Gaussian input file is below: # opt=( modredundant,maxcycles=250 ) rhf/3-21g Stepwise mechanism: pulling H towards other Oxygen 0 1 Let's start from pulling the Hydrogen atom to other Oxygen: We shall pull Hydrogen from the OH group either to Oxygen or Nitrogen atom. The easiest way to start exploration of the Potential Energy Surface of a stepwise mechanism is to use a Tetrahedral Intermediate (TI) as a starting point. Stepwise Mechanism of the Peptide Bond Hydrolysis Two main reaction mechanisms were proposed in the literature, Concerted and Stepwise:įor the purpose of this tutorial it's easier to start from the stepwise mechanism. In this tutorial we shall investigate Potential Energy Surface of different reaction mechanisms of the peptide bond hydrolysis. So, now we can use a structure corresponding to the Saddle Point as a starting structure for finding a "true" Transition State. The animation can then be stopped via the red X icon which replaces it. We shall select a structure corresponding to the highest Total Energy (Saddle Point):īy pressing the green circle button in the toolbar of the Molecular View window you can animate the various structures. A plot is interactive, so you can click on the various points in the plot, and the corresponding structure will appear in the Molecular View window. We can visualize the results of the PES in GaussView:Ī plot of the Potential Energy Surface Scan shows that we have a saddle point. Numbers " -0.100000" and " 21" are used because of the initial 3.21 Å distance between the Hydrogen and Carbon atoms (you can check it in your favorite molecular editor), so a PES scan is supposed to run for a C-H distance from 3.21 to 1.11 Å with a -0.1 increment (or 0.1 decrement). " S" tells Gaussian to perform a relaxed Potential Energy Surface Scan incrementing the coordinate by a stepsize " -0.100000" a total of nsteps " 21" times, performing an optimization from each resulting starting geometry. Modreduntant option tells Gaussian to modify coordinate definition before performing the calculation and it requires a separate input section following the geometry specification.ī 1 8 S 21 -0.100000 is a Modreduntant section where " B" means a bond length defined by atoms " 1" and " 8".
The resulting Gaussian input is below: # opt=modredundant hf/3-21g Hydrogen atom migration PES 0 1 We shall study a double bond migration in CH 3CHCH 2:Īnd perform a PES of a Hydrogen atom migration from one Carbon atom to another, so we shall define a distance between a Hydrogen and distant Carbon atom as a reaction coordinate:
Case Study: Migration of a double bond in CH 3CHCH 2 It's advisable to start PES using the inexpensive computational methods, for example, HF/3-21G to get quickly the overall picture of the Potential Energy Surface along the reaction coordinate(s). Molecular structure at each point of the scan can be either kept rigid (a rigid PES scan which consists of single point energy evaluations) or be optimized (a relaxed PES scan with geometry optimization at each point which is requested with the Opt keyword). To request a PES in Gaussian one needs to specify the reaction variable(s) and their range for scan. So, prior to applying the exact methods for finding the Transition State it is a good idea to perform the Potential Energy Scan (PES) to explore a region of a potential energy surface. Though Gaussian has necessary facilities for finding the exact stationary points (either equilibrium structures or Saddle Points of the nth order), locating the Transition States is usually more tricky task than a simple geometry minimization.
0 kommentar(er)
