Organic Chemistry

Kekule’s Benzene vs Actual Benzene — On a cold winter afternoon, sitting in an armchair and sipping hot cocoa, August Kekule was lost in thoughts. He was in deep thought about what the structure of benzene would be like. He soon fell asleep, dreaming about benzene. In his dreams, he saw a “snake biting its own…

Organic Chemistry This came at the request of a redditor to teach stereochemistry in SMILES and I completely forgot about how important this was to teach at the beginning. It’s good to ask questions, helps me know what to teach. So let’s go back to a simple stereoisomer, valine: Where the amine…

Continuing on the standardizing of mechanisms in SMILES. Friedel-Crafts is a common reaction to learn electrophilic substitution. The best explanation of the mechanism I found through this Reddit post from OchemWizz. So let’s start writing this into SMILES starting_product = 'O=C(C)C1=CC=CC=C1' reactant_one = 'CC(Cl)C' reactant_two = '[Al](Cl)(Cl)(Cl)' The first step…

Our goal is to start recording mechanisms in SMILES langauge that is intuitive for an organic chemist to write. A lot of the mechanisms I will be abstracting from are Reddit and will be going with what the community agrees is the standard way of arrow pushing. …

In Organic Chemistry, we enter mechanisms through substitution and elimination reactions. Which you should remember from organic chemistry but good to review on your own. Sn1, Sn2 — Substitution nucleophile and the amount of steps. 2 is one step. 1 is 2 step. E1, E2 — Elimination Reactions to the…

Organic chemistry can be a challenging subject, but with the right approach, you can master it and achieve success in your coursework. …

When we add elements in KingDraw, the element is displayed in color by default.

Welcome to advanced cheminformatics where you will be learning more tricks of the trade in doing more fun things with large datasets. This course assumes you have a proficient understanding in both chemistry and computer science and have completed the undergraduate course. This is your first 1,000,000 Million molecules that…

Okay, let’s start pushing some boundaries of theory in SMILES. Here’s the colab notebook. Do you remember in organic chemistry we used to denote an “R” group as a placeholder for a substituent.