Author Archives: alan
Setting up Spartan icons
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 … finish reading Setting up Spartan icons
Posted in Molecular modeling
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When the heat is ON
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
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: … finish reading Models for Sigmatropic Rearrangements & Migrations
Posted in Molecular modeling
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Organic chemistry! Puzzle chemistry!
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 … finish reading Organic chemistry! Puzzle chemistry!
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Error: maximum number of optimization cycles was reached
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 … finish reading Error: maximum number of optimization cycles was reached
Posted in Homework, Molecular modeling
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Converting published models into Spartan models
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:
Posted in Molecular modeling
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Hard and Soft Lewis Acids
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 … finish reading Hard and Soft Lewis Acids
Posted in Molecular modeling
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Diffusion-controlled rate constants are the MAX
Today’s class presented two formalisms that organic chemists use for connecting rates, rate constants, and the shapes of PE surfaces: Arrhenius equation (old-school but still useful and still widely used; go here for more background on collisions & kinetics) transition … finish reading Diffusion-controlled rate constants are the MAX
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Anions that can tolerate 2-norbornyl cation
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 … finish reading Anions that can tolerate 2-norbornyl cation
Posted in Molecular modeling, Papers for discussion
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Welcome back to Reed – Spring 2015
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 … finish reading Welcome back to Reed – Spring 2015
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