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Re: Next Organic Chemistry Brain Storming Session

From: Volker Sorge <volker.sorge@gmail.com>
Date: Thu, 29 Apr 2021 17:07:58 +0100
Message-ID: <CAE5-06QiTjdO9OUuT3jH7TPFiSOgO3PjXDh+w3S1ZkT6H13wBQ@mail.gmail.com>
To: "Stefan M. Kilyanek" <kilyanek@uark.edu>
Cc: Chemistry CG <public-chem-web-pub@w3.org>
These are links to all the diagrams for all the SMILES elements I
found in Stefan's text file.

https://speech-rule-engine.github.io/a11y-math-graphics/chemistry/ex1

https://speech-rule-engine.github.io/a11y-math-graphics/chemistry/ex2

https://speech-rule-engine.github.io/a11y-math-graphics/chemistry/ex3

https://speech-rule-engine.github.io/a11y-math-graphics/chemistry/ex4

On Thu, 22 Apr 2021 at 20:39, Stefan M. Kilyanek <kilyanek@uark.edu> wrote:
>
> Dear All,
>
>
>
> Our next brainstorming session for organic reaction mechanism descriptions is scheduled for 4-29-21 at 12:00 EDT.  The zoom information is given below. An invitation will also be sent shortly.
>
>
>
> For this discission we will brainstorm ways to describe a more complicated reaction mechanism.  Given the time constraints we will discuss the first order nucleophilic substation reaction (SN1) of tert-butyl alcohol by hydroiodic acid.  The SVG file “SN1.svg” is attached. A text file containing the SMILES description of the reactants products and intermediates is also attached.
>
>
>
> Additionally a summary of the brainstormed conventions for describing reactions and reaction mechanism are given below. I have attached these as PDF as well for convenience. The attached svg file “reaction.svg” shows the reaction discussed during our last meeting.
>
>
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> Hope you can join us next week!
>
>
>
> Stefan
>
>
>
> Stefan M. Kilyanek
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> Associate Professor
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> Department of Chemistry and Biochemistry
>
> University of Arkansas
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> Fayetteville, AR 72701
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>
>
> Summary of previous brainstorming session
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>
>
> General rules
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> Whenever possible carbon numbers / position numbers will correspond to IUPAC conventions.
> Carbon numbers / positions are not always IUPAC numbers especially when describing reaction mechanisms.  After reactions, the carbon numbers of a reactant or product will often change.
> Hierarchy of descriptions of structures and reactions.
>
> Reactant 1, reactant 2, product 1, product 2 etc. This is effectively the molecularity of the reaction.
> Functional groups on a carbon chain. Here we describe the molecule as a “n” number of carbons with a “name” functional group at either “position 1” or “C1” or some convention describing location within a structure.
> Stereochemistry. Here we describe “position 1” or “C1” as having an R or S stereochemistry. Or “X group on CX and Y group on CY have a cis stereochemistry” or “double bond between position C2 and C3 has an E stereochemistry”.
>
> Mechanistic descriptions
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> When electron pairs are moving in a typical reaction the terms “is attacked by” or “attacks” should be used.
> These terms are coupled to a bond breaking or making event for example “C1 of reactant 1 is attacked by C2 of reactant 2 to form a bond between C1 of reactant 1 and C2 of reactant 2.”
> “bond formed” “bond broken” including bond orders “double bond formed” double bond broken” should be used.
>
> For the reaction shown in the attached svg image.
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> The reaction would be described using the general language of
>
> “Reactant 1 and reactant 2 reacts to form product 1 and product 2.”
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> Specifically, the reaction description would be:
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> “n-butyl lithium and S-2-bromobutane reacts to form LiBr and R-3-methyl heptane. “
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>
>
> describing the mechanism requires a more detailed or “deeper level” of description of reactants and products.  A proposed description of reactants would be:
>
> Reactant 1, n-BuLi, is described as “a four-carbon chain with a lithium atom bonded to the terminal carbon, carbon position 1.”
>
> Reactant 2, S-2-bromo butane is described as “a four-carbon chain with a bromine bonded to carbon position 2” followed by “the bromine atom is attached to carbon 2 which has an S stereochemistry”
>
> A proposed description of the reaction mechanism would be:
>
> “the C-Li bond, at position C1 of reactant 1 attacks position C2 of reactant 2. A bond is formed between the C1 position of reactant 1 and the C2 position of reactant 2. The C-Br bond at position C2 of reactant 2 is broken. The C-Li bond at position C1 of reactant 1 is broken.”
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> Zoom information
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>
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> Stefan M. Kilyanek is inviting you to a scheduled Zoom meeting.
>
>
>
> Topic: Organic Chemistry Brainstorming Session
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> Time: Apr 29, 2021 11:00 AM Central Time (US and Canada)
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>
>
> Join Zoom Meeting
>
> https://uark.zoom.us/j/87506382772?pwd=VjdUNE1IMXVLeExuMkhka0dTamRLUT09
>
>
>
> Meeting ID: 875 0638 2772
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> Passcode: K8mCz$M3
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> One tap mobile
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> +19292056099,,87506382772#,,,,*53626706# US (New York)
>
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>
>
>
> Dial by your location
>
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>
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>
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> Find your local number: https://uark.zoom.us/u/keDvo99fRW
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>
> Join by SIP
>
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>
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Received on Thursday, 29 April 2021 16:08:23 UTC

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