Organic Chemistry I : Crash Course Part 1

(1) Structure of organic molecules
(a) connectivity and structural isomerism
(b) electron delocalization and drawing/evaluating resonance contributors
(c) conformational analysis (draw/evaluate chair forms and Newman projections)
(d) stereochemical analysis (E/Z alkenes; 1, 2 similar, or 2 dissimilar sterecenters)


(2) Prediction and explanation of Bronsted Acid-Base reactions (use of pKa table)
(3) Reactions of polar C-X sigma bonds (SNand E reactions & mechanisms)(4) Electrophilic addition reactions of C-C pi bonds (regioselectivity & mechanisms)(a) addition of H/eN (strong & weak Bronsted acids)
(b) addition of X/eN (halogenation; halogens & other nucleophiles)
(c) oxidation (mCPBA; OsO4; ozonolysis)
(d) reduction (hydrogenation with regular & poison catalyst; dissolving metal redn)
(5) EAS: Electrophilic Aromatic Substitution (regioselectivity & mechanisms)

This might be the typical curriculum of an Organic Chemistry I course. In this article I’ll be breaking down each of these concepts and adding some resources I found helpful for studying. This is the first of a 5 part series on Organic Chemistry.

Structure of Organic Molecules
Organic molecules usually are Carbon containing. This definition is a bit reductionist, but Carbon is really the star of the show for the majority of your Organic Chemistry experience. Make sure that you can look at a formula like C6H9 and know how to draw the Lewis Structure. A Lewis Structure shows how all the electrons are interacting with each other in a simple drawing. The number of valence electrons an atom has is determined by its place on the periodic table. Some atoms can have expanded octets such as Sulfur (S) and Phosphorous (P) so make note of any exceptions.
To make accurate complex representations of a molecule from its formula we use Units of Unsaturation. The formula for UU is ((2n+ 2)- # Hydrogens – # Monovalents – #Trivalent ))/ 2.
n represents the number of Carbons , monovalent means any of the halogens and trivalent means Nitrogen, Phosphorous and etc.
Units of Unsaturation help you determine where and if there are any multiple bonds (i.e. double bonds) or rings to factor in to your drawing. This can help guide your thinking.

a)Connectivity and Structural Isomerism
Connectivity, like it sounds, are how different atoms are connected to each other in a compound.
A structural, or constitutional, isomer of another compound is a compound that has the SAME MOLECULAR FORMULA but different CONNECTIVITY. This means that there should be the same number of let’s say Cs, Os and Hs, but they could be connected to each other in a different way. Structural Isomers can differ in chain, position or functional group. This can be seen as different arrangements of the carbon skeleton, differing position of the same functional group or differing position resulting in a different functional group. It is NOT the same molecule.

(b) electron delocalization and drawing/evaluating resonance contributors
This is a crucial skill to hone in on for organic chemistry. You’ll want to make sure of what electrons are localized (meaning that they cannot move) or delocalized (meaning that they can move to different parts of the structure). Recognizing the DELOCALIZABLE electrons helps you to create Resonance Structures which are differing representations of the same molecule that places charges (due to the movement of electrons) on different atoms.

How to Determine if an Electron is Localized or Delocalized
1.Look at any multiple bonds. Double bonds and triple bonds are sources of electrons and those electrons can possibly move to nearby atoms.
2.Look at adjacent atoms or groups. Determine whether the nearby atoms can receive the electrons from another spot.

Resonance Structure Merit
Resonance structures are different representations of the same molecule.There are better and worse resonance structures. The major forms of a resonance structure are the best looking forms with the most merit. However, the minor forms of a resonance structure can help you determine the reactivity of the compound by showing areas that are electron rich or electron poor (nucleophilic and electrophilic respectively).
1. Closed shell resonance contributors or structures > open shell. A closed shell means that the atom has all the electrons that it needs whereas an open shell means its missing some and thus is not happy!
2.Place the charges (-) on most electronegative atom and (+) on electropositive atom.
3.Have separation of charges. Do not put a (-) and (-) together or a (+) and (+) nearby because they repel each other which is problematic.

(c) conformational analysis (draw/evaluate chair forms and Newman projections)
To understand conformational isomerism we first need to determine a working definition for stereoisomerism. Stereoisomers are another branch of isomers, they have the same functional groups and connectivities, but they differ in the arrangement of atoms in space. Conformational isomers are often visualized as Newman Projections and Chair Forms because they showcase if there is a different arrangement of atoms in space. Just because you see a Newman Projection or Chair Form does not automatically mean that they are conformational isomers, but you should evaluate to see if that is the case.
The image below shows the line structure of a Newman projection and below that a chair form. As you can see here, the differences between the left and the right are in the arrangement of atoms in space. To show the different arrangement of atoms in space, you’ll often see dashes or wedges in a structure. Furthermore, you’ll also have axial and equatorial positions for the chair structures.

Newman Projections
Newman Projections require a lot of spatial reasoning skills. I recommend using 3D visual aids either online or physical kits to help with figuring out what is happening in the molecule.
How to Draw a Newman Projection
You’ll be given a structure with 2 carbons that are attached to each other and a bunch of other structures attached to those 2 carbons. You’ll want to make one carbon the “front” and one carbon the “back.” Once that has been determined look at all the components attached to the carbon in the front and determine what goes on a dash, a wedge or just a line. Once you do that move to the “back” carbon and determine what goes on a dash, a wedge or just a line. Dashed lines are the moving into the page or up and wedges are moving out of the page or down. I recommend practicing this a lot!
There are different types of Newman Projection phenomenon to look at and know.
Anti, Gauche, Staggered and Eclipsed Forms.
1.Anti forms are more stable than gauche forms. They have the bulky or large groups at 180 degrees from each other rather than gauche which has them “next to each other” relatively speaking.
2.Staggered forms are more stable than eclipsed forms. Again they have the separation of the statically large groups rather than having the groups close to each other. Staggered forms will often have the groups be Anti to each other whereas the Eclipsed forms will often have the groups be gauche to each other.

Source: http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch03/ch3-0-2.html
Source: http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch03/ch3-0-2.html
Source: https://www.youtube.com/watch?v=PCsfXIpMfcM

Chair Formations
These are representations of something called cyclohexanes (these are rings that are 6 membered). The chair formation includes axial bonds and equatorial bonds. To draw a chair follow the steps as outlined below. Then number your cyclohexane and chair to have an accurate drawing. Equatorial and Axial forms can be generated. Axial position is usually not preferred because when substituents are in the axial position, there tends to be more unfavorable interactions with other axial atoms on the same side. … When substituents are in the equatorial position, they are farther away from each other. This increases the stability of the conformation. For this same reason axial positions suffer from gauche interactions of statically bulky groups and are higher in energy overall.

Source: Lumen Learning
Source: Leah 4 Sci

d) Stereochemical Analysis
Recall the definition of stereoisomers as being the molecule with the same connectivity but different arrangements in space. You’ll want to recognize sources of stereoisomerism and what a stereo center is.
A stereocenter or chiral center is an atom with three or more different attachments, interchanging of two of these attachments leads to another stereoisomer. Most commonly, but not limited to, an sp3 (tetrahedral) carbon atom bearing four different attachments.

Here are 3 sources of stereoisomerism to recognize:
1) pi bonds with E/Z diastereomers: assign atom number priority, 1:1 comparison only
E is for opposite side!
Z is for Z same side!
2) oppositely-substituted even-sized rings with cis/trans diastereomers (need a pair of H’s to label)
cis is the same side
trans is the opposite side
3) tetrahedral stereocenters with 4 different groups
a) 1 stereocenter
2 stereoisomers (R) and (S)both chiral, both optically active(R) vs (S) : enantiomers1:1 mixture of (R)/(S) enantiomers: optically inactive, “racemic mixture”
b) 2 dissimilar stereocenters
4 stereoisomers(R,R), (S,S), (R,S), (S,R)all 4 are chiral, optically active(R,R) vs (S,S) : enantiomers(R,R) has 2 diastereomers
c) 2 similar stereocenters
3 stereoisomers(R,R), (S,S), (R,S-meso) 2 are chiral, optically activemeso: achiral, opt inactive(R,R) vs (S,S) : enantiomers(R,R) has 1 diastereomer(R,S) has no enantiomers(R,S) has 2 diastereomers
d) easy to extraopolate for N dissimilar stereocenters
4 dissimilar stereocenters -> 16 chiral stereoisomers(R,R,R,R) has one enantiomer, (S,S,S,S) and 14 diastereomers

Published by Magda Wojtara

Magda Wojtara is Junior at the LSA Honors College at the University of Michigan-Ann Arbor on a pre-med track with a major in Neuroscience. In her free time, she write articles, volunteers at a chronic pain outpatient facility with UM Medicine, does research, competes in HOSA, and, of course, enjoys photography and singing. In her spare time she manages her own travel and lifestyle blog: @journeythedestiantion on instagram and journeythedestination.weebly.com

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