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Related Concept Videos

Chemical Reactions01:19

Chemical Reactions

81.9K
A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely, the rearrangement of chemical bonds produces new compounds.
Chemical Reactions Rearrange Atoms into New Substances
A chemical reaction takes starting materials—the reactants—and changes them...
81.9K
Chemical Reactions02:26

Chemical Reactions

9.2K
A balanced chemical equation provides the information of chemical formulas of the reactants and products involved in the chemical change. A reaction’s stoichiometry helps predict how much of the reactant is needed to produce the desired amount of product, or in some cases, how much product will be formed from a specific amount of the reactant.
The relative amounts of reactants and products represented in a balanced chemical equation are often referred to as stoichiometric amounts.
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Radical Reactivity: Overview01:11

Radical Reactivity: Overview

2.2K
Radicals, the highly reactive species, gain stability by undergoing three different reactions. The first reaction involves a radical-radical coupling, in which a radical combines with another radical, forming a spin‐paired molecule. The second reaction is between a radical and a spin‐paired molecule, generating a new radical and a new spin‐paired molecule. The third reaction is radical decomposition in a unimolecular reaction, forming a new radical and a spin‐paired...
2.2K
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

15.7K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
15.7K
Reaction Mechanisms03:06

Reaction Mechanisms

24.5K
Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
24.5K
Chemical Equations03:10

Chemical Equations

67.1K
Chemical equations represent the identities and relative quantities of substances involved in a chemical reaction. The substances undergoing reaction are called reactants, and their formulas are placed on the left side of the equation. The substances generated by the reaction are called products, and their formulas are placed on the right side of the equation. Plus signs (+) separate individual reactant and product formulas, and an arrow (→) separates the reactant and product (left and...
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Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization
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ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

David Fooshee1, Alessio Andronico, Pierre Baldi

  • 1Institute for Genomics and Bioinformatics and School of Information and Computer Sciences, University of California , Irvine, California 92697, United States.

Journal of Chemical Information and Modeling
|October 29, 2013
PubMed
Summary
This summary is machine-generated.

ReactionMap is a novel algorithm for atom-mapping chemical reactions, improving data quality in large reaction databases. It accurately maps 96% of reactions, outperforming existing tools.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Data science

Background:

  • Large chemical reaction databases present data-mining opportunities but suffer from imperfect quality, including unbalanced and unmapped reactions.
  • Accurate atom-mapping is crucial for leveraging these databases for chemical research and discovery.

Purpose of the Study:

  • To develop and validate an efficient and accurate algorithm for atom-mapping chemical reactions.
  • To improve the quality and usability of large chemical reaction datasets.

Main Methods:

  • Developed ReactionMap, an algorithm combining maximum common chemical subgraph search and cost function minimization.
  • Trained ReactionMap on over 259,000 balanced, atom-mapped reactions from the SPRESI database.
  • Validated ReactionMap on large, diverse test sets of chemical reactions.

Main Results:

  • ReactionMap achieves high accuracy, correctly mapping approximately 99% of atoms and 96% of reactions.
  • The algorithm demonstrates a mean mapping time of 2 seconds per reaction.
  • ReactionMap's accuracy surpasses that of ChemAxon's AutoMapper and the DREAM Web tool on the same datasets.

Conclusions:

  • ReactionMap is an efficient and highly accurate solution for atom-mapping chemical reactions.
  • The algorithm significantly enhances the quality of data in large chemical reaction databases.
  • A ReactionMap server is publicly accessible for broader use in chemical informatics.