulation was performed with the CASTEP
module 16 in the Materials Studio software. A (6 × 6) supercell
with 3 layers in thickness was used to simulate the Au(111)
substrate. Periodic boundary conditions were used in the
calculations. The DFT with Perdew-Burke-Ernzerhof (PBE) 17
version of the generalized gradient approximation (GGA) for the
exchange-correlation functional was employed to optimize the
structure and simulate the STM images of the molecules on
Au(111).
3 Results and discussion Fig. 2a shows a typical STM topographic image of the B2P
molecules adsorbed on Au(111). The B2P molecules are
randomly dispersed on the Au(111) surface and form monomer,
dimer, trimer and tetramer. A close-up of the B2P monomer is
given in Fig. 2b. Based on the dimension of the B2P molecule,
the elliptical large bright and two small round protrusions are
attributed to be the BTBT protecting group and the verdazyl
radical ring, respectively. With the assignment of the single B2P
molecule in the STM image, its dimer, trimer and tetramer are
correspondingly depicted in Fig. 2c through 2e.
To verify the interaction in multimers, STM tip manipulation
was applied to the B2P dimer. The experimental results showed
that the B2P trimer could be feasibly separated into one
monomer and one dimer, demonstrating that the B2P molecules
are actually held together by weak intermolecular interaction
rather than chemical bond. For most B2P molecules scrutinized
in this work, the monomer exhibited two conformations, namely,
the “T” and “P” ones. The former appeared in the STM image
with a large elliptical protrusion and two small ones of different
size, while the latter appeared with a large protrusion and two
small ones of equal size.
Interestingly, the “T” conformation of B2P can be switched to
the “P” one by the tip disturbance. As shown in Fig. 3a, b, the
STM images of B2P before the switching are nearly identical at
the bias of +0.5 V and +1.5 V, demonstrating the same
conformation at both biases. When the scanning bias changes to
+2.0 V, the “T” conformation turns into the “P” one, as shown in
Fig. 3c. Subsequent STM images of the B2P molecule at biases
of +2.0 V and +0.5 V confirm the successful conformational
switching from “T” to “P”, as pictorially shown in Fig. 3d and e,
respectively. However, the switch from the “P” conformation
cannot be switched back to the “T” one at all biases tried
experimentally.
adsorbed B4P molecules on Au(111) were also investigated by
STM. As shown in Fig. 4, B4P can form various structures at
different coverages. The topographic STM images of the B4P
molecules at low, medium and high coverages are
correspondingly shown in Fig. 4a, b and c. At low coverage,
most B4Ps exist in dimers and adsorb at the elbow sites on
Au(111). The high-resolution STM image and proposed model
of the dimer are given in Fig. 4d where the verdazyl radical in
one B4P faces toward that in the other. At medium coverage, the
dimers tend to assemble into a strip structure while some B4Ps
form a trimer-like structure, as shown in Fig. 4e. At high
coverage, the B4Ps form an assembled structure. The basic unit
in this structure is marked by the blue circle in Fig. 4f which
consists of one B4P molecule. In Fig. 4f, a unit cell (a = 1.4 nm,
Fig. 2 STM topography of B2P molecules on Au(111).
(a) Large scale STM image of the B2P molecules on Au(111);
(b) B2P monomer with its molecular structure superimposed;
(c) dimer; (d) trimer; and (e) tetramer.
Fig. 3 The conformational switching process of B2P molecules from “T” conformation to “P” conformation. For each part, the top section is the
STM image with a regular color bar and the bottom with a more prominent color bar. (a) B2P before switching, bias: +0.5 V. (b) B2P before
switching, bias: +1.5 V. (c) B2P is switched at +2.0 V. (d) B2P after switching, bias: +2.0 V. (e) B2P after switching, bias: +0.5 V.
b = 1.3 nm, θ = 121°) in blue diamond can also be identified. The
STM tip manipulation can also feasibly separate the B4P dimer
or other structure into monomers, showing that the B4P
molecules stick to each other via weak intermolecular interaction
rather than chemical bond. As can be seen in Fig. 4e and f, the
B4P absorbed on Au(111) exhibits two conformations, namely,
the “T” and “P” ones, in their STM images which display two
protrusions in different and similar brightness, respectively. For
B4P, the “T” conformation is more stable upon tip disturbance at
the bias of +2.0 V and below while the “P” conformation
undergoes conformational switch under the same condition.
Fig. 5 demonstrates the conformational switch from “P” to
“T”. As shown in Fig. 5a and b, all B4P molecules maintain their
conformation during the tip scanning over the bias range of +0.5
to +1.5 V. As the bias rises to +2.0 V, one B4P molecule in “P”
conformation (marked by the dashed circle) is disturbed by the
tip and transforms into the “T” conformation (Fig. 5c), which is
verified by the STM image after the switching (Fig. 5d). It
should be noted that such a conformational switch does not
necessarily work for all molecules in “P” conformation. It’s
experimentally shown that conformational switching of the
molecules in the assembled structure turns out to be quite
difficult, but rather easy for the molecules in the trimer-like
assemblies.
In order to determine the “P” and “T” conformations, DFT
calculations are employed to simulate the STM images of several
possible structures. The used models are first optimized prior to
the STM image simulations. Obviously, the main imaging
difference between “P” and “T” conformations stems from the
feature of the nitrogen heterocycle in two aspects: one is the
rotation of the isopropyl and the other, the tilting angle of the
nitrogen heterocycle against the Au(111) surface. To discern the
above-mentioned two situations, DFT simulation is performed.
In terms of the isopropyl rotation, B2P is used an example in the
simulation, as shown in Fig. 6. In Fig. 6a, both the dihedral
angles between two nitrogen heterocycles and the isopropyl C-
N-C-H are 0°. Meanwhile, the methylene group in isopropyl is
nearly parallel to the substrate surface. Fig. 6b and c show the
modelled and simulated results of other two possible
conformations. In Fig. 6b, the isopropyl marked by the red
dashed circle differs from the one in Fig. 6a in the dihedral angle
C-N-C-H which is about 180°. The green dashed circle in Fig.
6c highlights the difference that the dihedral angle C-N-C-H is
about 90° and the methylene group in isopropyl is perpendicular
to the surface. There exists no apparent difference among these
structures, which accordingly suggests that the difference
between the “P” and “T” conformations is not the reason for the
rotation of the isopropyl moiety.
Therefore, the conformations are simulated as a function of
the tilting angle of the nitrogen heterocycle. In all three
conformations simulated in Fig. 6, the structure in Fig. 6a
possesses the lowest energy. Hence subsequent simulation
maintains restricts the isopropyl moiety in the conformation in
Fig. 6a. Fig. 7 shows the stimulated results of different 6-
oxoverdazyl ring conformations in the B4P model. The dihedral
angle between BTBT and the nitrogen heterocycle is 0° (Fig. 7a),
Fig. 4 STM topographic images of B4P molecules on Au(111).
Image of B4P molecules on Au(111) at (a) low coverage, (b) medium
coverage and (c) high coverage. High-resolution STM images of
B4P molecules on Au(111) at (d) low coverage, (e) medium
coverage and (f) high coverage.
Fig. 5 The conformational switch of B4P molecules from “P” conformation to “T” conformation. For each part, the top section is the STM
image with a regular color bar, the bottom with a prominent color bar. (a) B4P before switching, bias: +0.5 V.
(b) B4P before switching, bias: +1.5 V. (c) B4P is switched at +2.0 V. (d) B4P after switching, bias: 0.5 V.
+50° (Fig. 7b) and −50° (Fig. 7c), correspondingly. Once the
nitrogen heterocycle is parallel to the Au(111) surface (Fig. 7a),
the brightness of each part in the radical appears similar.
However, the tilted nitrogen heterocycle (Fig. 7b and c) results
in a large brightness difference in the STM images. The farthest
part from the surface is brightest in the simulated STM image,
which is in excellent agreement with the experimental STM
image for the “T” conformation. Thus, the structures of the “P”
and “T” conformations for B4P correspond to the modelled ones
in Fig. 7a and b, respectively. The DFT calculation results also
show that the energy for the “T” conformation of B4P is about
0.23 eV lower than the “P” conformation, indicating that the
former is more stable. The reason is likely to be that a steric
hindrance exists between the nitrogen heterocycle and the BTBT
in the “P” conformation. It echoes the experimental result that
only the “P” conformation for B4P can be converted to the “T”
one. However, the “P” conformation becomes more stable due
to the absence of the steric hindrance in B2P.
4 Conclusions The adsorption of two verdazyl radicals like B2P and B4P
molecules on Au(111) are explored with STM. Experimental
results show that adsorbed B2P exists in monomers, dimers,
trimers and tetramers at surface. B4P forms dimers or assembled
structures, depending on its coverage. Both B2P and B4P
molecules adopt two conformations, namely, the “P”
conformation where the nitrogen heterocycle lies parallel to the
surface and the “T” one where the nitrogen heterocycle tilts
against the surface. At the bias voltage of +2.0 V, the STM tip
exerts a disturbance that converts the B2P molecule from “T” to
“P” conformation or transforms the B4P from “P” to “T”
conformation. For both molecules, such a conformational
transition is irreversible. The main difference in the most stable
conformation for both molecules originates from the steric
hindrance of the BTBT group. The conformational change can
be employed as the working principle to achieve molecular
switches based on these molecules.
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Conformational Switching of Verdazyl Radicals on Au(111)

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