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  1. Article ; Online: Location of the Shared Proton in Proton-Bound Dimer Compound of Hydrogen Sulfate and Formate: Path Integral Molecular Dynamics Study.

    Udagawa, Taro / Tanaka, Hikaru / Kuwahata, Kazuaki / Tachikawa, Masanori

    The journal of physical chemistry. A

    2024  Volume 128, Issue 11, Page(s) 2103–2110

    Abstract: The structure of the proton-bound dimer compound of hydrogen sulfate and formate has been studied by considering nuclear quantum effects (NQEs) using the path integral molecular dynamics method. This study unveiled the location of the shared proton and ... ...

    Abstract The structure of the proton-bound dimer compound of hydrogen sulfate and formate has been studied by considering nuclear quantum effects (NQEs) using the path integral molecular dynamics method. This study unveiled the location of the shared proton and answered the following question: "Is the shared proton localized on either an anion or located around the center of two anions?" We have elucidated that the shared proton is distributed in the region beyond the transition state due to the NQEs, even though the shared proton did not completely overcome the transition state for the proton shuttle.
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.4c00239
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2.

    Shimazaki, Tomomi / Tachikawa, Masanori

    ACS omega

    2022  Volume 7, Issue 12, Page(s) 10372–10381

    Abstract: To improve virtual screening for drug discovery, we present a collaborative approach between explainable artificial intelligence (AI) and simplified chemical interaction scores to efficiently search for active ligands bound to the target receptor. In ... ...

    Abstract To improve virtual screening for drug discovery, we present a collaborative approach between explainable artificial intelligence (AI) and simplified chemical interaction scores to efficiently search for active ligands bound to the target receptor. In particular, we focus on cyclin-dependent kinase 2 (CDK2), which is well known as a cancer target protein. Docking simulation alone is insufficient to distinguish active ligands from decoy molecules. To identify active ligands, in this paper, machine learning is employed together with scoring functions that simplify the screened Coulomb and Lennard-Jones interactions between the ligands and residues of the target receptor. We demonstrate that these simplified interaction scores can significantly improve the classification ability of machine learning models. We also demonstrate that explainable AI together with the simplified scoring method can highlight the important residues of CDK2 for recognizing active ligands.
    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.1c06976
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transport Characteristics of Placenta-Derived Extracellular Vesicles and Their Relevance to Placenta-to-Maternal Tissue Communication.

    Inagaki, Mai / Tachikawa, Masanori

    Chemical & pharmaceutical bulletin

    2022  Volume 70, Issue 5, Page(s) 324–329

    Abstract: The placenta, a unique organ that helps maintain a healthy pregnancy, plays a pivotal role in maternal adaptation to pregnancy and releases extracellular vesicles (EVs), autacoids, and hormones. EVs are membranous vesicles released by all types of cells, ...

    Abstract The placenta, a unique organ that helps maintain a healthy pregnancy, plays a pivotal role in maternal adaptation to pregnancy and releases extracellular vesicles (EVs), autacoids, and hormones. EVs are membranous vesicles released by all types of cells, including placental trophoblasts, which are involved in intracellular communication by delivering their cargo, such as proteins, nucleic acids, and lipids, to the targeted cells in a neighboring or distant location. Recently, an increasing number of publications have reported that EVs secreted from the placenta into maternal circulation deliver their cargo to maternal organs and mediate placenta-to-maternal communication during pregnancy. This review provides an overview of the transport mechanism of placenta-derived EVs to maternal organs.
    MeSH term(s) Extracellular Vesicles/metabolism ; Female ; Humans ; Nucleic Acids ; Placenta ; Pregnancy ; Proteins/metabolism
    Chemical Substances Nucleic Acids ; Proteins
    Language English
    Publishing date 2022-05-01
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 213307-6
    ISSN 1347-5223 ; 0009-2363
    ISSN (online) 1347-5223
    ISSN 0009-2363
    DOI 10.1248/cpb.c22-00072
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 770: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Foreword.

    Ishida, Tatsuhiro / Kogure, Kentaro / Tachikawa, Masanori / Baba, Kazuhiko

    Chemical & pharmaceutical bulletin

    2022  Volume 70, Issue 5, Page(s) 309

    Language English
    Publishing date 2022-04-28
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 213307-6
    ISSN 1347-5223 ; 0009-2363
    ISSN (online) 1347-5223
    ISSN 0009-2363
    DOI 10.1248/cpb.c22-ctf7005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 770: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2

    Tomomi Shimazaki / Masanori Tachikawa

    ACS Omega, Vol 7, Iss 12, Pp 10372-

    2022  Volume 10381

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: A path integral molecular dynamics study on the muoniated xanthene-thione molecule.

    Kuwahata, Kazuaki / Ito, Shigekazu / Tachikawa, Masanori

    The Journal of chemical physics

    2023  Volume 159, Issue 10

    Abstract: A positive Mu is a useful tool for investigating the spin density of radical species. The theoretical estimation of its behavior in a molecule requires the inclusion of a quantum effect due to the small mass of muonium. Herein, we performed ab initio a ... ...

    Abstract A positive Mu is a useful tool for investigating the spin density of radical species. The theoretical estimation of its behavior in a molecule requires the inclusion of a quantum effect due to the small mass of muonium. Herein, we performed ab initio a path integral molecular dynamics (PIMD) simulation, which accurately included a multi-dimensional quantum effect, for muoniated 9H-xanthene-9-thione (μXT). Our results showed that the quantum effect significantly increased the hyperfine coupling constant (HFCC) value of μXT, which qualitatively improved the calculated HFCC value, compared to the experimental one. In the PIMD simulation, the bond length between muonium and sulfur in μXT is longer than that between hydrogen and sulfur in a hydrogenated 9H-xanthene-9-thione (HXT), leading to a spin density transfer from XT (9H-xanthene-9-thione) to muonium due to neutral dissociations. Additionally, we found that the S-Mu bond in μXT prefers a structure perpendicular to the molecular plane, where the interaction between Mu and the singly occupied molecular orbital of μXT is the strongest. These structural changes resulted in a larger HFCC value in the PIMD simulation of μXT.
    Language English
    Publishing date 2023-09-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0159207
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 4' 49/16: Show issues

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  7. Article ; Online: Low-Barrier Hydrogen Bond in Fujikurin A-D: A Computational Study.

    Tanaka, Hikaru / Kuwahata, Kazuaki / Tachikawa, Masanori / Udagawa, Taro

    ACS omega

    2022  Volume 7, Issue 16, Page(s) 14244–14251

    Abstract: The compounds Fujikurin A, B, and D, recently isolated ... ...

    Abstract The compounds Fujikurin A, B, and D, recently isolated from
    Language English
    Publishing date 2022-04-15
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c00857
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A path integral molecular dynamics study on the NH

    Udagawa, Taro / Kinoshita, Amane / Kuwahata, Kazuaki / Tachikawa, Masanori

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 28, Page(s) 17295–17302

    Abstract: The nuclear quantum effects (NQEs) in dihydrogen bond (DHB) complexes, ...

    Abstract The nuclear quantum effects (NQEs) in dihydrogen bond (DHB) complexes,
    Language English
    Publishing date 2022-07-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d2cp01999j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Nuclear quantum and H/D isotope effects on intramolecular hydrogen bond in curcumin.

    Udagawa, Taro / Yabushita, Hinata / Tanaka, Hikaru / Kuwahata, Kazuaki / Tachikawa, Masanori

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 23, Page(s) 15798–15806

    Abstract: Curcumin and its derivatives possess intramolecular low-barrier hydrogen bonds for intramolecular proton transfer. The π-delocalization in the OCCCO framework of the hydrogen bond in these compounds is reorganized concomitantly with the proton transfer. ... ...

    Abstract Curcumin and its derivatives possess intramolecular low-barrier hydrogen bonds for intramolecular proton transfer. The π-delocalization in the OCCCO framework of the hydrogen bond in these compounds is reorganized concomitantly with the proton transfer. To characterize the hydrogen bond and π-delocalization, we performed path integral molecular dynamics simulations, revealing that although the proton migration and reorganization of the π-delocalized structure showed a positive correlation, the correlation was weak.
    Language English
    Publishing date 2023-06-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp01821k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A theoretical study on solvatofluorochromic asymmetric thiazolothiazole (TTz) dyes using dielectric-dependent density functional theory.

    Shimazaki, Tomomi / Tachikawa, Masanori

    Physical chemistry chemical physics : PCCP

    2021  Volume 23, Issue 37, Page(s) 21078–21086

    Abstract: In this work, the excitation energies of asymmetric thiazolothizaole (TTz) dye molecules have been theoretically studied using dielectric-dependent density functional theory (DFT). In the dielectric-dependent DFT approach, the ratio (fraction) of the ... ...

    Abstract In this work, the excitation energies of asymmetric thiazolothizaole (TTz) dye molecules have been theoretically studied using dielectric-dependent density functional theory (DFT). In the dielectric-dependent DFT approach, the ratio (fraction) of the nonlocal Hartree exchange term incorporated into the DFT exchange-correlation functional is a system-dependent parameter, which is inversely proportional to the dielectric constant of the target material. The dielectric-dependent DFT method is closely related to the Coulomb hole and screened exchange (COHSEX) approximation in the GW method and therefore has been applied to crystalline systems with periodic boundary conditions, such as semiconductors and inorganic materials. By focusing on the solvatofluorochromic phenomena of asymmetric TTz dyes, we show that excitation energy calculations obtained from the dielectric-dependent DFT method can reproduce the corresponding experimental UV-vis absorption and emission spectra of dyes in solvents.
    Language English
    Publishing date 2021-09-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp02047a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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