scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

Methylamination of some 3,6-dinitro-1,8-naphthyridines with liquid methylamine – potassium permanganate

2000 ◽  
Vol 78 (7) ◽  
pp. 950-956
Author(s):  
Marian Wozniak ◽  
Maria Grzegozek ◽  
Piotr Surylo
Keyword(s):  
Quantum Chemical Calculations ◽  
Potassium Permanganate ◽  
Satisfactory Agreement ◽  
Quantum Chemical ◽  
Transition States ◽  
Molecular Orbitals ◽  
Heats Of Formation ◽  
Convenient Synthesis

3,6-Dinitro-1,8-naphthyridine and its 2-substituted derivatives are dehydro-methylaminated with the solution of potassium permanganate in liquid methylamine (LMA–PP) to the corresponding mono- or mono- and bis(methylamino)-3,6-dinitro-1,8-naphthyridines. In the case of 2-chloro- and 2-methoxy-3,6-dinitro-1,8-naphthyridine the replacement of chloro and methoxy substituents by the NHCH3 group occurs as well. Quantum-chemical calculations indicate the reactions to be controlled by the interaction of the frontal molecular orbitals (FMO) of the reagents. Moreover the heats of formation of intermediary methylamino-σ-adducts and transition states are calculated for the reaction studied. The calculations show satisfactory agreement between calculated and observed results. A convenient synthesis of some 2-substituted-3,6-dinitro-1,8-naphthyridines is reported.Key words: methylaminations, calculations PM3, nitro-1,8-naphthyridines, oxidation.

Strukturen ladungsgestörter oder räumlich überfüllter Moleküle, 80 [1 - 3] Strukturänderungen von p-Benzochinon durch Donator- und Akzeptor-Substituenten

1996 ◽  
Vol 51 (2) ◽  
pp. 153-171 ◽  
Author(s):  
Hans Bock ◽  
Sabine Nick ◽  
Wolfgang Seitz ◽  
Christian Näther ◽  
Jan W. Bats
Keyword(s):  
Charge Distribution ◽  
Quantum Chemical Calculations ◽  
Satisfactory Agreement ◽  
Quantum Chemical ◽  
Structural Changes ◽  
Structural Data ◽  
Semiempirical Calculations ◽  
Reduction Potentials ◽  
Donor Acceptor ◽  
Structural Summary

Abstract The structures of seven di- or tetrasubstituted p-benzoquinone derivatives O=C(XC=CH )2C=O and O=C(XC=CX)2C=O with substituents X = -OCH3, -N(CH2)5, - N(CH2CH2)2O, -Cl, -CN and -⊕N(HC=CH)2C-N(CH3)2 are presented and discussed in comparison with published ones substituted by X = -Si(CH3)3, -C6H5, -N(CH3)2, -⊕N(HC=CH)2CN(CH3)2, -O⊖ , and - NO2. Based on the introduction, in which halfwave-reduction potentials, geometry-optimized quantum-chemical calculations on substituent perturbation and known structural data of p-benzoquinone derivatives are used to characterize their molecular ground states. The structural changes indicate how substituent perturbations might be rationalized. Of the categories defined - imperturbed, donor, donor/acceptor and acceptor perturbed - the donorsubstituted p-benzoquinones do exhibit the largest differences, often called cyanine distorsion. In very satisfactory agreement with extensive semiempirical calculations, all effects determined experimentally are discussed in terms of varying charge distribution. With respect to the biochemical importance of p-benzoquinone derivatives, this first structural summary points out important facets.

Security of NoSQL Database Against Intruders

2019 ◽  
Vol 13 (1) ◽  
pp. 5-12 ◽  
Author(s):  
Khaleel Ahmad ◽  
Mohammad Shoaib Alam ◽  
Nur Izura Udzir
Keyword(s):  
Big Data ◽  
Relational Database ◽  
Large Scale ◽  
Distributed Databases ◽  
Structural Data ◽  
Database Management System ◽  
Base System ◽  
Security Measures ◽  
Nosql Databases ◽  
Nosql Database

Background: The evolution of distributed web-based applications and cloud computing has brought about the demand to store a large amount of big data in distributed databases. Such efficient systems offer excessive availability and scalability to users. The new type of database resolves many new challenges especially in large-scale and high concurrency applications which are not present in the relational database. NoSQL refers to non-relational databases that are different from the Relational Database Management System. Objective: NoSQL has many features over traditional databases such as high scalability, distributed computing, lower cost, schema flexibility, semi or un-semi structural data and no complex relationship. Method: NoSQL databases are “BASE” Systems. The BASE (Basically Available, Soft state, Eventual consistency), formulates the CAP theorem the properties of which are used by BASE System. The distributed computer system cannot guarantee all of the following three properties at the same time that is consistency, availability and partition tolerance. Results: As progressively sharp big data is saved in NoSQL databases, it is essential to preserve higher security measures to ensure safe and trusted communication across the network. In this patent, we describe the security of NoSQL database against intruders which is growing rapidly. Conclusion: This patent also defines probably the most prominent NoSQL databases and describes their security aspects and problems.

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations

2020 ◽  
Author(s):  
Tsuyoshi Mita ◽  
Yu Harabuchi ◽  
Satoshi Maeda
Keyword(s):  
Quantum Chemical Calculations ◽  
Experimental Verification ◽  
Quantum Chemical ◽  
Synthesis Method ◽  
Target Product ◽  
Systematic Exploration ◽  
Hands On ◽  
Retrosynthetic Analysis ◽  
Synthetic Routes ◽  
Verification Process

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

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