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Related Concept Videos

Transition State Theory01:25

Transition State Theory

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
SN2 Reaction: Transition State02:26

SN2 Reaction: Transition State

An SN2 reaction of an alkyl halide is a single-step process in which bond formation between the nucleophile and the substrate and bond breaking between the substrate and the halide occurs simultaneously through a transition state without forming an intermediate.
When the nucleophile approaches the electrophilic carbon with its lone pairs, the halide acts as a leaving group and moves away with the electron-pair bonded to the carbon. Dotted partial bonds represent the bonds being formed or broken...
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

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 other...

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Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
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Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

Published on: September 6, 2019

A hierarchical transition state search algorithm.

Jorge M Del Campo1, Andreas M Köster

  • 1Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A. P. 14-740, México DF 07000, Mexico. jmartin@cinvestav.mx

The Journal of Chemical Physics
|July 16, 2008
PubMed
Summary

A new hierarchical transition state search algorithm combines saddle interpolation and trust region optimization for complex chemical reactions. This method aids in understanding reaction mechanisms, particularly for challenging systems like intramolecular Diels-Alder reactions.

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Area of Science:

  • Computational Chemistry
  • Theoretical Chemistry
  • Chemical Kinetics

Background:

  • Transition state (TS) search is crucial for understanding chemical reaction mechanisms.
  • Existing methods can struggle with complex molecules featuring multiple internal rotors.
  • Accurate TS identification is essential for predicting reaction pathways and kinetics.

Purpose of the Study:

  • To develop and implement a robust hierarchical transition state search algorithm.
  • To improve the efficiency and reliability of automated TS searches.
  • To investigate complex reaction mechanisms computationally.

Main Methods:

  • Developed a hierarchical TS search algorithm combining double-ended saddle interpolation with local uphill trust region optimization.
  • Derived a new formalism for incorporating distance constraints into the saddle interpolation method.
  • Validated the algorithm on 28 diverse chemical reactions using density functional theory (DFT) in the deMon2k program.

Main Results:

  • The hierarchical algorithm successfully located transition states for a challenging intramolecular Diels-Alder reaction with internal rotors.
  • The method demonstrated effectiveness in handling complex molecular systems.
  • The computational findings provide insights into the reaction mechanism and its relation to experimental product distribution.

Conclusions:

  • The developed hierarchical TS search algorithm offers a reliable approach for complex chemical systems.
  • This computational tool enhances the ability to elucidate reaction mechanisms.
  • The findings contribute to a deeper understanding of reaction dynamics and stereochemistry.