User's Guide

Introduction

The OrgoChemVisualizer software

Installation

To install OrgoChemVisualizer, see the releases tab on our Github.

Reaction Descriptions

The following are long-form descriptions of the reactions that are animated in OrgoChemVisualizer. Please see [insert reference here] for more details.

Addition of HBr to Alkenes

The Addition of HBr to Alkenes mechanism follows the reaction of an alkene, which is a molecule with a double bond between two Carbon molecules, and Hydrogen Bromide, or HBr. This mechanism takes place in two steps: Protonation of alkene and Addition of Br to carbocation. In the protonation step, the Hydrogen in HBr is drawn towards the double bond of the alkene while the bond between the Hydrogen and Bromide atoms stretches until it is broken, and simultaneously, the double bond in the alkene is also broken into a single bond. The Hydrogen bonds with one of the Carbons, and leaves the other Carbon, that was part of the C=C bond, with a positive charge. In the second step, the Bromide ion, Br-, is drawn to the positive charge left on the other Carbon, and forms a single bond with it. This molecule is called an alkyl bromide. This mechanism can also be performed with HCl, Hydrogen Chloride.

SN2 Reaction with Alkyl Halides

An SN2 reaction mechanism is a Nucleophilic Substitution in which the Rate Determining Step of the reaction involves 2 components: the concentration of both the substrate and the nucleophile. Alkyl Halides are compounds in which one or more Hydrogen atoms in an alkane have been replaced by halogen atoms, such as Fluorine, Chlorine, Bromine, or Iodine). This SN2 reaction with Alkyl Halides consists of 2-bromopropane, an alkane of three Carbon atoms with 7 Hydrogen atoms and one Bromine atom attached with single bonds, this is the Alkyl Halide; and a Hydroxide which consists of one Oxygen atom and one Hydrogen atom, this is the nucleophile. A Hydroxide molecule has a negative charge since the Oxygen atom has one extra pair of electrons, the molecule does not have the same amount of positive charges as negative charges. Because of this, the Hydroxide wants to become neutral. In this reaction, the extra pair of electrons in the Oxygen atom of the Hydroxide are drawn to the Alkyl Halide. Simultaneously, the electron pair breaks the bond between the Bromine and Carbon atoms and forms a new bond with the Carbon. This new molecule is called Methanol and is an alcohol.

E1 Mechanism

An E1 mechanism is also known as an Elimination 1 reaction, in this mechanism two substituents, any atom/group other than Hydrogen on a molecule, are removed. This reaction includes an alcohol and H2SO4 to eliminate the oxygen from the molecule, and eventually forming an alkene. For this reaction, the alcohol is a molecule called: ethanol and the alkene formed from this reaction is ethanol. This reaction is also known as the dehydration of ethanol. The first step of this reaction is the protonation of the alcohol which is achieved when the lone pairs of elections on the oxygen picks up a hydrogen ion from the sulphuric acid (H2SO4), the -OH group then becomes -OH2 with the addition of the hydrogen ion. In the next step, the H2O leaves the molecule because it is a good leaving group, this forms a carbocation. The carbocation molecule experiences the removal of a hydrogen ion in order to form a double bond between the two Carbons, and forming ethene (CH2=CH2).