Posts Tagged ‘Molecular dynamics’

Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.

Monday, March 20th, 2017
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The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).

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Dynamic effects in nucleophilic substitution at trigonal carbon.

Monday, July 16th, 2012
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Singleton and co-workers have produced some wonderful work showing how dynamic effects and not just transition states can control the outcome of reactions. Steve Bachrach’s blog contains many examples, including this recent one.

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