Related Experiment Video
Updated: Jul 11, 2026
05:51
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
Published on: July 19, 2019
Comparison of double-ended transition state search methods
Elena F Koslover1, David J Wales
1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
The Journal of Chemical Physics
|October 9, 2007
Summary
Comparing three double-ended transition state search methods reveals their performance is highly dependent on the specific molecular system and chosen parameters, with no single method consistently outperforming others for complex pathways.
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Chemical Physics
Background:
- Double-ended transition state search methods are crucial for understanding molecular transformations.
- The comparative performance of these methods for complex, multistep pathways is not well-established.
- Characterizing pathways between structurally diverse molecular conformations presents a significant challenge.
Purpose of the Study:
- To compare the performance of three prominent double-ended transition state search methods.
- To evaluate their effectiveness in characterizing complex reaction pathways.
- To identify system and parameter dependencies influencing method performance.
Main Methods:
- Comparison of doubly-nudged elastic band, string method, and growing string method.
- Application to benchmark systems: Lennard-Jones clusters (LJ(7), LJ(13), LJ(38), LJ(75)) and peptide folding.
- Utilizing a missing connection network flow algorithm to build complex pathways.
Main Results:
- No single method demonstrated superior performance across all tested systems.
- Method effectiveness was found to be strongly dependent on the specific molecular system.
- Parameter choices significantly impacted the success and efficiency of each method.
- A database of paths for LJ(13) was used to suggest optimal parameter values.
Conclusions:
- The choice of double-ended transition state search method should be guided by system-specific characteristics and parameter optimization.
- Further research is needed to develop more robust and universally applicable methods for complex pathway searches.
- Current double-ended methods offer valuable but context-dependent tools for exploring molecular transformations.
Related Concept Videos
01:25Transition 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...
02:13Energy 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...
01:12Double Resonance Techniques: Overview
Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...
Spin decoupling is usually achieved by...
02:26SN2 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...
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...
01:58Cooperative 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...
01:58Cooperative 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...