W3C home > Mailing lists > Public > public-chem-web-pub@w3.org > April 2021

Next Organic Chemistry Brain Storming Session

From: Stefan M. Kilyanek <kilyanek@uark.edu>
Date: Thu, 22 Apr 2021 19:38:46 +0000
To: Chemistry CG <public-chem-web-pub@w3.org>
Message-ID: <SN4PR0401MB363193B1B7C5B3E424532F1ABB469@SN4PR0401MB3631.namprd04.prod.outlook.com>
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.

Hope you can join us next week!


Stefan M. Kilyanek
Associate Professor
Department of Chemistry and Biochemistry
University of Arkansas
Fayetteville, AR 72701

Summary of previous brainstorming session

General rules

  1.  Whenever possible carbon numbers / position numbers will correspond to IUPAC conventions.
  2.  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.
  3.  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".
  4.  Mechanistic descriptions
     *   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.
The reaction would be described using the general language of
"Reactant 1 and reactant 2 reacts to form product 1 and product 2."
Specifically, the reaction description would be:
"n-butyl lithium and S-2-bromobutane reacts to form LiBr and R-3-methyl heptane. "

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."

Zoom information

Stefan M. Kilyanek is inviting you to a scheduled Zoom meeting.

Topic: Organic Chemistry Brainstorming Session
Time: Apr 29, 2021 11:00 AM Central Time (US and Canada)

Join Zoom Meeting

Meeting ID: 875 0638 2772
Passcode: K8mCz$M3
One tap mobile
+19292056099,,87506382772#,,,,*53626706# US (New York)
+13017158592,,87506382772#,,,,*53626706# US (Washington DC)

Dial by your location
        +1 929 205 6099 US (New York)
        +1 301 715 8592 US (Washington DC)
        +1 312 626 6799 US (Chicago)
        +1 669 900 6833 US (San Jose)
        +1 253 215 8782 US (Tacoma)
        +1 346 248 7799 US (Houston)
Meeting ID: 875 0638 2772
Passcode: 53626706
Find your local number: https://uark.zoom.us/u/keDvo99fRW

Join by SIP

Join by H.323 (US West) (US East) (India Mumbai) (India Hyderabad) (Amsterdam Netherlands) (Germany) (Australia Sydney) (Australia Melbourne) (Singapore) (Brazil) (Canada Toronto) (Canada Vancouver) (Japan Tokyo) (Japan Osaka)
Meeting ID: 875 0638 2772
Passcode: 53626706

Received on Thursday, 22 April 2021 19:39:08 UTC

This archive was generated by hypermail 2.4.0 : Thursday, 22 April 2021 19:39:10 UTC