MANABIYA Topics

MAEDA, Satoshi

Theoretical analysis and prediction of reaction mechanism using automated reaction path search methods

Participants will investigate the reaction path of chemical reactions such as organic reactions using the automated reaction path search program GRRM. The important reaction routes are extracted from the obtained reaction route data, and the reaction mechanism of the chemical reaction is discussed from the kinetic analysis for their energy profiles.

The target chemical reaction will be decided in consultation with the faculty in charge.

Since participants will be using a computer with a UNIX/Linux operating system, they should be familiar with the UNIX/Linux operating system, not Windows or Mac before attending.

Click here for more information on Professor Maeda.

TAKETSUGU, Tetsuya

Calculation of excited state species and design of heterogeneous catalysts

  • Electronic structure calculation for excited states
  • Calculation of heterogeneous catalytic reactions
  • Electronic structure calculation of large systems
  • Catalyst informatics

Click here for more information on Professor Taketsugu.

YAMAMOTO, Tetsuya (Rubinstein group)

Theoretical calculation of polymer materials and macromolecules

  • Soft matter physics (theory)—Polymer melting/solution, polymer network, liquid crystal, colloid, surface/interface/membrane, electrostatics/dynamics, etc.
  • Physics of gene regulation and the nucleus—Combining the kinetic theory of (bio)chemical reactions and the theory of soft-matter physics to understand the physics of systems in the nucleus, such as the dynamics/regulation of genetic expression, chromatin structure/dynamics, the assembly of nuclear bodies, etc.

Click here for more information on Professor Rubinstein.

YOSHIOKA, Masaharu

Information extraction from chemical research papers

  • Chemical Named Entity Recognition (CNER): Extraction of chemical named entity (e.g., name of chemical compounds and atoms) from the text
  • Technical term extraction: Extract technical term candidates from the text
  • Research trend analysis using a time series of research paper sets (e.g., annual conference proceedings and/or articles of a particular journal title over 10 years)

Since participants will be using a computer with a UNIX/Linux operating system, they should be familiar with the UNIX/Linux operating system, not Windows or Mac before attending.

Click here for more information on Professor Yoshioka.

SIDOROV, Pavel (Varnek group)

Chemoinformatics tools for chemical data management, analysis and QSAR modeling

Participants will study chemoinformatics tools and approaches that are used for collecting and cleaning chemical compound data and building Quantitative Structure-Activity Relationship models to predict biological activities against a specific target, physico-chemical properties of molecules or properties of reactions.

Studied techniques:

  • Computer representation of chemical structures (text strings, 2D and 3D structures)
  • Chemical data cleaning
  • Chemical database tools (e.g., ChemAxon’s InstantJChem)
  • Molecular descriptors and Quantitative Structure-Activity Relationships (QSAR) for biological activity or physico-chemical properties
  • Chemical cartography: data visualisation and analysis using Generative Topographic Maps
  • Condensed Graph of Reaction representation of chemical reactions; reaction databases and reaction properties modelling

Click here for more information on Professor Varnek.

TAKIGAWA, Ichigaku

Methods and practices for data-intensive research

  • Prediction and data analysis based on machine learning, data mining, and database-related technologies
  • Development and improvement of algorithms and data analysis pipelines

Click here for more information on Professor Takigawa.

KOMATSUZAKI, Tamiki

Phase space geometry of chemical reactions and on-line machine learning to accelerate experiments

  • Theoretical development of chemical reaction systems which conventional statistical transition state theories cannot capture
  • Bandits algorithm to drastically accelerate experiments and drug screening within a chosen tolerance by exploring the optimal condition with a feedback from exploiting the knowledge acquired during the experiment
  • Molecular data science on the reconstruction of the energy landscape and reaction network from time series data and on classifying different roles of composite elements from an image data set
  • Network theory for complex reacting systems

Click here for more information on Professor Komatsuzaki.

ITO, Hajime

Development of new reactions of small molecules with various elements

  • Mechanochemistry: Development of new organic synthetic methods without solvents using a ball mill
  • Development of luminescent sensing materials for mechanical stimulation: Mechanochromism and crystal phase change
  • Novel catalyst design using computational chemistry: Asymmetric borylation and aromatic borylation
  • Synthesis of new functionalized organosilicon compounds

Click here for more information on Professor Ito.

SAWAMURA, Masaya

Development of new catalytic reactions using transition metals

  • Design, synthesis and application of chiral transition metal catalysts and ligands guided by quantum chemical calculations
  • Design, synthesis and application of highly active transition metal catalysts based on solid-supported ligands
  • Development and application of photo-driven transition metal-catalyzed reactions for organic synthesis
  • Synthesis of bioactive organic compounds through catalytic C–H borylation reactions

Click here for more information on Professor Sawamura.

TSUJI, Nobuya (List group)

Development of new reactions using organocatalysis

Participants will work on developing organocatalytic reactions as follows:

  • Brønsted acid catalysis
  • Organic Lewis acid catalysis
  • Asymmetric Couteranion Directed Catalysis (ACDC)
  • Design of novel chemical reactions using CO and CO2

Click here for more information on Professor List.

INOKUMA, Yasuhide

Small to medium-size molecule synthesis and crystallography

  • Synthesis of polyketones and related compounds
  • Design and synthesis of π-conjugated organic chromophores
  • Crystallization and single crystal X-ray analysis of organic compounds

Click here for more information on Professor Inokuma.

HASEGAWA, Yasuchika

Light-emitting materials with high brightness and durability

  • Development of luminescent lanthanide complexes and coordination polymers
  • Applications using luminescent lanthanide complexes and coordination polymers (wavelength converter etc.)
  • Measurements and analysis of luminescence properties (low and high-temperature measurements, emission lifetime, nanosecond time-resolved measurements, near-infrared luminescence measurements)
  • Measurements and analysis of circularly polarized absorption and luminescence

Click here for more information on Professor Hasegawa.

GONG, Jian Ping

Synthesis of biocompatible/self-evolving gels and macromolecules

Participants will learn about the sacrificial bond principle, which is a basic principle for the toughening of soft materials, and synthesize a tough hydrogel whose toughness is comparable to that of industrial rubbers. Then, they will describe the mechanical properties of the synthesized gel by multiple measurements. The target gel will be decided after discussion with the staff members.

Click here for more information on Professor Gong.

TANAKA, Shinya

Cell control by new materials, development of next-generation diagnosis tools

  • Theoretical prediction of catalytic proteins for chemical reactions and introduction of mutations into catalytic proteins (collaboration with Maeda group)
  • Induction of cancer stem cells by hydrogels
  • Chemical library screening for anti-cancer stem cell drug through mathematical theory

Click here for more information on Professor Tanaka.