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Related Concept Videos

Transition State Theory01:25

Transition State Theory

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Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...
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Energy Diagrams, Transition States, and Intermediates02:13

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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...
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Induced-fit Model01:13

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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Reaction Mechanisms: The Steady-State Approximation01:26

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The steady-state approximation, also referred to as the quasi-steady-state approximation to differentiate it from a true steady state, is a widely used method for simplifying calculations in complex reaction mechanisms. This approach is particularly useful when dealing with multi-step reactions that involve reverse reactions or several steps, which can significantly increase mathematical complexity and make the reactions nearly unsolvable analytically.The steady-state approximation operates on...
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Reaction Mechanisms03:06

Reaction Mechanisms

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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:
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Radical Reactivity: Intramolecular vs Intermolecular01:33

Radical Reactivity: Intramolecular vs Intermolecular

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Radical reactions can occur either intermolecularly or intramolecularly. In an intermolecular radical reaction, a nucleophilic radical adds to an electrophilic alkene or vice versa. In such reactions, the radical and generally the alkene, which is also called the radical trap, are two different molecules. Additionally, for such intermolecular reactions to occur, the radical trap must be active, present in an excess concentration, and the radical starting material must have a weak...
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Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method.

Satoshi Maeda1, Tetsuya Taketsugu, Keiji Morokuma

  • 1Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.

Journal of Computational Chemistry
|November 5, 2013
PubMed
Summary

This study introduces single-component artificial force induced reaction (SC-AFIR), a fully automated method for finding transition states in intramolecular reactions. SC-AFIR successfully maps complex reaction pathways, improving theoretical chemical reaction studies.

Keywords:
potential energy surface • transition state • reaction path • artificial force induced reaction

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Area of Science:

  • Computational Chemistry
  • Theoretical Chemistry
  • Reaction Mechanism Studies

Background:

  • Identifying transition states (TS) is crucial for understanding complex reaction mechanisms but remains challenging.
  • Existing artificial force induced reaction (AFIR) methods are primarily for intermolecular reactions.
  • Manual fragmentation for intramolecular AFIR lacks automation and efficiency.

Purpose of the Study:

  • To develop a fully automated algorithm for searching intramolecular reaction pathways.
  • To extend the artificial force induced reaction (AFIR) method for intramolecular reactions.
  • To introduce the single-component AFIR (SC-AFIR) method.

Main Methods:

  • Proposed an automated fragmentation scheme for intramolecular molecules.
  • Integrated the automated fragmentation with the AFIR method to create SC-AFIR.
  • Applied SC-AFIR to study the Claisen rearrangement and cobalt-catalyzed hydroformylation.

Main Results:

  • Successfully developed and implemented a fully automated search algorithm for intramolecular pathways (SC-AFIR).
  • SC-AFIR efficiently located all significant pathways for the tested reactions.
  • Demonstrated the method's effectiveness in theoretical studies of complex reaction mechanisms.

Conclusions:

  • SC-AFIR provides an efficient and automated approach for exploring intramolecular reaction pathways.
  • This advancement simplifies the identification of transition states in complex chemical reactions.
  • The method enhances the capabilities of theoretical chemistry in reaction mechanism elucidation.