Faculty Profiles - YAMAGUCHI, Shigehiro

Papers - YAMAGUCHI, Shigehiro

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Dual Circular Polarized Luminescence from Chiral Boron-Embedded Polycyclic Aromatic Hydrocarbons Reviewed

T. Mori, Y. Sano, T. Ikai, Y. Kawasaki, K. Tomooka, T. Sasamori, S. Yamaguchi

Angew. Chem. Int. Ed. Vol. 65 page： e22746 2026.3

Temperature-responsive near-infrared emission enabled by reversible π-umpolung with an alkenyl-strapped diarylboryl unit Reviewed

S. Kitamura, M. Sakai, S. Yamaguchi

Angew. Chem. Int. Ed. Vol. 65 page： e23338 2026.3

Kinetically controlled self-assembly of a lipophilic fluorophore with phenylalanine-based diamides in artificial lipid droplets Reviewed

2. M. Naruse, S. Ogi, K. Kajiwara, N. Fukaya, Y. Sato, M. Taki, S. Yamaguchi

Small Vol. 22 page： e13411 2026.2

Reaction of Blatter and Verdazyl Radicals with Arynes: Synthesis and Investigation of N-Chiral, Antiaromatic Triazines and Tetrazinones Reviewed International coauthorship

4. L. Lezius, E. S. Horst, M. Scherübl, J. Lammert, C. G. Daniliuc, T. Mori, S. Yamaguchi, A. Studer

Angew. Chem. Int. Ed. Vol. 65 page： e22746 2026.1

Tunable Thermally Activated Delayed Fluorescence from Supramolecular Polymers towards Application in Aqueous Media Reviewed International coauthorship

10. N. Bäumer, P. Hu, M. Naruse, S. Ogi, Z. M. Hudson, S. Yamaguchi

Angew. Chem., Int. Ed. Vol. 64 page： e202509241 2025.8

Kinetic Control over Social and Narcissistic Self-Sorting from Multicomponent Mixtures in Seed-Initiated Supramolecular Polymerization by Fine-Tuning of Steric Effects Reviewed Open Access

Matsumoto, K; Bäumer, N; Ogi, S; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 64 ( 4 ) page： e202416361 2025.1

Near-infrared fluorescent HaloTag ligands for efficient organelle labelling in live cells

Tanaka, Y; Taki, M; Yamaguchi, S

CHEMICAL COMMUNICATIONS Vol. 61 ( 6 ) page： 1164 - 1167 2025.1

Dithieno[3,2-b; 2′,3′-f]phosphepinium-Based Near-Infrared Fluorophores: px-π* Conjugation Inherent to Seven-Membered Phosphacycles Reviewed International coauthorship Open Access

Andoh, K; Murai, M; Bouit, PA; Hissler, M; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 63 ( 39 ) page： e202410204 2024.9

Sulfur-Bridged Cationic Diazulenomethenes: Formation of Charge-Segregated Assembly with High Charge-Carrier Mobility Reviewed

Takahashi, S; Murai, M; Hattori, Y; Seki, S; Yanai, T; Yamaguchi, S

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 146 ( 32 ) page： 22642 - 22649 2024.8

Bis-Ortho-Donor-Modification of Boracyclic π-Electron Systems beyond Steric Protection to Produce Thermally Activated Delayed Fluorescence Materials Reviewed Open Access

Narita, H; Min, H; Kubo, N; Hattori, I; Yasuda, T; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 63 ( 30 ) page： e202405412 2024.7

Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super‐photostable Environment‐Sensitive Probe Reviewed Open Access

Junwei Wang, Masayasu Taki, Yohsuke Ohba, Makoto Arita, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 63 ( 28 ) page： e202404328 2024.7

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

Abstract

The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red‐emissive IMM‐labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super‐resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.

DOI： 10.1002/anie.202404328

Open Access

Web of Science

PubMed

In‐Silico Screening and Experimental Verification of Near‐Infrared‐Emissive Two‐Boron‐Doped Polycyclic Aromatic Hydrocarbons Reviewed Open Access

Izumi Hattori, Masaya Hagai, Masato Ito, Mika Sakai, Hiroki Narita, Kazuhiro J. Fujimoto, Takeshi Yanai, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 63 ( 22 ) page： e202403829 2024.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

Embedding two boron atoms into a polycyclic aromatic hydrocarbon (PAH) leads to the formation of a neutral analogue that is isoelectronic to the corresponding dicationic PAH skeleton, which can significantly alter its electronic structure. Based on this concept, we explore herein the identification of near‐infrared (NIR)‐emissive PAHs with the aid of an in‐silico screening method. Using perylene as the PAH scaffold, we embedded two boron atoms and fused two thiophene rings to it. Based on this design concept, all possible structures (~2500 entities) were generated using a comprehensive structure generator. Time‐dependent DFT calculations were conducted on all these structures, and promising candidates were extracted based on the vertical excitation energy, transition dipole moment, and atomization energy per bond. One of the extracted dithieno‐diboraperylene candidates was synthesized and indeed exhibited emission at 724 nm with a quantum yield of 0.40 in toluene, demonstrating the validity of this screening method. This modification was further applied to other PAHs, and a series of thienobora‐modified PAHs was synthesized.

DOI： 10.1002/anie.202403829

Open Access

Web of Science

PubMed

Stereochemistry‐Dependent Labeling of Organelles with a Near‐Infrared‐Emissive Phosphorus‐Bridged Rhodamine Dye in Live‐Cell Imaging Reviewed Open Access

Qian Wu, Masayasu Taki, Yoshiki Tanaka, Manish Kesherwani, Quan Manh Phung, Sawako Enoki, Yasushi Okada, Florence Tama, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 63 ( 15 ) page： e202400711 2024.4

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

The development of near‐infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha‐rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2‐carboxy‐3‐benzothiophenyl group at the 9‐position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X‐ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non‐specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag‐fused proteins, enabling the long‐term imaging of cell division and the 5‐color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR‐emissive properties, multi‐color time‐lapse super‐resolution 3D imaging, namely super‐resolution 5D‐imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.

DOI： 10.1002/anie.202400711

Open Access

Web of Science

PubMed

Dithienoazepine-Based Near-Infrared Dyes: Janus-Faced Effects of a Thiophene-Fused Structure on Antiaromatic Azepines Reviewed Open Access

Murai, M; Enoki, T; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 62 ( 49 ) page： e202311445 2023.12

Theoretical Insight into the Effect of Phosphorus Oxygenation on Nonradiative Decays: Comparative Analysis of P-Bridged Stilbene Analogs Reviewed Open Access

Inai, N; Yamaguchi, S; Yanai, T

ACS PHYSICAL CHEMISTRY AU Vol. 3 ( 6 ) page： 540 - 552 2023.10

Biomimetic Design of a Robustly Stabilized Folded State Enabling Seed-Initiated Supramolecular Polymerization under Microfluidic Mixing Reviewed Open Access

Ogi, S; Takamatsu, A; Matsumoto, K; Hasegawa, S; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 62 ( 34 ) page： e202306428 2023.8

Amphiphile desymmetrisation-induced steric relief governs self-assembly pathways in aqueous media Reviewed International coauthorship

Bäumer, N; Ogi, S; Borsdorf, L; Yamaguchi, S; Fernández, G

CHEMICAL COMMUNICATIONS Vol. 59 ( 58 ) page： 8937 - 8940 2023.7

Germanium- and tin-bridged diazulenylmethyl cations: effects of group 14 elements on the structure and properties of π-extended cations Reviewed Open Access

Murai, M; Ito, M; Takahashi, S; Yamaguchi, S

DALTON TRANSACTIONS Vol. 52 ( 25 ) page： 8631 - 8635 2023.6

Impact of Hydrophobic/Hydrophilic Balance on Aggregation Pathways, Morphologies, and Excited-State Dynamics of Amphiphilic Diketopyrrolopyrrole Dyes in Aqueous Media. Reviewed International coauthorship International journal

Natsumi Fukaya, Soichiro Ogi, Hikaru Sotome, Kazuhiro J Fujimoto, Takeshi Yanai, Nils Bäumer, Gustavo Fernández, Hiroshi Miyasaka, Shigehiro Yamaguchi

Journal of the American Chemical Society Vol. 144 ( 49 ) page： 22479 - 22492 2022.12

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.

DOI： 10.1021/jacs.2c07299

Web of Science

PubMed

Diazulenylmethyl Cations with a Silicon Bridge: A π-Extended Cationic Motif to Form J-Aggregates with Near-Infrared Absorption and Emission Reviewed

Murai, M; Abe, M; Ogi, S; Yamaguchi, S

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 144 ( 44 ) page： 20385 - 20393 2022.10

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Papers - YAMAGUCHI, Shigehiro