Related Experiment Video
Updated: Jul 19, 2026
09:09
A Modified Heterotopic Swine Hind Limb Transplant Model for Translational Vascularized Composite Allotransplantation (VCA) Research
Published on: October 14, 2013
Mechanism of ligand exchange studied using transition path sampling
Preston T Snee1, Jennifer Shanoski, Charles B Harris
1Department of Chemistry, University of California, Berkeley, California 94720, USA.
Journal of the American Chemical Society
|January 27, 2005
Summary
This study used transition path sampling molecular dynamics to reveal the multi-step mechanism of intermolecular ligand exchange for chromium pentacarbonyl in methanol. Favorable interactions were found between the reaction center and solvent bath.
Area of Science:
- Chemical Dynamics
- Computational Chemistry
- Coordination Chemistry
Background:
- Intermolecular ligand exchange is a fundamental process in coordination chemistry.
- Understanding the detailed mechanism of ligand exchange is crucial for controlling chemical reactions.
- Chromium pentacarbonyl (Cr(CO)5) serves as a model system for studying ligand substitution reactions.
Purpose of the Study:
- To elucidate the microscopic mechanism of intermolecular solvent ligand exchange.
- To investigate the exchange of methanol molecules bound to unsaturated Cr(CO)5.
- To analyze the role of solvent interactions in the ligand exchange process.
Main Methods:
- Utilized transition path sampling (TPS) combined with molecular dynamics (MD) simulations.
- Simulated the exchange of solvent molecules in methanol solution.
- Analyzed the reaction pathway and free energy landscape.
Main Results:
- Identified a multi-step mechanism involving partial dissociation and re-association of ligands.
- Observed specific solvent layer interactions during the exchange process.
- Found favorable interactions between the reaction center and the solvent bath, attributed to the adiabatic nature of the transition.
Conclusions:
- The study provides a detailed molecular-level understanding of intermolecular ligand exchange.
- Highlights the importance of solvent interactions and adiabaticity in the reaction mechanism.
- Demonstrates the utility of TPS-MD simulations for analyzing complex chemical processes and free energy landscapes.
Related Concept Videos
02:08Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
02:08Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
01:30Crossing Over
Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...