Dialogue

9/05/24

I am confused about the difference between cis/trans and Z/E. I was under the impression that you explained them as they were the same thing and interchangeable. However, just before the quiz today, the TA said they were different but did not explain how they were different. What is the difference between them and why are they not interchangeable?

Response:

I consider Z/E and cis/trans to be essentially identical for describing molecular structure.  There is a difference however, in the formality of the two terms. The term Z/E is a specific nomenclature with specifically defined rules (priority rules) that are used for each substituent at the alkene carbons. The term cis/trans can be used in a more casual way; for example, in discussing molecular structure one can talk about two specified groups being cis to each other or two groups being trans to each other. These are relative terms.

In other words, cis/trans can be vague whereas E/Z is exact and unambiguous.  Consider a tetra-substituted or tri-substituted alkene.  Without use of the priority rules that underlie Z/E, the meaning of cis/trans is subjective, and hence arbitrary.  For a disubstituted alkene, Z/E and cis/trans would be identical, and that was the case I showed in class. But again, suppose there are two or more alkenes in a compound.  The rules of nomenclature are that each alkene in the compound be named with Z/E (not cis/trans) terms.

8/28/24

Hello Professor Lindsey! I am in the CH 225 class and I was wondering for the quiz tomorrow if we would need to know how to identify all of the functional groups in a large molecule such as in 2.59 in the Chapter 2 problems we were given? I also wanted to ask if we would be expected to know names such as Isopentane and Neopentae as in 2.58 in the given problems?

Response:

Thank you for your message. Instead of asking a question that can be translated into the form of “what is the least I have to know?“  –  I think you want to ask “do you consider knowing exotic names to be important?“ The answer is I do not consider knowing exotic names to be important.

Knowledge of functional groups is absolutely essential for understanding organic chemistry. However, we will get to functional groups in due course. It is not expected that anyone would know any functional groups after two weeks of organic chemistry. The assigned problem was simply meant as a preview that there is a richness and beauty to organic chemistry that’s deeper and more profound than simply the line drawings of alkanes. 

8/28/24

The question was posed today as to where the term "tropane" originates.  Here is an expanded answer:

Since antiquity, an extract of a particular plant has been used to dilate the pupils.  This was done not for medical purposes but to create allure.  Eventually, the plant was named (by Linnaeus) as Atropa belladonna to denote the physiological effects and use of the extract.  https://en.wikipedia.org/wiki/Atropa_belladonna

Centuries later the molecular structure of the active ingredient was identified; it was named atropine because it came from the plant Atropa belladonna.  Taking the structure of atropine and stripping it down (conceptually) to the core structure lacking substituents, that was very reasonably given the name tropane.  https://en.wikipedia.org/wiki/Tropane

Tropane is a non-systematic, legacy name.  The systematic name of tropane is N-methyl 8-azabicyclo[3.2.1]octane.  The "N-methyl" indicates a methyl group is attached to the nitrogen atom.  The "8-aza" describes the location of the nitrogen atom.  All of this is in the category of cultural enrichment.  We are not going to cover formal naming of bicyclo or spiro compounds.  One can see the utility of non-systematic names even though they are bewildering at first.