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Shinsaku Fujita - One of the best experts on this subject based on the ideXlab platform.

  • Stereoisomerism accompanied with bond rotations characterization of propane derivatives by correlation diagrams of epimeric stereoisograms
    Bulletin of the Chemical Society of Japan, 2018
    Co-Authors: Shinsaku Fujita
    Abstract:

    The Stereoisomerism of propane derivatives with bond rotations is investigated by means of correlation diagrams of stereoisograms, where the diagrams are governed by epimeric RS-stereoisomeric grou...

  • Hierarchical enumeration of Kekulé’s benzenes, Ladenburg’s benzenes, Dewar’s benzenes, and benzvalenes by using combined-permutation representations
    Journal of Mathematical Chemistry, 2018
    Co-Authors: Shinsaku Fujita
    Abstract:

    The group hierarchy for each skeleton of ligancy 6 is formulated to be: point group (PG $${\varvec{G}}_{\sigma }$$ G σ ) $$\subseteq $$ ⊆ RS -stereoisomeric group ( RS -SIG $${\varvec{G}}_{\sigma \widetilde{\sigma }\widehat{I}}$$ G σ σ ~ I ^ ) $$\subseteq $$ ⊆ stereoisomeric group (SIG $$\widetilde{{\varvec{G}}}_{\sigma \widetilde{\sigma }\widehat{I}}$$ G ~ σ σ ~ I ^ ) $$\subseteq $$ ⊆ isoskeletomeric group (ISG $$\widetilde{\widetilde{{\varvec{G}}}}_{\sigma \widetilde{\sigma }\widehat{I}}$$ G ~ ~ σ σ ~ I ^ = $${\varvec{S}}^{[6]}_{\sigma \widehat{I}}$$ S σ I ^ [ 6 ] ), where we start from the PG $${\varvec{G}}_{\sigma }$$ G σ = $${\varvec{D}}_{6h}$$ D 6 h for the Kekulé benzene skeleton, from the PG $${\varvec{G}}_{\sigma }$$ G σ = $${\varvec{D}}_{3h}$$ D 3 h for the Ladenburg benzene skeleton, from the PG $${\varvec{G}}_{\sigma }$$ G σ = $${\varvec{C}}_{2v}$$ C 2 v for the Dewar benzene skeleton, or from the PG $${\varvec{G}}_{\sigma }$$ G σ = $${\varvec{C}}_{2v}$$ C 2 v for the benzvalene skeleton. After these groups are constructed as combined-permutation representations, the calculation of the respective cycle indices with chirality fittingness (CI-CFs) and the introduction of ligand-inventory functions are conducted to give generation functions for 3D-based enumerations (for PGs and RS -SIGs) and 2D-based enumerations (for SIGs and ISGs). The enumeration results are discussed by means of isomer-classification diagrams, in which equivalence classes under enantiomerism (for PGs), RS -Stereoisomerism (for RS -SIGs), Stereoisomerism (for SIGs), and isoskeletomerism (for ISGs) are illustrated schematically. The implicit connotations of the conventional terms “skeletal isomerism”, “positional isomerism”, and “constitutional isomerism” are discussed, where the effects of the concept of isoskeletomerism are emphasized.

  • correlation diagrams of epimeric stereoisograms for Stereoisomerism of cyclopropane derivatives
    Bulletin of the Chemical Society of Japan, 2018
    Co-Authors: Shinsaku Fujita
    Abstract:

    Stereoisomerism of cyclopropanes is systematically discussed by means of stereoisograms and their correlation diagrams. A cyclopropane skeleton is governed by a main RS-stereoisomeric group constru...

  • Isoskeletomerism as an intermediate concept for mediating between Stereoisomerism and isomerism. A remedy for conceptual defects of organic chemistry
    Tetrahedron: Asymmetry, 2017
    Co-Authors: Shinsaku Fujita
    Abstract:

    Abstract After isoskeletomerism is introduced as an intermediate concept for mediating between Stereoisomerism and isomerism, so-called ‘constitutional isomerism’ is critically discussed as one of the roots of confusion in organic chemistry. The convention that isomerism is subdivided into Stereoisomerism and ‘constitutional isomerism’ is concluded to be misleading, because these concepts are conceptually distinct from a viewpoint of the concepts of equivalence relationships and equivalence classes. The indifference toward these concepts is one of the conceptual defects of organic chemistry. A new flowchart for judging enantiomerism, RS-Stereoisomerism, Stereoisomerism, isoskeletomerism, and isomerism is discussed to generate an isomer-classification diagram, where RS-Stereoisomerism and isoskeletomerism are contained as new matters for remedying the conceptual defects. Skeletons are derived from basic skeletons by three operations (the bond operation, the replacement operation, and the substitutive operation), and they are used to examine the action of isoskeletomeric relationships. Equivalent molecular entities under an isoskeletomeric relationship are collected to give a set of isoskeletomers, which is concluded to be an equivalence class. The confusion caused by so-called ‘constitutional isomerism’ and its subcategories (‘skeletal isomerism’, ‘positional isomerism’, and so on) is critically discussed from the viewpoint of isoskeletomerism as a missing link. The double-entendre of the term constitution is examined when applied to both a 3D entity (a set of stereoisomers) and a 2D entity (a graph). Taxonomy of organic compounds and rational formulas, nomenclature of organic compounds, and combinatorial enumeration of chemical compounds are discussed from the viewpoint of isoskeletomerism.

  • Conceptual defects of modern stereochemistry. Comprehensive remedy by stereoisograms based on RS-Stereoisomerism for mediating between enantiomerism and Stereoisomerism
    Tetrahedron: Asymmetry, 2017
    Co-Authors: Shinsaku Fujita
    Abstract:

    Abstract The recognition of chirality as a single kind of handedness is a conceptual defect of modern stereochemistry, which has caused serious confusion in its theoretical foundations and stereochemical nomenclature. To remedy this defect, RS -stereogenicity is developed as another kind of handedness. These two kinds of handedness are integrated to give RS -Stereoisomerism, which is formulated diagrammatically by stereoisograms. During the process of the remedy, the lack of the concept of ligand reflections has been revealed as another conceptual defect. The lack of the concept of orbits (equivalence classes) has been found to be one more defect, which has caused a misleading classification of isomers. By adopting the concept of orbits, the revised hierarchy of isomerism is developed, i.e., isomers ⊇ isoskeletomers ⊇ stereoisomers ⊇ RS -stereoisomers ⊇ enantiomers ⊇ 3D-structures. Thereby, the theoretical foundations of modern stereochemistry are restructured rationally.

Nikos Chronakis - One of the best experts on this subject based on the ideXlab platform.

Maria Riala - One of the best experts on this subject based on the ideXlab platform.

Lingyu Zhu - One of the best experts on this subject based on the ideXlab platform.

  • tunable supramolecular helical aggregate and optoelectrical properties of perylene diimides by Stereoisomerism of sugar
    Journal of Physical Chemistry C, 2017
    Co-Authors: Xiaotian Liu, Zhijian Huang, Yongwei Huang, Lingyu Zhu
    Abstract:

    In the present study, two sugar-based perylenediimide derivatives (PDIs) substituted at the imide positions with carbohydrate groups were synthesized to investigate the impact of the Stereoisomerism of the sugar on the aggregation morphology and optoelectrical properties. The results showed that right-handed and left-handed helical nanowire fibers were obtained in tetrahydrofuran (THF)/H2O solution for α-d-glucopyranoside- and β-d-glucopyranoside-substituted PDIs, respectively. Determination of the electrical current in hydrazine vapor revealed that both sugar-based chiral PDIs exhibited enhanced current changes compared to their achiral counterpart because of the larger π–π orbital overlap between their adjacent perylene cores. A larger π–π orbital overlap and a smaller π–π interplanar spacing increased the electrical current of the α-d-glucopyranoside-substituted PDI more markedly than that of the β-d-glucopyranoside-substituted PDI. The results of this study suggest that the Stereoisomerism of chiral s...

  • Tunable Supramolecular Helical Aggregate and Optoelectrical Properties of Perylene Diimides by Stereoisomerism of Sugar
    2017
    Co-Authors: Xiaotian Liu, Zhijian Huang, Yongwei Huang, Lingyu Zhu
    Abstract:

    In the present study, two sugar-based perylenediimide derivatives (PDIs) substituted at the imide positions with carbohydrate groups were synthesized to investigate the impact of the Stereoisomerism of the sugar on the aggregation morphology and optoelectrical properties. The results showed that right-handed and left-handed helical nanowire fibers were obtained in tetrahydrofuran (THF)/H2O solution for α-d-glucopyranoside- and β-d-glucopyranoside-substituted PDIs, respectively. Determination of the electrical current in hydrazine vapor revealed that both sugar-based chiral PDIs exhibited enhanced current changes compared to their achiral counterpart because of the larger π–π orbital overlap between their adjacent perylene cores. A larger π–π orbital overlap and a smaller π–π interplanar spacing increased the electrical current of the α-d-glucopyranoside-substituted PDI more markedly than that of the β-d-glucopyranoside-substituted PDI. The results of this study suggest that the Stereoisomerism of chiral sugar groups significantly influences the aggregation morphology and optoelectrical properties of PDIs by adjusting their intermolecular interactions, π–π overlap, and π–π distance

Didier Villemin - One of the best experts on this subject based on the ideXlab platform.

  • Chemoinformatics and Stereoisomerism
    Pattern Recognition Letters, 2017
    Co-Authors: Pierre-Anthony Grenier, Luc Brun, Didier Villemin
    Abstract:

    The framework is the prediction of molecules properties thanks to graph kernels.A graph kernel which take into account Stereoisomerism is proposed.This kernel use a set of subgraphs to compare molecules.Two extensions of this kernel allow to compare the neighborhood of those subgraphs.A measure of similarity between those subgraphs is proposed. In chemoinformatics, Quantitative Structure Activity and Property Relationships (QSAR and QSPR) are two fields which aim to predict properties of molecules thanks to computational techniques. In these fields, graph kernels provide a powerful tool which allows to combine the natural encoding of molecules by graphs with usual statistical tools. However, some molecules may have a same graph but differ by the three dimensional orientation of their atoms in space. These molecules, called stereoisomers, may have different properties which cannot be correctly predicted using usual graph encodings. In a previous study we proposed to encode the Stereoisomerism property of each atom by a local subgraph, called minimal stereo subgraph, and we designed a kernel based on the comparison of bags of such subgraphs. This kernel allows to predict properties induced by the Stereoisomerism which cannot be correctly predicted using usual graph kernels. However, it has two major drawbacks : it considers each minimal stereo subgraph without taking into account its surroundings, and it considers that two non identical minimal stereo subgraphs have a null similarity. In this paper we present three extensions to tackle those drawbacks. The first extension allows to take into account interactions between minimal stereo subgraphs. The second extension allows to compare the neighborhood of minimal stereo subgraphs. And finally, the third extension provides a measure of similarity between different minimal stereo subgraphs.

  • Taking into account Stereoisomerism in the prediction of molecular properties
    2016
    Co-Authors: Pierre-Anthony Grenier, Luc Brun, Didier Villemin
    Abstract:

    The prediction of molecule's properties through Quantitative Structure Activity (resp. Property) Relationships are two active research fields named QSAR and QSPR. Within these frameworks Graph kernels allow to combine a natural encoding of a molecule by a graph with classical statistical tools such as SVM or kernel ridge regression. Unfortunately some molecules encoded by a same graph and differing only by the three dimensional orientation of their atoms in space have different properties. Such molecules are called stereoisomers. These latter properties can not be predicted by usual graph methods which do not encode Stereoisomerism. In a previous paper, we proposed to encode the stereoiso-merism property of each atom by a local subgraph, called minimal stereo subgraph, and we designed a kernel based on the comparison of bags of such subgraphs. However, the encoding of a molecule by a bag of subgraphs induces an important loss of information. In this paper, we propose a new kernel based both on the spatial relationships between minimal stereo subgraphs and the local neighbourhood of each minimal stereo subgraph within its supergraph. Our experiments show the benefits of taking into account such information.

  • taking into account Stereoisomerism in the prediction of molecular properties
    International Conference on Pattern Recognition, 2016
    Co-Authors: Pierre-Anthony Grenier, Luc Brun, Didier Villemin
    Abstract:

    The prediction of molecule's properties through Quantitative Structure Activity (resp. Property) Relationships are two active research fields named QSAR and QSPR. Within these frameworks Graph kernels allow to combine a natural encoding of a molecule by a graph with classical statistical tools such as SVM or kernel ridge regression. Unfortunately some molecules encoded by a same graph and differing only by the three dimensional orientation of their atoms in space have different properties. Such molecules are called stereoisomers. These latter properties can not be predicted by usual graph methods which do not encode Stereoisomerism.

  • Incorporating Molecule's Stereisomerism within the Machine Learning Framework
    2016
    Co-Authors: Pierre-Anthony Grenier, Luc Brun, Didier Villemin
    Abstract:

    An important field of chemoinformatics consists in the prediction of molecule's properties, and within this field, graph kernels constitute a powerful framework thanks to their ability to combine a natural encoding of molecules by graphs, with classical statistical tools. Unfortunately some molecules encoded by a same graph and differing only by the three dimensional orientation of their atoms in space have different properties. Such molecules are called stereoisomers. These latter properties can not be predicted by usual graph methods which do not encode Stereoisomerism. In this paper we propose to encode the Stereoisomerism property of each atom of a molecule by a local subgraph. A kernel between bags of such subgraphs provides a similarity measure incorporating Stereoisomerism properties. We then propose two extensions of this kernel incorporating in each sub graph information about its surroundings.

  • Taking into account interaction between stereocenters in a graph kernel framework
    2015
    Co-Authors: Pierre-Anthony Grenier, Luc Brun, Didier Villemin
    Abstract:

    An important field of chemoinformatics consists in the pre-diction of molecule's properties, and within this field, graph kernels con-stitute a powerful framework thanks to their ability to combine a natural encoding of molecules by graphs, with classical statistical tools. Unfor-tunately some molecules encoded by a same graph and differing only by the three dimensional orientation of their atoms in space have different properties. Such molecules are called stereoisomers. These latter proper-ties can not be predicted by usual graph methods. In this report, ordered graphs are introduced in order to represent those molecules. Then the Stereoisomerism property of each atom of a molecule is encoded by a lo-cal ordered subgraph. Finally a graph of interactions between those local subgraphs is constructed.