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Organic Chemistry Study Guide

Jocilyn Cara Pak

Topic 1: Nuclear atom

Anion -, Cation +
Charge= # of protons - # of electrons
Atomic #Z: # of protons
Mass #: # of protons + # of neutrons
Valence electron # = group #

Topic 2: Molecular Shape

Types of electron domains
1. 2 electrons in nonbonding domain (lone pair)
2. 2 electrons in a single bond domain
3. 4 electrons in a double bond domain
4. 6 electrons in a triple bond domain

VSEPR Theory: domains of electrons around a central atom will orient themselves to minimize the electron- electron repulsion
between the domains

Bond Angles
# of Domains 2 180 BeH2, O2N+, CO2
3 120 BH3, H3C+, CH2
4 109.5 Ch4, NH3, H2O

5 Molecular Shapes
Name AXmEn Notation Geometry Idealized Bond Angles
Linear AX2 180

Bent (V-Shaped) AX2E <180

Trigonal Planar AX2 120

Trigonal Pyramidal AX3E <120

Tetrahedral AX4 <180

Topic 3: Lewis Structures

Formal Charge: Group # - (# of nonbonded + bonded)
Net Charge: total charge of a molecule = sum of all formal charges
Carbocation: three single bonds with a positive charge on carbon

R, Y, Z placeholders
1. R H or Alkyl Group (CnHm)
2. X F, Cl, Br, or I (halogens)
3. Z any group/ group of atoms

Recognizing Formal Charges

1. Carbon
a. (+) 3 bonds, no lone pairs
b. (0) 4 bonds, no long pairs
c. (-) 3 bonds, with 1 lone pair
2. Oxygen
a. (+) 3 bonds, with 1 lone pair
b. (0) 2 bonds, with 2 lone pairs
c. (-) 1 bond, with 3 lone pairs
3. X Group (F, Cl, Br, or I)
a. (+) 2 bonds with 2 lone pairs
b. (0) 1 bond with 3 lone pairs
c. (-) no bond with lone pairs

Topic 4: Electron Orbitals

Covalent bond is formed by an overlap of orbitals

Types of Orbitals
1. Head to head overlaps sigma () bonds
2. Side to side overlaps- pi () bonds

Bonds between atoms

1. Single bond- one bond
2. Double bond- one bond plus one bond
3. Triple bond- one bond plus two bonds
* bonds form from hybridized p orbitals

Hybrid Orbital Sets

, , 109.5 sp3 tetrahedral 4 Domains
, 120 sp2 trigonal planar/ bent 3 Domains
2 , 180 sp linear 2 domains

Hybridization; combining s and p orbitals to form an equal number of new orbitals that are averages of the originals

Single bonds can rotate freely but double bonds cannot because the portion of a double bond prevents the bond axis from rotating

Common examples of hybridized orbitals

Hybrid Orbital # of Domains Angle
sp3 4 109.5

sp2 3 120

sp 2 180

Topic 5: Polar Bonds

Covalent bonds: strong attractions between atoms within a molecule (ex: H 2O)
Intermolecular forces: weak attractions between separate molecules (ex: between H 2O molecules)
Nonpolar covalent bonds: bonding electrons are shared equally (ex: C-H)
Polar covalent bonds: electrons shared unequally (ex: H-F)
Ionic bonds: extreme case of polarized bond (ex: NaCl)
Partial charges: or +

Electronegativity on periodic chart: EN increases, atoms get bigger

Polarity of bond: dipole moment arrow

-Arrow points to negative end

EN= | EN of atom1 EN of atom 2|

If net dipole = 0, molecule is nonpolar

Boiling Points: stronger IMF forces (hydrogen bonding) + surface area

Dipole-Dipole: Polar
Dipole Induced Dipole: Polar + Nonpolar
London Dispersion Force: Non-polar
Topic 6: Polar reactions (Proton Transfer Reactions)
Hydrogen bond: strongest type of dipole- dipole reaction, only forms between a lone pair on N, O, F and an H attached to a N, O, or X
Hydrogen bond donor: H suitable for hydrogen bonding
Hydrogen bond acceptor: lone pair suitable for hydrogen bonding
*Extreme H bond donor/acceptor will transfer H+ (with no electrons) from donor to acceptor one gets electrons, one get protons
(proton transfer reaction)

Strong Acids- Donates H+, extreme H bond donor

1. Hydroiodic acid

2. Hydrobromic acid

3. Hydrochloric acid

4. Sulfuric Acid (R=OH)

5. Nitric Acid

6. Hydronium Ion (R=H)

Strong Bases- Accepts an H+, an ion with lone pair and -1 formal charge localized on an H, C, N, or O atom
1. Hydride Ion

2. Hydroxide

3. Methoxide

4. Ethoxide

5. Tert-butoxide

Any molecule containing an H can serve as an acid, and any molecule with a lone pair (or a bond) can be a base

Weak acid: H2O, HOR (alcohol), HF, HNR3+, H2CO3

Weak base: H2O, HOR (alcohol), NR3, NaHCO3, ROR

Conjugate acid- base pairs examples

Arrow Rules
1. Arrow must come from either a lone pair or a bond
2. Arrows point to atoms that either get a new lone pair or make a new bond

Topic 7: Polar Reactions- Acid Base Reactions & pKa

Energy Diagram Conventions
1. Potential Energy (P.E) change ( H) from high to low is considered downhill or negative (-) or exothermic
2. P.E. change ( H) from low to high is considered uphill or positive or endothermic
3. Making a bond is downhill, negative, exothermic energy is released by the molecule
4. Breaking a bond is uphill, positive, endothermic energy must be added to the molecule

pKa: measure of the energy difference between the conjugate acid (H-Z) and the conjugate base (Z-) in the solvent, water
Positive pKa breaking bond (+/uphill);
Negative pKa making bond (-/downhill)

High pKa = weak acid; Low pKa = strong acid assume all six strong acids are pKa = 0

Strong base= molecule with lone pair and -1 charge on H, C, N, O assume that strong bases have a pKa > 14
For a given base, the higher the pKa of its conjugate acid, the stronger the base
For a given base, the lower the pKa of its conjugate acid, the weaker the base

Most acidic H requires the least amount of energy to remove and tied to the strongest acid molecule

Inductive Effect: polarization caused by an electronegative atom (ex: F) can induce minor polarization in neighboring bonds (localized
effect); weak so it cannot change that an H on a positively charged atom is more acidic than an H on a neutral atom, or that an H on N
or O is more acidic than an H on C

Nomenclature Workshop
Alkane= molecule consisting entirely of carbon and hydrogen atoms connected by single bonds

Straight Chain Alkanes

# Cs Condensed Structure Name
1 CH4 Methane
2 CH3 CH3 Ethane
3 CH3CH2CH3 Propane
4 CH3CH2CH2CH3 Butane
5 CH3CH2CH2CH2CH3 Pentane
6 CH3CH2CH2CH2CH2CH3 Hexane
7 CH3CH2CH2CH2CH2CH2CH3 Heptane

Parent chain= longest continuous chain of carbon atoms found in branched molecule
Molecule can have more than one parent chain of equal length

Naming Branched Alkanes + Alkyl Groups

1. Identify parent chain
2. Number the carbons in the chain starting with the end thats closest to a branch
3. Count the number of carbon in each branch (-yl suffix)
4. Attach the number of the carbon from which each substituent branches to the front of the alkyl group name
5. Check for repeated alkyl groups (di-, tri-, tetra-)
6. Place the names of the substituent groups in front of the name of the parent chain in alphabetical order (ex: 3-ethyl-4,5-

Naming Cyclic Alkanes

1. If a ring is present in a molecule, this ring almost always is considered the parent chain
2. Number ring carbons starting at a branch point (alkyl group), and number around the ring in a direction toward the closer
3. If there are exactly two alkyl groups, decide which gets 1 based on alphabetical order

Names of commonly found branches (Alkyl Groups)

#Cs Structure IUPAC Name
1 -CH3 Methyl
2 -CH2CH3 Ethyl
3 -CH2CH2CH3 Propyl or n-propyl
3 Isopropyl

4 -CH2CH2CH2CH3 Butyl or n-butyl

4 Isobutyl

4 sec-butyl

4 tert-butyl or t-butyl

5 -CH2CH2CH2CH2CH3 pentyl

Topic 8: Drawing Resonance Structures

-1 Anions: HO-, Cl-, (CH3)2N-, HCO3-, etc.
Counterion balances the charge
Assume that positive counterions are inert and that their only function is to balance the negative charge of the ion
Use of superscript zero after an element (ex: Li0) indicates that the element is in an uncharged metallic state (zero oxidations state)

Strong Base: a molecule with a -1 formal charge localized on a single H, C, N, or O atom

Resonance: demonstrates charges that are delocalized (shared) among multiple atoms

Arrow Rules
1. Type 1: A lone pair of electrons becomes a bond to an adjacent (next- door) atom
2. Type 2: A pair of electrons in a bond slides down to become a lone pair on one atom in that bond
3. Type 3: A pair of electrons in a bond to an adjacent (next-door) atom
4. For most Anions: Use one Type 1 and one Type 2 in tandem to move a (-) charge
5. For most Cations: Use on Type 3 to move a (+) charge
6. Arrows are only used to move electrons to an adjacent (next-door) atom or bond
7. You may not move electrons in a sigma bond, move any atoms, change the total number of electrons, or change the number
of formal charges
8. Each C, N, O, X atom must have an octet (carbocation [R3C+] are acceptable)

Important or first order resonance structures defined as those with the minimum number of +1 and -1 formal charges (and no
formal chargers larger than +/- 1)

Carbonyl Bond: C=O double bond

Topic 9: Resonance Stabilization

Light with a short wavelength is high in energy; Light with a long wavelength is low in energy

Electron in a Box analogy: for two similar molecules, the one with more resonance structures will be lower in potential energy
because they are resonance stabilized

Resonance Effect
1. Delocalized electrons have a greater wavelength because they spread out electrons (decrease in reactivity)
2. Resonance structures increase wavelength (low P.E. more stable)
3. Electrons can behave like waves
4. (-) Charge stuck on more electronegative atom for stabilization
Carboxylic acids [RCOOH] are acidic (pKa=5, ex: Acetic Acid)

Resonance structures of neutral molecules

1. Aromatic molecules= benzene and similar molecules Type 3 arrow
2. Zwitterions= overall neutral molecules with both + and formal charges (delocalized electrons) Type 1 & 2 arrow

Identifying most acidic hydrogen atoms

1. Atom type
2. Resonance
3. Inductive Effects
4. Orbital Type

Strongest acid has the weakest conjugate base + more resonance

Topic 10: Conformers of Alkanes

Alkanes: hydrocarbons with only bonds (sp3, tetrahedral)

Types of Conformations
Staggered (180): bonds on one carbon bisect the bond angle on the adjacent carbon when viewed looking down the C-C
bond, H is staggered; favorable (downhill)
Staggered Anti (180): two largest groups are on opposite sides of the structure/diagram
Eclipsed (120): bonds on adjacent carbons are aligned as viewed looking down the C-C bond; H is lined up eclipsing one
another; most unfavorable (uphill)
Staggered Gauche (60): methyl groups are staggered but next to each other
Fully eclipsed (0): when the methyl groups eclipse each other

Most favorable conformation is the relative position in space that H is occupying Steric
1. Steric hindrance- positioning of atoms forces them closer together, increasing the amount of steric strain in the molecule
2. Stabilization of the staggered conformation by hyperconjugation
3. Repulsion between bonding pairs (electrons in C-H bonds)

In general, high potential energy systems are unstable and likely to change if they have a way to change

Ethane spends the most time in the lowest PE position (staggered) so you would be most likely to catch ethane in that position
Potential energy wells of the staggered conformations

Newman Projection: focuses on rotation of one bond

1. Identify molecule with a small chain of carbons
2. Line up two of the center carbons (ex: 2, 3)
3. Draw the front carbon first and all of its attachments; angles should be about 120
4. Draw in the back carbon and all of its attachments

Topic 11: Constitutional isomers

# of hydrogen on a particular carbon is determined by
1. If one bond is present there should be three hydrogen, etc.
2. Formal charge

Isomers: compounds with the same molecular formula but have different structures

Constitutional isomers: same molecular formula with different atom connectivity

*Two molecules are the same if they can be interconverted without breaking any bonds

Conformers: molecules can be interconverted simply by rotations about single bonds

Molecular formula of an noncyclic alkane = CnH2n+2 (N= no. of Cs)

Noncyclic alkane= molecule with only C & H, and no bonds or rings

Alkenes: compounds containing only C and H with a C=C bond are known

Degree of unsaturation: [# of bonds] + [# of rings]

Because introducing a bond or ring has the same effect on the molecular formula of a molecule (to decrease the number of
hydrogen by two) the total number of bonds + rings in a molecule is given a special name (reduces hydrogen count by

Saturated single bonds

Unsaturated double bonds

Determining degree of unsaturation from molecular formula

Degree of unsaturation = No. of missing Hs/ 2

Topic 12: Alkene Stereoisomers

If circled groups are on opposite sides of this line double bond is E (trans)
If circled groups are on the same side of this line double bond is Z (cis)

E/Z Assignment: Cahn- Ingold- Prelog Rules

1. Atomic #
2. Isotopes (heavier atom wins)
3. Multiple bonds (double bond counts double)

Rules and conventions for naming alkenes

1. Use a number to designate where a double bond is located on carbon skeleton (ex: but-1-ene)
2. To name a molecule with one double bond that is Z or E, include the appropriate prefix before the name (ex: E-but-2-ene)
a. * Exception: double bond in a ring is assumed to be Z (ex: cyclohexene)
3. Molecules with two, three, or four double bonds have the base names diene, triene, and tetraene respectively

Z isomers require higher activation energy than E isomers

Topic 13: Cycloalkane Stereoisomers

Two molecules are the same if they can be interconverted without breaking bonds

Determining cis/trans for rings that lie in the plane of the paper (wedge vs. dash)
If both groups are attached to the same carbon groups are neither cis or trans to one another
If both groups lie on the same side of the plane of the paper groups are cis to one another (both wedge)
If the groups lie on opposite sides of the paper groups are trans to one another (one wedge, one dash)

Determining cis and trans for 3D diagrams of cyclohexane

Draw a dotted line to define the plane of the average carbon position, which is often horizontal
If bonds to both groups point toward the same side of this line groups are cis to one another
If bonds to the group point toward opposite sides of this line groups are trans to one another
If the groups are attached to the same carbon, they are neither cis nor trans to one another

Review: Terms and Definitions

Conformers (conformational stereoisomers) can be
interconverted via single bond rotation (without breaking bonds).
Two conformers are usually considered the same molecule

Constitutional isomers have the same molecular formula but

different atom connectivity

Configurational Stereoisomers have the same molecular

formula and the same atom connectivity, but cannot be
interconverted via single bond rotation

*You cannot buy a bottle of anti butane because in any sample of butane at normal temperatures the molecules are rapidly
interconverting among al possible conformations. You can buy a bottle of cis-1, 3-dimethylcyclohexane

Ring strain: type of instability that exists when bonds in a molecule form angles (>109.5) that are abnormal (ex: cyclopropane)

Chair conformation: cyclohexane is the only size of ring that adopts this conformation lowest potential energy of cyclohexane and
looks like a side view of a recliner with a footrest

Building models of cyclohexane focus on the axial Hs and check if:

Axial Hs alternate up, down, up, down, etc. around the ring
Bonds to all six axial Hs are parallel

Groups attached to a cyclohexane chair

Axial: Perpendicular to the ring, attached to a chair via a bond that points straight up or down like an Axis
Equatorial: Attached to a chair via a bond that points slightly up or down; imaginary equator circling the cyclohexane