A5025423742- Computational Drug Discovery Methods
- Analytical Chemistry and Chromatography
- Molecular spectroscopy and chirality
- Machine Learning in Materials Science
- Carbohydrate Chemistry and Synthesis
- Various Chemistry Research Topics
- Glycosylation and Glycoproteins Research
- Advanced Chemical Physics Studies
- Chemical Synthesis and Analysis
- Metabolomics and Mass Spectrometry Studies
- Fullerene Chemistry and Applications
- Neural Networks and Applications
- Boron and Carbon Nanomaterials Research
- Virtual Reality Applications and Impacts
- Synthesis and Properties of Aromatic Compounds
- Educational Robotics and Engineering
- Advanced Chemical Sensor Technologies
- Synthetic Organic Chemistry Methods
- Catalysis and Oxidation Reactions
- History and advancements in chemistry
- Innovative Educational Techniques
- Polymer Nanocomposite Synthesis and Irradiation
- Enzyme Catalysis and Immobilization
- Molecular Sensors and Ion Detection
- Spectroscopy and Quantum Chemical Studies
University of Zurich
2015-2024
Research Organization of Information and Systems
2015-2024
Quantum Chemistry Research Institute
2017-2020
National Institute of Informatics
2005-2016
RIKEN
1998-2013
RIKEN Advanced Science Institute
2010-2013
Gunma University
1993-2009
Japan Atomic Energy Agency
2009
ETH Zurich
2009
Future University Hakodate
2006-2008
The mechanism of solvent effects on the stereoselectivity glycosylation reactions is investigated using quantum-mechanical (QM) calculations and molecular dynamics (MD) simulations, considering a methyl-protected glucopyranoside triflate as glycosyl donor equivalent solvents acetonitrile, ether, dioxane, or toluene, well gas-phase conditions (vacuum). QM oxacarbenium-solvent complexes do not provide support to usual solvent-coordination hypothesis, suggesting that an experimentally observed...
Abstract Catalysis research is on the verge of experiencing a paradigm shift regarding how catalysts are designed and characterized due to rise catalyst informatics. The details informatics reviewed where following three key concepts proposed: data, data design via science, platform. Additionally, progress opportunities within explored introduced. If field grows in appropriate manner, methods approaches taken for would be fundamentally altered, leading towards great advancement catalysis research.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSOPHIA, a Knowledge Base-Guided Reaction Prediction System - Utilization of Base Derived from DatabaseHiroko Satoh and Kimito FunatsuCite this: J. Chem. Inf. Comput. Sci. 1995, 35, 1, 34–44Publication Date (Print):January 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ci00023a005https://doi.org/10.1021/ci00023a005research-articleACS PublicationsRequest reuse permissionsArticle...
An endocyclic pathway is proposed as a reaction mechanism for the anomerization from β (1,2-trans) to α (1,2-cis) configuration observed in glycosides carrying 2,3-trans cyclic protecting groups. This occurs presence of weak Lewis or Brønsted acid, while cleavage (endocleavage) typical was only when mediated by protic media strong acids. To rationalize behavior this class compounds, and promoting factors endocleavage are investigated using quantum-mechanical (QM) calculations experimental...
Abstract We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate minimal RMSD value of two atomic structures by optimal superimposition. not restricted systems with equal number atoms compare or a unique atom mapping between molecules. The can handle any type chemical structure, including transition states and which cannot be explained only valence bond (VB) theory (non-VB structures). It requires Cartesian coordinates for...
Micropollutants have become a serious environmental problem by threatening ecosystems and the quality of drinking water. This account investigates if advanced AI can be used to find solutions for this problem. We review background, challenges involved, current state-of-the-art quantitative structure-biodegradation relationships (QSBR). report on recent progress combining experiment, quantum chemistry (QC) chemoinformatics, provide perspective potential future uses technology help improve...
Abstract Generalized root mean square deviation (G-RMSD) is an optimization method for three-dimensional molecular similarity determination. It calculates the minimum value of RMSD among all possible one-to-one matchings between atoms and positions molecules. The first paper on G-RMSD introduced two approaches called alternating (AO) tangent space relaxation (TSR) methods, which give local optimum solutions. We propose here a new using branch-and-bound (BnB) isometric transformations,...
Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry 1960s. Most existing elucidators a structure-spectrum database to obtain clues about correct structure. Such is expected grow on daily basis. Hence, necessity develop an efficient system that can adapt growth also growing. Therefore, we have developed new elucidator using practically graph algorithms, including convex bipartite matching, weighted and Bron-Kerbosch...
Organic reactions occur as a result of complicated interactions among many factors: structural and electronic features reactants, reagents, catalysts, temperature, etc. In this study, organic were automatically classified based on these factors. A dataset 131 was investigated focusing the changes oxygen atoms at reaction sites by principal component analysis self-organizing neural networks analyses. Good correlations found between similarities in substructural transformations well with known...
This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. automatically deduces a transition network, called reaction route map (r-map), by using Scaled Hypersphere Search of Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based search has been achieved large ADDF, which makes it possible to trace only low state (TS) barriers while restraining bond lengths and structures with high free energy. It performs...
Synthesis of (23E)-cycloart-23-ene-3β,25-diol (1) and its 23Z-isomer 2 was achieved by using cycloartenol as a starting material, thus revising the proposed structure natural to 1 unequivocally. These synthetic studies revealed that structural revision (Z-form → E-form) should also be applied terpenoids such (23Z)-3β-acetoxyeupha-7,23-diene-25-ol, (23Z)-tirucalla-7,23-diene-3β,25-diol, quadrangularol A, quadrangularic acid K, daurichromene C.
Abstract Aminoglycosides containing a 2,3‐ trans carbamate group easily undergo anomerization from the 1,2‐ glycoside to cis isomer under mild acidic conditions. The N‐substituent of has significant effect on reaction; in particular, an N ‐acetyl facilitated rapid and complete α‐anomerization. differences reactivity due various N‐substituents were supported by results DFT calculations; orientation acetyl carbonyl close anomeric position was found contribute significantly directing reaction....
Abstract Pyranosides with N ‐benzyl‐2,3‐ trans ‐oxazolidinone undergo anomerization from the β form to α even in presence of a weak Lewis acid. Experimental evidence for endo ‐cleavage, breaking bond between pyran‐oxygen and anomeric carbon atoms, reactions was obtained. This unexpected phenomenon investigated by quantum mechanical calculations, which found clear differences transition states anomerized non‐anomerized substrates. The computations suggest that BF 3 induces ‐cleavage followed...
グリコシル化反応は、グリコシド結合を形成し糖鎖を生成する化学反応であり、グライコサイエンスにおける重要な化学反応の1つである。この糖鎖合成における鍵反応のメカニズムを理解することは、生体内におけるグリコシル化反応についての洞察を深めるだけでなく、合理的な戦略に基づいた化学合成技術の発展にも貢献すると期待される。本稿では、グリコシル化の反応機構に関する研究について、計算化学的アプローチによる取組みに焦点をあてて概説する。具体的には、本反応機構についての理論的研究の中で、一般に広く議論されている、隣接基関与、溶媒効果、立体電子効果に絡んだ 研究について紹介する。また、糖供与体の立体配座が、その化学反応性や立体選択性に与える影響や、ピラノシド環のエキソ開裂反応とエンド開裂反応についてなされている議論についても述べる。
A reaction generator in SOPHIA ( for by ) generates all possible product structures reconnections of free bonds obtained cutting a site which is automatically perceived the input reactantt structure and additions atoms and/or atomic groups (AAG) to bonds. The has been extended recognize add suitable AAG utilizing knowledge base derived from database. Contents are structural information characteristics sites their environments added during reactions considers conditions condition...
A new type of crown compounds (crownopaddlanes) bearing two cyclobutane rings were efficiently and selectively prepared by means intramolecular [2 + 2] photocycloaddition appropriate styrene derivatives, which was successfully carried out in cyclohexane under irradiation through a Pyrex filter. Crownopaddlanes 4a, 5, 6 exclusively quantitatively extracted Li(+) on the solid-liquid extraction. Upon competitive extraction, 4a showed highest selectivity toward over Na(+) K(+) (Li(+)/Na(+) =...
We describe a rigorous and fast algorithm for advanced canonical coding of planar chemical structures based on the Faulon et al. (J. Chem. Inf. Comput. Sci. 2004, 44, 427-436). Our works well even highly symmetric structures; moreover, an advantage our includes providing numbering atoms with consideration stereochemistry recognizing moieties. The structural line notation is also fit use stereochemical notation. These capabilities are usable general purposes in particularly essential...