Charge not recognized in allylic cation (vs anion)

[JW_UMiami]

I've tried to show the MO and electrostatic potential maps in class, but ran into the following issue:

1. after constructing the molecule, I've changed the formal charge on the terminal carbon with out the pi bond to 1 (entered as +1).
2. After optimizing the geometry or using the remote server (which recognizes the +1 charge), generating the MOs shows the 2nd pi MO as occupied, i.e. at some point it has picked up a -1 charge.

The second pi MO is occupied in the cation:



The electrostatic potential map of the cation and anion are the same, despite the difference in charge:

[webmo]

Can you please clarify the problem? Note that you must correctly specify the total charge of the molecule when running the actual calculation. The format charges do not actually enter a MO calculation. They are for display / generation of an initial geometry only.

Note that your images do not display, so that may be part of the confusion.

[November_SSN]

I had run into a similar issue when using WebMO on my tablet in class last week, and it looks like I didn't indicate the charge of the molecule correctly. If I do it the right way, the problem does not appear again. Thank you for your explanation!

[jwk]

I am still having trouble with MO calculations on carbocations (see also post on MO visualizations). But first consider t-butyl anion: Build C3C and set central atom charge to -1. Cleanup Mechanics - gives pyramidal central carbon. Thus WebMO recognizes the correct hybridization of that atom and the correct total charge on the ion. Calculate, Molecular Orbitals shows HOMO with sp3-like geometry. (Fig. 1) All well and good.
Now Reset. Use the Adjust tool to change the charge on central C to +1. Cleanup Mechanics - gives trigonal planar central carbon. So again WebMO recognizes the correct hybridization of that atom (its not just a label for display). (see Fig.2) Calculate, Molecular Orbitals shows incorrect LUMO (Fig.3) and a HOMO with 2e in p-orbital on central carbon. (Fig. 4).
BTW, in WebMO 23 itself, the above procedure for t-butyl anion and t-butyl cation (Build; Set Charge on central atom; Cleanup-Mechanics; Huckel Orbitals tool) shows the same set of MOs as the tablet app.
Please explain again how to do this calculation correctly.

[OllyBe]

jwk wrote: ↑
I am still having trouble with MO calculations on carbocations (see also post on MO visualizations). But first consider t-butyl anion: Build C3C and set central atom charge to -1. Cleanup Mechanics - gives pyramidal central carbon. Thus WebMO recognizes the correct hybridization of that atom and the correct total charge on the ion. Calculate, Molecular Orbitals shows HOMO with sp3-like geometry. (Fig. 1) All well and good.
Now Reset. Use the Adjust tool to change the charge on central C to +1. Cleanup Mechanics - gives trigonal planar central carbon. So again WebMO recognizes the correct hybridization of that atom (its not just a label for display). (see Fig.2) Calculate, Molecular Orbitals shows incorrect LUMO (Fig.3) and a HOMO with 2e in p-orbital on central carbon. (Fig. 4).
BTW, in WebMO 23 itself, the above procedure for t-butyl anion and t-butyl cation (Build; Set Charge on central atom; Cleanup-Mechanics; Huckel Orbitals tool) shows the same set of MOs as the tablet app.
Please explain again how to do this calculation correctly.

It appears you're encountering issues with molecular orbital (MO) calculations for the t-butyl cation in WebMO, particularly regarding the visualization of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Here's a step-by-step guide to ensure accurate calculations:

Building the Molecule:

Construct the t-butyl cation structure within WebMO.

Assign a +1 charge to the central carbon atom using the 'Adjust' tool.

Geometry Optimization:

After setting the charge, perform a 'Cleanup' using molecular mechanics to achieve a reasonable starting geometry.

For more accurate results, execute a full geometry optimization using an appropriate computational chemistry engine (e.g., GAMESS, Gaussian). This step ensures that the molecular structure corresponds to a true energy minimum, which is crucial for reliable MO analysis.

Setting the Total Molecular Charge:

When configuring the calculation, explicitly specify the total charge of the molecule as +1. This is essential because the formal charges assigned during molecule building are primarily for visualization and do not influence the actual quantum mechanical calculations. Properly setting the total molecular charge ensures that the computational engine accounts for the correct electronic structure.
webmo.net

Performing the MO Calculation:

Select 'Molecular Orbitals' as the calculation type.

Choose an appropriate level of theory and basis set suitable for carbocation systems.

Submit the job and allow the calculation to complete.

Visualizing the Results:

Once the calculation is finished, navigate to the 'Job Results' page.

Use the MO viewer to inspect the HOMO and LUMO. In WebMO, occupied orbitals are typically represented in red/blue, while unoccupied orbitals appear in yellow/green

By meticulously following these steps and ensuring that the total molecular charge is correctly specified during the calculation setup, you should obtain accurate and meaningful MO visualizations for the t-butyl cation.

[schmidt]

Adding to the above reply:

For a "real" MO calculation done on the WebMO server, the total molecular charge is used and relevant.

For the simple Huckel MO calculations done direcetly in the app (or in the editor), without using an external computational chemistry program, the charges are NOT used. The simple built-in Huckel only works (accurately) for closed shell singlets!