Chemical reaction with two different elementary transition states

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.

Download Full-text

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

10.26434/chemrxiv.13133465.v1 ◽

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.

Download Full-text

Favorable Direction in a Chemical Reaction Through the Maximum Hardness Principle

Journal of the Mexican Chemical Society ◽

10.29356/jmcs.v57i1.232 ◽

2017 ◽

Vol 57 (1) ◽

Author(s):

Sudip Pan ◽

Pratim K. Chattaraj

Keyword(s):

Electronic Structure ◽

Chemical Reactions ◽

Chemical Reaction ◽

Transition States ◽

Basis Sets ◽

Maximum Hardness ◽

Maximum Hardness Principle ◽

Hardness Values

Recently, an assessment regarding the validity of maximum hardness principle has been done taking 34 exothermic chemical reactions (Poater, J.; Swart, M.; Solà, M. J. Mex. Chem. Soc. 2012, 56, 311) in which only 46% and 53% of the total reactions have greater hardness for the products and the reactants than those for the reactants and the transition states, respectively. They have also mentioned that a larger set of reactions should be studied to draw a general conclusion regarding the validity of maximum hardness principle. We have noticed that the reactions having fewer number of reactants than that of products and / or very hard atoms like H, N, O, F or very hard molecules like H2, N2, HF, HCN, CH4, etc. appearing in the reactant side, are more likely to disobey maximum hardness principle. In addition, dependence of hardness values on level of theory, basis sets, definitions, formulas, approximations should be kept in mind before criticising the validity of maximum hardness principle. Since these electronic structure principles are qualitative in nature, one should not expect them to be valid in all cases.

Download Full-text

Directional observation on lipid of male nectary of Lindera megaphylla hemsl. by the rapid embedding method with polyethylene glycol (PEG)

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100161151 ◽

1990 ◽

Vol 48 (3) ◽

pp. 718-719

Author(s):

Dai Dalin ◽

Guo Jianmin

Keyword(s):

Electron Microscope ◽

Polyethylene Glycol ◽

Chemical Reaction ◽

Traditional Method ◽

Osmium Tetroxide ◽

Unsaturated Lipid ◽

Embedding Method ◽

Long Period ◽

New Methods

Lipid cytochemistry has not yet advanced far at the EM level. A major problem has been the loss of lipid during dehydration and embedding. Although the adoption of glutaraldehyde and osmium tetroxide accelerate the chemical reaction of lipid and osmium tetroxide can react on the double bouds of unsaturated lipid to from the osmium black, osmium tetroxide can be reduced in saturated lipid and subsequently some of unsaturated lipid are lost during dehydration. In order to reduce the loss of lipid by traditional method, some researchers adopted a few new methods, such as the change of embedding procedure and the adoption of new embedding media, to solve the problem. In a sense, these new methods are effective. They, however, usually require a long period of preparation. In this paper, we do research on the fiora nectary strucure of lauraceae by the rapid-embedding method wwith PEG under electron microscope and attempt to find a better method to solve the problem mentioned above.

Download Full-text