Molecular modeling

Instructions for in-class modeling activities

Setting up Spartan icons

February 1, 2021 in Molecular modeling | Permalink

I mentioned this topic briefly during a modeling session, but it went by fast and you may have missed the key instructions. The idea here is that Spartan lets you choose which icons to display in your Spartan window so that you can tailor things to match your needs and work more efficiently.

Because every icon corresponds to a menu item, you might think to yourself, “Why clutter up my window? I’ll just rely on the menus.” That would be a mistake. Not only do the icons save you mouse clicks, they also provide visual reminders about the tools that are available and work flow.

Here’s how you select icons for an Apple (Mac) computer. Choose Options > Preferences. When the Preferences window opens, choose the ICONS tab (it turns blue). The icons are listed by menu. Start with the File menu, click on the icons you want, and then continue working your way, menu by menu, all the way over to the Spectra menu, 12 menus in all. (Notes: 1) the Spectra menu doesn’t actually appear in the Spartan window, 2) my window doesn’t display all 12 menus at once so I had to use the slider at the bottom of the window to bring more menus into view.) When you’re done, click OK.

These thumbnail images show the icons that I currently rely on (click on the thumbnail for a more legible image):

Models for Sigmatropic Rearrangements & Migrations

April 11, 2017 in Molecular modeling | Permalink

The following models were optimized at EDF2/6-31G**. They include IR calculations (unscaled frequencies).

[1,n] migrations

  • 1,2-H in acyclic carbocation: TS | Rct
  • 1,5-H in acyclic system: TS | Rct
  • 1,5-H in cyclic system: TS | Rct
  • 1,7-H in acyclic system: TS | Rct
  • 1,5-CH3 in acyclic system: TS | Rct
  • 1,5-CH3 in cyclic system: TS | Rct
  • 1,5-H vs CH3 in 5-methyl-1,3-cyclopentadiene: H TS | CH3 TS | Rct

[3,3] rearrangements (unfinished 4/11/17)

 

Error: maximum number of optimization cycles was reached

February 23, 2015 in Homework, Molecular modeling | Permalink

Spartan can produce a number of “job failed” messages. The most frequent reason for failure is “maximum number of optimization cycles was reached.” I’ll explain what this message means, why it is so common, and what you can do about it.

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Converting published models into Spartan models

February 12, 2015 in Molecular modeling | Permalink

Most papers that include molecular models publish the atomic coordinates and total energies in the supporting information. The list of coordinates can be easily downloaded, saved on your computer, and converted into a Spartan’14 model by following these steps:

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Hard and Soft Lewis Acids

February 11, 2015 in Molecular modeling | Permalink

The authors of paper #2 reported on the behavior of a chiral dienophile in Diels-Alder reactions. For reasons that I will discuss on another day, they wanted to conduct their reactions at the lowest possible temperature and so a Lewis acid catalyst was required. They investigated several catalysts based on B and Al compounds and this raised some questions during our discussion last Monday.

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Anions that can tolerate 2-norbornyl cation

February 9, 2015 in Molecular modeling, Papers for discussion | Permalink

I forget whether this question came up in our discussion of the Scholz paper (paper #1), but 2-norbonyl cation was crystallized with Al2Br7 anion. The authors described this anion as “weakly coordinating,”

Our interest in binding challenging ions such as the [CX3]+ (X = Cl, Br, or I) cations (35–37) to weakly coordinating anions (38, 39) led us to exploit the ability of soft bromoaluminate anions, such as [Al2Br7]–, to stabilize, for example, the [C(CH3)3]+ carbocation in the solid state (40).

The unusual properties of this anion leap out from a comparison of potential maps of Al2Br7 anion (left) with BF4 anion (right) (EDF2/6-31g* made with iSpartan). Potentials on the former map never get more negative than approx. -340 kJ/mol, while those on the latter reach much more negative values (the extreme occurs at -615 kJ/mol in the orange-red bands between F’s).

Al2Br7 anion

Al2Br7 anion (EDF2/6-31G*, iSpartan)

BF4 anion

BF4 anion (EDF2/6-31G*, iSpartan)