ORGANIC CHEMISTRY FOR THE VISUAL LEARNER by Alexandra Ignacio
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INT RODUCT ION
Thanks for picking up this study guide! This guide was created as part of a summer research project for the Da Vinci Grant at the University of Notre Dame. It references the first semester of the Organic Chemistry course offered in the College of Science. As a disclaimer, this guide is not meant to teach organic chemistry, but rather act as a visual aid in studying and understanding the material. This project started as a means to illustrate organic chemistry in a way that organizes the difficult concepts into a visually communicated design, simple and accessible with a playful style similar to a children’s book. The work was done during the summer of 2014 while and created with a mix of Adobe Photoshop, Illustrator, and InDesign. Thank you, Professor Emily Beck, for advising me in the design aspects of this project, and ensuring I effectively communicate the material visually. Thank you, Professor James Parise, for providing reference material from your class and assuring the accuracy of the content of this study guide. This research was made possible in part by support from the Undergraduate Research Opportunity Program, Institute for Scholarship in the Liberal Arts, College of Arts and Letters, the University of Notre Dame.
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My name’s Amir, and I will pop out throughout the guide to provide instructions and aid! Let’s get started.
ELEMENTS The six most common elements in organic chemistry are...
oxygen carbon
phospherous
sulfur hydrogen
nitrogen 3
BASICS
NAME
FACE
# VALENCE ELECTRONS
carbon 4
nitrogen
oxygen
4
# PREFERRED LONE PAIRS
0
5
1
6
2
NAME
halogens fluroine chlorine bromine iodine
phosphorous
sulfur
FACE
# VALENCE ELECTRONS
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# PREFERRED LONE PAIRS
3
5
1
6
2
5
ORBITALS
Y
6
X
Z
Use these pages as a reminder of how orbitals are oriented and how they are merged.
1s
+
3p
3
=
4 sp3
4 7
POLARIT Y
+
-
H2O
O2 Covalent bonding is the equal sharing of electrons between two atoms that result in equal electron density
NaCl Polar covalent bonding is the unequal sharing of electrons between two atoms meaning electrons stay longer in the more electronegative atom
Ionic bonding is transfer of electrons between two atoms meaning giving them an ionic charge
The range of bonds can be viewed as a spectrum...
covalent bonding
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polar covalent bonding
ionic bonding
ACID-BASE
INCREASING PKA H2O
HX
(hydrogen halides)
+
R’
RCOOH
(carboxylic acids)
NH4+
R’
NH3
ROH
(alcohols)
H2SO4
<0
~5
~10
~15
>25
INCREASING ACIDITY
It’s important to know the general pKa trends of common compounds.
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ACID-BASE
Lewis acid:
Lewis base:
accepts an electron pair
donates an electron pair
conjugate base
H2O
+ H3O+
Cl-
Bronsted-Lowry acid:
Bronsted-Lowry base:
donates a hydrogen ion (H )/proton
accepts a hydrogen ion (H+)/proton
+
+
-
+ HCl
conjugate acid
+
-
+
+ HCl
H2O
Keep in mind that all Bronsted-Lowry Acids are Lewis acids, but not all Lewis Acids are Bronsted-Lowry Acids.
Cl-
Lewis Acids B-L Acids H2O
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H3O+
HBr HCl
AlCl3
BH3 FeBr3
FUNCT IONAL GROUPS A functional group is a group of atoms within a molecule that has a characterstic chemical behavior.
Common Function Groups name(ending)
name(ending)
structure
alkene
structure
name(ending)
imine
ester (-oate)
nitrile
thioester (-thioate)
thiol
amide
structure
alkyne
arene
halide or
sulfide
alcohol disulfide
carboxylic acid anhydride (-oic anhydride)
ether aldehyde diphosphate -
amine
-
-
ketone
carboxylic acid
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ALKANES AND CYCLOALKANES
PRACTICE! Can you label these conformations?
WORD BANK staggered anti eclipsed gauche cis trans axial equatorial
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1
5
2
6
3
7
4
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CHIRALIT Y
isomers same formula constitutional isomers
stereoisomers same connectivity
different connectivity enantiomers
diastereomers
mirror images
non-mirror images configurational diastereomers
cis-trans diastereomers
In enantiomers, their physical properties differ only in their behavior of polarized light. In diastereomers, their physical properties can differ in melting/ boiling points, densities, heat of formations, IR/NMR/UV-Vis spectra, and so on.
VOCAB racemic a 50:50 mixture of enantiomers that leads to a 0 degree specific rotation of polaraized light 13
T RANSIT ION STAT E GRAPH
TS
Imagine a hot air balloon. Heat must be added in order for it to rise in the air.
ENERGY
Similarly, compounds need energy in order to undergo a reaction. The transition state is the high energy structure in between the initial and final states
â&#x2C6;&#x2020;G°
(activation energy)
REACTION PROGRESS
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Recall that the highest point in the graph is the rate determining step.
EQUATIONS
∆G° = ∆H° – T∆S = –RT ln K eq
Free energy (∆Go) is directly related to the position of the equilibrium (K) ∆G° = –RT ln K
∆ G ° free energy + ∆G°: endergonic – ∆G°: exergonic
=
or
-∆G° = e
∆G° is determined by ∆Ho (enthalpy) and ∆So (entropy)
∆ H ° enthalpy + ∆H°: endothermic – ∆H°: exothermic
–
T ∆ S entropy (temperature dependant) + ∆S°: entropically favored – ∆S°: entropically disfavored
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POLAR REACT IONS
-
-
nucleophile
electrophile
electron source
electron sink
electron rich
electron poor
“nucleus loving” omg a nucleus
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-
δ+
δ+ δ+
+ δ+
“electron loving”
+
wow those electrons are attractive!
CURLY ARROW NOTAT ION
A-
Aâ&#x20AC;&#x201D;B
B+ -
Curly arrows depict electron pairs which always flow from nucleophile to source to
+
Electrons that flow from the nucleophile to form a covalent bond.
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ALKENE REACT IONS Addition Reactions Markovnikov regiochemistry
adding hydrogen halides
ether
addition of halogens Cl2 and Br2
anti-addition CH2 Cl2
halohydrin formation
addition of water by oxymercurationdemerucration addition of water by hydroboartionoxidation catalytic hydrogenation epoxidation with a peroxyacid
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+
1. Hg(OAc)2, H2O/THF
Markovnikov regiochemistry and anti-stereochemistry
Markovnikov regiochemistry
2. NaBH4
1. BH3, THF 2. H2O2, OH
-
Non-Markovnikov syn addition
syn addition Pd/C or PtO2
R
syn addition
Test your knowledge! What are some other alkene reactions?
ALKYNE REACT IONS Fill in the blanks! How well do you know your reactions?
Preparation of Alkynes dehydrohalogenation of vicinial dihalides
1.
R’
R
2.
1. 2.
R’
R
R
R’
+ 2
R
R’
+
1.
alkylation of acetylide anions
1.
R
R
-
+
1.
-
+
1.
+ 2
+ 2
R
R
R’
Preparation of Alkynes addition of HCl and HBr
addition of Cl2 and Br2
R R
R
ether
R ether
R
R
R’ R
R’
2.
R
R’ 2.
R
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