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):

When the heat is ON

April 15, 2019 in Homework, Resources | Permalink

The full version of Roberts’ Rule of Pericyclic Reactions:

When the heat is ON

Four pi is CON

If you can remember that, you’ve got the rest of them!

– Charis Roberts ’19

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)

 

Organic chemistry! Puzzle chemistry!

January 24, 2017 in Uncategorized | Permalink

Yesterday I referred to the book Arrowsmith by Sinclair Lewis, wherein one of the characters (Prof. Gottlieb) makes disparaging remarks about organic chemistry. I have duplicated the full passage from Chapter 2 at the bottom of this post. Enjoy! (And here’s a link to the entire book. You can read it for Spring Break.)

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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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Diffusion-controlled rate constants are the MAX

February 11, 2015 in Uncategorized | Permalink

Today’s class presented two formalisms that organic chemists use for connecting rates, rate constants, and the shapes of PE surfaces:

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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)

Welcome back to Reed – Spring 2015

January 25, 2015 in Resources | Permalink

Welcome back to Reed. And thank you for signing up for Chem 324 – Adv. Physical Organic Chemistry.

You are probably wondering what this course will be about and that’s why you came here looking for some information. Well, your curiosity is well warranted. The course always changes a little (sometimes a lot!) from year to year. Perhaps because this year is the second time that I am offering the course in just two years, this enrollment is much smaller than last year’s crazy number and this will require some changes to fit the new enrollment.

This year I plan to follow the trails that have been laid down in recent years so don’t hesitate to talk to some seniors who have taken the class, but you can also expect some changes to fit the smaller class size and the better access you will have to molecular modeling software (more on that to come).

For now, take a look at what I have planned for this semester by looking at the About page.