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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...
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...
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...

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Related Experiment Video

Updated: May 29, 2026

SwarmSight: Real-time Tracking of Insect Antenna Movements and Proboscis Extension Reflex Using a Common Preparation and Conventional Hardware
08:13

SwarmSight: Real-time Tracking of Insect Antenna Movements and Proboscis Extension Reflex Using a Common Preparation and Conventional Hardware

Published on: December 25, 2017

Using swarm intelligence for finding transition states and reaction paths.

René Fournier1, Satya Bulusu, Stephen Chen

  • 1Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada. renef@yorku.ca

The Journal of Chemical Physics
|September 22, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel algorithm for exploring potential energy surfaces (PES) to identify reaction pathways and transition states. The method uses "climbers" to efficiently navigate complex PES landscapes, discovering new minima and saddle points.

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Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling
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Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling

Published on: November 11, 2008

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SwarmSight: Real-time Tracking of Insect Antenna Movements and Proboscis Extension Reflex Using a Common Preparation and Conventional Hardware
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Published on: December 25, 2017

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling
08:24

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling

Published on: November 11, 2008

Area of Science:

  • Computational Chemistry
  • Chemical Physics
  • Materials Science

Background:

  • Exploring potential energy surfaces (PES) is crucial for understanding chemical reactions and molecular behavior.
  • Identifying transition states and reaction pathways is computationally challenging, often requiring extensive searches.

Purpose of the Study:

  • To present a new algorithm for efficient exploration of potential energy surfaces.
  • To locate approximate reaction paths and transition states on PES.
  • To discover previously unknown minima on the PES.

Main Methods:

  • The algorithm employs multiple atomic configurations, termed "climbers," initiated near a local minimum.
  • Climbers utilize energy and energy derivatives for individual pathfinding and relative fitness for collective decision-making.
  • The method iteratively moves climbers toward saddle points and down to new minima, avoiding revisits.

Main Results:

  • The algorithm successfully explored PES and identified reaction paths and transition states in eight small test systems.
  • The method demonstrated its capability to discover previously unknown minima and navigate complex PES landscapes.
  • Applied to systems like Li(8), Al(7)(+), Ag(7), and Ag(2)NH(3), showcasing potential applications.

Conclusions:

  • The developed algorithm offers an efficient approach for exploring complex potential energy surfaces.
  • This method can aid in the discovery of reaction mechanisms and stable configurations in various chemical systems.
  • The "climbers" approach provides a robust strategy for navigating PES and identifying critical points.