The Berkeley Review MCAT Organic Chemistry Part 1

332 Pages·2011·44.93 MB·English

by  The Berkeley Review

Organic
Chemistry
Part I
Sections I-IV
Section I
Structure, Bonding, and Reactivity
Section II
Structure Elucidation
Section III
Stereochemistry
Section IV
Hydrocarbon Reactions
,
BERKELEY
Specializing in MCAT Preparation
ERKELEY
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F.O. Box 40140, Berkeley, California 94704-0140
Phone: [phone] (800) M C AT-TBR
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Nomenclature
a) IUPAC Nomenclature
b) General nomenclature
Bonding and Molecular Orbitals
a) Lewis Dot Structures
b) Bonding Model
Section I c) Covalent Bonds
d) Molecular Orbitals and Bonds
i. Single Bonds
ii. Double Bonds
Structure, iii. Triple Bonds
e) Molecular Structures
0 Octet Rule (HONC Shortcut)
Bonding,
9) Charged Structures
and Hybridization
a) Hybridization of Atomic Orbitals
Reactivity i. sp-Iiybridzation
ii. sp2-Hybridzation
by Todd Bennett iii. sp3-Hybridzation
b) Common Shapes
H H
ii Bond Energy
*
C C/, a) Bond Dissociation Energy
b) Ionic Bonds
/ Y*H
H H Intramolecular Features
a) Resonance
b) Inductive Effect
c) Steric Hindrance
d) Aromaticity
Fundamental Reactivity
a) Proton Transfer Reactions
b) Lewis Acid-Base Reactions
c) Acid and Base Strength
i. Primary Effects
ii. Secondary Effects
iii. Values and Terminology
d) Electrophiles and Nucleophiles
Physical Properties
a) Hydrogen-Bonding
b) Polarity
c) Van der Waals Forces
d) Solubility and Miscibility
Berkel,eEyY
Ur-E-V-I^E'W®
Specializing in MCAT Preparation
Structure, Bonding, and Reactivity
Section Goals
Be able to correlate structures with common and 1UPAC nomenclature.
o»
It is expected that you can answer questionsabout organicmoleculeswhen given either the molecular
structure or the name of the compound. You will need to be able to rapidly convert from name to
the structure or from the structure to name. You are expected to be able to recognize common
structural features like substitution and functional groups. Youmust be able to name small organic
molecules according to IUPAC conventions.
Be able to predict relative bond lengths, bond strengths, and structural angles.
Therewill be questions that require you to comparethe structural features of similar molecules. You
should know the hybridization-to-bond angle correlation. Youshould also know what effect the s-
character of a hybrid orbital has on bond length and strength. Youmust know the common molecular
geometries and shapes and how they correlate to hybridization. Youmust be able to read data tables
and explains trends in bonding features.
Be able to draw resonance structures and determine which is the most stable.
Some questions on the MCATrequire you either to count the resonance structures or determine
whichresonance structureis moststable. Stable resonance structureshave octetstabilityabout all
atoms except hydrogen, haveminimal charges, andwhencharges arepresent, negative charge resides
on the more highly electronegative atom and positive charge resides on the less electronegative
Know the structure of aromatic compounds and their unusual stability.
Benzene isthetypical aromatic compound, because it iscompletely planar with a cyclic, conjugated
arrangement of ^-electrons that obey Huckel's rule. Huckefs rule states that aromatic compounds
must have 4n + 2 n electrons in a cyclic array ofp orbitals, where n is any integer (orzero). Benzene
has aromatic stability due to its sixnelectrons in a continuous cyclic arrayofp orbitals. You should
be able to recognize aromaticity in structures other than benzene too.
Know the common organic acids and bases and their reactivity.
Common organic acids include phenols, thiols, protonated amines, andcarboxylic acids. Common
organic bases include amines and carboxylates. Youshould be able to determine the direction of a
proton transferreaction fromthe pKa values. You shouldbe ableto giveapproximate ratiosof the
conjugate acid and base in a buffered solution. You must have a solid understanidng on the
relationship between pH and pKa.
Be able to predict the relative acidity and basicity of organic compounds.
Acidity is determined bybothprimaryeffects (involving atomsthat aredirectly bonded to theacidic
Proton) and secondary effects (involving atoms that are not directly bonded to the acidic proton),
rimaryeffects include atomic size, electronegativity, and hybridization. Secondary effects include
resonance, theinductive effect, aromaticity, andsteric hindrance. You mustknow therelative impact
of the various effects.
Be familiar with fundamental reactions, energetics, and mechanisms.
•> Knowing that reactions in organic chemistry involve the interaction of electron-rich sites with
electron-poor sites, be able to identify the reactive sites of organic molecules. You must have a
fundamental understanding of electrophiles and nucleophiles and how they interact in transition
states. It is alsoimportant that you be ableto correlate a reaction mechanism to an energydiagram,
identifying reactants, transitionstates,intermediates, and products.
Be able to determine relative boiling and melting points.
Physical properties like boiling and melting point are the result of intermolecular forces such as
hydrogen-bonding, dipole-dipole interactions, and Van der Waals forces. You should be able to
predict the effect ofintermolecular forces, molecular mass,and structuraldetails(like branchingand
the presence of rc-bonds) on the physical properties ofa compound. You shouldbe ableto predict
relative physical properties from functional groups.
Organic Chemistry Molecular Structure Introduction
Molecular Structure
The perfect place to start any review of organic chemistry is the basics of
molecular structure, which traditionally include bonding, hybridization, and
electronic distribution. We shall consider a chemical bond to be the result of
atomic orbitals overlapping to form molecular orbitals. We shall consider all
bonds involving carbon to be covalent in nature. A covalent bond is thought to
involve the sharing of electrons between two adjacent nuclei. According to the
rules of electrostatics, the region between two nuclei offers a highly favorable
environment for electrons, where they can be shared by neighboring atoms.
However, there are several other factors to consider in bonding. If bonding were
purely a matter of electrostatics, then all of the electrons would be found between
two neighboring nuclei, not just the bonding electrons. The sharing of electrons
may be either symmetric (when the two atoms of the bond are of equal
electronegativity) or asymmetric (when the two atoms of the bond are of unequal
electronegativity). Sharing of electrons occurs when the atoms of a bond lack a
complete valence electron shell. Bysharing electrons,each atom moves closer to
completing its shell. This is the driving force behind the formation of stable
covalent bonds.
Having looked briefly at electron distribution, we can introduce the idea of
electronic orbitals, which are three-dimensional probability maps of the location
of an electron. They represent the region in space where an electron is found
95% of the time. We shall consider the orbitals and the overlap of orbitals to
describe the electronic distribution within a molecule. Once one has established
a foundation in bonding, the classification of molecules can be made based on
similarities in their bonding of particular atoms, known asfunctional groups. Each
functional group shall be considered in terms of its unique electron distribution,
hybridization, and nomenclature. Nomenclature, both that of the International
Union of Pure and Applied Chemists (IUPAC) and more general methods
describing the substitution of carbon within a functional group, shall be used to
describe a particular organic molecule. The review of nomenclature is
continuous throughout all sections of this book.
Then, we shall consider the factors that affect the distribution of electron density
within a molecule, including resonance, the inductive effect, steric hindrance,
aromaticity, and hybridization. The distribution of electron density can be used
to explain and predict chemical behavior. The simplest rule of reactivity in
organic chemistry is that regions of high electron density act as nucleophiles by
sharing their electron cloud with regions of low electron density, which act as
electrophiles. If you can correctly label a molecule in terms of the region that
carries a partially negative charge (the electron-rich environment) and the region
that carries a partially positive charge (the electron-poor environment), you can
understand chemical reactions better.
And so begins your review of organic chemistry. Fortunately, much of organic
chemistry is taught from the perspective of logic, which makes preparing for
organic chemistry on the MCAT easier. In organic chemistry courses you are
required to process information and reach conclusions based on observations,
which is also required on the MCAT. Reviewing and relearning this material
will help you develop critical thinking skills, which will carry over into your
review for other portions of the exam. Despite what you may have perceived
was a girth of information when you initially studied organic chemistry, you
don't need to review that much material to prepare successfully for the MCAT.
Copyright © by The Berkeley Review 3 Exclusive MCAT Preparation
Organic Chemistry Molecular Structure Nomenclature
Nomenclature
IUPAC Nomenclature (Systematic Proper Naming)
IUPAC Nomenclature is an internationally used system for naming molecules.
Molecular names reflect the structural features (functional groups) and the
number of carbons in a molecule. In IUPAC nomenclature, the name is based on
the carbon chain length and the functional groups. The suffix indicates which
primary functional group is attached to the carbon chain. Table 1-1 lists prefixes
for carbon chains between one and twelve carbons in length. Table 1-2 lists the
suffices for various functional groups. Beaware that "R" stands for any generic
alkyl group. When R is used, it indicates that the carbon chain size is irrelevant
to the reaction. Table 1-3summarizes the nomenclature process by listing several
four-carbon compounds.
Carbons Prefix Carbons Prefix Carbons Prefix
1 meth- 5 pent- 9 non-
2 eth- 6 hex- 10 dec-
3 prop- 7 hept- 11 undec-
4 but- 8 oct- 12 dodec-
Table 1-1
Functionality Compound Name Bonding
R-CH3 Alkane C—C & C—H
R-O-R Ether C—O—C
O
R-CO-H Aldehyde II
C—C—H
R-CH2-OH Alcohol C—O—H
O
R-CO-R Ketone II
C—C—C
0
R-CO-OH Carboxylic acid II
C—C—OH
Table 1-2
Formula IUPAC Name Structural Class
H3CCH2CH2CH3 Butane Alkane
H3CCH=CHCH3 Butene Alkene
H3CCH2CH2CHO Butanal Aldehyde
H3CCH2COCH3 Butanone Ketone
H3CCH2CH2CH2OH Butanol Alcohol
H3CCH2CH(OH)CH3 2-butanol Alcohol
H3CCH2CH2CH2NH2 Butanamine Amine
H3CCH2CH2CO2H Butanoic acid Carboxylic acid
Table 1-3
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Organic Chemistry Molecular Structure nomenclature
Figure 1-1 shows examples of IUPAC nomenclature for four organic compounds
with variable functional groups:
®
l^.O
3-methylpentanoic acid 4-chloro-5-methyl-3-heptanol
Longest chain: 5 carbons Longest chain: 7 carbons
Carboxylic acid group Alcohol group
Methyl substituent at C-3 Chloro substituent at C-4
Methyl substituent at C-5
©
Br Br H
3-ethylcyclopentanone 3,3-dibromobutanal
Ring of 5 carbons Longest chain: 4 carbons
Ketone group Aldehyde group
Ethyl substituent at C-3 2 Bromo substituents at C-3
Figure 1-1
General Nomenclature (Common Naming Based on Substitution)
In addition to the IUPAC naming system, there is a less rigorous method of
naming compounds by functional group and carbon type (based on carbon
substitution). Carbon type refers to the number of carbonatoms attached to the
central carbon atom (carbon atom of interest). A carbon with one other carbon
attachedis referred to as a primary (1°) carbon. A carbonwith two other carbons
attached is secondary (2°). A carbon with three other carbonsattached is tertiary
(3°). Figure 1-2shows some sample structures.
H CH3 H CH3 H H
\ ^ Tertiary carbon ^ ? Secondary carbon \ ? Primary carbon
s<
H,C QH, H3CH2C OH H3CH2C CI
Isobutane Sec-butanol n-Propyl chloride
(2-Methylpropane) (2-Butanol) (1-Chlropropane)
Figure 1-2
Nomenclature is an area of organic chemistry best learned through practice and
experience. We will deal with nomenclature throughout the course, as we
introduceeachnew functional group. Understandingnomenclature is especially
important in MCAT passages where names rather than structuresare given. Be
sure to know the Greek prefixes for carbon chain lengths up to twelve carbons.
Copyright © by The Berkeley Review Exclusive MCAT Preparation
OrganiC ChemiStry Molecular Structure Bonding and Orbitals
Lewis Dot Structures (Two-Dimensional Depiction of Molecules)
Lewis dot structures represent the electrons in the valence shell of an atom or
bonding orbitals of a molecule. Typically, we consider the Lewis dot structures
of elements in the s-block and p-block of the periodic table. For every valence
electron, a dot is placed around the atom. Single bonds are represented by a pair
of dots in a line between the atoms, or by a line itself. A double bond is
represented by a double line (implying that four electrons are being shared.)
Likewise, a triple bond is represented by a triple line (implying that six electrons
are being shared.) Lewis dot structures are familiar to most chemistry students,
so recognize the exceptions to the rules, as they make good test questions.
Example 1.1
What is the Lewis dot structure for H2BF?
A. B.
• • • •
:h—b--f: :h--b—f:
• •
1 1 -
H H
• • • •
C. D.
• • • •
H—B--f: h--b—f:
• •
1 1 -
H H
Solution
Boron has only three valence electrons, hence it can make only three bonds.
There is no lone pairon theboron atom, elirninating choices A and C. Hydrogen
has onlyoneelectron, which is in thebond toboron,so thereis never a lonepair
on a bonded hydrogen. This eliminates choices A (already eliminated) and B.
Fluorine hasa completed octet, so it makes onebondandhas three lone pairs, as
depicted in choice D, the best answer.
Bonding Model
Bonding is defined as the sharing of electron pairs between two atoms in either
an equal or unequal manner. As a general rule, a bond is the sharing of two
electrons between two adjacent nuclei. The region between two nuclei is the
mostprobable location foran electron. In mostcases, with the exception of ligand
bonds (known also asLewis acid-base bonds), oneelectron from each atomgoes into
forming the bond. When electrons are shared evenly between two atoms, the
bond is said to be a covalent bond. When electrons are transferred from one atom
to another, the bond is said to be an ionic bond. The difference between a covalent
and ionicbond is measured in the degree of sharing of the electrons, which can
be determined from the dipole. The more evenly that the electrons are shared,
the less the polarityof the bond. Therelativeelectronegativity of two atoms can
be determined by measuring the dipole of the bond they form. When the
difference in electronegativitybetween two atoms is less than 1.5, then the bond
is said to be covalent. When the difference in electronegativity between two
atoms is greater than 2.0, then the bond is said to be ionic. When the difference
in electronegativity between two atoms is greater than 1.5but less than 2.0, then
the bond is said to be polar-covalent (or partially ionic).
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Organic Chemistry Molecular Structure Bonding and Orbitals
Example 1.2
Which of the following bonds is MOST likely to be ionic?
A. C—O
B. N—F
C. Li—H
D. Li—F
Solution
A bond is ionic when the difference in electronegativity between the two atoms
exceeds 2.0. This means that the bond that is most likely to be ionic is the one
between the two atoms with the greatest difference in electronegativity. Lithium
is a metal and fluorine is a halide, so they exhibit the greatest electronegativity
difference of the choices listed. The best answer is therefore choice D.
Covalent Bonds
Bonds can be classified in one of three ways: ionic, polar-covalent, and covalent.
A covalent bond occurs when electrons are shared between two atoms having
little to no difference in electronegativity. As the difference in electronegativity
decreases, the covalent nature of the bond increases. There are two types of
covalent bonds: sigma bonds (a), defined as having electron density shared
between the nuclei of the two atoms; and pi bonds (n), defined as having no
electron density shared between the nuclei of the two atoms, but instead only
above and below the internuclear region. Sigma bonds are made from many
types of atomic orbitals (including hybrids), while pi bonds are made exclusively
ofparallel p-orbitals. In almost all cases, the sigma bond is stronger than the pi
bond, with molecular fluorine (F2) being a notable exception. Figure 1-3shows a
generic sigma bond. You maynotice thatwithin a sigma bond, only about eighty
toninety percentof the electron density liesbetween thenuclei, not allof it.
.Nuclei
o CD
Electron density
Figure 1-3
Example 1.3
Which drawing depicts theelectron density ofa carbon-carbon sigma bond?
A.
L~D
C D
Solution
A sigma bond has its electron density between the two nuclei, which eliminates
choice D. The two atoms in the bond are identical, so the electron density should
be symmetrically displaced between the two nuclei. This eliminates choice B.
Mostof electron density is between the nuclei,so choice Ais a better answer than
choice C. These drawings are ugly, so focus on the concept, not the pictures.
Copyright © by The Berkeley Review Exclusive MCAT Preparation
Organic Chemistry Molecular Structure Bonding and Orbitals
Figure 1-4 shows a generic 7C-bond. Within a rc-bond, there is no electron density
between the two nuclei. The electron density hi a rc-bond results from electrons
being shared between the adjacent lobes of parallel p-orbitals.
Nuclei
Electron Density
Figure 1-4
In organic chemistry, covalent bonds are viewed in great detail, taking into
account hybridization and overlap. In alkanes, carbons have srAhybridization
and all of the bonds are sigma bonds. In alkanes, there are two types of bonds:
C— H (GSp3-s bonds) and C— C (CJSp3-Sp3 bonds). In alkenes, there are sigma
and pi bonds present. The 7t-bond consists of p-orbitals side by side, and its
carbons have sp2-hybridization. The C=C bond is made up of a GSp2_Sp2 bond
and a 7t2p-2p bond. Bond length varies with the size of the orbitals in the bond.
For instance, a sigma bond composed of an s/?2-hybridized carbon and an sp^-
hybridized carbon isshorter than a sigma bond comprised of two sp^-hybridized
carbons. Hydrogens use s-orbitals to form bonds. Figure 1-5shows three sigma
bonds with their relative bond lengths. The longer bond is associated with the
larger orbitals (bond radii: dz>dy >dx).
asp2-sp2 <V-sp3
Figure 1-5
Figure 1-5 confirms that most of the electron density lies between the two nuclei
in sigma bonds, no matter what the orbitals are from which the sigma bond
originates. In pi bonds, electron density does not lie between the two nuclei. The
length of a bond is defined as the distance between the nuclei of the two atoms
making the bond. Figure 1-6 shows an example of a re-bond between two 2pz-
orbitals, which is typical for nearly alln-bonds encountered in organic chemistry,
because carbon, nitrogen, and oxygen have 2p-orbitals in their valence shells.
2pz-2pz
Figure 1-6
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