Advanced Visualization of Electrons, Atoms,and Molecules

October 29, 2020 (Thu)
Progress in technologies of measurement and analysis is notable because it enables toenlarge the limitations such as sensitivity, spatial resolution, and data accumulation
time. Hardware like probing or detection system has been amazingly improving for acouple of decades. Furthermore, development in data processing software based on
application of statistical and information technologies has been drastically rising
nowadays. This topical meeting is focusing on state-of-the-art technologies in the fieldof measurement and analysis feasible to characterize emergent matter phenomena byvisualization of electrons, atoms, and molecules.

13:00–13:10

Opening

15:10–15:30

13:10–14:00 (*Long talk)

15:30–16:05

Shigeki Kawai

Ryo Ishikawa(NIMS)(The Univ. of Tokyo)“On-surface chemistry studied
with high-resolution scanningprobe microscopy”“Advanced electron
microscopy for point defects”

14:00–14:35

16:05–16:40

Manabu Hoshino

Keiki Fukumoto(RIKEN CEMS)(KEK)“Evaluation of ‘to-be-collected’
diffraction data using
information technology”“Electron dynamics inorganic heterostructures”

14:35–15:10

16:40–17:30 (*Long talk)Kenichi KatoKen Onda(RIKEN RSC)

(Kyushu Univ.)“Data-driven total scattering
measurements by synchrotron
X-rays ーAiming at
visualization of heterogeneous
phenomenaー”“Structural dynamics inphotofunctional materials
studied by time-resolved
infrared spectroscopy”
17:30–17:40

BreakClosing

https://cems.riken.jp/topicalmeeting/004_visualization/

Oc be 29, 2020
CEMS T ca Mee

O -face C e

S d edMcH g -RecScagOeg P beShigeki Kawai11

Research Center for Advanced Measurement and Characterization, National Institute forMaterials Science, 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
Email: KAWAI.Shigeki@nims.go.jp
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1 L. Ge al., S32 , 1110 (2009).
2 J. C e al., N
4 , 470 (2010)
3 K. Ne al., J. A C. S . 142, 11363 (2020)
4 S. Ke al. N . C. , 8098 (2015)
5 S. Ke al., S . A . 4,7181 (2018).
6 S. Ke al., S
3 1, 957 (2016).
7 S. Ke al., S . A . ,8913 (2020).

October 29, 2020
CEMS Topical Meeting Online

Evaluation of ‘to-be-collected’ diffraction data using
information technology
Manabu Hoshino
RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: manabu.hoshino@riken.jp

Crystal structure analysis essentially provides three-dimensional distribution of electron density
in a crystal specimen. Using that distribution, molecular and crystal structure are constructed,refined, and evaluated. Due to this principle of crystal structure analysis, researcher who will
perform crystal structure analysis carefully design a strategy of diffraction data collection forvisualizing realistic and informative electron density distribution. In this talk, our developed
methodology[1], which is useful to the strategy building via evaluation of to-be-collecteddiffraction data generated by information technology, is introduced with showing a practicalexample.
Generation of to-be-collected diffraction data is based on stochastic sampling from a probability
distribution using a computer. In our methodology, the parameter inherent in a probability
distribution of diffraction data peculiar to a subject crystal is precisely estimated from apreliminary-collected small diffraction data set by Bayes’ theorem, which is a theory basicallyused in information technologies. The generated data set is used for optimizing X-ray exposure
time to collect quantitative diffraction intensities. Crystal structure analysis using diffraction datacollected along the strategy with the optimized X-ray exposure time clearly visualized electron
density distributions of equivalent three lone-pairs around an oxygen atom in a sulfonyl group(Figure).
Figure. Electron density distribution arounda selected oxygen atom in taurine ((2aminoethane-1-sulfonic acid, C2H7NO3S).
Positive peak positions are marked by ‘*’with the corresponding amplitude. The color
scheme and the density limit [blue: positive(max.: 0.18 e Å−3); green: zero].
[1]

M.

Hoshino,Y.

Nakanishi-Ohno,

doi:10.1038/s41598-019-48362-3.

D.

Hashizume,

Sci.

Rep.,

2019,

9:11886

October 29, 2020
CEMS Topical Meeting Online

Data-driven total scattering measurements by synchrotron X-rays
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Kenichi Kato
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
Email: katok@spring8.or.jp
Synchrotron radiation (SR), which is recognized as one of the most powerful analytical tools formaterials and life sciences, allows us to visualize physical and chemical phenomena. Taking theadvantages of SR, such as high brilliance, adjustable energy and polarization, coherence, andpulsed beams, gives us crystal and electronic structures on a wide scale in space and time. FromSR X-ray diffraction data, crystal structure including electrondensity can be obtained [1]. In most cases, however, theapplications are limited to a perfectly periodic system. Total
scattering, which means both Bragg and diffuse scattering, isapplicable regardless of structural periodicity [2]. Diffuse
scattering is extremely broad and weak compared with Bragg
scattering, and therefore total scattering is technicallyFig. 1 Hardware development
demanding. We developed a total scattering measurement
system “OHGI” at the RIKEN Materials Science beamline
BL44B2 of SPring-8 to cover a wide range of scatteringvector Q with high Q resolution (Fig. 1) [3]. Furthermore, wehave recently developed a data-driven correction approach“ReLiEf” to achieve high signal-to-noise ratio (Fig. 2) [4]. A
data-driven analysis approach to atomic pair distributionfunctions is under development to visualize heterogeneous
structure inside nanocrystals on a sub-angstrom scale. In thispresentation, I will talk about recent advances in terms ofFig. 2 Software development
both hardware and software.
[1] K. Kato and H. Tanaka, Advances in Physics: X 1, 55-80 (2016).
[2] T. Egami and S. J. L. Billinge, Underneath the Bragg Peaks, Structural Analysis of Complex
Materials (2nd Edition), Pergamon (2012).
[3] K. Kato, Y. Tanaka, M. Yamauchi, K. Ohara, and T. Hatsui, J. Synchrotron Rad. 26, 762-773(2019).
[4] K. Kato and K. Shigeta, J. Synchrotron Rad. 27, 1172-1179 (2020).

Oc be 29, 2020
CEMS T ca MeegOe

Ad anced electron microscop for point defects
I hika a1,2, Na a Shiba a1,3, Y ichi Ik ha a1,3R

1Institute of Engineering Innovation, University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
2

PRESTO, Japan Science and Technology, Kawaguchi, Saitama 332-0012, Japan

3

Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya, Aichi 456-8587,
Japan
Email: ishikawa@sigma.t.u-tokyo.ac.jp
M,.I-(DPC)[1,2],-(STEM).I,S
DPC STEM.W[3]. TS,S-W.
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[5].

[1] N. S,N .P. , 611 (2012).

[2] N. S,N .C. , 15631 (2017).

[3] R. I,N .C. , 3878 (2018).

[4] R. I,P. R . L . 113, 155501 (2014).

[5] R. I,M

6 , 240 (2020).

(ADF) STEM

Oc be 29, 2020
CEMS T ca MeegOe

Electron d namics in organic heterostr ct res
Keiki FukumotoHigh Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801,JapanEmail: keiki@post.kek.jp
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Figure 1: Schematic view of the TR-PEEM system.

P C C60
by monitoring the electron
density in the LUMO of C60(red plots in Figure 2 (right))[5].

Figure 2: Results of TR-PEEM experiments on a
C60/Pen-SC organic heterostructure.

1 F., A

2 F., R .

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5 IF.P. L ., (2014).
., (2014).
P .N.P., J. P.:O2018/159272.

. 53, 405106 (2020).
.C. C 124, 13572 (2020).

October 29, 2020
CEMS Topical Meeting Online

Structural Dynamics in Photofunctional Materials Studied by Timeresolved Infrared Spectroscopy.HQ2QGD
Department of Chemistry, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
Email: konda@chem.kyushu-univ.jp
Recently a variety of photofunctional materials have been intensively developed for solving
energy and environment problems or for living a better life; however, there are a few in-situ andrealtime observation methods for analyzing dynamical processes in these materials though thequick processes upon photoexcitation play key roles for their photofunctions. For now, mostly
time-resolved photo-luminescent spectroscopy (TR-PL) and sometime time-resolved ultravioletvisible transient absorption spectroscopy (TR-UV/VIS) are utilized. Time-resolved infrared
vibrational spectroscopy (TR-IR) is potentially powerful tools for analyzing such functional
materials because complicated IR spectra particularly in the finger print region contain richinformation on not only electronic states but also molecular structures, nevertheless applicationsof TR-IR to photofunctional materials are limited. Therefore, we developed TR-IR systems for
exploring dynamics and unveiled many important phenomena or mechanism in a variety offunctional materials (Fig.1): molecular crystals showing photoinduced phase transition [1,2],
metal complexes for photocatalysts or artificial photosynthesis [3-6], photo-active liquid crystals[7], graphene oxide [8], and emissive materials for organic light emitting diodes (OLED) [9].

Figure 1. Examples of photofunctional materials studied by time-resolved infrared spectroscopy[1] N. Fukazawa, M. Shimizu, T. Ishikawa, et al. J. Phys. Chem. C, 116, 5892 (2012).
[2] N. Fukazawa, T. Tanaka, T. Ishikawa, et al. J. Phys. Chem. C, 117, 13187 (2013).
[3] T. Mukuta, N. Fukazawa, K. Murata, et al. Inorg. Chem. 53, 2481 (2014).
[4] T. Mukuta, S. Tanaka, A. Inagaki, et al. ChemistrySelect 1, 2802 (2016).
[5] T. Mukuta, P. V. Simpson, J. G. Vaughan, et al. Inorg. Chem. 56, 3404 (2017).
[6] Y. Yamazaki, K. Ohkubo, D. Saito, et al. Inorg. Chem. 58, 11480 (2019).
[7] M. Hada, S. Saito, S. Tanaka et al. J. Am. Chem. Soc. 2017, 139, 15792.
[8] M. Hada, K. Miyata, S. Ohmura, et al. ACS Nano, 13, 10103 (2019).
[9] M. Saigo, K. Miyata, S. Tanaka, et al. J. Phys. Chem. Lett. 10, 2475 (2019).